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Changeset 2452
- Timestamp:
- 12/03/09 15:44:36 (2 years ago)
- Location:
- molgenis4animaldb
- Files:
-
- 4 edited
-
WebContent/META-INF/context.xml (modified) (1 diff)
-
logger.out (modified) (23 diffs)
-
molgenis4animal_db.xml (modified) (4 diffs)
-
molgenis4animal_ui.xml (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
molgenis4animaldb/WebContent/META-INF/context.xml
r2414 r2452 8 8 password="molgenis" 9 9 driverClassName="com.mysql.jdbc.Driver" 10 url="jdbc:mysql://localhost/animaldb _proto?innodb_autoinc_lock_mode=2"10 url="jdbc:mysql://localhost/animaldb?innodb_autoinc_lock_mode=2" 11 11 removeAbandoned="true" 12 12 maxActive="8" -
molgenis4animaldb/logger.out
r2432 r2452 2 2 INFO main main - 3 3 MOLGENIS version 3.3.2-testing 4 INFO main main - working dir: C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb4 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 5 5 DEBUG main main - 6 6 Using generators: … … 43 43 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 44 44 DEBUG main org.molgenis.model.MolgenisModelParser - read: 45 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 46 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 47 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 45 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 46 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Name, type=string[0], auto=false, nillable=false, readonly=true, default=) 48 47 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 49 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 50 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 51 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 52 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 53 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 54 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 55 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 56 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 57 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 58 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 59 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 60 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 61 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 62 ( 63 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 64 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 65 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 66 Unique(id, ) 67 Unique(name, ) 68 ); 69 ENTITY: Entity(animaldb.Event) 70 ( 71 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 72 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 73 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 74 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 75 ); 76 ENTITY: Entity(animaldb.Animal) 77 ( 78 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 79 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 80 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 81 ); 82 ENTITY: Entity(animaldb.Animal_group) 83 ( 84 ); 85 ENTITY: Entity(animaldb.Location) 86 ( 87 ); 88 ENTITY: Entity(animaldb.Event_type) 89 ( 48 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 49 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 50 DEBUG main org.molgenis.model.MolgenisModelParser - read: Experiment 51 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Species, type=string[0], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 52 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Tissue, type=string[0], auto=false, nillable=true, readonly=false, default=) 53 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=) 54 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 55 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 56 DEBUG main org.molgenis.model.MolgenisModelParser - read: Sample 57 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=SpecialSample, name=detail, type=string[0], auto=false, nillable=false, readonly=false, default=) 58 DEBUG main org.molgenis.model.MolgenisModelParser - read: SpecialSample 59 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 60 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 61 DEBUG main org.molgenis.model.MolgenisModelParser - read: Trait 62 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 63 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 64 DEBUG main org.molgenis.model.MolgenisModelParser - read: Measurement 65 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 66 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Measurement, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 67 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Sample, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 68 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Trait, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 69 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Value, type=string[0], auto=false, nillable=false, readonly=false, default=) 70 DEBUG main org.molgenis.model.MolgenisModelParser - read: Data 71 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(example.Identifiable) 72 ( 73 Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 74 Field(entity=Identifiable, name=Name, type=string[255], auto=false, nillable=false, readonly=true, default=) 75 Unique(Id, ) 76 Unique(Name, ) 77 ); 78 ENTITY: Entity(example.Experiment) 79 ( 80 Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 81 Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 82 ); 83 ENTITY: Entity(example.Sample) 84 ( 85 Field(entity=Sample, name=Species, type=string[255], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 86 Field(entity=Sample, name=Tissue, type=string[255], auto=false, nillable=true, readonly=false, default=) 87 Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=, enum_options=[male, female, unknown]) 88 Field(entity=Sample, name=Experiment, type=xref[Experiment->Id], xref_label=Id, auto=false, nillable=false, readonly=false, default=) 89 Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 90 ); 91 ENTITY: Entity(example.SpecialSample) 92 ( 93 Field(entity=SpecialSample, name=detail, type=string[255], auto=false, nillable=false, readonly=false, default=) 94 ); 95 ENTITY: Entity(example.Trait) 96 ( 97 Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 98 Field(entity=Trait, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 99 ); 100 ENTITY: Entity(example.Measurement) 101 ( 102 Field(entity=Measurement, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 103 Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 104 ); 105 ENTITY: Entity(example.Data) 106 ( 107 Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 108 Field(entity=Data, name=Measurement, type=xref[Measurement->id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 109 Field(entity=Data, name=Sample, type=xref[Sample->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 110 Field(entity=Data, name=Trait, type=xref[Trait->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 111 Field(entity=Data, name=Value, type=string[255], auto=false, nillable=false, readonly=false, default=) 112 Unique(Id, ) 113 Unique(Measurement, Sample, Trait, ) 90 114 ); 91 115 … … 111 135 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 112 136 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 113 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event114 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal115 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group116 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location117 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type137 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Experiment 138 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Sample 139 DEBUG main MolgenisModelValidator - copy primary key Id from superclass Sample to SpecialSample 140 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Trait 141 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Measurement 118 142 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 119 143 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... … … 124 148 INFO main MolgenisModel - parsing ui-schema 125 149 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 126 DEBUG main main - using file generated/sql\create_tables.sql 127 INFO main main - Updating database.... 128 INFO main main - MOLGENIS database updated succesfully 150 INFO main main - generating .... 151 INFO main main - 152 Using options: 153 model_database = [molgenis4animal_db.xml, molgenis_auth.xml] #File with data structure specification (in MOLGENIS DSL). 154 model_userinterface = molgenis4animal_ui.xml #File with user interface specification (in MOLGENIS DSL). Can be same file as model_database 155 output_src = generated/java/ #Output-directory for the generated project. 156 output_hand = handwritten/java/ #Output-directory for the generated project. 157 output_sql = generated/sql #Output-directory for the generated sql files. 158 output_doc = WebContent/generated-doc #Output-directory for the generated documentation. 159 output_web = WebContent #Output-directory for any generated web resources 160 db_driver = com.mysql.jdbc.Driver #Driver of database. Any JDBC compatible driver should work. 161 db_user = molgenis #Username for database. 162 db_password = xxxxxx #Password for database. 163 db_uri = jdbc:mysql://localhost/animaldb_proto?innodb_autoinc_lock_mode=2 #Uri of the database. Default: localhost 164 db_filepath = attachedfiles #Path where the database should store file attachements. Default: null 165 db_jndiname = jdbc/molgenisdb #Used to create a JDBC database resource for the application 166 object_relational_mapping = subclass_per_table #Expert option: Choosing OR strategy. Either 'class_per_table', 'subclass_per_table', 'hierarchy_per_table'. Default: class_per_table 167 mapper_implementation = multiquery #Expert option: Choosing wether multiquery is used instead of prepared statements. Default: false 168 exclude_system = true #Expert option: Whether system tables should be excluded from generation. Default: true 169 auth_loginclass = org.molgenis.framework.security.SimpleLogin #Expert option. 170 mail_smtp_protocol = smtps #Sets the email protocol, either smtp, smtps or null. Default: null meaning email disabled 171 mail_smtp_hostname = smtp.gmail.com #SMTP host server. Default: localhost 172 mail_smtp_port = 465 #SMTP host server port. Default: 25 173 mail_smtp_user = molgenis #SMTP user for authenticated emailing. Default: null. 174 mail_smtp_password = molgenispass #SMTP user for authenticated emailing. Default: null. 175 176 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors.css to WebContent\generated-res\css\colors.css 177 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors_blue.css to WebContent\generated-res\css\colors_blue.css 178 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors_blue2.css to WebContent\generated-res\css\colors_blue2.css 179 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors_bluegrey.css to WebContent\generated-res\css\colors_bluegrey.css 180 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors_grey.css to WebContent\generated-res\css\colors_grey.css 181 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\colors_maroon.css to WebContent\generated-res\css\colors_maroon.css 182 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\data.css to WebContent\generated-res\css\data.css 183 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\dateinput.css to WebContent\generated-res\css\dateinput.css 184 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\dateipnut.css to WebContent\generated-res\css\dateipnut.css 185 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\main.css to WebContent\generated-res\css\main.css 186 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\menu.css to WebContent\generated-res\css\menu.css 187 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\css\xrefinput.css to WebContent\generated-res\css\xrefinput.css 188 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\cancel.png to WebContent\generated-res\img\cancel.png 189 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\close.png to WebContent\generated-res\img\close.png 190 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\delete.png to WebContent\generated-res\img\delete.png 191 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\deselect.png to WebContent\generated-res\img\deselect.png 192 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\deselectall.png to WebContent\generated-res\img\deselectall.png 193 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\down.png to WebContent\generated-res\img\down.png 194 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\download.png to WebContent\generated-res\img\download.png 195 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\editview.gif to WebContent\generated-res\img\editview.gif 196 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\exit.bmp to WebContent\generated-res\img\exit.bmp 197 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\filter.png to WebContent\generated-res\img\filter.png 198 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\first.png to WebContent\generated-res\img\first.png 199 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\info.png to WebContent\generated-res\img\info.png 200 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\last.png to WebContent\generated-res\img\last.png 201 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\limit.png to WebContent\generated-res\img\limit.png 202 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\listview.png to WebContent\generated-res\img\listview.png 203 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\logo_molgenis.gif to WebContent\generated-res\img\logo_molgenis.gif 204 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\new.png to WebContent\generated-res\img\new.png 205 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\next.png to WebContent\generated-res\img\next.png 206 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\none.png to WebContent\generated-res\img\none.png 207 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\open.png to WebContent\generated-res\img\open.png 208 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\prev.png to WebContent\generated-res\img\prev.png 209 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\pulldown.gif to WebContent\generated-res\img\pulldown.gif 210 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\recordview.png to WebContent\generated-res\img\recordview.png 211 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\reset.png to WebContent\generated-res\img\reset.png 212 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\rowStart.png to WebContent\generated-res\img\rowStart.png 213 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\rowStop.png to WebContent\generated-res\img\rowStop.png 214 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\save.png to WebContent\generated-res\img\save.png 215 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\select.png to WebContent\generated-res\img\select.png 216 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\sort_asc.gif to WebContent\generated-res\img\sort_asc.gif 217 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\sort_desc.gif to WebContent\generated-res\img\sort_desc.gif 218 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\up.png to WebContent\generated-res\img\up.png 219 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\update.gif to WebContent\generated-res\img\update.gif 220 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\upload.png to WebContent\generated-res\img\upload.png 221 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\_logo_molgenis.gif to WebContent\generated-res\img\_logo_molgenis.gif 222 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\img\_logo_molgenis_old.gif to WebContent\generated-res\img\_logo_molgenis_old.gif 223 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\all.js to WebContent\generated-res\scripts\all.js 224 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\Copy of datetimeinput.js to WebContent\generated-res\scripts\Copy of datetimeinput.js 225 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\Copy of mrefinput.js to WebContent\generated-res\scripts\Copy of mrefinput.js 226 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\dateinput.js to WebContent\generated-res\scripts\dateinput.js 227 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\datetimeinput.js to WebContent\generated-res\scripts\datetimeinput.js 228 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\menu.js to WebContent\generated-res\scripts\menu.js 229 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\mrefinput.js to WebContent\generated-res\scripts\mrefinput.js 230 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\popup.js to WebContent\generated-res\scripts\popup.js 231 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\rest.js to WebContent\generated-res\scripts\rest.js 232 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\textinput.js to WebContent\generated-res\scripts\textinput.js 233 DEBUG main MolgenisResourceCopyGen - copied C:\Users\Erik\workspace\molgenis32_workspace\molgenis\bin\org\molgenis\framework\ui\res\scripts\xrefinput.js to WebContent\generated-res\scripts\xrefinput.js 234 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 235 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 236 INFO main TableDocGen - generated WebContent\generated-doc\tabledoc.html 237 INFO main EntityModelDocGen - generated WebContent\generated-doc\entitymodel.html 238 INFO main DotDocGen - generated WebContent\generated-doc\objectmodel-uml-diagram.dot 239 DEBUG main DotDocGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 240 DEBUG main DotDocGen - Data model image was generated succesfully. 241 Output: 242 243 DEBUG main DotDocGen - Executing: dot -Tsvg -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 244 DEBUG main DotDocGen - Data model image was generated succesfully. 245 Output: 246 247 INFO main CsvDocGen - generated WebContent\generated-doc\tab-format-reference.html 248 INFO main DotDocMinimalGen - generated WebContent\generated-doc\entity-uml-minimal-diagram.dot 249 DEBUG main DotDocMinimalGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\entity-uml-minimal-diagram.dot 250 DEBUG main DotDocMinimalGen - Data model image was generated succesfully. 251 Output: 252 253 DEBUG main freemarker.beans - Key 'version' was not found on instance of org.molgenis.model.elements.Model. Introspection information for the class is: {methods=java.beans.PropertyDescriptor@bc153021, userinterface=java.beans.PropertyDescriptor@dcfeec9a, getEntity=public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String), getDBDescription=public java.lang.String org.molgenis.model.elements.Model.getDBDescription(), methodSchema=java.beans.PropertyDescriptor@f7024bd8, getUserinterface=public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface(), hashCode=public native int java.lang.Object.hashCode(), setLabel=public void org.molgenis.model.elements.Model.setLabel(java.lang.String), concreteEntities=java.beans.PropertyDescriptor@d79123b5, wait=freemarker.ext.beans.MethodMap@175d6ab, getMethods=public java.util.Vector org.molgenis.model.elements.Model.getMethods(), getEntities=public java.util.Vector org.molgenis.model.elements.Model.getEntities(), setDBDescription=public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String), getConcreteEntities=public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities(), findField=public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException, getModules=public java.util.List org.molgenis.model.elements.Model.getModules(), matrices=java.beans.PropertyDescriptor@41f81961, java.lang.Object@6b7920=public org.molgenis.model.elements.Model(java.lang.String), name=java.beans.PropertyDescriptor@c6a5b168, notify=public final native void java.lang.Object.notify(), PRDescription=java.beans.PropertyDescriptor@e9965887, notifyAll=public final native void java.lang.Object.notifyAll(), setPRDescription=public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String), getClass=public final native java.lang.Class java.lang.Object.getClass(), UIDescription=java.beans.PropertyDescriptor@2d918cf5, getViews=public java.util.Vector org.molgenis.model.elements.Model.getViews(), equals=public boolean java.lang.Object.equals(java.lang.Object), java.lang.Object@e3b895={public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema()=[Ljava.lang.Class;@160a26f, public boolean java.lang.Object.equals(java.lang.Object)=[Ljava.lang.Class;@1484a05, public java.lang.String org.molgenis.model.elements.Model.getLabel()=[Ljava.lang.Class;@f39b3a, public java.util.Vector org.molgenis.model.elements.Model.getMatrices()=[Ljava.lang.Class;@1542a75, public final native java.lang.Class java.lang.Object.getClass()=[Ljava.lang.Class;@af993e, public java.lang.String org.molgenis.model.elements.Model.getPRDescription()=[Ljava.lang.Class;@75e4fc, public java.util.Vector org.molgenis.model.elements.Model.getViews()=[Ljava.lang.Class;@c62c8, public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String)=[Ljava.lang.Class;@12940b3, public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)=[Ljava.lang.Class;@156b6b9, public java.lang.String org.molgenis.model.elements.Model.toString()=[Ljava.lang.Class;@1f66cff, public void org.molgenis.model.elements.Model.setName(java.lang.String)=[Ljava.lang.Class;@16de49c, public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String)=[Ljava.lang.Class;@1bbf1ca, public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase()=[Ljava.lang.Class;@1ff0dde, public java.lang.String org.molgenis.model.elements.Model.getName()=[Ljava.lang.Class;@1e78fc6, public java.lang.String org.molgenis.model.elements.Model.getUIDescription()=[Ljava.lang.Class;@1901437, public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface()=[Ljava.lang.Class;@1f6226, public void org.molgenis.model.elements.Model.setLabel(java.lang.String)=[Ljava.lang.Class;@64ea66, public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String)=[Ljava.lang.Class;@158f9d3, public java.lang.String org.molgenis.model.elements.Model.getDBDescription()=[Ljava.lang.Class;@79a2e7, public org.molgenis.model.elements.Model(java.lang.String)=[Ljava.lang.Class;@1b60280, public native int java.lang.Object.hashCode()=[Ljava.lang.Class;@5e55ab, public final native void java.lang.Object.notify()=[Ljava.lang.Class;@14a55f2, public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException=[Ljava.lang.Class;@15093f1, public java.util.List org.molgenis.model.elements.Model.getModules()=[Ljava.lang.Class;@120bf2c, public final native void java.lang.Object.notifyAll()=[Ljava.lang.Class;@e6f7d2, public java.util.Vector org.molgenis.model.elements.Model.getMethods()=[Ljava.lang.Class;@19836ed, public java.util.Vector org.molgenis.model.elements.Model.getEntities()=[Ljava.lang.Class;@3e0ebb, public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String)=[Ljava.lang.Class;@39443f, public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities()=[Ljava.lang.Class;@1afae45}, class=java.beans.PropertyDescriptor@d1681043, getPRDescription=public java.lang.String org.molgenis.model.elements.Model.getPRDescription(), label=java.beans.PropertyDescriptor@57b39921, DBDescription=java.beans.PropertyDescriptor@1504bab, entities=java.beans.PropertyDescriptor@901555c8, getMethodSchema=public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema(), database=java.beans.PropertyDescriptor@fccd564d, getLabel=public java.lang.String org.molgenis.model.elements.Model.getLabel(), getMatrices=public java.util.Vector org.molgenis.model.elements.Model.getMatrices(), getUIDescription=public java.lang.String org.molgenis.model.elements.Model.getUIDescription(), setUIDescription=public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String), views=java.beans.PropertyDescriptor@e35eab55, getDatabase=public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase(), getName=public java.lang.String org.molgenis.model.elements.Model.getName(), toString=public java.lang.String org.molgenis.model.elements.Model.toString(), setName=public void org.molgenis.model.elements.Model.setName(java.lang.String), modules=java.beans.PropertyDescriptor@34394f50, getRecord=public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)} 254 INFO main ObjectModelDocGen - generated WebContent\generated-doc\objectmodel.html 255 INFO main MySqlCreateSubclassPerTableGen - generated generated\sql\create_tables.sql 256 INFO main MySqlAlterSubclassPerTableGen - generated generated\sql\alter_tables.sql 257 INFO main JDBCDatabaseGen - generated generated\java\app\JDBCDatabase.java 258 INFO main DataTypeGen - generated generated\java\example\Identifiable.java 259 INFO main DataTypeGen - generated generated\java\example\Experiment.java 260 INFO main DataTypeGen - generated generated\java\example\Sample.java 261 INFO main DataTypeGen - generated generated\java\example\SpecialSample.java 262 INFO main DataTypeGen - generated generated\java\example\Trait.java 263 INFO main DataTypeGen - generated generated\java\example\Measurement.java 264 INFO main DataTypeGen - generated generated\java\example\Data.java 265 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup.java 266 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUser.java 267 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisEntityMetaData.java 268 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_members.java 269 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canRead.java 270 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canWrite.java 271 INFO main MultiqueryMapperGen - generated generated\java\example\db\ExperimentMapper.java 272 INFO main MultiqueryMapperGen - generated generated\java\example\db\SampleMapper.java 273 INFO main MultiqueryMapperGen - generated generated\java\example\db\SpecialSampleMapper.java 274 INFO main MultiqueryMapperGen - generated generated\java\example\db\TraitMapper.java 275 INFO main MultiqueryMapperGen - generated generated\java\example\db\MeasurementMapper.java 276 INFO main MultiqueryMapperGen - generated generated\java\example\db\DataMapper.java 277 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroupMapper.java 278 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserMapper.java 279 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisEntityMetaDataMapper.java 280 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_membersMapper.java 281 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canReadMapper.java 282 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canWriteMapper.java 283 INFO main JDBCMetaDatabaseGen - generated generated\java\app\JDBCMetaDatabase.java 284 INFO main CountPerEntityGen - generated generated\sql\count_per_entity.sql 285 INFO main CountPerTableGen - generated generated\sql\count_per_table.sql 286 INFO main FillMetadataTablesGen - generated generated\sql\insert_metadata.sql 287 INFO main CsvReaderGen - generated generated\java\example\csv\ExperimentCsvReader.java 288 INFO main CsvReaderGen - generated generated\java\example\csv\SampleCsvReader.java 289 INFO main CsvReaderGen - generated generated\java\example\csv\SpecialSampleCsvReader.java 290 INFO main CsvReaderGen - generated generated\java\example\csv\TraitCsvReader.java 291 INFO main CsvReaderGen - generated generated\java\example\csv\MeasurementCsvReader.java 292 INFO main CsvReaderGen - generated generated\java\example\csv\DataCsvReader.java 293 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroupCsvReader.java 294 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserCsvReader.java 295 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisEntityMetaDataCsvReader.java 296 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_membersCsvReader.java 297 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canReadCsvReader.java 298 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canWriteCsvReader.java 299 INFO main REntityGen - generated generated\java\example\R\Experiment.R 300 INFO main REntityGen - generated generated\java\example\R\Sample.R 301 INFO main REntityGen - generated generated\java\example\R\SpecialSample.R 302 INFO main REntityGen - generated generated\java\example\R\Trait.R 303 INFO main REntityGen - generated generated\java\example\R\Measurement.R 304 INFO main REntityGen - generated generated\java\example\R\Data.R 305 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup.R 306 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUser.R 307 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisEntityMetaData.R 308 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_members.R 309 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canRead.R 310 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canWrite.R 311 INFO main RApi - generated generated\java\app\servlet\source.R 312 INFO main HtmlFormGen - generated generated\java\example\ui\IdentifiableHtmlForm.java 313 INFO main HtmlFormGen - generated generated\java\example\ui\ExperimentHtmlForm.java 314 INFO main HtmlFormGen - generated generated\java\example\ui\SampleHtmlForm.java 315 INFO main HtmlFormGen - generated generated\java\example\ui\SpecialSampleHtmlForm.java 316 INFO main HtmlFormGen - generated generated\java\example\ui\TraitHtmlForm.java 317 INFO main HtmlFormGen - generated generated\java\example\ui\MeasurementHtmlForm.java 318 INFO main HtmlFormGen - generated generated\java\example\ui\DataHtmlForm.java 319 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroupHtmlForm.java 320 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserHtmlForm.java 321 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisEntityMetaDataHtmlForm.java 322 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_membersHtmlForm.java 323 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_canReadHtmlForm.java 324 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_canWriteHtmlForm.java 325 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 326 INFO main MolgenisContextListenerGen - generated generated\java\app\servlet\ContextListener.java 327 INFO main MolgenisServletGen - generated generated\java\app\servlet\MolgenisServlet.java 328 INFO main FormScreenGen - generated generated\java\app\ui\ExperimentForm.java 329 INFO main FormScreenGen - generated generated\java\app\ui\SamplesForm.java 330 INFO main FormScreenGen - generated generated\java\app\ui\TraitsForm.java 331 INFO main FormScreenGen - generated generated\java\app\ui\MeasurementsForm.java 332 INFO main FormScreenGen - generated generated\java\app\ui\DataForm.java 333 INFO main MenuScreenGen - generated generated\java\app\ui\TopmenuMenu.java 334 INFO main MenuScreenGen - generated generated\java\app\ui\MainMenu.java 335 INFO main MenuScreenGen - generated generated\java\app\ui\ExperimentMenuMenu.java 336 INFO main MenuScreenGen - generated generated\java\app\ui\PluginexamplesMenu.java 337 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\GooglePlugin.java 338 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\HelloWorldPlugin.java 339 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\ExperimentQueryPlugin.java 340 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\WizardPluginPlugin.java 341 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\FileServingPluginPlugin.java 342 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\MartViewPlugin.java 343 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\Model_documentationPlugin.java 344 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\APIsPlugin.java 345 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\LoginPlugin.java 346 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\examples\portal\PortalIntegrationPlugin.ftl 347 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\examples\helloworld\HelloWorldPlugin.ftl 348 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\examples\dbquery\ExperimentQueryPlugin.ftl 349 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\examples\wizard\WizardPlugin.ftl 350 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\examples\file\FileServingPlugin.ftl 351 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\query\view\MartView.ftl 352 