List of Plugins

• Lucene indexing created on molgenis DB tables
  • Location : http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugins/LuceneIndex/
    • DBIndexPlugin.ftl
    • DBIndexPlugin.java
  • Functionality : creation of index , deletion of index , search on index, query expansion
    • Documentation : http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/Lucene_OntoCAT_Indexing_manual.docx
  • Despoina , Dasha
• Lucene indexing created on molgenis ontocat results on specific terms
  • Location : http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugins/LuceneIndex/
    • OntoCatIndexPlugin2.ftl
    • OntoCatIndexPlugin2.java
  • Functionality: Indexes all ontologies specified in ontologyNamesMap (creation of index ). The ontologies should be downloaded on the computer in ONTOLOGIES_DIRECTORY, searches through the index , deletion of index , query expansion
  • Documentation : http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/Lucene_OntoCAT_Indexing_manual.docx
  • Despoina , Dasha
• AddAnimalPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/addanimal/
  • Author: Erik
  • Function: Add one or more animals to the database, specifying their name, species, sex and genotype.
• RemAnimalPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/addanimal/
  • Author: Erik
  • Function: Terminate an animal. Its status is set to 'Dead' and it is removed from any experiments it may be part of, allowing the user to set some end state parameters.
• AddEvent
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/addevent/
  • Author: Erik
  • Function: Apply a protocol to one or more targets. Upon choosing the protocol, the AddEventMenuServlet gives back HTML for inputs to set the appropriate feature-values.
• AddLocation
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/addlocation/
  • Author: Erik
  • Function: Add a location to the database. It is possible to set it as a sublocation of another one, so you can construct hierarchies of locations.
• BreedingModule
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/breedingplugin/
  • Author: Erik
  • Function: This plugin consists of 5 screens. Screen 1 is to make a parent group, a group of one or more females and one or more males that have been put together in the hope that they will produce offspring. Screen 2 is to edit parant groups (under construction). Screen 3 is to register litters, specifying the parent group that produced it, the birth date and the (approximate) size. Screen 4 is to edit litters (under construction). Screen 5 is also still under construction and will enable the user to wean a litter (mammals only), whereupon the pups will be entered into the database as real animals that count for the Yearly Report.
• EventViewer
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/eventviewer/
  • Author: Erik
  • Function: Choose an animal and then you are shown all the feature-values that have been applied to it. The ViewEventsServlet produces the right HTML.
• ShowAnimalsInSubprojects
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/experiments/
  • Author: Erik
  • Function: Under construction. Show a table of all DEC Subprojects (experiments) and the animals that participate in them. The user should be able to add animals to experiments, edit their properties or remove them from experiments for whatever reason.
• ShowDecProjects
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/experiments/
  • Author: Erik
  • Function: Show all DEC Projects (applications), allowing the user to add or edit.
• ShowDecSubprojects
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/experiments/
  • Author: Erik
  • Function: Show all DEC Subprojects (experiments), allowing the user to add or edit.
• FillDatabasePlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/fillanimaldb/
  • Author: Erik
  • Function: Fill the database with targets, features, protocols and values needed to make the system run. For instance, generate a list of species, make a protocol for adding animals to experiments etc. It is also possible to load one or more tables from the old version of AnimalDB (in practice this is for Ate Boerema only).
• ListPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/listplugin/
  • Author: Erik
  • Function: Show a matrix of targets x features. The user can select from a selectbox features they want to be shown. Selecting again removes the feature from the matrix again. It is possible to browse through the targets. Furthermore, the user can search in the whole table or in one or more columns, of which the result set can be saved into a targetgroup. jQuery technology is used to construct this matrix. The EventViewerJSONServlet is the underlying datasource, spitting out the data the user wants to see formatted in JSON, so jQuery can parse it into the matrix.
• ListPlugin2
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/animaldb/listplugin2/
  • Author: Ate
  • Function: Under construction. An attempt at the same functionality as the ListPlugin, except this plugin uses ExtJS technology.
• LocationInfoPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/locationinfo/
  • Author: Erik
  • Function: Select a location and this plugin shows how it fits into the location hierarchy. The LocationInformationServlet provides the appropriate HTML.
• AddSpecialGroupPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/specialgroups/
  • Author: Erik
  • Function: Add a targetgroup. Optionally, the user can label it, either with an existing label (Species, Sex) or a new one.
• AnimalDBWelcomeScreenPlugin
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/welcome/
  • Author: Erik
  • Function: Show an AnimalDB-specific welcome screen.
• YearlyReportModule
  • Location: http://www.molgenis.org/svn/molgenis_projects/molgenis4phenotype/handwritten/java/plugin/yearlyreportplugin/
  • Author: Erik
  • Function: Show a VWA Yearly Report of a chosen type (4A, 4B, 4C or 5) for a chosen year (max. 5 years back).
• Lanes plugin
  • Location: http://www.molgenis.org/svn/sequence_lims/handwritten/java/plugins/
  • Author: Joris
  • Function: assign sample to lanes in a sequence LIMS platform
•  Matrix plugin
  • Location: http://www.molgenis.org/svn/molgenis_distro/3.5/handwritten/java/Matrix/
  • Author: Joris
  • Function: browse data in pheno-model, support search (expression), sort and add/remove column. Only db backend supported at the moment.