Changeset 2618


Ignore:
Timestamp:
02/02/10 17:42:10 (2 years ago)
Author:
jlops
Message:

commit

Location:
maven_sequence_lims/sequence_lims_maven
Files:
2 added
2 deleted
49 edited

Legend:

Unmodified
Added
Removed

  • maven_sequence_lims/sequence_lims_maven

    • Property svn:ignore

      •  

        old new  
        11target 
         2profiles.xml 

  • maven_sequence_lims/sequence_lims_maven/WebContent/doc/classmodel.html

    r2582 r2618  
    7474<a href="#_top_of_page">go to top</a> 
    7575 
    76 <div align="center">Documentation generated on October 13, 2009 by MOLGENIS <a href="http://www.molgenis.org">http://www.molgenis.org</a></div> 
     76<div align="center">Documentation generated on February 2, 2010 by MOLGENIS <a href="http://www.molgenis.org">http://www.molgenis.org</a></div> 
    7777</body></html> 
    7878 

  • maven_sequence_lims/sequence_lims_maven/WebContent/doc/objectmodel.html

    r2582 r2618  
    13531353<a href="#_top_of_page">go to top</a> 
    13541354 
    1355 <div align="center">Documentation generated on October 13, 2009 by MOLGENIS <a href="http://www.molgenis.org">http://www.molgenis.org</a></div> 
     1355<div align="center">Documentation generated on February 2, 2010 by MOLGENIS <a href="http://www.molgenis.org">http://www.molgenis.org</a></div> 
    13561356</body></html> 
    13571357 