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.ftl 353 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\ApiScreen.ftl 354 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\LoginScreen.ftl 355 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\examples\portal\PortalIntegrationPlugin.java 356 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\examples\helloworld\HelloWorldPlugin.java 357 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\examples\dbquery\ExperimentQueryPlugin.java 358 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\examples\wizard\WizardPlugin.java 359 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\examples\file\FileServingPlugin.java 360 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\query\view\MartView.java 361 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.java 362 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\ApiScreen.java 363 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\topmenu\LoginScreen.java 364 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 365 INFO main SoapApiGen - generated generated\java\app\servlet\SoapApi.java 366 INFO main CsvExportGen - generated generated\java\app\CsvExport.java 367 INFO main CsvImportGen - generated generated\java\app\CsvImport.java 129 368 DEBUG main MolgenisOptions - parsed properties file. 130 369 INFO main main - 131 370 MOLGENIS version 3.3.2-testing 132 INFO main main - working dir: C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb371 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 133 372 DEBUG main main - 134 373 Using generators: … … 171 410 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 172 411 DEBUG main org.molgenis.model.MolgenisModelParser - read: 412 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 413 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Name, type=string[0], auto=false, nillable=false, readonly=true, default=) 414 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 415 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 416 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 417 DEBUG main org.molgenis.model.MolgenisModelParser - read: Experiment 418 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Species, type=string[0], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 419 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Tissue, type=string[0], auto=false, nillable=true, readonly=false, default=) 420 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=) 421 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 422 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 423 DEBUG main org.molgenis.model.MolgenisModelParser - read: Sample 424 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=SpecialSample, name=detail, type=string[0], auto=false, nillable=false, readonly=false, default=) 425 DEBUG main org.molgenis.model.MolgenisModelParser - read: SpecialSample 426 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 427 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 428 DEBUG main org.molgenis.model.MolgenisModelParser - read: Trait 429 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 430 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 431 DEBUG main org.molgenis.model.MolgenisModelParser - read: Measurement 432 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 433 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Measurement, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 434 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Sample, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 435 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Trait, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 436 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Value, type=string[0], auto=false, nillable=false, readonly=false, default=) 437 DEBUG main org.molgenis.model.MolgenisModelParser - read: Data 438 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(example.Identifiable) 439 ( 440 Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 441 Field(entity=Identifiable, name=Name, type=string[255], auto=false, nillable=false, readonly=true, default=) 442 Unique(Id, ) 443 Unique(Name, ) 444 ); 445 ENTITY: Entity(example.Experiment) 446 ( 447 Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 448 Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 449 ); 450 ENTITY: Entity(example.Sample) 451 ( 452 Field(entity=Sample, name=Species, type=string[255], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 453 Field(entity=Sample, name=Tissue, type=string[255], auto=false, nillable=true, readonly=false, default=) 454 Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=, enum_options=[male, female, unknown]) 455 Field(entity=Sample, name=Experiment, type=xref[Experiment->Id], xref_label=Id, auto=false, nillable=false, readonly=false, default=) 456 Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 457 ); 458 ENTITY: Entity(example.SpecialSample) 459 ( 460 Field(entity=SpecialSample, name=detail, type=string[255], auto=false, nillable=false, readonly=false, default=) 461 ); 462 ENTITY: Entity(example.Trait) 463 ( 464 Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 465 Field(entity=Trait, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 466 ); 467 ENTITY: Entity(example.Measurement) 468 ( 469 Field(entity=Measurement, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 470 Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 471 ); 472 ENTITY: Entity(example.Data) 473 ( 474 Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 475 Field(entity=Data, name=Measurement, type=xref[Measurement->id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 476 Field(entity=Data, name=Sample, type=xref[Sample->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 477 Field(entity=Data, name=Trait, type=xref[Trait->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 478 Field(entity=Data, name=Value, type=string[255], auto=false, nillable=false, readonly=false, default=) 479 Unique(Id, ) 480 Unique(Measurement, Sample, Trait, ) 481 ); 482 483 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 484 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 485 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 486 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 487 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 488 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 489 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 490 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 491 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 492 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 493 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 494 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 495 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 496 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 497 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 498 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 499 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 500 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 501 DEBUG main MolgenisModelValidator - validating model and adding defaults: 502 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 503 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 504 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Experiment 505 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Sample 506 DEBUG main MolgenisModelValidator - copy primary key Id from superclass Sample to SpecialSample 507 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Trait 508 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Measurement 509 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 510 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 511 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 512 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 513 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 514 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 515 INFO main MolgenisModel - parsing ui-schema 516 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 517 ERROR main main - org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Access denied for user 'molgenis'@'localhost' to database 'animaldb_proto') 518 DEBUG main MolgenisOptions - parsed properties file. 519 INFO main main - 520 MOLGENIS version 3.3.2-testing 521 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 522 DEBUG main main - 523 Using generators: 524 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 525 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 526 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 527 generators.doc.DotDocGen #Generates one documentation file describing all entities. 528 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 529 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 530 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 531 generators.db.ViewMapperGen #generate the mappers for each database view 532 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 533 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 534 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 535 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 536 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 537 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 538 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 539 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 540 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 541 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 542 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 543 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 544 generators.R.RMatrixGen #Generates access methods in R for each matrix. 545 generators.R.RApi #Generates a R file that sources all R files. 546 generators.ui.HtmlFormGen #Generates html form class for each entity. 547 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 548 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 549 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 550 generators.ui.FormScreenGen #Generates form screens. 551 generators.ui.MenuScreenGen #Generates menu screens. 552 generators.ui.TreeScreenGen #Generates Tree screens. 553 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 554 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 555 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 556 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 557 generators.csv.CsvExportGen #Generates CsvImportExport 558 generators.csv.CsvImportGen #Generates CsvImportExport 559 560 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 561 DEBUG main org.molgenis.model.MolgenisModelParser - read: 562 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 563 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=Name, type=string[0], auto=false, nillable=false, readonly=true, default=) 564 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 565 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 566 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 567 DEBUG main org.molgenis.model.MolgenisModelParser - read: Experiment 568 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Species, type=string[0], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 569 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Tissue, type=string[0], auto=false, nillable=true, readonly=false, default=) 570 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=) 571 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 572 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 573 DEBUG main org.molgenis.model.MolgenisModelParser - read: Sample 574 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=SpecialSample, name=detail, type=string[0], auto=false, nillable=false, readonly=false, default=) 575 DEBUG main org.molgenis.model.MolgenisModelParser - read: SpecialSample 576 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 577 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Trait, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 578 DEBUG main org.molgenis.model.MolgenisModelParser - read: Trait 579 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=Experiment, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 580 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 581 DEBUG main org.molgenis.model.MolgenisModelParser - read: Measurement 582 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 583 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Measurement, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 584 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Sample, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 585 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Trait, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 586 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Data, name=Value, type=string[0], auto=false, nillable=false, readonly=false, default=) 587 DEBUG main org.molgenis.model.MolgenisModelParser - read: Data 588 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(example.Identifiable) 589 ( 590 Field(entity=Identifiable, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 591 Field(entity=Identifiable, name=Name, type=string[255], auto=false, nillable=false, readonly=true, default=) 592 Unique(Id, ) 593 Unique(Name, ) 594 ); 595 ENTITY: Entity(example.Experiment) 596 ( 597 Field(entity=Experiment, name=Description, type=text, auto=false, nillable=true, readonly=false, default=) 598 Field(entity=Experiment, name=Date, type=date, auto=true, nillable=false, readonly=false, default=) 599 ); 600 ENTITY: Entity(example.Sample) 601 ( 602 Field(entity=Sample, name=Species, type=string[255], auto=false, nillable=false, readonly=false, default=Arabidopsis thaliana) 603 Field(entity=Sample, name=Tissue, type=string[255], auto=false, nillable=true, readonly=false, default=) 604 Field(entity=Sample, name=Sex, type=enum, auto=false, nillable=false, readonly=false, default=, enum_options=[male, female, unknown]) 605 Field(entity=Sample, name=Experiment, type=xref[Experiment->Id], xref_label=Id, auto=false, nillable=false, readonly=false, default=) 606 Field(entity=Sample, name=SampleTime, type=datetime, auto=false, nillable=false, readonly=false, default=) 607 ); 608 ENTITY: Entity(example.SpecialSample) 609 ( 610 Field(entity=SpecialSample, name=detail, type=string[255], auto=false, nillable=false, readonly=false, default=) 611 ); 612 ENTITY: Entity(example.Trait) 613 ( 614 Field(entity=Trait, name=Molcular, type=bool, auto=false, nillable=false, readonly=false, default=) 615 Field(entity=Trait, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 616 ); 617 ENTITY: Entity(example.Measurement) 618 ( 619 Field(entity=Measurement, name=Experiment, type=xref[Experiment->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 620 Field(entity=Measurement, name=DataFile, type=file, auto=false, nillable=false, readonly=false, default=) 621 ); 622 ENTITY: Entity(example.Data) 623 ( 624 Field(entity=Data, name=Id, type=int, auto=true, nillable=false, readonly=true, default=) 625 Field(entity=Data, name=Measurement, type=xref[Measurement->id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 626 Field(entity=Data, name=Sample, type=xref[Sample->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 627 Field(entity=Data, name=Trait, type=xref[Trait->Id], xref_label=Name, auto=false, nillable=false, readonly=false, default=) 628 Field(entity=Data, name=Value, type=string[255], auto=false, nillable=false, readonly=false, default=) 629 Unique(Id, ) 630 Unique(Measurement, Sample, Trait, ) 631 ); 632 633 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 634 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 635 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 636 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 637 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 638 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 639 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 640 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 641 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 642 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 643 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 644 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 645 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 646 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 647 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 648 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 649 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 650 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 651 DEBUG main MolgenisModelValidator - validating model and adding defaults: 652 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 653 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 654 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Experiment 655 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Sample 656 DEBUG main MolgenisModelValidator - copy primary key Id from superclass Sample to SpecialSample 657 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Trait 658 DEBUG main MolgenisModelValidator - copy primary key Id from interface Identifiable to Measurement 659 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 660 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 661 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 662 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 663 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 664 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 665 INFO main MolgenisModel - parsing ui-schema 666 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 667 DEBUG main main - using file generated/sql\create_tables.sql 668 INFO main main - Updating database.... 669 INFO main main - MOLGENIS database updated succesfully 670 DEBUG main MolgenisOptions - parsed properties file. 671 INFO main main - 672 MOLGENIS version 3.3.2-testing 673 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 674 DEBUG main main - 675 Using generators: 676 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 677 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 678 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 679 generators.doc.DotDocGen #Generates one documentation file describing all entities. 680 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 681 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 682 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 683 generators.db.ViewMapperGen #generate the mappers for each database view 684 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 685 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 686 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 687 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 688 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 689 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 690 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 691 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 692 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 693 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 694 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 695 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 696 generators.R.RMatrixGen #Generates access methods in R for each matrix. 697 generators.R.RApi #Generates a R file that sources all R files. 698 generators.ui.HtmlFormGen #Generates html form class for each entity. 699 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 700 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 701 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 702 generators.ui.FormScreenGen #Generates form screens. 703 generators.ui.MenuScreenGen #Generates menu screens. 704 generators.ui.TreeScreenGen #Generates Tree screens. 705 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 706 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 707 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 708 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 709 generators.csv.CsvExportGen #Generates CsvImportExport 710 generators.csv.CsvImportGen #Generates CsvImportExport 711 712 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 713 DEBUG main org.molgenis.model.MolgenisModelParser - read: 173 714 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 174 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 175 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 715 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 176 716 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 177 717 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) … … 190 730 ( 191 731 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 192 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 193 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 732 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=false, readonly=false, default=) 194 733 Unique(id, ) 195 734 Unique(name, ) … … 278 817 mail_smtp_password = molgenispass #SMTP user for authenticated emailing. Default: null. 279 818 280 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res 819 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors.css 820 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_blue.css 821 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_blue2.css 822 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_bluegrey.css 823 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_grey.css 824 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_maroon.css 825 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\data.css 826 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\dateinput.css 827 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\dateipnut.css 828 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\main.css 829 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\menu.css 830 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\xrefinput.css 831 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\cancel.png 832 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\close.png 833 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\delete.png 834 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\deselect.png 835 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\deselectall.png 836 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\down.png 837 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\download.png 838 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\editview.gif 839 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\exit.bmp 840 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\filter.png 841 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\first.png 842 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\info.png 843 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\last.png 844 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\limit.png 845 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\listview.png 846 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\logo_molgenis.gif 847 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\new.png 848 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\next.png 849 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\none.png 850 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\open.png 851 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\prev.png 852 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\pulldown.gif 853 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\recordview.png 854 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\reset.png 855 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\rowStart.png 856 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\rowStop.png 857 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\save.png 858 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\select.png 859 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\sort_asc.gif 860 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\sort_desc.gif 861 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\up.png 862 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\update.gif 863 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\upload.png 864 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\_logo_molgenis.gif 865 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\_logo_molgenis_old.gif 866 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\all.js 867 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\Copy of datetimeinput.js 868 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\Copy of mrefinput.js 869 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\dateinput.js 870 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\datetimeinput.js 871 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\menu.js 872 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\mrefinput.js 873 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\popup.js 874 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\rest.js 875 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\textinput.js 876 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\xrefinput.js 281 877 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 282 878 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res … … 289 885 INFO main EntityModelDocGen - generated WebContent\generated-doc\entitymodel.html 290 886 INFO main DotDocGen - generated WebContent\generated-doc\objectmodel-uml-diagram.dot 291 DEBUG main DotDocGen - Executing: dot -Tpng -O C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\objectmodel-uml-diagram.dot887 DEBUG main DotDocGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 292 888 DEBUG main DotDocGen - Data model image was generated succesfully. 293 889 Output: 294 890 295 DEBUG main DotDocGen - Executing: dot -Tsvg -O C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\objectmodel-uml-diagram.dot891 DEBUG main DotDocGen - Executing: dot -Tsvg -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 296 892 DEBUG main DotDocGen - Data model image was generated succesfully. 297 893 Output: … … 304 900 INFO main CsvDocGen - generated WebContent\generated-doc\tab-format-reference.html 305 901 INFO main DotDocMinimalGen - generated WebContent\generated-doc\entity-uml-minimal-diagram.dot 306 DEBUG main DotDocMinimalGen - Executing: dot -Tpng -O C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\entity-uml-minimal-diagram.dot902 DEBUG main DotDocMinimalGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\entity-uml-minimal-diagram.dot 307 903 DEBUG main DotDocMinimalGen - Data model image was generated succesfully. 308 904 Output: … … 313 909 DEBUG main MolgenisModel - swapped Animal with Animal_group 314 910 DEBUG main MolgenisModel - swapped Event with Event_type 315 DEBUG main freemarker.beans - Key 'version' was not found on instance of org.molgenis.model.elements.Model. Introspection information for the class is: { methods=java.beans.PropertyDescriptor@1aca7055, userinterface=java.beans.PropertyDescriptor@1d7a1ce7, getEntity=public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String), getDBDescription=public java.lang.String org.molgenis.model.elements.Model.getDBDescription(), methodSchema=java.beans.PropertyDescriptor@42b30dec, getUserinterface=public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface(), hashCode=public native int java.lang.Object.hashCode(), setLabel=public void org.molgenis.model.elements.Model.setLabel(java.lang.String), concreteEntities=java.beans.PropertyDescriptor@364663e9, wait=freemarker.ext.beans.MethodMap@1f4e571, getMethods=public java.util.Vector org.molgenis.model.elements.Model.getMethods(), setDBDescription=public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String), getEntities=public java.util.Vector org.molgenis.model.elements.Model.getEntities(), getConcreteEntities=public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities(), findField=public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException, getModules=public java.util.List org.molgenis.model.elements.Model.getModules(), matrices=java.beans.PropertyDescriptor@a0ad5995, java.lang.Object@16de49c={public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema()=[Ljava.lang.Class;@1038de7, public boolean java.lang.Object.equals(java.lang.Object)=[Ljava.lang.Class;@5976c2, public java.lang.String org.molgenis.model.elements.Model.getLabel()=[Ljava.lang.Class;@183e7de, public java.util.Vector org.molgenis.model.elements.Model.getMatrices()=[Ljava.lang.Class;@ebcdbb, public final native java.lang.Class java.lang.Object.getClass()=[Ljava.lang.Class;@10fe2b9, public java.lang.String org.molgenis.model.elements.Model.getPRDescription()=[Ljava.lang.Class;@1ee148b, public java.util.Vector org.molgenis.model.elements.Model.getViews()=[Ljava.lang.Class;@186d484, public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String)=[Ljava.lang.Class;@ea48be, public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)=[Ljava.lang.Class;@14dd758, public java.lang.String org.molgenis.model.elements.Model.toString()=[Ljava.lang.Class;@174d93a, public void org.molgenis.model.elements.Model.setName(java.lang.String)=[Ljava.lang.Class;@61a907, public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String)=[Ljava.lang.Class;@1a0225b, public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase()=[Ljava.lang.Class;@2f8b5a, public java.lang.String org.molgenis.model.elements.Model.getName()=[Ljava.lang.Class;@165c7f6, public java.lang.String org.molgenis.model.elements.Model.getUIDescription()=[Ljava.lang.Class;@12aea3e, public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface()=[Ljava.lang.Class;@78bc3b, public void org.molgenis.model.elements.Model.setLabel(java.lang.String)=[Ljava.lang.Class;@8ddc4c, public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String)=[Ljava.lang.Class;@17a1767, public java.lang.String org.molgenis.model.elements.Model.getDBDescription()=[Ljava.lang.Class;@968fda, public org.molgenis.model.elements.Model(java.lang.String)=[Ljava.lang.Class;@be41ec, public native int java.lang.Object.hashCode()=[Ljava.lang.Class;@da2cef, public final native void java.lang.Object.notify()=[Ljava.lang.Class;@1bc16f0, public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException=[Ljava.lang.Class;@18622f3, public java.util.List org.molgenis.model.elements.Model.getModules()=[Ljava.lang.Class;@160877b, public final native void java.lang.Object.notifyAll()=[Ljava.lang.Class;@5eb489, public java.util.Vector org.molgenis.model.elements.Model.getMethods()=[Ljava.lang.Class;@19ec4ed, public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String)=[Ljava.lang.Class;@92dcdb, public java.util.Vector org.molgenis.model.elements.Model.getEntities()=[Ljava.lang.Class;@1e1be92, public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities()=[Ljava.lang.Class;@1a6684f}, name=java.beans.PropertyDescriptor@e0aa5f55, notify=public final native void java.lang.Object.notify(), PRDescription=java.beans.PropertyDescriptor@39b0674, notifyAll=public final native void java.lang.Object.notifyAll(), setPRDescription=public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String), getClass=public final native java.lang.Class java.lang.Object.getClass(), UIDescription=java.beans.PropertyDescriptor@47963ae2, getViews=public java.util.Vector org.molgenis.model.elements.Model.getViews(), equals=public boolean java.lang.Object.equals(java.lang.Object), class=java.beans.PropertyDescriptor@52b1c6cd, getPRDescription=public java.lang.String org.molgenis.model.elements.Model.getPRDescription(), label=java.beans.PropertyDescriptor@71b8470e, DBDescription=java.beans.PropertyDescriptor@1b54f998, entities=java.beans.PropertyDescriptor@eeca95fc, getMethodSchema=public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema(), database=java.beans.PropertyDescriptor@202e32be, getLabel=public java.lang.String org.molgenis.model.elements.Model.getLabel(), getMatrices=public java.util.Vector org.molgenis.model.elements.Model.getMatrices(), getUIDescription=public java.lang.String org.molgenis.model.elements.Model.getUIDescription(), setUIDescription=public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String), java.lang.Object@1ff0dde=public org.molgenis.model.elements.Model(java.lang.String), views=java.beans.PropertyDescriptor@4213eb89, getDatabase=public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase(), getName=public java.lang.String org.molgenis.model.elements.Model.getName(), toString=public java.lang.String org.molgenis.model.elements.Model.toString(), setName=public void org.molgenis.model.elements.Model.setName(java.lang.String), modules=java.beans.PropertyDescriptor@829fc63f, getRecord=public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)}911 DEBUG main freemarker.beans - Key 'version' was not found on instance of org.molgenis.model.elements.Model. Introspection information for the class is: {java.lang.Object@1908ca1=public org.molgenis.model.elements.Model(java.lang.String), methods=java.beans.PropertyDescriptor@d3835edc, userinterface=java.beans.PropertyDescriptor@3b9c579f, getEntity=public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String), getDBDescription=public java.lang.String org.molgenis.model.elements.Model.getDBDescription(), methodSchema=java.beans.PropertyDescriptor@5fdc322e, getUserinterface=public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface(), hashCode=public native int java.lang.Object.hashCode(), setLabel=public void org.molgenis.model.elements.Model.setLabel(java.lang.String), concreteEntities=java.beans.PropertyDescriptor@eeff5270, wait=freemarker.ext.beans.MethodMap@16e1fb1, getMethods=public java.util.Vector org.molgenis.model.elements.Model.getMethods(), getEntities=public java.util.Vector org.molgenis.model.elements.Model.getEntities(), setDBDescription=public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String), getConcreteEntities=public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities(), findField=public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException, getModules=public java.util.List org.molgenis.model.elements.Model.getModules(), matrices=java.beans.PropertyDescriptor@5966481c, name=java.beans.PropertyDescriptor@713926fc, notify=public final native void java.lang.Object.notify(), PRDescription=java.beans.PropertyDescriptor@9429ce1b, notifyAll=public final native void java.lang.Object.notifyAll(), java.lang.Object@503429={public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema()=[Ljava.lang.Class;@e2cb55, public boolean java.lang.Object.equals(java.lang.Object)=[Ljava.lang.Class;@19360e2, public java.lang.String org.molgenis.model.elements.Model.getLabel()=[Ljava.lang.Class;@bdb503, public java.util.Vector org.molgenis.model.elements.Model.getMatrices()=[Ljava.lang.Class;@b6e39f, public final native java.lang.Class java.lang.Object.getClass()=[Ljava.lang.Class;@119dc16, public java.lang.String org.molgenis.model.elements.Model.getPRDescription()=[Ljava.lang.Class;@c05d3b, public java.util.Vector org.molgenis.model.elements.Model.getViews()=[Ljava.lang.Class;@128f6ee, public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String)=[Ljava.lang.Class;@6bade9, public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)=[Ljava.lang.Class;@166afb3, public java.lang.String org.molgenis.model.elements.Model.toString()=[Ljava.lang.Class;@9945ce, public void org.molgenis.model.elements.Model.setName(java.lang.String)=[Ljava.lang.Class;@b5dac4, public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String)=[Ljava.lang.Class;@12d96f2, public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase()=[Ljava.lang.Class;@110003, public java.lang.String org.molgenis.model.elements.Model.getName()=[Ljava.lang.Class;@17e4ca, public java.lang.String org.molgenis.model.elements.Model.getUIDescription()=[Ljava.lang.Class;@adb1d4, public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface()=[Ljava.lang.Class;@175d6ab, public void org.molgenis.model.elements.Model.setLabel(java.lang.String)=[Ljava.lang.Class;@160a26f, public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String)=[Ljava.lang.Class;@1484a05, public java.lang.String org.molgenis.model.elements.Model.getDBDescription()=[Ljava.lang.Class;@f39b3a, public org.molgenis.model.elements.Model(java.lang.String)=[Ljava.lang.Class;@1542a75, public native int java.lang.Object.hashCode()=[Ljava.lang.Class;@af993e, public final native void java.lang.Object.notify()=[Ljava.lang.Class;@75e4fc, public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException=[Ljava.lang.Class;@c62c8, public java.util.List org.molgenis.model.elements.Model.getModules()=[Ljava.lang.Class;@12940b3, public final native void java.lang.Object.notifyAll()=[Ljava.lang.Class;@156b6b9, public java.util.Vector org.molgenis.model.elements.Model.getMethods()=[Ljava.lang.Class;@1f66cff, public java.util.Vector org.molgenis.model.elements.Model.getEntities()=[Ljava.lang.Class;@16de49c, public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String)=[Ljava.lang.Class;@1bbf1ca, public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities()=[Ljava.lang.Class;@1ff0dde}, setPRDescription=public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String), getClass=public final native java.lang.Class java.lang.Object.getClass(), UIDescription=java.beans.PropertyDescriptor@d8250289, getViews=public java.util.Vector org.molgenis.model.elements.Model.getViews(), equals=public boolean java.lang.Object.equals(java.lang.Object), class=java.beans.PropertyDescriptor@e08218f8, getPRDescription=public java.lang.String org.molgenis.model.elements.Model.getPRDescription(), label=java.beans.PropertyDescriptor@2470eb5, DBDescription=java.beans.PropertyDescriptor@abe3c13f, entities=java.beans.PropertyDescriptor@a7838483, getMethodSchema=public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema(), database=java.beans.PropertyDescriptor@e363d93a, getLabel=public java.lang.String org.molgenis.model.elements.Model.getLabel(), getMatrices=public java.util.Vector org.molgenis.model.elements.Model.getMatrices(), getUIDescription=public java.lang.String org.molgenis.model.elements.Model.getUIDescription(), setUIDescription=public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String), views=java.beans.PropertyDescriptor@faccda10, getDatabase=public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase(), getName=public java.lang.String org.molgenis.model.elements.Model.getName(), toString=public java.lang.String org.molgenis.model.elements.Model.toString(), setName=public void org.molgenis.model.elements.Model.setName(java.lang.String), modules=java.beans.PropertyDescriptor@dd1ecca2, getRecord=public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)} 316 912 INFO main ObjectModelDocGen - generated WebContent\generated-doc\objectmodel.html 317 913 DEBUG main MolgenisModel - swapped Event with Animal … … 402 998 INFO main FormScreenGen - generated generated\java\app\ui\AnimalForm.java 403 999 INFO main FormScreenGen - generated generated\java\app\ui\Event_typeForm.java 1000 INFO main FormScreenGen - generated generated\java\app\ui\EventForm.java 404 1001 INFO main MenuScreenGen - generated generated\java\app\ui\MainmenuMenu.java 405 1002 INFO main MenuScreenGen - generated generated\java\app\ui\TopmenuMenu.java 406 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\WelcomeScreenPlugin.java 407 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\ManageEventsPlugin.java 408 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\MakeReportPlugin.java 1003 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\WelcomeScreenPlugin.java 1004 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\MakeReportPlugin.java 409 1005 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.ftl 410 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\eventman\ManageEventsPlugin.ftl411 1006 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\reports\MakeReportPlugin.ftl 412 1007 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.java 413 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\eventman\ManageEventsPlugin.java414 1008 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\reports\MakeReportPlugin.java 415 1009 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml … … 427 1021 DEBUG main MolgenisModel - swapped Event with Event_type 428 1022 INFO main CsvImportGen - generated generated\java\app\CsvImport.java 429 DEBUG main MolgenisModelValidator - validating model and adding defaults:430 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words...431 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships...432 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints...433 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references...434 DEBUG main MolgenisModelValidator - correct case of names in xrefs...435 DEBUG main MolgenisModelValidator - add linktable entities for mrefs...436 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level...437 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking...438 DEBUG main MolgenisModelValidator - validating model and adding defaults:439 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words...440 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships...441 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints...442 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references...443 DEBUG main MolgenisModelValidator - correct case of names in xrefs...444 DEBUG main MolgenisModelValidator - add linktable entities for mrefs...445 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level...446 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking...447 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51opened database connection, connectioncount=1448 DEBUG main JDBCDatabase - begin transaction449 INFO main JDBCDatabase - rolled back transaction450 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51closed connection back to pool, connectioncount=0451 ERROR main Event_typeMapper - ADD failed on Event_type: Unknown column 'comment' in 'field list'452 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51opened database connection, connectioncount=1453 DEBUG main JDBCDatabase - begin transaction454 INFO main JDBCDatabase - rolled back transaction455 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51closed connection back to pool, connectioncount=0456 ERROR main Animal_groupMapper - ADD failed on Animal_group: Unknown column 'comment' in 'field list'457 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51opened database connection, connectioncount=1458 DEBUG main JDBCDatabase - begin transaction459 INFO main JDBCDatabase - rolled back transaction460 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51closed connection back to pool, connectioncount=0461 ERROR main LocationMapper - ADD failed on Location: Unknown column 'comment' in 'field list'462 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51opened database connection, connectioncount=1463 DEBUG main JDBCDatabase - begin transaction464 INFO main JDBCDatabase - rolled back transaction465 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51closed connection back to pool, connectioncount=0466 ERROR main AnimalMapper - ADD failed on Animal: Unknown column 'comment' in 'field list'467 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51opened database connection, connectioncount=1468 DEBUG main JDBCDatabase - begin transaction469 INFO main JDBCDatabase - rolled back transaction470 INFO main JDBCDatabase - app.JDBCDatabase@1d9fd51closed connection back to pool, connectioncount=0471 ERROR main EventMapper - ADD failed on Event: Unknown column 'comment' in 'field list'472 1023 DEBUG main MolgenisOptions - parsed properties file. 473 1024 INFO main main - 474 1025 MOLGENIS version 3.3.2-testing 475 INFO main main - working dir: C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb1026 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 476 1027 DEBUG main main - 477 1028 Using generators: … … 498 1049 generators.R.RMatrixGen #Generates access methods in R for each matrix. 499 1050 generators.R.RApi #Generates a R file that sources all R files. 500 generators.ui.HtmlFormGen #Generates html form class for each entity.501 1051 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 502 1052 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. … … 518 1068 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 519 1069 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 520 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1070 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=litterid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1071 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=customid, type=string[0], auto=false, nillable=true, readonly=false, default=) 1072 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1073 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=sourceid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1074 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1075 DEBUG main org.molgenis.model.MolgenisModelParser - read: AbstractAnimal 1076 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=identifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1077 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=unidentifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1078 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=experimentid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 521 1079 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 522 1080 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 523 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1081 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=timestamp, type=datetime, auto=true, nillable=false, readonly=false, default=) 1082 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 524 1083 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 525 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=)526 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=)527 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=)528 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal529 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group530 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location531 1084 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 532 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 533 ( 534 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 535 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 536 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 537 Unique(id, ) 538 Unique(name, ) 539 ); 540 ENTITY: Entity(animaldb.Event) 541 ( 542 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 543 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 544 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 545 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 546 ); 547 ENTITY: Entity(animaldb.Animal) 548 ( 549 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 550 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 551 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 552 ); 553 ENTITY: Entity(animaldb.Animal_group) 554 ( 555 ); 556 ENTITY: Entity(animaldb.Location) 557 ( 558 ); 559 ENTITY: Entity(animaldb.Event_type) 560 ( 561 ); 562 563 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 564 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 565 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 566 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 567 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 568 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 569 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 570 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 571 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 572 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 573 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 574 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 575 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 576 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 577 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 578 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 579 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 580 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 581 DEBUG main MolgenisModelValidator - validating model and adding defaults: 582 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 583 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 584 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 585 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 586 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 587 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 588 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 589 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 590 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 591 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 592 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 593 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 594 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 595 INFO main MolgenisModel - parsing ui-schema 596 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 597 DEBUG main main - using file generated/sql\create_tables.sql 598 INFO main main - Updating database.... 599 INFO main main - MOLGENIS database updated succesfully 1085 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identified, name=genotypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1086 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identified 1087 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Unidentified, name=quantity, type=int, auto=false, nillable=false, readonly=false, default=) 1088 ERROR main DSLParser - type 'boolean' unknown for field 'exact' of entity 'Unidentified' 1089 ERROR main MolgenisModel - Parsing failed: type 'boolean' unknown for field 'exact' of entity 'Unidentified' 600 1090 DEBUG main MolgenisOptions - parsed properties file. 601 1091 INFO main main - 602 1092 MOLGENIS version 3.3.2-testing 603 INFO main main - working dir: C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb1093 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 604 1094 DEBUG main main - 605 1095 Using generators: … … 626 1116 generators.R.RMatrixGen #Generates access methods in R for each matrix. 627 1117 generators.R.RApi #Generates a R file that sources all R files. 628 generators.ui.HtmlFormGen #Generates html form class for each entity.629 1118 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 630 1119 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. … … 646 1135 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 647 1136 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 648 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1137 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=litterid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1138 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=customid, type=string[0], auto=false, nillable=true, readonly=false, default=) 1139 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1140 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=sourceid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1141 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1142 DEBUG main org.molgenis.model.MolgenisModelParser - read: AbstractAnimal 1143 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=identifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1144 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=unidentifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1145 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=experimentid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 649 1146 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 650 1147 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 651 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1148 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=timestamp, type=datetime, auto=true, nillable=false, readonly=false, default=) 1149 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 652 1150 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 653 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 654 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 655 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 656 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 657 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1151 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1152 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identified, name=genotypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1153 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identified 1154 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Unidentified, name=quantity, type=int, auto=false, nillable=false, readonly=false, default=) 1155 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Unidentified, name=exact, type=bool, auto=false, nillable=false, readonly=false, default=) 1156 DEBUG main org.molgenis.model.MolgenisModelParser - read: Unidentified 1157 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1158 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=identified_locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1159 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=unidentified_locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1160 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=fromdate, type=date, auto=true, nillable=false, readonly=false, default=) 1161 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=todate, type=date, auto=true, nillable=true, readonly=false, default=) 1162 DEBUG main org.molgenis.model.MolgenisModelParser - read: Loc_bridge 1163 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Location, name=address, type=string[0], auto=false, nillable=false, readonly=false, default=) 1164 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Location, name=inlocationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 658 1165 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 659 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1166 DEBUG main org.molgenis.model.MolgenisModelParser - read: Source 1167 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Genotype, name=genotype_description, type=string[0], auto=false, nillable=false, readonly=false, default=) 1168 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Genotype, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1169 DEBUG main org.molgenis.model.MolgenisModelParser - read: Genotype 1170 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=fatherid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1171 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=motherid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1172 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=fromdatepair, type=date, auto=true, nillable=false, readonly=false, default=) 1173 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=todatepair, type=date, auto=true, nillable=true, readonly=false, default=) 1174 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=birthdate, type=date, auto=true, nillable=false, readonly=false, default=) 1175 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=birthsize, type=int, auto=false, nillable=false, readonly=false, default=) 1176 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=weandate, type=date, auto=true, nillable=false, readonly=false, default=) 1177 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=weansize, type=int, auto=false, nillable=false, readonly=false, default=) 1178 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1179 DEBUG main org.molgenis.model.MolgenisModelParser - read: Litter 1180 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=experiment_description, type=string[0], auto=false, nillable=false, readonly=false, default=) 1181 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=decnumber, type=string[0], auto=false, nillable=false, readonly=false, default=) 1182 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expentrydate, type=date, auto=true, nillable=false, readonly=false, default=) 1183 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expexitdate_est, type=date, auto=true, nillable=false, readonly=false, default=) 1184 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expexitdate_real, type=date, auto=true, nillable=true, readonly=false, default=) 1185 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=inconvenience_est, type=int, auto=false, nillable=false, readonly=false, default=) 1186 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=inconvenience_real, type=int, auto=false, nillable=false, readonly=false, default=) 1187 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1188 DEBUG main org.molgenis.model.MolgenisModelParser - read: Experiment 1189 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=protocol_eventid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1190 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=key, type=string[0], auto=false, nillable=false, readonly=false, default=) 1191 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=value, type=string[0], auto=false, nillable=false, readonly=false, default=) 1192 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=unit, type=string[0], auto=false, nillable=true, readonly=false, default=) 1193 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1194 DEBUG main org.molgenis.model.MolgenisModelParser - read: Protocol 1195 DEBUG main org.molgenis.model.MolgenisModelParser - read: Owner 660 1196 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 661 1197 ( … … 666 1202 Unique(name, ) 667 1203 ); 1204 ENTITY: Entity(animaldb.AbstractAnimal) 1205 ( 1206 Field(entity=AbstractAnimal, name=litterid, type=xref[Litter->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1207 Field(entity=AbstractAnimal, name=customid, type=string[255], auto=false, nillable=true, readonly=false, default=) 1208 Field(entity=AbstractAnimal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1209 Field(entity=AbstractAnimal, name=sourceid, type=xref[Source->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1210 Field(entity=AbstractAnimal, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1211 ); 668 1212 ENTITY: Entity(animaldb.Event) 669 1213 ( 670 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1214 Field(entity=Event, name=identifiedid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1215 Field(entity=Event, name=unidentifiedid, type=xref[Unidentified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1216 Field(entity=Event, name=experimentid, type=xref[Experiment->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 671 1217 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 672 1218 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 673 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 674 ); 675 ENTITY: Entity(animaldb.Animal) 676 ( 677 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 678 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 679 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 680 ); 681 ENTITY: Entity(animaldb.Animal_group) 682 ( 1219 Field(entity=Event, name=timestamp, type=datetime, auto=true, nillable=false, readonly=false, default=) 1220 Field(entity=Event, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1221 ); 1222 ENTITY: Entity(animaldb.Event_type) 1223 ( 1224 ); 1225 ENTITY: Entity(animaldb.Identified) 1226 ( 1227 Field(entity=Identified, name=genotypeid, type=xref[Genotype->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1228 ); 1229 ENTITY: Entity(animaldb.Unidentified) 1230 ( 1231 Field(entity=Unidentified, name=quantity, type=int, auto=false, nillable=false, readonly=false, default=) 1232 Field(entity=Unidentified, name=exact, type=bool, auto=false, nillable=false, readonly=false, default=) 1233 ); 1234 ENTITY: Entity(animaldb.Loc_bridge) 1235 ( 1236 Field(entity=Loc_bridge, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1237 Field(entity=Loc_bridge, name=identified_locationid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1238 Field(entity=Loc_bridge, name=unidentified_locationid, type=xref[Unidentified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1239 Field(entity=Loc_bridge, name=fromdate, type=date, auto=true, nillable=false, readonly=false, default=) 1240 Field(entity=Loc_bridge, name=todate, type=date, auto=true, nillable=true, readonly=false, default=) 683 1241 ); 684 1242 ENTITY: Entity(animaldb.Location) 685 1243 ( 686 ); 687 ENTITY: Entity(animaldb.Event_type) 1244 Field(entity=Location, name=address, type=string[255], auto=false, nillable=false, readonly=false, default=) 1245 Field(entity=Location, name=inlocationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1246 ); 1247 ENTITY: Entity(animaldb.Source) 1248 ( 1249 ); 1250 ENTITY: Entity(animaldb.Genotype) 1251 ( 1252 Field(entity=Genotype, name=genotype_description, type=string[255], auto=false, nillable=false, readonly=false, default=) 1253 Field(entity=Genotype, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1254 ); 1255 ENTITY: Entity(animaldb.Litter) 1256 ( 1257 Field(entity=Litter, name=fatherid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1258 Field(entity=Litter, name=motherid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1259 Field(entity=Litter, name=fromdatepair, type=date, auto=true, nillable=false, readonly=false, default=) 1260 Field(entity=Litter, name=todatepair, type=date, auto=true, nillable=true, readonly=false, default=) 1261 Field(entity=Litter, name=birthdate, type=date, auto=true, nillable=false, readonly=false, default=) 1262 Field(entity=Litter, name=birthsize, type=int, auto=false, nillable=false, readonly=false, default=) 1263 Field(entity=Litter, name=weandate, type=date, auto=true, nillable=false, readonly=false, default=) 1264 Field(entity=Litter, name=weansize, type=int, auto=false, nillable=false, readonly=false, default=) 1265 Field(entity=Litter, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1266 ); 1267 ENTITY: Entity(animaldb.Experiment) 1268 ( 1269 Field(entity=Experiment, name=experiment_description, type=string[255], auto=false, nillable=false, readonly=false, default=) 1270 Field(entity=Experiment, name=decnumber, type=string[255], auto=false, nillable=false, readonly=false, default=) 1271 Field(entity=Experiment, name=expentrydate, type=date, auto=true, nillable=false, readonly=false, default=) 1272 Field(entity=Experiment, name=expexitdate_est, type=date, auto=true, nillable=false, readonly=false, default=) 1273 Field(entity=Experiment, name=expexitdate_real, type=date, auto=true, nillable=true, readonly=false, default=) 1274 Field(entity=Experiment, name=inconvenience_est, type=int, auto=false, nillable=false, readonly=false, default=) 1275 Field(entity=Experiment, name=inconvenience_real, type=int, auto=false, nillable=false, readonly=false, default=) 1276 Field(entity=Experiment, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1277 ); 1278 ENTITY: Entity(animaldb.Protocol) 1279 ( 1280 Field(entity=Protocol, name=protocol_eventid, type=xref[Event->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1281 Field(entity=Protocol, name=key, type=string[255], auto=false, nillable=false, readonly=false, default=) 1282 Field(entity=Protocol, name=value, type=string[255], auto=false, nillable=false, readonly=false, default=) 1283 Field(entity=Protocol, name=unit, type=string[255], auto=false, nillable=true, readonly=false, default=) 1284 Field(entity=Protocol, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1285 ); 1286 ENTITY: Entity(animaldb.Owner) 688 1287 ( 689 1288 ); … … 709 1308 DEBUG main MolgenisModelValidator - validating model and adding defaults: 710 1309 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 711 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 712 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 713 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 714 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 715 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 716 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 717 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 718 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 719 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 720 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 721 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 722 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 723 INFO main MolgenisModel - parsing ui-schema 724 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 725 INFO main main - generating .... 