  • maven_sequence_lims/sequence_lims_maven/pom.xml

    r2585 r2618  
    22         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> 
    33    <modelVersion>4.0.0</modelVersion> 
    4     <groupId>com.umcg</groupId> 
    5     <artifactId>sequence_lims_maven</artifactId> 
     4    <groupId>nl.umcg.gcc</groupId> 
     5    <artifactId>SimpleEE6AppMaven</artifactId> 
    66    <packaging>war</packaging> 
    77    <version>1.0-SNAPSHOT</version> 
    8     <name>sequence_lims_maven JEE5 Webapp</name> 
     8    <name>Sequence Lims Java EE 6 Webapp</name> 
    99    <url>http://maven.apache.org</url> 
     10    <repositories> 
     11        <repository> 
     12            <id>java.net2</id> 
     13            <name>Repository hosting the jee6 artifacts</name> 
     14            <url>http://download.java.net/maven/2</url> 
     15        </repository> 
     16    </repositories> 
    1017    <dependencies> 
    11         <dependency> 
    12             <groupId>com.sun.xml.ws</groupId> 
    13             <artifactId>jaxws-rt</artifactId> 
    14             <version>2.1.3</version> 
    15             <scope>compile</scope> 
    16             <exclusions> 
    17                 <exclusion> 
    18                     <artifactId>stax-api</artifactId> 
    19                     <groupId>javax.xml.stream</groupId> 
    20                 </exclusion> 
    21             </exclusions> 
    22         </dependency> 
    23         <dependency> 
    24             <groupId>log4j</groupId> 
    25             <artifactId>log4j</artifactId> 
    26             <version>1.2.13</version> 
    27             <scope>compile</scope> 
    28         </dependency> 
    29         <dependency> 
    30             <groupId>javax.servlet</groupId> 
    31             <artifactId>servlet-api</artifactId> 
    32             <version>2.5</version> 
    33             <scope>provided</scope> 
    34         </dependency> 
    35         <dependency> 
    36             <groupId>javax.servlet.jsp</groupId> 
    37             <artifactId>jsp-api</artifactId> 
    38             <version>2.1</version> 
    39             <scope>provided</scope> 
    40         </dependency> 
    41         <dependency> 
    42             <groupId>junit</groupId> 
    43             <artifactId>junit</artifactId> 
    44             <version>3.8.1</version> 
    45             <scope>test</scope> 
    46         </dependency> 
    4718        <dependency> 
    4819            <groupId>org.molgenis</groupId> 
    4920            <artifactId>molgenis3_4_maven</artifactId> 
    5021            <version>1.0-SNAPSHOT</version> 
    51             <exclusions> 
    52                 <exclusion> 
    53                     <artifactId>log4j</artifactId> 
    54                     <groupId>log4j</groupId> 
    55                 </exclusion> 
    56             </exclusions> 
    5722        </dependency> 
     23 
    5824        <dependency> 
    59             <groupId>cmdLine</groupId> 
    60             <artifactId>cmdLine</artifactId> 
    61             <version>1.2</version> 
     25            <groupId>javax</groupId> 
     26            <artifactId>javaee-web-api</artifactId> 
     27            <version>6.0</version> 
     28            <scope>provided</scope> 
     29        </dependency> 
     30 
     31        <dependency> 
     32            <groupId>junit</groupId> 
     33            <artifactId>junit</artifactId> 
     34            <version>3.8.2</version> 
     35            <scope>test</scope> 
    6236        </dependency> 
    6337        <dependency> 
    6438            <groupId>org.hibernate</groupId> 
    6539            <artifactId>hibernate</artifactId> 
    66             <version>3.2.6.ga</version> 
     40            <version>3.2.5.ga</version> 
    6741        </dependency> 
    6842        <dependency> 
    … …  
    7549            <artifactId>hibernate-entitymanager</artifactId> 
    7650            <version>3.3.2.GA</version> 
    77             <exclusions> 
    78                 <exclusion> 
    79                     <artifactId>hibernate</artifactId> 
    80                     <groupId>org.hibernate</groupId> 
    81                 </exclusion> 
    82             </exclusions> 
    8351        </dependency> 
    8452        <dependency> 
    … …  
    9260            <version>1.0.1B</version> 
    9361        </dependency> 
    94         <dependency> 
    95             <groupId>javax.xml.stream</groupId> 
    96             <artifactId>stax-api</artifactId> 
    97             <version>1.0-2</version> 
    98         </dependency> 
    9962    </dependencies> 
    10063    <build> 
    101  
    10264        <resources> 
    10365            <resource> 
    … …  
    11476            </resource> 
    11577        </resources> 
    116  
    11778        <plugins> 
    11879            <plugin> 
    … …  
    12586                </configuration> 
    12687            </plugin> 
     88            <plugin> 
     89                <groupId>org.apache.maven.plugins</groupId> 
     90                <artifactId>maven-war-plugin</artifactId> 
     91                <version>2.1-beta-1</version> 
     92                <configuration> 
     93                    <failOnMissingWebXml>false</failOnMissingWebXml> 
     94                </configuration> 
     95            </plugin> 
     96        </plugins> 
     97        <finalName>Sequence Lims</finalName> 
     98    </build> 
     99    <profiles> 
     100        <profile> 
     101            <id>endorsed</id> 
     102            <activation> 
     103                <property> 
     104                    <name>sun.boot.class.path</name> 
     105                </property> 
     106            </activation> 
     107            <build> 
     108                <plugins> 
     109                    <plugin> 
     110                        <groupId>org.apache.maven.plugins</groupId> 
     111                        <artifactId>maven-compiler-plugin</artifactId> 
     112                        <version>2.0.2</version> 
     113                        <configuration> 
     114                            <!-- javaee6 contains upgrades of APIs contained within the JDK itself. 
     115                                 As such these need to be placed on the bootclasspath, rather than classpath of the 
     116                                 compiler. 
     117                                 If you don't make use of these new updated API, you can delete the profile. 
     118                                 On non-SUN jdk, you will need to create a similar profile for your jdk, with the similar property as sun.boot.class.path in Sun's JDK.--> 
     119                            <compilerArguments> 
     120                                <bootclasspath>${settings.localRepository}/javax/javaee-endorsed-api/6.0/javaee-endorsed-api-6.0.jar${path.separator}${sun.boot.class.path}</bootclasspath> 
     121                            </compilerArguments> 
     122                        </configuration> 
     123                        <dependencies> 
     124                            <dependency> 
     125                                <groupId>javax</groupId> 
     126                                <artifactId>javaee-endorsed-api</artifactId> 
     127                                <version>6.0</version> 
     128                            </dependency> 
     129                        </dependencies> 
     130                    </plugin> 
     131                </plugins> 
     132            </build> 
     133        </profile> 
     134    </profiles> 
    127135 
    128             <plugin> 
    129                 <groupId>org.codehaus.mojo</groupId> 
    130                 <artifactId>jaxws-maven-plugin</artifactId> 
    131                 <executions> 
    132                     <execution> 
    133                         <goals> 
    134                             <goal>wsgen</goal> 
    135                         </goals> 
    136                         <configuration> 
    137                             <sei>handwritten.MySoapApi</sei> 
    138                             <!--for demo purpose only, the webapp does not--> 
    139                             <!--need the generated wsdl files--> 
    140                             <genWsdl>true</genWsdl> 
    141                             <keep>true</keep> 
    142                         </configuration> 
    143                     </execution> 
    144                 </executions> 
    145             </plugin> 
    146  
    147         </plugins> 
    148         <finalName>sequence_lims_maven</finalName> 
    149     </build> 
    150     <repositories> 
    151         <repository> 
    152             <url>http://download.java.net/maven/2/</url> 
    153             <id>hibernate-persistence</id> 
    154             <layout>default</layout> 
    155             <name>Repository for library Library[hibernate-persistence]</name> 
    156         </repository> 
    157     </repositories> 
    158     <properties> 
    159         <netbeans.hint.deploy.server>Tomcat60</netbeans.hint.deploy.server> 
    160     </properties> 
    161136</project> 
    162137 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/MolgenisServlet.java