726 INFO main main - 727 Using options: 728 model_database = [molgenis4animal_db.xml, molgenis_auth.xml] #File with data structure specification (in MOLGENIS DSL). 729 model_userinterface = molgenis4animal_ui.xml #File with user interface specification (in MOLGENIS DSL). Can be same file as model_database 730 output_src = generated/java/ #Output-directory for the generated project. 731 output_hand = handwritten/java/ #Output-directory for the generated project. 732 output_sql = generated/sql #Output-directory for the generated sql files. 733 output_doc = WebContent/generated-doc #Output-directory for the generated documentation. 734 output_web = WebContent #Output-directory for any generated web resources 735 db_driver = com.mysql.jdbc.Driver #Driver of database. Any JDBC compatible driver should work. 736 db_user = molgenis #Username for database. 737 db_password = xxxxxx #Password for database. 738 db_uri = jdbc:mysql://localhost/animaldb_proto?innodb_autoinc_lock_mode=2 #Uri of the database. Default: localhost 739 db_filepath = attachedfiles #Path where the database should store file attachements. Default: null 740 db_jndiname = jdbc/molgenisdb #Used to create a JDBC database resource for the application 741 object_relational_mapping = subclass_per_table #Expert option: Choosing OR strategy. Either 'class_per_table', 'subclass_per_table', 'hierarchy_per_table'. Default: class_per_table 742 mapper_implementation = multiquery #Expert option: Choosing wether multiquery is used instead of prepared statements. Default: false 743 exclude_system = true #Expert option: Whether system tables should be excluded from generation. Default: true 744 auth_loginclass = org.molgenis.framework.security.SimpleLogin #Expert option. 745 mail_smtp_protocol = smtps #Sets the email protocol, either smtp, smtps or null. Default: null meaning email disabled 746 mail_smtp_hostname = smtp.gmail.com #SMTP host server. Default: localhost 747 mail_smtp_port = 465 #SMTP host server port. Default: 25 748 mail_smtp_user = molgenis #SMTP user for authenticated emailing. Default: null. 749 mail_smtp_password = molgenispass #SMTP user for authenticated emailing. Default: null. 750 751 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res 752 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 753 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 754 INFO main TableDocGen - generated WebContent\generated-doc\tabledoc.html 755 DEBUG main MolgenisModel - swapped Event with Animal 756 DEBUG main MolgenisModel - swapped Animal with Location 757 DEBUG main MolgenisModel - swapped Event with Animal 758 DEBUG main MolgenisModel - swapped Animal with Animal_group 759 DEBUG main MolgenisModel - swapped Event with Event_type 760 INFO main EntityModelDocGen - generated WebContent\generated-doc\entitymodel.html 761 INFO main DotDocGen - generated WebContent\generated-doc\objectmodel-uml-diagram.dot 762 DEBUG main DotDocGen - Executing: dot -Tpng -O C:\Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\objectmodel-uml-diagram.dot 763 DEBUG main DotDocGen - Data model image was generated succesfully. 764 Output: 765 766 DEBUG main DotDocGen - Executing: dot -Tsvg -O C:\Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\objectmodel-uml-diagram.dot 767 DEBUG main DotDocGen - Data model image was generated succesfully. 768 Output: 769 770 DEBUG main MolgenisModel - swapped Event with Animal 771 DEBUG main MolgenisModel - swapped Animal with Location 772 DEBUG main MolgenisModel - swapped Event with Animal 773 DEBUG main MolgenisModel - swapped Animal with Animal_group 774 DEBUG main MolgenisModel - swapped Event with Event_type 775 INFO main CsvDocGen - generated WebContent\generated-doc\tab-format-reference.html 776 INFO main DotDocMinimalGen - generated WebContent\generated-doc\entity-uml-minimal-diagram.dot 777 DEBUG main DotDocMinimalGen - Executing: dot -Tpng -O C:\Documents and Settings\Administrator\workspace\molgenis4animaldb\WebContent\generated-doc\entity-uml-minimal-diagram.dot 778 DEBUG main DotDocMinimalGen - Data model image was generated succesfully. 779 Output: 780 781 DEBUG main MolgenisModel - swapped Event with Animal 782 DEBUG main MolgenisModel - swapped Animal with Location 783 DEBUG main MolgenisModel - swapped Event with Animal 784 DEBUG main MolgenisModel - swapped Animal with Animal_group 785 DEBUG main MolgenisModel - swapped Event with Event_type 786 DEBUG main freemarker.beans - Key 'version' was not found on instance of org.molgenis.model.elements.Model. Introspection information for the class is: {methods=java.beans.PropertyDescriptor@1aca7055, userinterface=java.beans.PropertyDescriptor@9bdbee0e, getEntity=public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String), getDBDescription=public java.lang.String org.molgenis.model.elements.Model.getDBDescription(), methodSchema=java.beans.PropertyDescriptor@65428cdc, getUserinterface=public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface(), hashCode=public native int java.lang.Object.hashCode(), setLabel=public void org.molgenis.model.elements.Model.setLabel(java.lang.String), concreteEntities=java.beans.PropertyDescriptor@364663e9, wait=freemarker.ext.beans.MethodMap@174d93a, getMethods=public java.util.Vector org.molgenis.model.elements.Model.getMethods(), setDBDescription=public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String), getEntities=public java.util.Vector org.molgenis.model.elements.Model.getEntities(), getConcreteEntities=public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities(), findField=public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException, getModules=public java.util.List org.molgenis.model.elements.Model.getModules(), matrices=java.beans.PropertyDescriptor@a0ad5995, name=java.beans.PropertyDescriptor@e0aa5f55, notify=public final native void java.lang.Object.notify(), java.lang.Object@1f66cff=public org.molgenis.model.elements.Model(java.lang.String), PRDescription=java.beans.PropertyDescriptor@39b0674, notifyAll=public final native void java.lang.Object.notifyAll(), setPRDescription=public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String), getClass=public final native java.lang.Class java.lang.Object.getClass(), UIDescription=java.beans.PropertyDescriptor@47963ae2, getViews=public java.util.Vector org.molgenis.model.elements.Model.getViews(), equals=public boolean java.lang.Object.equals(java.lang.Object), class=java.beans.PropertyDescriptor@346fdd19, getPRDescription=public java.lang.String org.molgenis.model.elements.Model.getPRDescription(), label=java.beans.PropertyDescriptor@71b8470e, DBDescription=java.beans.PropertyDescriptor@1b54f998, entities=java.beans.PropertyDescriptor@eeca95fc, getMethodSchema=public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema(), database=java.beans.PropertyDescriptor@202e32be, getLabel=public java.lang.String org.molgenis.model.elements.Model.getLabel(), getMatrices=public java.util.Vector org.molgenis.model.elements.Model.getMatrices(), getUIDescription=public java.lang.String org.molgenis.model.elements.Model.getUIDescription(), setUIDescription=public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String), views=java.beans.PropertyDescriptor@4213eb89, getDatabase=public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase(), getName=public java.lang.String org.molgenis.model.elements.Model.getName(), toString=public java.lang.String org.molgenis.model.elements.Model.toString(), setName=public void org.molgenis.model.elements.Model.setName(java.lang.String), modules=java.beans.PropertyDescriptor@4ff7dd6, java.lang.Object@156b6b9={public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema()=[Ljava.lang.Class;@1a0225b, public boolean java.lang.Object.equals(java.lang.Object)=[Ljava.lang.Class;@2f8b5a, public java.lang.String org.molgenis.model.elements.Model.getLabel()=[Ljava.lang.Class;@165c7f6, public java.util.Vector org.molgenis.model.elements.Model.getMatrices()=[Ljava.lang.Class;@12aea3e, public final native java.lang.Class java.lang.Object.getClass()=[Ljava.lang.Class;@78bc3b, public java.lang.String org.molgenis.model.elements.Model.getPRDescription()=[Ljava.lang.Class;@8ddc4c, public java.util.Vector org.molgenis.model.elements.Model.getViews()=[Ljava.lang.Class;@17a1767, public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String)=[Ljava.lang.Class;@968fda, public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)=[Ljava.lang.Class;@be41ec, public java.lang.String org.molgenis.model.elements.Model.toString()=[Ljava.lang.Class;@da2cef, public void org.molgenis.model.elements.Model.setName(java.lang.String)=[Ljava.lang.Class;@1bc16f0, public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String)=[Ljava.lang.Class;@18622f3, public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase()=[Ljava.lang.Class;@160877b, public java.lang.String org.molgenis.model.elements.Model.getName()=[Ljava.lang.Class;@5eb489, public java.lang.String org.molgenis.model.elements.Model.getUIDescription()=[Ljava.lang.Class;@19ec4ed, public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface()=[Ljava.lang.Class;@92dcdb, public void org.molgenis.model.elements.Model.setLabel(java.lang.String)=[Ljava.lang.Class;@1e1be92, public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String)=[Ljava.lang.Class;@1a6684f, public java.lang.String org.molgenis.model.elements.Model.getDBDescription()=[Ljava.lang.Class;@a3d3b, public org.molgenis.model.elements.Model(java.lang.String)=[Ljava.lang.Class;@3a1ec6, public native int java.lang.Object.hashCode()=[Ljava.lang.Class;@1ba6076, public final native void java.lang.Object.notify()=[Ljava.lang.Class;@112e7f7, public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException=[Ljava.lang.Class;@3b1f38, public java.util.List org.molgenis.model.elements.Model.getModules()=[Ljava.lang.Class;@17ec9f7, public final native void java.lang.Object.notifyAll()=[Ljava.lang.Class;@fd918a, public java.util.Vector org.molgenis.model.elements.Model.getMethods()=[Ljava.lang.Class;@15e2075, public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String)=[Ljava.lang.Class;@a522a6, public java.util.Vector org.molgenis.model.elements.Model.getEntities()=[Ljava.lang.Class;@1860038, public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities()=[Ljava.lang.Class;@787c16}, getRecord=public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)} 787 INFO main ObjectModelDocGen - generated WebContent\generated-doc\objectmodel.html 788 DEBUG main MolgenisModel - swapped Event with Animal 789 DEBUG main MolgenisModel - swapped Animal with Location 790 DEBUG main MolgenisModel - swapped Event with Animal 791 DEBUG main MolgenisModel - swapped Animal with Animal_group 792 DEBUG main MolgenisModel - swapped Event with Event_type 793 INFO main MySqlCreateSubclassPerTableGen - generated generated\sql\create_tables.sql 794 DEBUG main MolgenisModel - swapped Event with Animal 795 DEBUG main MolgenisModel - swapped Animal with Location 796 DEBUG main MolgenisModel - swapped Event with Animal 797 DEBUG main MolgenisModel - swapped Animal with Animal_group 798 DEBUG main MolgenisModel - swapped Event with Event_type 799 INFO main MySqlAlterSubclassPerTableGen - generated generated\sql\alter_tables.sql 800 INFO main JDBCDatabaseGen - generated generated\java\app\JDBCDatabase.java 801 INFO main DataTypeGen - generated generated\java\animaldb\Identifiable.java 802 INFO main DataTypeGen - generated generated\java\animaldb\Event.java 803 INFO main DataTypeGen - generated generated\java\animaldb\Animal.java 804 INFO main DataTypeGen - generated generated\java\animaldb\Animal_group.java 805 INFO main DataTypeGen - generated generated\java\animaldb\Location.java 806 INFO main DataTypeGen - generated generated\java\animaldb\Event_type.java 807 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup.java 808 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUser.java 809 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisEntityMetaData.java 810 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_members.java 811 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canRead.java 812 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canWrite.java 813 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\EventMapper.java 814 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\AnimalMapper.java 815 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\Animal_groupMapper.java 816 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\LocationMapper.java 817 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\Event_typeMapper.java 818 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroupMapper.java 819 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserMapper.java 820 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisEntityMetaDataMapper.java 821 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_membersMapper.java 822 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canReadMapper.java 823 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canWriteMapper.java 824 DEBUG main MolgenisModel - swapped Event with Animal 825 DEBUG main MolgenisModel - swapped Animal with Location 826 DEBUG main MolgenisModel - swapped Event with Animal 827 DEBUG main MolgenisModel - swapped Animal with Animal_group 828 DEBUG main MolgenisModel - swapped Event with Event_type 829 INFO main JDBCMetaDatabaseGen - generated generated\java\app\JDBCMetaDatabase.java 830 INFO main CountPerEntityGen - generated generated\sql\count_per_entity.sql 831 INFO main CountPerTableGen - generated generated\sql\count_per_table.sql 832 INFO main FillMetadataTablesGen - generated generated\sql\insert_metadata.sql 833 INFO main CsvReaderGen - generated generated\java\animaldb\csv\EventCsvReader.java 834 INFO main CsvReaderGen - generated generated\java\animaldb\csv\AnimalCsvReader.java 835 INFO main CsvReaderGen - generated generated\java\animaldb\csv\Animal_groupCsvReader.java 836 INFO main CsvReaderGen - generated generated\java\animaldb\csv\LocationCsvReader.java 837 INFO main CsvReaderGen - generated generated\java\animaldb\csv\Event_typeCsvReader.java 838 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroupCsvReader.java 839 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserCsvReader.java 840 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisEntityMetaDataCsvReader.java 841 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_membersCsvReader.java 842 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canReadCsvReader.java 843 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canWriteCsvReader.java 844 INFO main REntityGen - generated generated\java\animaldb\R\Event.R 845 INFO main REntityGen - generated generated\java\animaldb\R\Animal.R 846 INFO main REntityGen - generated generated\java\animaldb\R\Animal_group.R 847 INFO main REntityGen - generated generated\java\animaldb\R\Location.R 848 INFO main REntityGen - generated generated\java\animaldb\R\Event_type.R 849 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup.R 850 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUser.R 851 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisEntityMetaData.R 852 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_members.R 853 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canRead.R 854 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canWrite.R 855 INFO main RApi - generated generated\java\app\servlet\source.R 856 INFO main HtmlFormGen - generated generated\java\animaldb\ui\IdentifiableHtmlForm.java 857 INFO main HtmlFormGen - generated generated\java\animaldb\ui\EventHtmlForm.java 858 INFO main HtmlFormGen - generated generated\java\animaldb\ui\AnimalHtmlForm.java 859 INFO main HtmlFormGen - generated generated\java\animaldb\ui\Animal_groupHtmlForm.java 860 INFO main HtmlFormGen - generated generated\java\animaldb\ui\LocationHtmlForm.java 861 INFO main HtmlFormGen - generated generated\java\animaldb\ui\Event_typeHtmlForm.java 862 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroupHtmlForm.java 863 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserHtmlForm.java 864 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisEntityMetaDataHtmlForm.java 865 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_membersHtmlForm.java 866 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_canReadHtmlForm.java 867 INFO main HtmlFormGen - generated generated\java\org\molgenis\auth\ui\MolgenisUserGroup_canWriteHtmlForm.java 868 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 869 INFO main MolgenisContextListenerGen - generated generated\java\app\servlet\ContextListener.java 870 INFO main MolgenisServletGen - generated generated\java\app\servlet\MolgenisServlet.java 871 INFO main FormScreenGen - generated generated\java\app\ui\LocationForm.java 872 INFO main FormScreenGen - generated generated\java\app\ui\Animal_groupForm.java 873 INFO main FormScreenGen - generated generated\java\app\ui\AnimalForm.java 874 INFO main FormScreenGen - generated generated\java\app\ui\Event_typeForm.java 875 INFO main MenuScreenGen - generated generated\java\app\ui\MainmenuMenu.java 876 INFO main MenuScreenGen - generated generated\java\app\ui\TopmenuMenu.java 877 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\WelcomeScreenPlugin.java 878 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\ManageEventsPlugin.java 879 INFO main PluginScreenGen - generated d Settings\Administrator\workspace\molgenis4animaldb\generated\java\app\ui\MakeReportPlugin.java 880 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.ftl 881 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\eventman\ManageEventsPlugin.ftl 882 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\reports\MakeReportPlugin.ftl 883 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.java 884 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\eventman\ManageEventsPlugin.java 885 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\reports\MakeReportPlugin.java 886 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 887 INFO main SoapApiGen - generated generated\java\app\servlet\SoapApi.java 888 DEBUG main MolgenisModel - swapped Event with Animal 889 DEBUG main MolgenisModel - swapped Animal with Location 890 DEBUG main MolgenisModel - swapped Event with Animal 891 DEBUG main MolgenisModel - swapped Animal with Animal_group 892 DEBUG main MolgenisModel - swapped Event with Event_type 893 INFO main CsvExportGen - generated generated\java\app\CsvExport.java 894 DEBUG main MolgenisModel - swapped Event with Animal 895 DEBUG main MolgenisModel - swapped Animal with Location 896 DEBUG main MolgenisModel - swapped Event with Animal 897 DEBUG main MolgenisModel - swapped Animal with Animal_group 898 DEBUG main MolgenisModel - swapped Event with Event_type 899 INFO main CsvImportGen - generated generated\java\app\CsvImport.java 900 DEBUG main MolgenisModelValidator - validating model and adding defaults: 901 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 902 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 903 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 904 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 905 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 906 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 907 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 908 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 909 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 910 DEBUG main JDBCDatabase - begin transaction 911 INFO main JDBCDatabase - rolled back transaction 912 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 913 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 914 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 915 DEBUG main JDBCDatabase - begin transaction 916 INFO main JDBCDatabase - rolled back transaction 917 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 918 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Gerard's mice' for key 'name' 919 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 920 DEBUG main JDBCDatabase - begin transaction 921 INFO main JDBCDatabase - rolled back transaction 922 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 923 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'Climate Room 2' for key 'name' 924 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 925 DEBUG main JDBCDatabase - begin transaction 926 INFO main JDBCDatabase - rolled back transaction 927 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 928 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 929 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 930 DEBUG main JDBCDatabase - begin transaction 931 INFO main JDBCDatabase - rolled back transaction 932 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 933 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 10:42:37 CET 2009' for column 'date' at row 1 1310 ERROR main DSLParser - field name 'Protocol.key' illegal: key is a reserved JAVA and/or SQL word 1311 ERROR main MolgenisModel - Parsing failed: field name 'Protocol.key' illegal: key is a reserved JAVA and/or SQL word 934 1312 DEBUG main MolgenisOptions - parsed properties file. 935 1313 INFO main main - 936 1314 MOLGENIS version 3.3.2-testing 937 INFO main main - working dir: C:\ Documents and Settings\Administrator\workspace\molgenis4animaldb1315 INFO main main - working dir: C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro 938 1316 DEBUG main main - 939 1317 Using generators: … … 960 1338 generators.R.RMatrixGen #Generates access methods in R for each matrix. 961 1339 generators.R.RApi #Generates a R file that sources all R files. 962 generators.ui.HtmlFormGen #Generates html form class for each entity.963 1340 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 964 1341 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. … … 980 1357 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 981 1358 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 982 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1359 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=litterid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1360 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=customid, type=string[0], auto=false, nillable=true, readonly=false, default=) 1361 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1362 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=sourceid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1363 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=AbstractAnimal, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1364 DEBUG main org.molgenis.model.MolgenisModelParser - read: AbstractAnimal 1365 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=identifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1366 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=unidentifiedid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1367 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=experimentid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 983 1368 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 984 1369 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 985 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1370 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=timestamp, type=datetime, auto=true, nillable=false, readonly=false, default=) 1371 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 986 1372 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 987 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 988 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 989 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 990 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 991 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1373 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1374 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identified, name=genotypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1375 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identified 1376 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Unidentified, name=quantity, type=int, auto=false, nillable=false, readonly=false, default=) 1377 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Unidentified, name=exact, type=bool, auto=false, nillable=false, readonly=false, default=) 1378 DEBUG main org.molgenis.model.MolgenisModelParser - read: Unidentified 1379 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1380 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=identified_locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1381 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=unidentified_locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1382 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=fromdate, type=date, auto=true, nillable=false, readonly=false, default=) 1383 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Loc_bridge, name=todate, type=date, auto=true, nillable=true, readonly=false, default=) 1384 DEBUG main org.molgenis.model.MolgenisModelParser - read: Loc_bridge 1385 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Location, name=address, type=string[0], auto=false, nillable=false, readonly=false, default=) 1386 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Location, name=inlocationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 992 1387 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 993 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1388 DEBUG main org.molgenis.model.MolgenisModelParser - read: Source 1389 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Genotype, name=genotype_description, type=string[0], auto=false, nillable=false, readonly=false, default=) 1390 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Genotype, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1391 DEBUG main org.molgenis.model.MolgenisModelParser - read: Genotype 1392 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=fatherid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1393 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=motherid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1394 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=fromdatepair, type=date, auto=true, nillable=false, readonly=false, default=) 1395 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=todatepair, type=date, auto=true, nillable=true, readonly=false, default=) 1396 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=birthdate, type=date, auto=true, nillable=false, readonly=false, default=) 1397 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=birthsize, type=int, auto=false, nillable=false, readonly=false, default=) 1398 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=weandate, type=date, auto=true, nillable=false, readonly=false, default=) 1399 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=weansize, type=int, auto=false, nillable=false, readonly=false, default=) 1400 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Litter, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1401 DEBUG main org.molgenis.model.MolgenisModelParser - read: Litter 1402 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=experiment_description, type=string[0], auto=false, nillable=false, readonly=false, default=) 1403 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=decnumber, type=string[0], auto=false, nillable=false, readonly=false, default=) 1404 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expentrydate, type=date, auto=true, nillable=false, readonly=false, default=) 1405 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expexitdate_est, type=date, auto=true, nillable=false, readonly=false, default=) 1406 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=expexitdate_real, type=date, auto=true, nillable=true, readonly=false, default=) 1407 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=inconvenience_est, type=int, auto=false, nillable=false, readonly=false, default=) 1408 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=inconvenience_real, type=int, auto=false, nillable=false, readonly=false, default=) 1409 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Experiment, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1410 DEBUG main org.molgenis.model.MolgenisModelParser - read: Experiment 1411 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=protocol_eventid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1412 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=protkey, type=string[0], auto=false, nillable=false, readonly=false, default=) 1413 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=value, type=string[0], auto=false, nillable=false, readonly=false, default=) 1414 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=unit, type=string[0], auto=false, nillable=true, readonly=false, default=) 1415 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Protocol, name=ownerid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1416 DEBUG main org.molgenis.model.MolgenisModelParser - read: Protocol 1417 DEBUG main org.molgenis.model.MolgenisModelParser - read: Owner 994 1418 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 995 1419 ( … … 1000 1424 Unique(name, ) 1001 1425 ); 1426 ENTITY: Entity(animaldb.AbstractAnimal) 1427 ( 1428 Field(entity=AbstractAnimal, name=litterid, type=xref[Litter->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1429 Field(entity=AbstractAnimal, name=customid, type=string[255], auto=false, nillable=true, readonly=false, default=) 1430 Field(entity=AbstractAnimal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1431 Field(entity=AbstractAnimal, name=sourceid, type=xref[Source->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1432 Field(entity=AbstractAnimal, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1433 ); 1002 1434 ENTITY: Entity(animaldb.Event) 1003 1435 ( 1004 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1436 Field(entity=Event, name=identifiedid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1437 Field(entity=Event, name=unidentifiedid, type=xref[Unidentified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1438 Field(entity=Event, name=experimentid, type=xref[Experiment->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1005 1439 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1006 1440 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1007 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1008 ); 1009 ENTITY: Entity(animaldb.Animal) 1010 ( 1011 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1012 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1013 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1014 ); 1015 ENTITY: Entity(animaldb.Animal_group) 1016 ( 1441 Field(entity=Event, name=timestamp, type=datetime, auto=true, nillable=false, readonly=false, default=) 1442 Field(entity=Event, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1443 ); 1444 ENTITY: Entity(animaldb.Event_type) 1445 ( 1446 ); 1447 ENTITY: Entity(animaldb.Identified) 1448 ( 1449 Field(entity=Identified, name=genotypeid, type=xref[Genotype->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1450 ); 1451 ENTITY: Entity(animaldb.Unidentified) 1452 ( 1453 Field(entity=Unidentified, name=quantity, type=int, auto=false, nillable=false, readonly=false, default=) 1454 Field(entity=Unidentified, name=exact, type=bool, auto=false, nillable=false, readonly=false, default=) 1455 ); 1456 ENTITY: Entity(animaldb.Loc_bridge) 1457 ( 1458 Field(entity=Loc_bridge, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1459 Field(entity=Loc_bridge, name=identified_locationid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1460 Field(entity=Loc_bridge, name=unidentified_locationid, type=xref[Unidentified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1461 Field(entity=Loc_bridge, name=fromdate, type=date, auto=true, nillable=false, readonly=false, default=) 1462 Field(entity=Loc_bridge, name=todate, type=date, auto=true, nillable=true, readonly=false, default=) 1017 1463 ); 1018 1464 ENTITY: Entity(animaldb.Location) 1019 1465 ( 1020 ); 1021 ENTITY: Entity(animaldb.Event_type) 1466 Field(entity=Location, name=address, type=string[255], auto=false, nillable=false, readonly=false, default=) 1467 Field(entity=Location, name=inlocationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1468 ); 1469 ENTITY: Entity(animaldb.Source) 1470 ( 1471 ); 1472 ENTITY: Entity(animaldb.Genotype) 1473 ( 1474 Field(entity=Genotype, name=genotype_description, type=string[255], auto=false, nillable=false, readonly=false, default=) 1475 Field(entity=Genotype, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1476 ); 1477 ENTITY: Entity(animaldb.Litter) 1478 ( 1479 Field(entity=Litter, name=fatherid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1480 Field(entity=Litter, name=motherid, type=xref[Identified->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1481 Field(entity=Litter, name=fromdatepair, type=date, auto=true, nillable=false, readonly=false, default=) 1482 Field(entity=Litter, name=todatepair, type=date, auto=true, nillable=true, readonly=false, default=) 1483 Field(entity=Litter, name=birthdate, type=date, auto=true, nillable=false, readonly=false, default=) 1484 Field(entity=Litter, name=birthsize, type=int, auto=false, nillable=false, readonly=false, default=) 1485 Field(entity=Litter, name=weandate, type=date, auto=true, nillable=false, readonly=false, default=) 1486 Field(entity=Litter, name=weansize, type=int, auto=false, nillable=false, readonly=false, default=) 1487 Field(entity=Litter, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1488 ); 1489 ENTITY: Entity(animaldb.Experiment) 1490 ( 1491 Field(entity=Experiment, name=experiment_description, type=string[255], auto=false, nillable=false, readonly=false, default=) 1492 Field(entity=Experiment, name=decnumber, type=string[255], auto=false, nillable=false, readonly=false, default=) 1493 Field(entity=Experiment, name=expentrydate, type=date, auto=true, nillable=false, readonly=false, default=) 1494 Field(entity=Experiment, name=expexitdate_est, type=date, auto=true, nillable=false, readonly=false, default=) 1495 Field(entity=Experiment, name=expexitdate_real, type=date, auto=true, nillable=true, readonly=false, default=) 1496 Field(entity=Experiment, name=inconvenience_est, type=int, auto=false, nillable=false, readonly=false, default=) 1497 Field(entity=Experiment, name=inconvenience_real, type=int, auto=false, nillable=false, readonly=false, default=) 1498 Field(entity=Experiment, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1499 ); 1500 ENTITY: Entity(animaldb.Protocol) 1501 ( 1502 Field(entity=Protocol, name=protocol_eventid, type=xref[Event->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1503 Field(entity=Protocol, name=protkey, type=string[255], auto=false, nillable=false, readonly=false, default=) 1504 Field(entity=Protocol, name=value, type=string[255], auto=false, nillable=false, readonly=false, default=) 1505 Field(entity=Protocol, name=unit, type=string[255], auto=false, nillable=true, readonly=false, default=) 1506 Field(entity=Protocol, name=ownerid, type=xref[Owner->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1507 ); 1508 ENTITY: Entity(animaldb.Owner) 1022 1509 ( 1023 1510 ); … … 1044 1531 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1045 1532 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1533 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to AbstractAnimal 1046 1534 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1047 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1048 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1535 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1536 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Identified 1537 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Unidentified 1538 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Loc_bridge 1049 1539 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1050 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1540 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Source 1541 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Genotype 1542 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Litter 1543 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Experiment 1544 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Protocol 1545 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Owner 1051 1546 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1052 1547 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... … … 1057 1552 INFO main MolgenisModel - parsing ui-schema 1058 1553 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1059 DEBUG main main - using file generated/sql\create_tables.sql 1060 INFO main main - Updating database.... 1061 INFO main main - MOLGENIS database updated succesfully 1062 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1063 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1064 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1065 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1066 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1067 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1068 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1069 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1070 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1071 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1072 DEBUG main JDBCDatabase - begin transaction 1073 INFO main JDBCDatabase - rolled back transaction 1074 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1075 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1076 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1077 DEBUG main JDBCDatabase - begin transaction 1078 INFO main JDBCDatabase - rolled back transaction 1079 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1080 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Gerard's mice' for key 'name' 1081 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1082 DEBUG main JDBCDatabase - begin transaction 1083 INFO main JDBCDatabase - rolled back transaction 1084 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1085 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'Climate Room 2' for key 'name' 1086 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1087 DEBUG main JDBCDatabase - begin transaction 1088 INFO main JDBCDatabase - rolled back transaction 1089 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1090 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 1091 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1092 DEBUG main JDBCDatabase - begin transaction 1093 INFO main JDBCDatabase - rolled back transaction 1094 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1095 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 10:45:45 CET 2009' for column 'date' at row 1 1096 DEBUG main MolgenisOptions - parsed properties file. 1554 INFO main main - generating .... 1097 1555 INFO main main - 1098 MOLGENIS version 3.3.2-testing 1099 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 1100 DEBUG main main - 1101 Using generators: 1102 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 1103 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 1104 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 1105 generators.doc.DotDocGen #Generates one documentation file describing all entities. 1106 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 1107 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 1108 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 1109 generators.db.ViewMapperGen #generate the mappers for each database view 1110 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 1111 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 1112 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1113 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 1114 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 1115 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 1116 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1117 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 1118 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 1119 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 1120 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 1121 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 1122 generators.R.RMatrixGen #Generates access methods in R for each matrix. 1123 generators.R.RApi #Generates a R file that sources all R files. 1124 generators.ui.HtmlFormGen #Generates html form class for each entity. 1125 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 1126 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 1127 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 1128 generators.ui.FormScreenGen #Generates form screens. 1129 generators.ui.MenuScreenGen #Generates menu screens. 1130 generators.ui.TreeScreenGen #Generates Tree screens. 1131 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 1132 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 1133 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 1134 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 1135 generators.csv.CsvExportGen #Generates CsvImportExport 1136 generators.csv.CsvImportGen #Generates CsvImportExport 1137 1138 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 1139 DEBUG main org.molgenis.model.MolgenisModelParser - read: 1140 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1141 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 1142 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 1143 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 1144 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1145 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1146 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1147 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1148 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 1149 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1150 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 1151 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1152 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 1153 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1154 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 1155 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1156 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 1157 ( 1158 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1159 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 1160 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 1161 Unique(id, ) 1162 Unique(name, ) 1163 ); 1164 ENTITY: Entity(animaldb.Event) 1165 ( 1166 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1167 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1168 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1169 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1170 ); 1171 ENTITY: Entity(animaldb.Animal) 1172 ( 1173 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1174 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1175 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1176 ); 1177 ENTITY: Entity(animaldb.Animal_group) 1178 ( 1179 ); 1180 ENTITY: Entity(animaldb.Location) 1181 ( 1182 ); 1183 ENTITY: Entity(animaldb.Event_type) 1184 ( 1185 ); 1186 1187 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1188 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1189 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 1190 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1191 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1192 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1193 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 1194 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1195 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1196 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 1197 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 1198 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 1199 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 1200 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 1201 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1202 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1203 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 1204 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 1205 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1206 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1207 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1208 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1209 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1210 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1211 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1212 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1213 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1214 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1215 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1216 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1217 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1218 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1219 INFO main MolgenisModel - parsing ui-schema 1220 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1221 DEBUG main main - using file generated/sql\create_tables.sql 1222 INFO main main - Updating database.... 1223 INFO main main - MOLGENIS database updated succesfully 1224 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1225 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1226 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1227 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1228 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1229 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1230 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1231 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1232 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1233 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1234 DEBUG main JDBCDatabase - begin transaction 1235 INFO main JDBCDatabase - rolled back transaction 1236 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1237 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1238 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1239 DEBUG main JDBCDatabase - begin transaction 1240 INFO main JDBCDatabase - rolled back transaction 1241 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1242 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Gerard's mice' for key 'name' 1243 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1244 DEBUG main JDBCDatabase - begin transaction 1245 INFO main JDBCDatabase - rolled back transaction 1246 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1247 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'Climate Room 2' for key 'name' 1248 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1249 DEBUG main JDBCDatabase - begin transaction 1250 INFO main JDBCDatabase - rolled back transaction 1251 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1252 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 1253 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1254 DEBUG main JDBCDatabase - begin transaction 1255 INFO main JDBCDatabase - rolled back transaction 1256 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1257 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 10:52:50 CET 2009' for column 'date' at row 1 1258 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1259 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1260 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1261 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1262 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1263 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1264 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1265 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1266 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1267 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059opened database connection, connectioncount=1 1268 DEBUG main JDBCDatabase - begin transaction 1269 INFO main JDBCDatabase - rolled back transaction 1270 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059closed connection back to pool, connectioncount=0 1271 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1272 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059opened database connection, connectioncount=1 1273 DEBUG main JDBCDatabase - begin transaction 1274 INFO main JDBCDatabase - rolled back transaction 1275 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059closed connection back to pool, connectioncount=0 1276 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Gerard's mice' for key 'name' 1277 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059opened database connection, connectioncount=1 1278 DEBUG main JDBCDatabase - begin transaction 1279 INFO main JDBCDatabase - rolled back transaction 1280 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059closed connection back to pool, connectioncount=0 1281 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'Climate Room 2' for key 'name' 1282 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059opened database connection, connectioncount=1 1283 DEBUG main JDBCDatabase - begin transaction 1284 INFO main JDBCDatabase - rolled back transaction 1285 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059closed connection back to pool, connectioncount=0 1286 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 1287 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059opened database connection, connectioncount=1 1288 DEBUG main JDBCDatabase - begin transaction 1289 INFO main JDBCDatabase - rolled back transaction 1290 INFO main JDBCDatabase - app.JDBCDatabase@1b8e059closed connection back to pool, connectioncount=0 1291 ERROR main EventMapper - ADD failed on Event: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`event`, CONSTRAINT `event_ibfk_1` FOREIGN KEY (`animalid`) REFERENCES `animal` (`id`)) 1292 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1293 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1294 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1295 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1296 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1297 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1298 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1299 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1300 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1301 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1302 DEBUG main JDBCDatabase - begin transaction 1303 INFO main JDBCDatabase - rolled back transaction 1304 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1305 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1306 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1307 DEBUG main JDBCDatabase - begin transaction 1308 INFO main JDBCDatabase - rolled back transaction 1309 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1310 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Gerard's mice' for key 'name' 1311 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1312 DEBUG main JDBCDatabase - begin transaction 1313 INFO main JDBCDatabase - rolled back transaction 1314 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1315 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'Climate Room 2' for key 'name' 1316 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1317 DEBUG main JDBCDatabase - begin transaction 1318 INFO main JDBCDatabase - rolled back transaction 1319 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1320 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 1321 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1322 DEBUG main JDBCDatabase - begin transaction 1323 INFO main JDBCDatabase - rolled back transaction 1324 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1325 ERROR main EventMapper - ADD failed on Event: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`event`, CONSTRAINT `event_ibfk_1` FOREIGN KEY (`animalid`) REFERENCES `animal` (`id`)) 1326 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1327 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1328 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1329 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1330 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1331 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1332 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1333 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1334 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1335 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1336 DEBUG main JDBCDatabase - begin transaction 1337 INFO main JDBCDatabase - rolled back transaction 1338 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1339 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1340 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1341 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1342 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1343 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1344 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1345 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1346 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1347 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1348 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1349 INFO main JDBCDatabase - app.JDBCDatabase@121f1dopened database connection, connectioncount=1 1350 DEBUG main JDBCDatabase - begin transaction 1351 INFO main JDBCDatabase - rolled back transaction 1352 INFO main JDBCDatabase - app.JDBCDatabase@121f1dclosed connection back to pool, connectioncount=0 1353 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1354 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1355 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1356 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1357 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1358 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1359 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1360 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1361 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1362 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1363 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 1364 DEBUG main JDBCDatabase - begin transaction 1365 INFO main JDBCDatabase - commited transaction 1366 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 1367 INFO main Event_typeMapper - 1 Event_type objects added 1368 DEBUG main MolgenisOptions - parsed properties file. 1369 INFO main main - 1370 MOLGENIS version 3.3.2-testing 1371 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 1372 DEBUG main main - 1373 Using generators: 1374 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 1375 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 1376 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 1377 generators.doc.DotDocGen #Generates one documentation file describing all entities. 1378 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 1379 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 1380 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 1381 generators.db.ViewMapperGen #generate the mappers for each database view 1382 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 1383 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 1384 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1385 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 1386 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 1387 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 1388 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1389 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 1390 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 1391 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 1392 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 1393 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 1394 generators.R.RMatrixGen #Generates access methods in R for each matrix. 1395 generators.R.RApi #Generates a R file that sources all R files. 1396 generators.ui.HtmlFormGen #Generates html form class for each entity. 1397 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 1398 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 1399 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 1400 generators.ui.FormScreenGen #Generates form screens. 1401 generators.ui.MenuScreenGen #Generates menu screens. 1402 generators.ui.TreeScreenGen #Generates Tree screens. 1403 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 1404 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 1405 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 1406 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 1407 generators.csv.CsvExportGen #Generates CsvImportExport 1408 generators.csv.CsvImportGen #Generates CsvImportExport 1409 1410 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 1411 DEBUG main org.molgenis.model.MolgenisModelParser - read: 1412 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1413 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 1414 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 1415 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 1416 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1417 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1418 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1419 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1420 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 1421 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1422 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 1423 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1424 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 1425 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1426 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 1427 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1428 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 1429 ( 1430 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1431 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 1432 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 1433 Unique(id, ) 1434 Unique(name, ) 1435 ); 1436 ENTITY: Entity(animaldb.Event) 1437 ( 1438 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1439 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1440 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1441 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1442 ); 1443 ENTITY: Entity(animaldb.Animal) 1444 ( 1445 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1446 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1447 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1448 ); 1449 ENTITY: Entity(animaldb.Animal_group) 1450 ( 1451 ); 1452 ENTITY: Entity(animaldb.Location) 1453 ( 1454 ); 1455 ENTITY: Entity(animaldb.Event_type) 1456 ( 1457 ); 1458 1459 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1460 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1461 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 1462 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1463 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1464 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1465 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 1466 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1467 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1468 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 1469 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 1470 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 1471 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 1472 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 1473 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1474 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1475 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 1476 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 1477 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1478 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1479 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1480 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1481 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1482 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1483 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1484 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1485 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1486 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1487 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1488 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1489 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1490 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1491 INFO main MolgenisModel - parsing ui-schema 1492 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1493 DEBUG main main - using file generated/sql\create_tables.sql 1494 INFO main main - Updating database.... 1495 INFO main main - MOLGENIS database updated succesfully 1496 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1497 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1498 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1499 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1500 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1501 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1502 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1503 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1504 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1505 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1506 DEBUG main JDBCDatabase - begin transaction 1507 INFO main JDBCDatabase - commited transaction 1508 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1509 INFO main Event_typeMapper - 1 Event_type objects added 1510 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1511 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1512 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1513 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1514 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1515 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1516 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1517 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1518 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1519 INFO main JDBCDatabase - app.JDBCDatabase@d251a3opened database connection, connectioncount=1 1520 DEBUG main JDBCDatabase - begin transaction 1521 INFO main JDBCDatabase - rolled back transaction 1522 INFO main JDBCDatabase - app.JDBCDatabase@d251a3closed connection back to pool, connectioncount=0 1523 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Measurement' for key 'name' 1524 DEBUG main MolgenisOptions - parsed properties file. 1525 INFO main main - 1526 MOLGENIS version 3.3.2-testing 1527 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 1528 DEBUG main main - 1529 Using generators: 1530 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 1531 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 1532 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 1533 generators.doc.DotDocGen #Generates one documentation file describing all entities. 1534 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 1535 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 1536 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 1537 generators.db.ViewMapperGen #generate the mappers for each database view 1538 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 1539 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 1540 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1541 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 1542 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 1543 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 1544 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1545 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 1546 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 1547 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 1548 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 1549 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 1550 generators.R.RMatrixGen #Generates access methods in R for each matrix. 1551 generators.R.RApi #Generates a R file that sources all R files. 1552 generators.ui.HtmlFormGen #Generates html form class for each entity. 