    r2582 r2618  
    11/* 
    22 * Created by: org.molgenis.generators.servlet.MolgenisServletGen 
    3  * Date: October 13, 2009 
     3 * Date: February 2, 2010 
    44 */ 
    55 
     6import java.io.File; 
    67 
     8import javax.naming.NamingException; 
    79import javax.servlet.http.HttpServletRequest; 
     10import javax.sql.DataSource; 
    811 
    912import org.molgenis.framework.Database; 
    … …  
    1619import org.molgenis.util.email.SimpleEmailService; 
    1720 
     21import org.molgenis.framework.data.jdbc.datasource.JndiDataSourceWrapper; 
    1822import jpa.EMFactory; 
     23import javax.persistence.EntityManagerFactory; 
     24import javax.persistence.Persistence; 
    1925 
    2026public class MolgenisServlet extends AbstractMolgenisServlet 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/CustomerJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Customer.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/FlowcellJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Flowcell.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/GA_RunJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA GA_Run.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/LaneJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Lane.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/Lane_AssignmentJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Lane_Assignment.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/Lane_ConfigJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Lane_Config.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/LibprepJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Libprep.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/LimsUserJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA LimsUser.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/Pipeline_RUNJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Pipeline_RUN.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/ReagentJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Reagent.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/Reagent_UsageJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Reagent_Usage.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/RecipeJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Recipe.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/SampleJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Sample.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/TaskJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Task.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/handwritten/sequencing/data/types/TechnicianJPAListener.java

    r2582 r2618  
    11 
    22/* File:        ui/model/JPA Technician.java 
    3  * Copyright:   GBIC 2000-2,009, all rights reserved 
    4  * Date:        October 13, 2009 
     3 * Copyright:   GBIC 2000-2,010, all rights reserved 
     4 * Date:        February 2, 2010 
    55 * 
    66 * generator:   org.molgenis.generators.data.types.JpaDataTypeListenerGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/source.R

    r2582 r2618  
    11 
    22# File:        ui/R/src/main/java/source.R 
    3 # Copyright:   GBIC 2000-2,009, all rights reserved 
    4 # Date:        October 13, 2009 
     3# Copyright:   GBIC 2000-2,010, all rights reserved 
     4# Date:        February 2, 2010 
    55# 
    66# generator:   org.molgenis.generators.R.RApi 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/tools/CsvExport.java

    r2582 r2618  
    11 
    2 /* Date:        October 13, 2009 
     2/* Date:        February 2, 2010 
    33 *  
    44 * generator:   org.molgenis.generators.tools.CsvExportGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/tools/CsvImportByName.java

    r2582 r2618  
    11 
    2 /* Date:        October 13, 2009 
     2/* Date:        February 2, 2010 
    33 *  
    44 * generator:   org.molgenis.generators.tools.CsvImportByNameGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/JDBCMetaDatabase.java

    r2582 r2618  
    11/* File:        ui/model/JDBCDatabase 
    2  * Copyright:   Inventory 2000-2,009, GBIC 2002-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   Inventory 2000-2,010, GBIC 2002-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.data.JDBCMetaDatabaseGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/JpaDatabase.java

    r2582 r2618  
    11/* File:        ui/model/JDBCDatabase 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.data.JpaDatabaseGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/SoapApi.java

    r2582 r2618  
    3030import generated.sequencing.data.types.Pipeline_RUN; 
    3131import generated.sequencing.data.types.Lane_Config; 
    32 import jpa.EMFactory; 
    3332 
    3433import org.apache.commons.dbcp.BasicDataSource; 
    … …  
    4443 
    4544 
    46 //@WebService() 
    47 //@SOAPBinding(style = Style.DOCUMENT) 
     45@WebService() 
     46@SOAPBinding(style = Style.DOCUMENT) 
    4847public class SoapApi 
    4948{ 
    … …  
    13621361//CUSTOM SERVICES (defined by 'method' entries in MOLGENIS xml) 
    13631362 
    1364         public SoapApi() { 
    1365             new ui.JpaDatabase(EMFactory.createEntityManager());     
    1366         } 
    1367  
    1368         public SoapApi(Database database) 
     1363        public SoapApi(Database database) 
    13691364        { 
    13701365                this.database = database; 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/data/InMemoryDatabase.java