1553 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 1554 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 1555 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 1556 generators.ui.FormScreenGen #Generates form screens. 1557 generators.ui.MenuScreenGen #Generates menu screens. 1558 generators.ui.TreeScreenGen #Generates Tree screens. 1559 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 1560 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 1561 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 1562 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 1563 generators.csv.CsvExportGen #Generates CsvImportExport 1564 generators.csv.CsvImportGen #Generates CsvImportExport 1565 1566 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 1567 DEBUG main org.molgenis.model.MolgenisModelParser - read: 1568 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1569 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 1570 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 1571 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 1572 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1573 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1574 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1575 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1576 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 1577 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1578 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 1579 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1580 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 1581 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1582 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 1583 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1584 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 1585 ( 1586 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1587 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 1588 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 1589 Unique(id, ) 1590 Unique(name, ) 1591 ); 1592 ENTITY: Entity(animaldb.Event) 1593 ( 1594 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1595 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1596 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1597 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1598 ); 1599 ENTITY: Entity(animaldb.Animal) 1600 ( 1601 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1602 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1603 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1604 ); 1605 ENTITY: Entity(animaldb.Animal_group) 1606 ( 1607 ); 1608 ENTITY: Entity(animaldb.Location) 1609 ( 1610 ); 1611 ENTITY: Entity(animaldb.Event_type) 1612 ( 1613 ); 1614 1615 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1616 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1617 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 1618 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1619 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1620 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1621 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 1622 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1623 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1624 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 1625 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 1626 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 1627 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 1628 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 1629 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1630 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1631 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 1632 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 1633 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1634 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1635 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1636 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1637 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1638 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1639 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1640 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1641 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1642 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1643 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1644 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1645 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1646 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1647 INFO main MolgenisModel - parsing ui-schema 1648 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1649 DEBUG main main - using file generated/sql\create_tables.sql 1650 INFO main main - Updating database.... 1651 INFO main main - MOLGENIS database updated succesfully 1652 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1653 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1654 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1655 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1656 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1657 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1658 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1659 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1660 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1661 INFO main JDBCDatabase - app.JDBCDatabase@1edc073opened database connection, connectioncount=1 1662 DEBUG main JDBCDatabase - begin transaction 1663 INFO main JDBCDatabase - rolled back transaction 1664 INFO main JDBCDatabase - app.JDBCDatabase@1edc073closed connection back to pool, connectioncount=0 1665 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Feeding' for key 'name' 1666 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1667 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1668 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1669 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1670 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1671 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1672 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1673 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1674 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1675 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1676 DEBUG main JDBCDatabase - begin transaction 1677 INFO main JDBCDatabase - commited transaction 1678 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1679 INFO main Event_typeMapper - 2 Event_type objects added 1680 DEBUG main MolgenisOptions - parsed properties file. 1681 INFO main main - 1682 MOLGENIS version 3.3.2-testing 1683 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 1684 DEBUG main main - 1685 Using generators: 1686 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 1687 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 1688 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 1689 generators.doc.DotDocGen #Generates one documentation file describing all entities. 1690 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 1691 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 1692 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 1693 generators.db.ViewMapperGen #generate the mappers for each database view 1694 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 1695 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 1696 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1697 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 1698 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 1699 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 1700 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1701 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 1702 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 1703 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 1704 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 1705 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 1706 generators.R.RMatrixGen #Generates access methods in R for each matrix. 1707 generators.R.RApi #Generates a R file that sources all R files. 1708 generators.ui.HtmlFormGen #Generates html form class for each entity. 1709 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 1710 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 1711 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 1712 generators.ui.FormScreenGen #Generates form screens. 1713 generators.ui.MenuScreenGen #Generates menu screens. 1714 generators.ui.TreeScreenGen #Generates Tree screens. 1715 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 1716 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 1717 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 1718 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 1719 generators.csv.CsvExportGen #Generates CsvImportExport 1720 generators.csv.CsvImportGen #Generates CsvImportExport 1721 1722 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 1723 DEBUG main org.molgenis.model.MolgenisModelParser - read: 1724 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1725 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 1726 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 1727 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 1728 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1729 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1730 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1731 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1732 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 1733 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1734 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 1735 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1736 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 1737 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1738 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 1739 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1740 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 1741 ( 1742 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1743 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 1744 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 1745 Unique(id, ) 1746 Unique(name, ) 1747 ); 1748 ENTITY: Entity(animaldb.Event) 1749 ( 1750 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1751 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1752 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1753 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1754 ); 1755 ENTITY: Entity(animaldb.Animal) 1756 ( 1757 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1758 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1759 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1760 ); 1761 ENTITY: Entity(animaldb.Animal_group) 1762 ( 1763 ); 1764 ENTITY: Entity(animaldb.Location) 1765 ( 1766 ); 1767 ENTITY: Entity(animaldb.Event_type) 1768 ( 1769 ); 1770 1771 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1772 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1773 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 1774 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1775 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1776 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1777 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 1778 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1779 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1780 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 1781 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 1782 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 1783 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 1784 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 1785 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1786 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1787 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 1788 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 1789 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1790 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1791 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1792 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1793 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1794 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1795 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1796 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1797 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1798 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1799 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1800 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1801 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1802 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1803 INFO main MolgenisModel - parsing ui-schema 1804 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1805 DEBUG main main - using file generated/sql\create_tables.sql 1806 INFO main main - Updating database.... 1807 INFO main main - MOLGENIS database updated succesfully 1808 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1809 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1810 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1811 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1812 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1813 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1814 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1815 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1816 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1817 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1818 DEBUG main JDBCDatabase - begin transaction 1819 INFO main JDBCDatabase - commited transaction 1820 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1821 INFO main Event_typeMapper - 2 Event_type objects added 1822 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1823 DEBUG main JDBCDatabase - begin transaction 1824 INFO main JDBCDatabase - commited transaction 1825 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1826 INFO main Animal_groupMapper - 2 Animal_group objects added 1827 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1828 DEBUG main JDBCDatabase - begin transaction 1829 INFO main JDBCDatabase - commited transaction 1830 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1831 INFO main LocationMapper - 2 Location objects added 1832 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1833 DEBUG main JDBCDatabase - begin transaction 1834 INFO main JDBCDatabase - rolled back transaction 1835 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1836 ERROR main AnimalMapper - ADD failed on Animal: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`animal`, CONSTRAINT `animal_ibfk_1` FOREIGN KEY (`locationid`) REFERENCES `location` (`id`)) 1837 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 1838 DEBUG main JDBCDatabase - begin transaction 1839 INFO main JDBCDatabase - rolled back transaction 1840 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 1841 ERROR main EventMapper - ADD failed on Event: Cannot add or update a child row: a foreign key constraint fails (`animaldb_proto`.`event`, CONSTRAINT `event_ibfk_1` FOREIGN KEY (`animalid`) REFERENCES `animal` (`id`)) 1842 DEBUG main MolgenisOptions - parsed properties file. 1843 INFO main main - 1844 MOLGENIS version 3.3.2-testing 1845 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 1846 DEBUG main main - 1847 Using generators: 1848 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 1849 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 1850 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 1851 generators.doc.DotDocGen #Generates one documentation file describing all entities. 1852 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 1853 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 1854 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 1855 generators.db.ViewMapperGen #generate the mappers for each database view 1856 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 1857 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 1858 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1859 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 1860 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 1861 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 1862 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 1863 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 1864 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 1865 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 1866 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 1867 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 1868 generators.R.RMatrixGen #Generates access methods in R for each matrix. 1869 generators.R.RApi #Generates a R file that sources all R files. 1870 generators.ui.HtmlFormGen #Generates html form class for each entity. 1871 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 1872 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 1873 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 1874 generators.ui.FormScreenGen #Generates form screens. 1875 generators.ui.MenuScreenGen #Generates menu screens. 1876 generators.ui.TreeScreenGen #Generates Tree screens. 1877 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 1878 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 1879 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 1880 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 1881 generators.csv.CsvExportGen #Generates CsvImportExport 1882 generators.csv.CsvImportGen #Generates CsvImportExport 1883 1884 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 1885 DEBUG main org.molgenis.model.MolgenisModelParser - read: 1886 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1887 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 1888 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 1889 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 1890 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1891 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1892 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1893 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1894 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 1895 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 1896 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 1897 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 1898 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 1899 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 1900 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 1901 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 1902 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 1903 ( 1904 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1905 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 1906 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 1907 Unique(id, ) 1908 Unique(name, ) 1909 ); 1910 ENTITY: Entity(animaldb.Event) 1911 ( 1912 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1913 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1914 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1915 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 1916 ); 1917 ENTITY: Entity(animaldb.Animal) 1918 ( 1919 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 1920 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 1921 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 1922 ); 1923 ENTITY: Entity(animaldb.Animal_group) 1924 ( 1925 ); 1926 ENTITY: Entity(animaldb.Location) 1927 ( 1928 ); 1929 ENTITY: Entity(animaldb.Event_type) 1930 ( 1931 ); 1932 1933 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1934 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1935 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 1936 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1937 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1938 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 1939 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 1940 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1941 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1942 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 1943 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 1944 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 1945 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 1946 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 1947 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 1948 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 1949 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 1950 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 1951 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1952 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1953 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1954 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 1955 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 1956 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 1957 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 1958 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 1959 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1960 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1961 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1962 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1963 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1964 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1965 INFO main MolgenisModel - parsing ui-schema 1966 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 1967 DEBUG main main - using file generated/sql\create_tables.sql 1968 INFO main main - Updating database.... 1969 INFO main main - MOLGENIS database updated succesfully 1970 DEBUG main MolgenisModelValidator - validating model and adding defaults: 1971 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 1972 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 1973 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 1974 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 1975 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 1976 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 1977 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 1978 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 1979 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 1980 DEBUG main JDBCDatabase - begin transaction 1981 INFO main JDBCDatabase - commited transaction 1982 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 1983 INFO main Event_typeMapper - 2 Event_type objects added 1984 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 1985 DEBUG main JDBCDatabase - begin transaction 1986 INFO main JDBCDatabase - commited transaction 1987 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 1988 INFO main Animal_groupMapper - 2 Animal_group objects added 1989 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 1990 DEBUG main JDBCDatabase - begin transaction 1991 INFO main JDBCDatabase - commited transaction 1992 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 1993 INFO main LocationMapper - 2 Location objects added 1994 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 1995 DEBUG main JDBCDatabase - begin transaction 1996 INFO main JDBCDatabase - commited transaction 1997 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 1998 INFO main AnimalMapper - 2 Animal objects added 1999 INFO main JDBCDatabase - app.JDBCDatabase@910040opened database connection, connectioncount=1 2000 DEBUG main JDBCDatabase - begin transaction 2001 INFO main JDBCDatabase - commited transaction 2002 INFO main JDBCDatabase - app.JDBCDatabase@910040closed connection back to pool, connectioncount=0 2003 INFO main EventMapper - 2 Event objects added 2004 DEBUG main MolgenisOptions - parsed properties file. 2005 INFO main main - 2006 MOLGENIS version 3.3.2-testing 2007 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 2008 DEBUG main main - 2009 Using generators: 2010 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 2011 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 2012 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 2013 generators.doc.DotDocGen #Generates one documentation file describing all entities. 2014 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 2015 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 2016 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 2017 generators.db.ViewMapperGen #generate the mappers for each database view 2018 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 2019 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 2020 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2021 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 2022 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 2023 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 2024 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2025 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 2026 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 2027 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 2028 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 2029 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 2030 generators.R.RMatrixGen #Generates access methods in R for each matrix. 2031 generators.R.RApi #Generates a R file that sources all R files. 2032 generators.ui.HtmlFormGen #Generates html form class for each entity. 2033 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 2034 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 2035 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 2036 generators.ui.FormScreenGen #Generates form screens. 2037 generators.ui.MenuScreenGen #Generates menu screens. 2038 generators.ui.TreeScreenGen #Generates Tree screens. 2039 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 2040 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 2041 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 2042 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 2043 generators.csv.CsvExportGen #Generates CsvImportExport 2044 generators.csv.CsvImportGen #Generates CsvImportExport 2045 2046 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 2047 DEBUG main org.molgenis.model.MolgenisModelParser - read: 2048 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2049 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 2050 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 2051 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 2052 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2053 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2054 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2055 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2056 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 2057 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2058 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 2059 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 2060 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 2061 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 2062 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 2063 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 2064 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 2065 ( 2066 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2067 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 2068 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 2069 Unique(id, ) 2070 Unique(name, ) 2071 ); 2072 ENTITY: Entity(animaldb.Event) 2073 ( 2074 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2075 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2076 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2077 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2078 ); 2079 ENTITY: Entity(animaldb.Animal) 2080 ( 2081 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2082 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 2083 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 2084 ); 2085 ENTITY: Entity(animaldb.Animal_group) 2086 ( 2087 ); 2088 ENTITY: Entity(animaldb.Location) 2089 ( 2090 ); 2091 ENTITY: Entity(animaldb.Event_type) 2092 ( 2093 ); 2094 2095 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2096 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2097 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 2098 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2099 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2100 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2101 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 2102 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2103 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2104 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 2105 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 2106 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 2107 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 2108 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 2109 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2110 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2111 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 2112 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 2113 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2114 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2115 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2116 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 2117 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 2118 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 2119 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 2120 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 2121 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2122 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2123 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2124 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2125 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2126 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2127 INFO main MolgenisModel - parsing ui-schema 2128 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 2129 DEBUG main main - using file generated/sql\create_tables.sql 2130 INFO main main - Updating database.... 2131 INFO main main - MOLGENIS database updated succesfully 2132 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2133 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2134 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2135 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2136 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2137 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2138 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2139 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2140 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2141 INFO main JDBCDatabase - app.JDBCDatabase@860d49opened database connection, connectioncount=1 2142 DEBUG main JDBCDatabase - begin transaction 2143 INFO main JDBCDatabase - commited transaction 2144 INFO main JDBCDatabase - app.JDBCDatabase@860d49closed connection back to pool, connectioncount=0 2145 INFO main Event_typeMapper - 2 Event_type objects added 2146 INFO main JDBCDatabase - app.JDBCDatabase@860d49opened database connection, connectioncount=1 2147 DEBUG main JDBCDatabase - begin transaction 2148 INFO main JDBCDatabase - commited transaction 2149 INFO main JDBCDatabase - app.JDBCDatabase@860d49closed connection back to pool, connectioncount=0 2150 INFO main Animal_groupMapper - 2 Animal_group objects added 2151 INFO main JDBCDatabase - app.JDBCDatabase@860d49opened database connection, connectioncount=1 2152 DEBUG main JDBCDatabase - begin transaction 2153 INFO main JDBCDatabase - commited transaction 2154 INFO main JDBCDatabase - app.JDBCDatabase@860d49closed connection back to pool, connectioncount=0 2155 INFO main LocationMapper - 2 Location objects added 2156 INFO main JDBCDatabase - app.JDBCDatabase@860d49opened database connection, connectioncount=1 2157 DEBUG main JDBCDatabase - begin transaction 2158 INFO main JDBCDatabase - commited transaction 2159 INFO main JDBCDatabase - app.JDBCDatabase@860d49closed connection back to pool, connectioncount=0 2160 INFO main AnimalMapper - 2 Animal objects added 2161 INFO main JDBCDatabase - app.JDBCDatabase@860d49opened database connection, connectioncount=1 2162 DEBUG main JDBCDatabase - begin transaction 2163 INFO main JDBCDatabase - rolled back transaction 2164 INFO main JDBCDatabase - app.JDBCDatabase@860d49closed connection back to pool, connectioncount=0 2165 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 12:02:45 CET 2009' for column 'date' at row 1 2166 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2167 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2168 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2169 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2170 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2171 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2172 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2173 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2174 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2175 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 2176 DEBUG main JDBCDatabase - begin transaction 2177 INFO main JDBCDatabase - rolled back transaction 2178 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 2179 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Measurement' for key 'name' 2180 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 2181 DEBUG main JDBCDatabase - begin transaction 2182 INFO main JDBCDatabase - rolled back transaction 2183 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 2184 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Ate's hamsters' for key 'name' 2185 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 2186 DEBUG main JDBCDatabase - begin transaction 2187 INFO main JDBCDatabase - rolled back transaction 2188 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 2189 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'ChronoBio 0.11' for key 'name' 2190 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 2191 DEBUG main JDBCDatabase - begin transaction 2192 INFO main JDBCDatabase - rolled back transaction 2193 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 2194 ERROR main AnimalMapper - ADD failed on Animal: Duplicate entry 'Henkie' for key 'name' 2195 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386opened database connection, connectioncount=1 2196 DEBUG main JDBCDatabase - begin transaction 2197 INFO main JDBCDatabase - rolled back transaction 2198 INFO main JDBCDatabase - app.JDBCDatabase@1f5d386closed connection back to pool, connectioncount=0 2199 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 00:00:00 CET 2009' for column 'date' at row 1 2200 DEBUG main MolgenisOptions - parsed properties file. 2201 INFO main main - 2202 MOLGENIS version 3.3.2-testing 2203 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 2204 DEBUG main main - 2205 Using generators: 2206 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 2207 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 2208 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 2209 generators.doc.DotDocGen #Generates one documentation file describing all entities. 2210 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 2211 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 2212 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 2213 generators.db.ViewMapperGen #generate the mappers for each database view 2214 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 2215 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 2216 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2217 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 2218 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 2219 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 2220 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2221 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 2222 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 2223 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 2224 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 2225 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 2226 generators.R.RMatrixGen #Generates access methods in R for each matrix. 2227 generators.R.RApi #Generates a R file that sources all R files. 2228 generators.ui.HtmlFormGen #Generates html form class for each entity. 2229 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 2230 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 2231 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 2232 generators.ui.FormScreenGen #Generates form screens. 2233 generators.ui.MenuScreenGen #Generates menu screens. 2234 generators.ui.TreeScreenGen #Generates Tree screens. 2235 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 2236 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 2237 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 2238 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 2239 generators.csv.CsvExportGen #Generates CsvImportExport 2240 generators.csv.CsvImportGen #Generates CsvImportExport 2241 2242 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 2243 DEBUG main org.molgenis.model.MolgenisModelParser - read: 2244 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2245 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 2246 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 2247 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 2248 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2249 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2250 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2251 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2252 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 2253 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2254 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 2255 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 2256 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 2257 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 2258 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 2259 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 2260 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 2261 ( 2262 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2263 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 2264 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 2265 Unique(id, ) 2266 Unique(name, ) 2267 ); 2268 ENTITY: Entity(animaldb.Event) 2269 ( 2270 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2271 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2272 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2273 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2274 ); 2275 ENTITY: Entity(animaldb.Animal) 2276 ( 2277 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2278 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 2279 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 2280 ); 2281 ENTITY: Entity(animaldb.Animal_group) 2282 ( 2283 ); 2284 ENTITY: Entity(animaldb.Location) 2285 ( 2286 ); 2287 ENTITY: Entity(animaldb.Event_type) 2288 ( 2289 ); 2290 2291 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2292 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2293 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 2294 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2295 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2296 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2297 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 2298 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2299 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2300 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 2301 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 2302 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 2303 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 2304 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 2305 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2306 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2307 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 2308 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 2309 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2310 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2311 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2312 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 2313 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 2314 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 2315 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 2316 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 2317 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2318 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2319 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2320 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2321 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2322 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2323 INFO main MolgenisModel - parsing ui-schema 2324 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 2325 DEBUG main main - using file generated/sql\create_tables.sql 2326 INFO main main - Updating database.... 2327 INFO main main - MOLGENIS database updated succesfully 2328 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2329 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2330 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2331 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2332 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2333 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2334 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2335 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2336 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2337 INFO main JDBCDatabase - app.JDBCDatabase@13f3045opened database connection, connectioncount=1 2338 DEBUG main JDBCDatabase - begin transaction 2339 INFO main JDBCDatabase - commited transaction 2340 INFO main JDBCDatabase - app.JDBCDatabase@13f3045closed connection back to pool, connectioncount=0 2341 INFO main Event_typeMapper - 2 Event_type objects added 2342 INFO main JDBCDatabase - app.JDBCDatabase@13f3045opened database connection, connectioncount=1 2343 DEBUG main JDBCDatabase - begin transaction 2344 INFO main JDBCDatabase - commited transaction 2345 INFO main JDBCDatabase - app.JDBCDatabase@13f3045closed connection back to pool, connectioncount=0 2346 INFO main Animal_groupMapper - 2 Animal_group objects added 2347 INFO main JDBCDatabase - app.JDBCDatabase@13f3045opened database connection, connectioncount=1 2348 DEBUG main JDBCDatabase - begin transaction 2349 INFO main JDBCDatabase - commited transaction 2350 INFO main JDBCDatabase - app.JDBCDatabase@13f3045closed connection back to pool, connectioncount=0 2351 INFO main LocationMapper - 2 Location objects added 2352 INFO main JDBCDatabase - app.JDBCDatabase@13f3045opened database connection, connectioncount=1 2353 DEBUG main JDBCDatabase - begin transaction 2354 INFO main JDBCDatabase - commited transaction 2355 INFO main JDBCDatabase - app.JDBCDatabase@13f3045closed connection back to pool, connectioncount=0 2356 INFO main AnimalMapper - 2 Animal objects added 2357 INFO main JDBCDatabase - app.JDBCDatabase@13f3045opened database connection, connectioncount=1 2358 DEBUG main JDBCDatabase - begin transaction 2359 INFO main JDBCDatabase - rolled back transaction 2360 INFO main JDBCDatabase - app.JDBCDatabase@13f3045closed connection back to pool, connectioncount=0 2361 ERROR main EventMapper - ADD failed on Event: Data truncation: Incorrect date value: 'Thu Nov 12 13:08:33 CET 2009' for column 'date' at row 1 2362 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2363 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2364 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2365 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2366 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2367 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2368 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2369 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2370 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2371 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2372 DEBUG main JDBCDatabase - begin transaction 2373 INFO main JDBCDatabase - rolled back transaction 2374 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2375 ERROR main Event_typeMapper - ADD failed on Event_type: Duplicate entry 'Measurement' for key 'name' 2376 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2377 DEBUG main JDBCDatabase - begin transaction 2378 INFO main JDBCDatabase - rolled back transaction 2379 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2380 ERROR main Animal_groupMapper - ADD failed on Animal_group: Duplicate entry 'Ate's hamsters' for key 'name' 2381 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2382 DEBUG main JDBCDatabase - begin transaction 2383 INFO main JDBCDatabase - rolled back transaction 2384 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2385 ERROR main LocationMapper - ADD failed on Location: Duplicate entry 'ChronoBio 0.11' for key 'name' 2386 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2387 DEBUG main JDBCDatabase - begin transaction 2388 INFO main JDBCDatabase - rolled back transaction 2389 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2390 ERROR main AnimalMapper - ADD failed on Animal: Duplicate entry 'Henkie' for key 'name' 2391 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2392 DEBUG main JDBCDatabase - begin transaction 2393 INFO main JDBCDatabase - commited transaction 2394 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2395 INFO main EventMapper - 2 Event objects added 2396 DEBUG main MolgenisOptions - parsed properties file. 2397 INFO main main - 2398 MOLGENIS version 3.3.2-testing 2399 INFO main main - working dir: C:\Documents and Settings\Administrator\workspace\molgenis4animaldb 2400 DEBUG main main - 2401 Using generators: 2402 generators.server.MolgenisResourceCopyGen #Copies all resources into ${output_web}/generated-res. 2403 generators.doc.TableDocGen #Generates one documentation file describing all generated tables. 2404 generators.doc.EntityModelDocGen #Generates one documentation file describing all entities. 2405 generators.doc.DotDocGen #Generates one documentation file describing all entities. 2406 generators.doc.CsvDocGen #Generates one documentation file describing all entities. 2407 generators.doc.DotDocMinimalGen #Generates one documentation file describing all entities. 2408 generators.doc.ObjectModelDocGen #Generates one documentation file describing all entities. 2409 generators.db.ViewMapperGen #generate the mappers for each database view 2410 generators.sql.MySqlCreateSubclassPerTableGen #Generates create tables and views for each entity. 2411 generators.sql.MySqlAlterSubclassPerTableGen #Generates create tables and views for each entity. 2412 generators.db.JDBCDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2413 generators.DataTypeGen #Generates classes for each entity (simple 'bean's or 'pojo's). 2414 generators.db.MultiqueryMapperGen #Generates database mappers for each entity (concrete class per table). Uses prepared statements. 2415 generators.db.MapperDecoratorGen #(Optional) Generates a template for mappers if decorator='path' is set and the class is not there. 2416 generators.db.JDBCMetaDatabaseGen #Generates one JDBCDatabase to talk to the data. Encapsulates Database Mappers to do this. 2417 generators.sql.CountPerEntityGen #Generates one query to count all entities in the database (without counting subclasses twice). 2418 generators.sql.CountPerTableGen #Generates one query to count all entities in the database (without counting subclasses twice). 2419 generators.sql.FillMetadataTablesGen #Fills the metadata tables. 2420 generators.csv.CsvReaderGen #Generates CsvReaders for each entity 2421 generators.R.REntityGen #Generates access methods in R for each (concrete) entity. 2422 generators.R.RMatrixGen #Generates access methods in R for each matrix. 2423 generators.R.RApi #Generates a R file that sources all R files. 2424 generators.ui.HtmlFormGen #Generates html form class for each entity. 2425 generators.server.MolgenisServletContextGen #Generates the central servlet for MOLGENIS. 2426 generators.server.MolgenisContextListenerGen #Generates a context listener for MOLGENIS. 2427 generators.server.MolgenisServletGen #Generates the central servlet for MOLGENIS. 2428 generators.ui.FormScreenGen #Generates form screens. 2429 generators.ui.MenuScreenGen #Generates menu screens. 2430 generators.ui.TreeScreenGen #Generates Tree screens. 2431 generators.ui.PluginScreenGen #Generates plugin screens (linking to hand-written code). 2432 generators.ui.PluginScreenFTLTemplateGen #Generates in the handwritten folder a template of an FTL. 2433 generators.ui.PluginScreenJavaTemplateGen #Generates in the handwritten folder a template of an FTL. 2434 generators.server.SoapApiGen #Generates soap service interfaces for each entity. 2435 generators.csv.CsvExportGen #Generates CsvImportExport 2436 generators.csv.CsvImportGen #Generates CsvImportExport 2437 2438 INFO main MolgenisModel - parsing db-schema from [molgenis4animal_db.xml, molgenis_auth.xml] 2439 DEBUG main org.molgenis.model.MolgenisModelParser - read: 2440 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2441 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=name, type=string[0], auto=false, nillable=true, readonly=false, default=) 2442 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Identifiable, name=comment, type=string[0], auto=false, nillable=true, readonly=false, default=) 2443 DEBUG main org.molgenis.model.MolgenisModelParser - read: Identifiable 2444 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=animalid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2445 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=eventtypeid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2446 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2447 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2448 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event 2449 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=locationid, type=xref[->], xref_label=, auto=false, nillable=false, readonly=false, default=) 2450 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=animalgroupid, type=xref[->], xref_label=, auto=false, nillable=true, readonly=false, default=) 2451 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=Animal, name=species, type=string[0], auto=false, nillable=false, readonly=false, default=) 2452 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal 2453 DEBUG main org.molgenis.model.MolgenisModelParser - read: Animal_group 2454 DEBUG main org.molgenis.model.MolgenisModelParser - read: Location 2455 DEBUG main org.molgenis.model.MolgenisModelParser - read: Event_type 2456 DEBUG main org.molgenis.model.MolgenisModelParser - read: ENTITY: Entity(animaldb.Identifiable) 2457 ( 2458 Field(entity=Identifiable, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2459 Field(entity=Identifiable, name=name, type=string[255], auto=false, nillable=true, readonly=false, default=) 2460 Field(entity=Identifiable, name=comment, type=string[255], auto=false, nillable=true, readonly=false, default=) 2461 Unique(id, ) 2462 Unique(name, ) 2463 ); 2464 ENTITY: Entity(animaldb.Event) 2465 ( 2466 Field(entity=Event, name=animalid, type=xref[Animal->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2467 Field(entity=Event, name=eventtypeid, type=xref[Event_type->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2468 Field(entity=Event, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2469 Field(entity=Event, name=date, type=date, auto=true, nillable=false, readonly=false, default=) 2470 ); 2471 ENTITY: Entity(animaldb.Animal) 2472 ( 2473 Field(entity=Animal, name=locationid, type=xref[Location->id], xref_label=name, auto=false, nillable=false, readonly=false, default=) 2474 Field(entity=Animal, name=animalgroupid, type=xref[Animal_group->id], xref_label=name, auto=false, nillable=true, readonly=false, default=) 2475 Field(entity=Animal, name=species, type=string[255], auto=false, nillable=false, readonly=false, default=) 2476 ); 2477 ENTITY: Entity(animaldb.Animal_group) 2478 ( 2479 ); 2480 ENTITY: Entity(animaldb.Location) 2481 ( 2482 ); 2483 ENTITY: Entity(animaldb.Event_type) 2484 ( 2485 ); 2486 2487 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2488 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2489 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=superuser, type=bool, auto=false, nillable=false, readonly=false, default=false) 2490 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=members, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2491 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canRead, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2492 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUserGroup, name=canWrite, type=mref[->], mref_name=null, mref_localid=null, mref_remoteid=null, xref_label=, auto=false, nillable=false, readonly=false, default=) 2493 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUserGroup 2494 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2495 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2496 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=password, type=string[0], auto=false, nillable=false, readonly=false, default=) 2497 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=emailaddress, type=string[0], auto=false, nillable=false, readonly=false, default=) 2498 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=activationCode, type=string[0], auto=false, nillable=false, readonly=false, default=) 2499 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisUser, name=active, type=bool, auto=false, nillable=false, readonly=false, default=false) 2500 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisUser 2501 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=id, type=int, auto=true, nillable=false, readonly=true, default=) 2502 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=name, type=string[0], auto=false, nillable=false, readonly=false, default=) 2503 DEBUG main org.molgenis.model.MolgenisModelParser - read: Field(entity=MolgenisEntityMetaData, name=className, type=string[0], auto=false, nillable=false, readonly=false, default=) 2504 DEBUG main org.molgenis.model.MolgenisModelParser - read: MolgenisEntityMetaData 2505 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2506 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2507 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2508 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event 2509 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal 2510 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Animal_group 2511 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Location 2512 DEBUG main MolgenisModelValidator - copy primary key id from interface Identifiable to Event_type 2513 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2514 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2515 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2516 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2517 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2518 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2519 INFO main MolgenisModel - parsing ui-schema 2520 DEBUG main org.molgenis.model.MolgenisModelParser - parsing ui file: molgenis4animal_ui.xml 2521 DEBUG main main - using file generated/sql\create_tables.sql 2522 INFO main main - Updating database.... 2523 INFO main main - MOLGENIS database updated succesfully 2524 DEBUG main MolgenisModelValidator - validating model and adding defaults: 2525 DEBUG main MolgenisModelValidator - check for JAVA and SQL reserved words... 2526 DEBUG main MolgenisModelValidator - validate 'extends' and 'implements' relationships... 2527 DEBUG main MolgenisModelValidator - validate the fields used in 'unique' constraints... 2528 DEBUG main MolgenisModelValidator - validate xref_field and xref_label references... 2529 DEBUG main MolgenisModelValidator - correct case of names in xrefs... 2530 DEBUG main MolgenisModelValidator - add linktable entities for mrefs... 2531 DEBUG main MolgenisModelValidator - add a 'type' field in subclasses to enable instanceof at database level... 2532 DEBUG main MolgenisModelValidator - copy fields to subclass for constrain checking... 2533 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2534 DEBUG main JDBCDatabase - begin transaction 2535 INFO main JDBCDatabase - commited transaction 2536 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2537 INFO main Event_typeMapper - 2 Event_type objects added 2538 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2539 DEBUG main JDBCDatabase - begin transaction 2540 INFO main JDBCDatabase - commited transaction 2541 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2542 INFO main Animal_groupMapper - 2 Animal_group objects added 2543 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2544 DEBUG main JDBCDatabase - begin transaction 2545 INFO main JDBCDatabase - commited transaction 2546 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2547 INFO main LocationMapper - 2 Location objects added 2548 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2549 DEBUG main JDBCDatabase - begin transaction 2550 INFO main JDBCDatabase - commited transaction 2551 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2552 INFO main AnimalMapper - 2 Animal objects added 2553 INFO main JDBCDatabase - app.JDBCDatabase@ed0338opened database connection, connectioncount=1 2554 DEBUG main JDBCDatabase - begin transaction 2555 INFO main JDBCDatabase - commited transaction 2556 INFO main JDBCDatabase - app.JDBCDatabase@ed0338closed connection back to pool, connectioncount=0 2557 INFO main EventMapper - 2 Event objects added 1556 Using options: 1557 model_database = [molgenis4animal_db.xml, molgenis_auth.xml] #File with data structure specification (in MOLGENIS DSL). 1558 model_userinterface = molgenis4animal_ui.xml #File with user interface specification (in MOLGENIS DSL). Can be same file as model_database 1559 output_src = generated/java/ #Output-directory for the generated project. 1560 output_hand = handwritten/java/ #Output-directory for the generated project. 1561 output_sql = generated/sql #Output-directory for the generated sql files. 1562 output_doc = WebContent/generated-doc #Output-directory for the generated documentation. 1563 output_web = WebContent #Output-directory for any generated web resources 1564 db_driver = com.mysql.jdbc.Driver #Driver of database. Any JDBC compatible driver should work. 1565 db_user = molgenis #Username for database. 1566 db_password = xxxxxx #Password for database. 1567 db_uri = jdbc:mysql://localhost/animaldb?innodb_autoinc_lock_mode=2 #Uri of the database. Default: localhost 1568 db_filepath = attachedfiles #Path where the database should store file attachements. Default: null 1569 db_jndiname = jdbc/molgenisdb #Used to create a JDBC database resource for the application 1570 object_relational_mapping = subclass_per_table #Expert option: Choosing OR strategy. Either 'class_per_table', 'subclass_per_table', 'hierarchy_per_table'. Default: class_per_table 1571 mapper_implementation = multiquery #Expert option: Choosing wether multiquery is used instead of prepared statements. Default: false 1572 exclude_system = true #Expert option: Whether system tables should be excluded from generation. Default: true 1573 auth_loginclass = org.molgenis.framework.security.SimpleLogin #Expert option. 1574 mail_smtp_protocol = smtps #Sets the email protocol, either smtp, smtps or null. Default: null meaning email disabled 1575 mail_smtp_hostname = smtp.gmail.com #SMTP host server. Default: localhost 1576 mail_smtp_port = 465 #SMTP host server port. Default: 25 1577 mail_smtp_user = molgenis #SMTP user for authenticated emailing. Default: null. 1578 mail_smtp_password = molgenispass #SMTP user for authenticated emailing. Default: null. 1579 1580 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors.css 1581 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_blue.css 1582 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_blue2.css 1583 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_bluegrey.css 1584 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_grey.css 1585 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\colors_maroon.css 1586 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\data.css 1587 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\dateinput.css 1588 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\dateipnut.css 1589 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\main.css 1590 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\menu.css 1591 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\css\xrefinput.css 1592 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\cancel.png 1593 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\close.png 1594 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\delete.png 1595 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\deselect.png 1596 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\deselectall.png 1597 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\down.png 1598 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\download.png 1599 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\editview.gif 1600 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\exit.bmp 1601 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\filter.png 1602 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\first.png 1603 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\info.png 1604 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\last.png 1605 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\limit.png 1606 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\listview.png 1607 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\logo_molgenis.gif 1608 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\new.png 1609 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\next.png 1610 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\none.png 1611 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\open.png 1612 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\prev.png 1613 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\pulldown.gif 1614 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\recordview.png 1615 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\reset.png 1616 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\rowStart.png 1617 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\rowStop.png 1618 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\save.png 1619 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\select.png 1620 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\sort_asc.gif 1621 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\sort_desc.gif 1622 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\up.png 1623 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\update.gif 1624 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\upload.png 1625 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\_logo_molgenis.gif 1626 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\img\_logo_molgenis_old.gif 1627 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\all.js 1628 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\Copy of datetimeinput.js 1629 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\Copy of mrefinput.js 1630 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\dateinput.js 1631 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\datetimeinput.js 1632 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\menu.js 1633 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\mrefinput.js 1634 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\popup.js 1635 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\rest.js 1636 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\textinput.js 1637 DEBUG main MolgenisResourceCopyGen - skipped because exists/svn: WebContent\generated-res\scripts\xrefinput.js 1638 INFO main MolgenisResourceCopyGen - generated WebContent\generated-res 1639 INFO main TableDocGen - generated WebContent\generated-doc\tabledoc.html 1640 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1641 DEBUG main MolgenisModel - loop detected between Litter and Identified 1642 DEBUG main MolgenisModel - loop detected between Litter and Identified 1643 DEBUG main MolgenisModel - swapped Litter with Owner 1644 DEBUG main MolgenisModel - swapped Event with Identified 1645 DEBUG main MolgenisModel - loop detected between Identified and Litter 1646 DEBUG main MolgenisModel - swapped Identified with Source 1647 DEBUG main MolgenisModel - swapped Event with Identified 1648 DEBUG main MolgenisModel - loop detected between Identified and Litter 1649 DEBUG main MolgenisModel - swapped Identified with Genotype 1650 DEBUG main MolgenisModel - swapped Unidentified with Litter 1651 DEBUG main MolgenisModel - loop detected between Litter and Identified 1652 DEBUG main MolgenisModel - loop detected between Litter and Identified 1653 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1654 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1655 DEBUG main MolgenisModel - swapped Event with Unidentified 1656 DEBUG main MolgenisModel - swapped Protocol with Event 1657 INFO main EntityModelDocGen - generated WebContent\generated-doc\entitymodel.html 1658 INFO main DotDocGen - generated WebContent\generated-doc\objectmodel-uml-diagram.dot 1659 DEBUG main DotDocGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 1660 DEBUG main DotDocGen - Data model image was generated succesfully. 