    r2582 r2618  
    11/* File:        ui/model/JDBCDatabase 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.data.InMemoryDatabaseGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Administration/CustomersForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Administration.Customers.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Administration/ReagentForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Administration.Reagent.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Administration/RecipeForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Administration.Recipe.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Administration/TechniciansForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Administration.Technicians.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/AdministrationMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Administration.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/ClusterStation/FlowcellForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.ClusterStation.flowcell.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/ClusterStation/flowcell/FlowcellMenuMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.ClusterStation.flowcell.flowcellMenu.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/ClusterStation/flowcell/flowcellMenu/LanePlugin.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.ClusterStation.flowcell.flowcellMenu.Lane.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.PluginScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/ClusterStationMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.ClusterStation.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/GA_Run/GA_Run/ReagentsUsedForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.GA_Run.GA_Run.reagentsUsed.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/GA_Run/GA_RunForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.GA_Run.GA_Run.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/GA_RunMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.GA_Run.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Pipeline/PIPELINE_RUN/CONFIG_PER_LANEForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Pipeline.PIPELINE_RUN.CONFIG_PER_LANE.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/Pipeline/PIPELINE_RUNForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Pipeline.PIPELINE_RUN.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/PipelineMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.Pipeline.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/SamplesAndLibprepMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.samplesAndLibprep.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/samplesAndLibprep/LibprepForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.samplesAndLibprep.libprep.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/Main/samplesAndLibprep/SamplesForm.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.samplesAndLibprep.samples.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.FormScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/java/ui/screen/MainMenu.java

    r2582 r2618  
    11/* File:        Ui/screen/molgenis.Main.java 
    2  * Copyright:   GBIC 2000-2,009, all rights reserved 
    3  * Date:        October 13, 2009 
     2 * Copyright:   GBIC 2000-2,010, all rights reserved 
     3 * Date:        February 2, 2010 
    44 *  
    55 * generator:   org.molgenis.generators.screen.MenuScreenGen 3.3.0-testing 

  • maven_sequence_lims/sequence_lims_maven/src/main/resources/META-INF/persistence.xml

    r2582 r2618  
    11<?xml version="1.0" encoding="UTF-8"?> 
    22<persistence version="1.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_1_0.xsd"> 
    3 <!-- 
     3  <!-- 
    44  <persistence-unit name="molgenis4LIMS" transaction-type="RESOURCE_LOCAL"> 
    55    <provider>org.hibernate.ejb.HibernatePersistence</provider> 
    … …  
    1111--> 
    1212  <persistence-unit name="molgenis4LIMS" transaction-type="RESOURCE_LOCAL"> 
    13     <provider>org.hibernate.ejb.HibernatePersistence</provider> 
     13    <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider> 
     14    <non-jta-data-source>molgenis4LIMS</non-jta-data-source> 
     15    <exclude-unlisted-classes>false</exclude-unlisted-classes> 
    1416    <properties> 
    15       <property name="hibernate.connection.username" value="molgenis"/> 
    16       <property name="hibernate.connection.driver_class" value="com.mysql.jdbc.Driver"/> 
    17       <property name="hibernate.connection.password" value="molgenis"/> 
    18       <property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/sequence_lims?sessionVariables=storage_engine=InnoDB"/> 
    1917      <property name="hibernate.cache.provider_class" value="org.hibernate.cache.NoCacheProvider"/> 
    20       <property name="dialect" value="org.hibernate.dialect.MySQLInnoDBDialect"/> 
    21       <property name="hibernate.hbm2ddl.auto" value="create"/> 
     18      <property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/sequence_lims"/> 
     19      <property name="javax.persistence.jdbc.password" value="molgenis"/> 
     20      <property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver"/> 
     21      <property name="javax.persistence.jdbc.user" value="molgenis"/> 
     22      <property name="eclipselink.logging.level" value="FINE"/> 
     23      <property name="eclipselink.ddl-generation" value="drop-and-create-tables"/> 
    2224    </properties> 
    2325  </persistence-unit> 

  • maven_sequence_lims/sequence_lims_maven/src/main/webapp/WEB-INF/sun-web.xml

    r2582 r2618  
    22<!DOCTYPE sun-web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Application Server 9.0 Servlet 2.5//EN" "http://www.sun.com/software/appserver/dtds/sun-web-app_2_5-0.dtd"> 
    33<sun-web-app error-url=""> 
    4   <context-root>/sequence_lims2</context-root> 
     4  <context-root>/Sequence Lims</context-root> 
    55  <class-loader delegate="true"/> 
    66  <jsp-config> 

  • maven_sequence_lims/sequence_lims_maven/src/main/webapp/WEB-INF/web.xml

    r2585 r2618  
    1212        <listener-class>servlet.ContextListener</listener-class> 
    1313    </listener> 
    14     <listener> 
    15         <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class> 
    16     </listener> 
    1714    <servlet> 
    1815        <servlet-name>MolgenisServlet</servlet-name> 
    1916        <servlet-class>MolgenisServlet</servlet-class> 
    20     </servlet> 
    21     <servlet> 
    22         <servlet-name>MySoapApi</servlet-name> 
    23         <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class> 
    24         <load-on-startup>1</load-on-startup> 
    2517    </servlet> 
    2618    <servlet-mapping> 
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