1661 Output: 1662 1663 DEBUG main DotDocGen - Executing: dot -Tsvg -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\objectmodel-uml-diagram.dot 1664 DEBUG main DotDocGen - Data model image was generated succesfully. 1665 Output: 1666 1667 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1668 DEBUG main MolgenisModel - loop detected between Litter and Identified 1669 DEBUG main MolgenisModel - loop detected between Litter and Identified 1670 DEBUG main MolgenisModel - swapped Litter with Owner 1671 DEBUG main MolgenisModel - swapped Event with Identified 1672 DEBUG main MolgenisModel - loop detected between Identified and Litter 1673 DEBUG main MolgenisModel - swapped Identified with Source 1674 DEBUG main MolgenisModel - swapped Event with Identified 1675 DEBUG main MolgenisModel - loop detected between Identified and Litter 1676 DEBUG main MolgenisModel - swapped Identified with Genotype 1677 DEBUG main MolgenisModel - swapped Unidentified with Litter 1678 DEBUG main MolgenisModel - loop detected between Litter and Identified 1679 DEBUG main MolgenisModel - loop detected between Litter and Identified 1680 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1681 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1682 DEBUG main MolgenisModel - swapped Event with Unidentified 1683 DEBUG main MolgenisModel - swapped Protocol with Event 1684 INFO main CsvDocGen - generated WebContent\generated-doc\tab-format-reference.html 1685 INFO main DotDocMinimalGen - generated WebContent\generated-doc\entity-uml-minimal-diagram.dot 1686 DEBUG main DotDocMinimalGen - Executing: dot -Tpng -O C:\Users\Erik\workspace\molgenis32_workspace\molgenis_distro\WebContent\generated-doc\entity-uml-minimal-diagram.dot 1687 DEBUG main DotDocMinimalGen - Data model image was generated succesfully. 1688 Output: 1689 1690 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1691 DEBUG main MolgenisModel - loop detected between Litter and Identified 1692 DEBUG main MolgenisModel - loop detected between Litter and Identified 1693 DEBUG main MolgenisModel - swapped Litter with Owner 1694 DEBUG main MolgenisModel - swapped Event with Identified 1695 DEBUG main MolgenisModel - loop detected between Identified and Litter 1696 DEBUG main MolgenisModel - swapped Identified with Source 1697 DEBUG main MolgenisModel - swapped Event with Identified 1698 DEBUG main MolgenisModel - loop detected between Identified and Litter 1699 DEBUG main MolgenisModel - swapped Identified with Genotype 1700 DEBUG main MolgenisModel - swapped Unidentified with Litter 1701 DEBUG main MolgenisModel - loop detected between Litter and Identified 1702 DEBUG main MolgenisModel - loop detected between Litter and Identified 1703 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1704 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1705 DEBUG main MolgenisModel - swapped Event with Unidentified 1706 DEBUG main MolgenisModel - swapped Protocol with Event 1707 DEBUG main freemarker.beans - Key 'version' was not found on instance of org.molgenis.model.elements.Model. Introspection information for the class is: {methods=java.beans.PropertyDescriptor@85468716, userinterface=java.beans.PropertyDescriptor@a2da2b4, getEntity=public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String), getDBDescription=public java.lang.String org.molgenis.model.elements.Model.getDBDescription(), methodSchema=java.beans.PropertyDescriptor@ddba3eb5, getUserinterface=public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface(), hashCode=public native int java.lang.Object.hashCode(), setLabel=public void org.molgenis.model.elements.Model.setLabel(java.lang.String), concreteEntities=java.beans.PropertyDescriptor@a0c27aaa, wait=freemarker.ext.beans.MethodMap@bc8e1e, getMethods=public java.util.Vector org.molgenis.model.elements.Model.getMethods(), getEntities=public java.util.Vector org.molgenis.model.elements.Model.getEntities(), setDBDescription=public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String), getConcreteEntities=public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities(), findField=public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException, getModules=public java.util.List org.molgenis.model.elements.Model.getModules(), matrices=java.beans.PropertyDescriptor@b297056, name=java.beans.PropertyDescriptor@8bda862f, notify=public final native void java.lang.Object.notify(), PRDescription=java.beans.PropertyDescriptor@aecb2d4e, notifyAll=public final native void java.lang.Object.notifyAll(), setPRDescription=public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String), getClass=public final native java.lang.Class java.lang.Object.getClass(), java.lang.Object@5e3974=public org.molgenis.model.elements.Model(java.lang.String), UIDescription=java.beans.PropertyDescriptor@f2c661bc, getViews=public java.util.Vector org.molgenis.model.elements.Model.getViews(), equals=public boolean java.lang.Object.equals(java.lang.Object), class=java.beans.PropertyDescriptor@50cf0ddd, getPRDescription=public java.lang.String org.molgenis.model.elements.Model.getPRDescription(), label=java.beans.PropertyDescriptor@1ce86de8, DBDescription=java.beans.PropertyDescriptor@c6852072, entities=java.beans.PropertyDescriptor@5946acbd, getMethodSchema=public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema(), database=java.beans.PropertyDescriptor@39a83c28, getLabel=public java.lang.String org.molgenis.model.elements.Model.getLabel(), getMatrices=public java.util.Vector org.molgenis.model.elements.Model.getMatrices(), getUIDescription=public java.lang.String org.molgenis.model.elements.Model.getUIDescription(), setUIDescription=public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String), views=java.beans.PropertyDescriptor@ac90024a, getDatabase=public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase(), getName=public java.lang.String org.molgenis.model.elements.Model.getName(), toString=public java.lang.String org.molgenis.model.elements.Model.toString(), setName=public void org.molgenis.model.elements.Model.setName(java.lang.String), java.lang.Object@1dd46f7={public org.molgenis.model.elements.MethodSchema org.molgenis.model.elements.Model.getMethodSchema()=[Ljava.lang.Class;@12452e8, public boolean java.lang.Object.equals(java.lang.Object)=[Ljava.lang.Class;@1bf3d87, public java.lang.String org.molgenis.model.elements.Model.getLabel()=[Ljava.lang.Class;@60991f, public java.util.Vector org.molgenis.model.elements.Model.getMatrices()=[Ljava.lang.Class;@1e4f7c2, public final native java.lang.Class java.lang.Object.getClass()=[Ljava.lang.Class;@145f0e3, public java.lang.String org.molgenis.model.elements.Model.getPRDescription()=[Ljava.lang.Class;@c9d92c, public java.util.Vector org.molgenis.model.elements.Model.getViews()=[Ljava.lang.Class;@1d0fafc, public void org.molgenis.model.elements.Model.setPRDescription(java.lang.String)=[Ljava.lang.Class;@10dc6b5, public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)=[Ljava.lang.Class;@170bea5, public java.lang.String org.molgenis.model.elements.Model.toString()=[Ljava.lang.Class;@f47396, public void org.molgenis.model.elements.Model.setName(java.lang.String)=[Ljava.lang.Class;@d0af9b, public void org.molgenis.model.elements.Model.setUIDescription(java.lang.String)=[Ljava.lang.Class;@b8f8eb, public org.molgenis.model.elements.DBSchema org.molgenis.model.elements.Model.getDatabase()=[Ljava.lang.Class;@1de17f4, public java.lang.String org.molgenis.model.elements.Model.getName()=[Ljava.lang.Class;@1f6ba0f, public java.lang.String org.molgenis.model.elements.Model.getUIDescription()=[Ljava.lang.Class;@1313906, public org.molgenis.model.elements.UISchema org.molgenis.model.elements.Model.getUserinterface()=[Ljava.lang.Class;@96cf11, public void org.molgenis.model.elements.Model.setLabel(java.lang.String)=[Ljava.lang.Class;@f47bf5, public org.molgenis.model.elements.Entity org.molgenis.model.elements.Model.getEntity(java.lang.String)=[Ljava.lang.Class;@f6438d, public java.lang.String org.molgenis.model.elements.Model.getDBDescription()=[Ljava.lang.Class;@1cd0888, public org.molgenis.model.elements.Model(java.lang.String)=[Ljava.lang.Class;@1eb2c1b, public native int java.lang.Object.hashCode()=[Ljava.lang.Class;@9cbd4b, public final native void java.lang.Object.notify()=[Ljava.lang.Class;@4f9fdc, public org.molgenis.model.elements.Field org.molgenis.model.elements.Model.findField(java.lang.String) throws org.molgenis.framework.db.DatabaseException,org.molgenis.model.MolgenisModelException=[Ljava.lang.Class;@18825b3, public java.util.List org.molgenis.model.elements.Model.getModules()=[Ljava.lang.Class;@1632847, public final native void java.lang.Object.notifyAll()=[Ljava.lang.Class;@e95a56, public java.util.Vector org.molgenis.model.elements.Model.getMethods()=[Ljava.lang.Class;@29e357, public java.util.Vector org.molgenis.model.elements.Model.getEntities()=[Ljava.lang.Class;@ca470, public void org.molgenis.model.elements.Model.setDBDescription(java.lang.String)=[Ljava.lang.Class;@1ffc686, public java.util.Vector org.molgenis.model.elements.Model.getConcreteEntities()=[Ljava.lang.Class;@142bece}, modules=java.beans.PropertyDescriptor@8bfbb355, getRecord=public org.molgenis.model.elements.Record org.molgenis.model.elements.Model.getRecord(java.lang.String)} 1708 INFO main ObjectModelDocGen - generated WebContent\generated-doc\objectmodel.html 1709 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1710 DEBUG main MolgenisModel - loop detected between Litter and Identified 1711 DEBUG main MolgenisModel - loop detected between Litter and Identified 1712 DEBUG main MolgenisModel - swapped Litter with Owner 1713 DEBUG main MolgenisModel - swapped Event with Identified 1714 DEBUG main MolgenisModel - loop detected between Identified and Litter 1715 DEBUG main MolgenisModel - swapped Identified with Source 1716 DEBUG main MolgenisModel - swapped Event with Identified 1717 DEBUG main MolgenisModel - loop detected between Identified and Litter 1718 DEBUG main MolgenisModel - swapped Identified with Genotype 1719 DEBUG main MolgenisModel - swapped Unidentified with Litter 1720 DEBUG main MolgenisModel - loop detected between Litter and Identified 1721 DEBUG main MolgenisModel - loop detected between Litter and Identified 1722 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1723 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1724 DEBUG main MolgenisModel - swapped Event with Unidentified 1725 DEBUG main MolgenisModel - swapped Protocol with Event 1726 INFO main MySqlCreateSubclassPerTableGen - generated generated\sql\create_tables.sql 1727 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1728 DEBUG main MolgenisModel - loop detected between Litter and Identified 1729 DEBUG main MolgenisModel - loop detected between Litter and Identified 1730 DEBUG main MolgenisModel - swapped Litter with Owner 1731 DEBUG main MolgenisModel - swapped Event with Identified 1732 DEBUG main MolgenisModel - loop detected between Identified and Litter 1733 DEBUG main MolgenisModel - swapped Identified with Source 1734 DEBUG main MolgenisModel - swapped Event with Identified 1735 DEBUG main MolgenisModel - loop detected between Identified and Litter 1736 DEBUG main MolgenisModel - swapped Identified with Genotype 1737 DEBUG main MolgenisModel - swapped Unidentified with Litter 1738 DEBUG main MolgenisModel - loop detected between Litter and Identified 1739 DEBUG main MolgenisModel - loop detected between Litter and Identified 1740 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1741 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1742 DEBUG main MolgenisModel - swapped Event with Unidentified 1743 DEBUG main MolgenisModel - swapped Protocol with Event 1744 INFO main MySqlAlterSubclassPerTableGen - generated generated\sql\alter_tables.sql 1745 INFO main JDBCDatabaseGen - generated generated\java\app\JDBCDatabase.java 1746 INFO main DataTypeGen - generated generated\java\animaldb\Identifiable.java 1747 INFO main DataTypeGen - generated generated\java\animaldb\AbstractAnimal.java 1748 INFO main DataTypeGen - generated generated\java\animaldb\Event.java 1749 INFO main DataTypeGen - generated generated\java\animaldb\Event_type.java 1750 INFO main DataTypeGen - generated generated\java\animaldb\Identified.java 1751 INFO main DataTypeGen - generated generated\java\animaldb\Unidentified.java 1752 INFO main DataTypeGen - generated generated\java\animaldb\Loc_bridge.java 1753 INFO main DataTypeGen - generated generated\java\animaldb\Location.java 1754 INFO main DataTypeGen - generated generated\java\animaldb\Source.java 1755 INFO main DataTypeGen - generated generated\java\animaldb\Genotype.java 1756 INFO main DataTypeGen - generated generated\java\animaldb\Litter.java 1757 INFO main DataTypeGen - generated generated\java\animaldb\Experiment.java 1758 INFO main DataTypeGen - generated generated\java\animaldb\Protocol.java 1759 INFO main DataTypeGen - generated generated\java\animaldb\Owner.java 1760 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup.java 1761 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUser.java 1762 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisEntityMetaData.java 1763 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_members.java 1764 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canRead.java 1765 INFO main DataTypeGen - generated generated\java\org\molgenis\auth\MolgenisUserGroup_canWrite.java 1766 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\EventMapper.java 1767 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\Event_typeMapper.java 1768 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\IdentifiedMapper.java 1769 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\UnidentifiedMapper.java 1770 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\Loc_bridgeMapper.java 1771 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\LocationMapper.java 1772 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\SourceMapper.java 1773 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\GenotypeMapper.java 1774 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\LitterMapper.java 1775 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\ExperimentMapper.java 1776 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\ProtocolMapper.java 1777 INFO main MultiqueryMapperGen - generated generated\java\animaldb\db\OwnerMapper.java 1778 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroupMapper.java 1779 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserMapper.java 1780 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisEntityMetaDataMapper.java 1781 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_membersMapper.java 1782 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canReadMapper.java 1783 INFO main MultiqueryMapperGen - generated generated\java\org\molgenis\auth\db\MolgenisUserGroup_canWriteMapper.java 1784 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1785 DEBUG main MolgenisModel - loop detected between Litter and Identified 1786 DEBUG main MolgenisModel - loop detected between Litter and Identified 1787 DEBUG main MolgenisModel - swapped Litter with Owner 1788 DEBUG main MolgenisModel - swapped Event with Identified 1789 DEBUG main MolgenisModel - loop detected between Identified and Litter 1790 DEBUG main MolgenisModel - swapped Identified with Source 1791 DEBUG main MolgenisModel - swapped Event with Identified 1792 DEBUG main MolgenisModel - loop detected between Identified and Litter 1793 DEBUG main MolgenisModel - swapped Identified with Genotype 1794 DEBUG main MolgenisModel - swapped Unidentified with Litter 1795 DEBUG main MolgenisModel - loop detected between Litter and Identified 1796 DEBUG main MolgenisModel - loop detected between Litter and Identified 1797 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1798 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1799 DEBUG main MolgenisModel - swapped Event with Unidentified 1800 DEBUG main MolgenisModel - swapped Protocol with Event 1801 INFO main JDBCMetaDatabaseGen - generated generated\java\app\JDBCMetaDatabase.java 1802 INFO main CountPerEntityGen - generated generated\sql\count_per_entity.sql 1803 INFO main CountPerTableGen - generated generated\sql\count_per_table.sql 1804 INFO main FillMetadataTablesGen - generated generated\sql\insert_metadata.sql 1805 INFO main CsvReaderGen - generated generated\java\animaldb\csv\EventCsvReader.java 1806 INFO main CsvReaderGen - generated generated\java\animaldb\csv\Event_typeCsvReader.java 1807 INFO main CsvReaderGen - generated generated\java\animaldb\csv\IdentifiedCsvReader.java 1808 INFO main CsvReaderGen - generated generated\java\animaldb\csv\UnidentifiedCsvReader.java 1809 INFO main CsvReaderGen - generated generated\java\animaldb\csv\Loc_bridgeCsvReader.java 1810 INFO main CsvReaderGen - generated generated\java\animaldb\csv\LocationCsvReader.java 1811 INFO main CsvReaderGen - generated generated\java\animaldb\csv\SourceCsvReader.java 1812 INFO main CsvReaderGen - generated generated\java\animaldb\csv\GenotypeCsvReader.java 1813 INFO main CsvReaderGen - generated generated\java\animaldb\csv\LitterCsvReader.java 1814 INFO main CsvReaderGen - generated generated\java\animaldb\csv\ExperimentCsvReader.java 1815 INFO main CsvReaderGen - generated generated\java\animaldb\csv\ProtocolCsvReader.java 1816 INFO main CsvReaderGen - generated generated\java\animaldb\csv\OwnerCsvReader.java 1817 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroupCsvReader.java 1818 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserCsvReader.java 1819 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisEntityMetaDataCsvReader.java 1820 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_membersCsvReader.java 1821 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canReadCsvReader.java 1822 INFO main CsvReaderGen - generated generated\java\org\molgenis\auth\csv\MolgenisUserGroup_canWriteCsvReader.java 1823 INFO main REntityGen - generated generated\java\animaldb\R\Event.R 1824 INFO main REntityGen - generated generated\java\animaldb\R\Event_type.R 1825 INFO main REntityGen - generated generated\java\animaldb\R\Identified.R 1826 INFO main REntityGen - generated generated\java\animaldb\R\Unidentified.R 1827 INFO main REntityGen - generated generated\java\animaldb\R\Loc_bridge.R 1828 INFO main REntityGen - generated generated\java\animaldb\R\Location.R 1829 INFO main REntityGen - generated generated\java\animaldb\R\Source.R 1830 INFO main REntityGen - generated generated\java\animaldb\R\Genotype.R 1831 INFO main REntityGen - generated generated\java\animaldb\R\Litter.R 1832 INFO main REntityGen - generated generated\java\animaldb\R\Experiment.R 1833 INFO main REntityGen - generated generated\java\animaldb\R\Protocol.R 1834 INFO main REntityGen - generated generated\java\animaldb\R\Owner.R 1835 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup.R 1836 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUser.R 1837 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisEntityMetaData.R 1838 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_members.R 1839 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canRead.R 1840 INFO main REntityGen - generated generated\java\org\molgenis\auth\R\MolgenisUserGroup_canWrite.R 1841 INFO main RApi - generated generated\java\app\servlet\source.R 1842 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 1843 INFO main MolgenisContextListenerGen - generated generated\java\app\servlet\ContextListener.java 1844 INFO main MolgenisServletGen - generated generated\java\app\servlet\MolgenisServlet.java 1845 INFO main MenuScreenGen - generated generated\java\app\ui\MainmenuMenu.java 1846 INFO main PluginScreenGen - generated orkspace\molgenis32_workspace\molgenis_distro\generated\java\app\ui\WelcomeScreenPlugin.java 1847 WARN main PluginScreenFTLTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.ftl 1848 WARN main PluginScreenJavaTemplateGen - Skipped because exists: handwritten\java\plugin\welcome\WelcomeScreenPlugin.java 1849 INFO main MolgenisServletContextGen - generated WebContent\META-INF\context.xml 1850 INFO main SoapApiGen - generated generated\java\app\servlet\SoapApi.java 1851 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1852 DEBUG main MolgenisModel - loop detected between Litter and Identified 1853 DEBUG main MolgenisModel - loop detected between Litter and Identified 1854 DEBUG main MolgenisModel - swapped Litter with Owner 1855 DEBUG main MolgenisModel - swapped Event with Identified 1856 DEBUG main MolgenisModel - loop detected between Identified and Litter 1857 DEBUG main MolgenisModel - swapped Identified with Source 1858 DEBUG main MolgenisModel - swapped Event with Identified 1859 DEBUG main MolgenisModel - loop detected between Identified and Litter 1860 DEBUG main MolgenisModel - swapped Identified with Genotype 1861 DEBUG main MolgenisModel - swapped Unidentified with Litter 1862 DEBUG main MolgenisModel - loop detected between Litter and Identified 1863 DEBUG main MolgenisModel - loop detected between Litter and Identified 1864 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1865 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1866 DEBUG main MolgenisModel - swapped Event with Unidentified 1867 DEBUG main MolgenisModel - swapped Protocol with Event 1868 INFO main CsvExportGen - generated generated\java\app\CsvExport.java 1869 DEBUG main MolgenisModel - swapped AbstractAnimal with Litter 1870 DEBUG main MolgenisModel - loop detected between Litter and Identified 1871 DEBUG main MolgenisModel - loop detected between Litter and Identified 1872 DEBUG main MolgenisModel - swapped Litter with Owner 1873 DEBUG main MolgenisModel - swapped Event with Identified 1874 DEBUG main MolgenisModel - loop detected between Identified and Litter 1875 DEBUG main MolgenisModel - swapped Identified with Source 1876 DEBUG main MolgenisModel - swapped Event with Identified 1877 DEBUG main MolgenisModel - loop detected between Identified and Litter 1878 DEBUG main MolgenisModel - swapped Identified with Genotype 1879 DEBUG main MolgenisModel - swapped Unidentified with Litter 1880 DEBUG main MolgenisModel - loop detected between Litter and Identified 1881 DEBUG main MolgenisModel - loop detected between Litter and Identified 1882 DEBUG main MolgenisModel - swapped Loc_bridge with Location 1883 DEBUG main MolgenisModel - swapped Loc_bridge with Identified 1884 DEBUG main MolgenisModel - swapped Event with Unidentified 1885 DEBUG main MolgenisModel - swapped Protocol with Event 1886 INFO main CsvImportGen - generated generated\java\app\CsvImport.java -
molgenis4animaldb/molgenis4animal_db.xml
r2432 r2452 6 6 <molgenis name="animaldb" label="AnimalDB"> 7 7 8 <description>This is an minimal exampledatabase to show how8 <description>This is an minimal database to show how 9 9 AnimalDB works in combination with Molgenis. The purpose of 10 this example database is to administrate animals, groups, 11 locations, events and event types. The name='example' will 12 result in a Java package 'example' being generated.</description> 10 this database is to administrate animals, groups of animals, 11 locations, events and event types.</description> 13 12 14 13 <!-- abstract data types --> … … 23 22 <field name="comment" nillable="true" description="optional comment string" label="Comment"/> 24 23 </entity> 24 25 <entity name="AbstractAnimal" implements="Identifiable" abstract="true"> 26 <description>Abstract class that contains the 27 common elements of identified (single) animals 28 and unidentified (groups of) animals</description> 29 <field name="litterid" type="xref" xref_field="Litter.id" 30 xref_label="name" label="Litter"/> 31 <field name="customid" type="string" nillable="true" label="Custom ID"/> 32 <field name="species" type="string" label="Species"/> 33 <field name="sourceid" type="xref" xref_field="Source.id" 34 xref_label="name" label="Source"/> 35 <field name="ownerid" type="xref" xref_field="Owner.id" 36 xref_label="name" label="Owner"/> 37 </entity> 25 38 26 39 <!-- event structure --> … … 28 41 <entity name="Event" implements="Identifiable" xref_label="id" label="Events"> 29 42 <description>Summary of an event</description> 30 <field name=" animalid" type="xref" xref_field="Animal.id"43 <field name="identifiedid" type="xref" xref_field="Identified.id" 31 44 xref_label="name" label="Animal"/> 45 <field name="unidentifiedid" type="xref" xref_field="Unidentified.id" 46 xref_label="name" label="Set of animals"/> 47 <field name="experimentid" type="xref" xref_field="Experiment.id" 48 xref_label="name" label="Experiment"/> 32 49 <field name="eventtypeid" type="xref" xref_field="Event_type.id" 33 50 xref_label="name" label="Type of event"/> 34 51 <field name="locationid" type="xref" xref_field="Location.id" 35 52 xref_label="name" label="Location"/> 36 <field name="date" type="date" auto="true" 37 description="Creation date, with an automatic default to 'today'" label="Date"/> 38 </entity> 39 40 <entity name="Animal" implements="Identifiable" xref_label="name" label="Animals"> 41 <description>Summary of an animal</description> 42 <field name="locationid" type="xref" xref_field="Location.id" 43 xref_label="name" label="Location"/> 44 <field name="animalgroupid" type="xref" xref_field="Animal_group.id" 45 xref_label="name" nillable="true" label="Group"/> 46 <field name="species" label="Species"/> 47 </entity> 48 49 <entity name="Animal_group" implements="Identifiable" xref_label="name" label="Groups"> 50 <description>Summary of a group of animals</description> 51 </entity> 52 53 <entity name="Location" implements="Identifiable" xref_label="name" label="Locations"> 54 <description>Summary of a location</description> 53 <field name="timestamp" type="datetime" auto="true" 54 description="Creation date and time, with an automatic default to 'now'" label="Date-Time"/> 55 <field name="ownerid" type="xref" xref_field="Owner.id" 56 xref_label="name" label="Owner"/> 55 57 </entity> 56 58 … … 59 61 </entity> 60 62 63 <entity name="Identified" implements="AbstractAnimal" xref_label="id" label="Identified"> 64 <field name="genotypeid" type="xref" xref_field="Genotype.id" 65 xref_label="name" label="Genotype"/> 66 </entity> 67 68 <entity name="Unidentified" implements="AbstractAnimal" xref_label="id" label="Unidentified"> 69 <field name="quantity" type="int" label="Quantity"/> 70 <field name="exact" type="bool" label="Exact quantity?"/> 71 </entity> 72 73 <entity name="Loc_bridge" implements="Identifiable" xref_label="name" label="Animal-Location-bridge"> 74 <description>Bridge table to couple an animal to a location</description> 75 <field name="locationid" type="xref" xref_field="Location.id" 76 xref_label="name" label="Location"/> 77 <field name="identified_locationid" type="xref" xref_field="Identified.id" 78 xref_label="name" label="Identified"/> 79 <field name="unidentified_locationid" type="xref" xref_field="Unidentified.id" 80 xref_label="name" label="Unidentified"/> 81 <field name="fromdate" type="date" auto="true" label="From date"/> 82 <field name="todate" type="date" nillable="true" auto="true" label="To date"/> 83 </entity> 84 85 <entity name="Location" implements="Identifiable" xref_label="name" label="Locations"> 86 <description>Summary of a location</description> 87 <field name="address" type="string" label="Address"/> 88 <field name="inlocationid" type="xref" xref_field="Location.id" 89 xref_label="name" label="In location"/> 90 </entity> 91 92 <entity name="Source" implements="Identifiable" xref_label="name" label="Sources"> 93 <description>A description of where the animal(s) came from</description> 94 </entity> 95 96 <entity name="Genotype" implements="Identifiable" xref_label="name" label="Genotypes"> 97 <description>A list of known genotypes</description> 98 <field name="genotype_description" type="string" label="Description"/> 99 <field name="ownerid" type="xref" xref_field="Owner.id" 100 xref_label="name" label="Owner"/> 101 </entity> 102 103 <entity name="Litter" implements="Identifiable" xref_label="name" label="Litters"> 104 <description>Litters, linking animals to their parents</description> 105 <field name="fatherid" type="xref" xref_field="Identified.id" 106 xref_label="name" label="Father"/> 107 <field name="motherid" type="xref" xref_field="Identified.id" 108 xref_label="name" label="Mother"/> 109 <field name="fromdatepair" type="date" auto="true" label="Pair from date"/> 110 <field name="todatepair" type="date" nillable="true" auto="true" label="Pair to date"/> 111 <field name="birthdate" type="date" auto="true" label="Birth date"/> 112 <field name="birthsize" type="int" label="Birth size"/> 113 <field name="weandate" type="date" auto="true" label="Wean date"/> 114 <field name="weansize" type="int" label="Wean size"/> 115 <field name="ownerid" type="xref" xref_field="Owner.id" 116 xref_label="name" label="Owner"/> 117 </entity> 118 119 <entity name="Experiment" implements="Identifiable" xref_label="name" label="Genotypes"> 120 <description>Experiments</description> 121 <field name="experiment_description" type="string" label="Description"/> 122 <field name="decnumber" type="string" label="DEC number"/> 123 <field name="expentrydate" type="date" auto="true" label="Experiment entry date"/> 124 <field name="expexitdate_est" type="date" auto="true" label="Estimated experiment exit date"/> 125 <field name="expexitdate_real" type="date" nillable="true" auto="true" label="Real experiment exit date"/> 126 <field name="inconvenience_est" type="int" label="Estimated inconvenience"/> 127 <field name="inconvenience_real" type="int" label="Real inconvenience"/> 128 <field name="ownerid" type="xref" xref_field="Owner.id" 129 xref_label="name" label="Owner"/> 130 </entity> 131 132 <entity name="Protocol" implements="Identifiable" xref_label="name" label="Protocols"> 133 <description>Protocols, for instance measurements</description> 134 <field name="protocol_eventid" type="xref" xref_field="Event.id" 135 xref_label="name" label="Event"/> 136 <field name="protkey" type="string" label="Key" description="These should come from an ontology"/> 137 <field name="value" type="string" label="Value"/> 138 <field name="unit" type="string" nillable="true" label="Unit of measurement"/> 139 <field name="ownerid" type="xref" xref_field="Owner.id" 140 xref_label="name" label="Owner"/> 141 </entity> 142 143 <entity name="Owner" implements="Identifiable" xref_label="name" label="Users"> 144 <description>Users, who can be owners of animals, experiments etc.</description> 145 </entity> 146 61 147 </molgenis> -
molgenis4animaldb/molgenis4animal_ui.xml
r2421 r2452 12 12 label="Welcome" /> 13 13 14 <!-- 14 15 <menu name="topmenu" label="Manage tables"> 15 16 <form name="Location" entity="Location" view="list" label="Locations" /> … … 25 26 <plugin name="MakeReport" type="plugin.reports.MakeReportPlugin" 26 27 label="Make reports" /> 27 28 --> 29 28 30 </menu> 29 31
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