source: extensions/net.sf.basedb.reggie/trunk/META-INF/extensions.xml

<?xml version="1.0" encoding="UTF-8" ?>
<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about safe-resources="1">
    <name>Reggie package</name>
    <description>
      A package for simplified registration of biosources
      and samples.
    </description>
    <version>4.34-dev</version>
    <min-base-version>3.19.0</min-base-version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie</url>
  </about>

  <plugin-definition id="CaliperSampleNameExporter">
    <about>
      <name>Caliper sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        CSV file that can be used by the Caliper software. The
        exported file has one line for each non-empty well with
        five columns. Only the first two columns are used:
        Well coordinate, sample name.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperRunParametersExporter">
    <about>
      <name>Caliper run parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperRunParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperLibPrepParametersExporter">
    <about>
      <name>Caliper library preparation parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="QubitSampleNameExporter">
    <about>
      <name>Qubit sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        tab-separated file that the operator can use to fill in
        concentration measurements from the Qubit. When all data
        has been filled in, the file can be uploaded to BASE and
        the concentration values are imported as annotations.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.QubitSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="MBafPlotterPlugin">
    <about>
      <name>mBAF plotter plug-in</name>
      <description>
        Plug-in for extracting and plotting mBAF data from existing
        VCF files.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.MBafPlotterPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="GeneReportPlugin">
    <about>
      <name>Report creator</name>
      <description>
        Plug-in for generating reports of cufflinks data.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.GeneReportPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="ReportsCombinerPlugin">
    <about>
      <name>Report combiner</name>
      <description>
        Plug-in for combining multiple existing 
        reports to a single PDF/ZIP file and adding
        personal information about the patients.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="ReleaseExporterPlugin">
    <about>
      <name>Release exporter</name>
      <description>
        Plug-in for exporting released data based
        on raw bioassays in a list.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.release.ReleaseExporterPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="TMASpecimenImporter">
    <about>
      <name>TMA Specimen importer</name>
      <description>
        Plug-in for importing TMA specimen.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.TMASpecimenImporter</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="SingleSamplePredictorPlugin">
    <about>
      <name>Single Sample Predictor plug-in</name>
      <description>
        Plug-in for running Single Sample Predictor models on raw
        bioassays with StringTie data.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.ssp.SspPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
    </settings>
  </plugin-definition>
  <plugin-definition id="SetPermissionsForDelivery">
    <about>
      <name>Set access permissions for delivery</name>
      <description>
        Plug-in for setting access permissions on items that
        are delivered to sites. This plug-in can't be used
        interactively. The plug-in gains elevated permissions
        for setting permissions on items that the user would 
        normally not be allowed to change.
      </description>
    </about>
    <plugin-class>net.sf.basedb.reggie.plugins.SetPermissionsForDeliveryPlugin</plugin-class>
    <settings>
      <property name="everyone-use">0</property>
    </settings>
  </plugin-definition>
  <extension
    id="net.sf.basedb.reggie"
    extends="net.sf.basedb.clients.web.menu.extensions"
    >
    <index>10</index>
    <about safe-scripts="1">
      <name>Reggie</name>
      <description>
        Menu entry for accessing reggie-specific operations.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.MenuItemFactory
      </factory-class>
      <parameters>
        <title>Reggie</title>
        <icon>~/images/snake-icon.png</icon>
        <tooltip>Access reggie operations</tooltip>
        <data-url>~/index.jsp?ID=$SESSION-ID$</data-url>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.start-page"
    extends="net.sf.basedb.clients.web.start-page"
    >
    <index>10</index>
    <about>
      <name>Reggie</name>
      <description>
        Use the Reggie index page as a start page.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.StartPageFactory
      </factory-class>
      <parameters>
        <name>Extensions › Reggie</name>
        <url>~/index.jsp?ID=$SESSION-ID$</url>
        <description>Use Reggie as the start page</description>
      </parameters>
    </action-factory>
  </extension>
  
  
  <extension
    id="net.sf.basedb.reggie.toolbar.case-summary"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.derivedbioassay</ref>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.rawbioassay</ref>
    </extends>
    <about safe-scripts="1">
      <name>Case summary</name>
      <description>
        Adds a button to the toolbar of sample, extracts, derived and
        raw bioassay pages that opens the 'case summary' for the case that the current
        item is part of. Works for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory
      </factory-class>
      <parameters>
        <title>Case summary</title>
        <clazz>button auto-init</clazz>
        <data-auto-init>reggie-case-summary-link</data-auto-init>
        <data-home>$HOME$</data-home>
        <icon>~/images/case_summary.png</icon>
        <script>~/scripts/case-summary.js</script>
        <stylesheet>~/css/reggie-inside-base.css</stylesheet>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.list-column"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.derivedbioassay</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.rawbioassay</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
    </extends>
    <index>2</index>
    <about safe-scripts="1">
      <name>Reggie column</name>
      <description>
        Add a column to the list page of samples, extract, derived bioassays,
        raw bioassays and bioplates for including some reggie-specific links.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.histology-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.sample"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>Stained image</name>
      <description>
        Add a column to the list page of samples that display
        a thumbnail of the stained histology image.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>his-image</id>
        <title>Stained image</title>
        <link-name>image</link-name>
        <subtype>STAINED</subtype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.ndpi-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.bioplate"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>NDPI image</name>
      <description>
        Add a column to the list page of bioplates that display
        a thumbnail of the NDPI image for HE glass slides.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>ndpi-thumbnail</id>
        <title>NDPI thumbnail</title>
        <link-name>NDPI Image</link-name>
        <platetype>HE_GLASS</platetype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.genereport-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>Gene report PDF</name>
      <description>
        Add a column to the list page of raw bioassays that display
        a thumbnail of the gene report PDF.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>genereport-pdf</id>
        <title>Gene report</title>
        <link-name>genereport.pdf</link-name>
        <rawdatatype>CUFFLINKS</rawdatatype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.pilot-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
    >
    <index>4</index>
    <about safe-scripts="1">
      <name>Pilot report PDF</name>
      <description>
        Add a column to the list page of raw bioassays that display
        a thumbnail of the pilot report PDF.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>pilotreport-pdf</id>
        <title>Pilot report</title>
        <link-name>pilotreport.pdf</link-name>
        <rawdatatype>CUFFLINKS</rawdatatype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.scanbreport-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>SCAN-B report PDF</name>
      <description>
        Add a column to the list page of raw bioassays that display
        a thumbnail of the SCAN-B report PDF.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>scanbreport-pdf</id>
        <title>SCAN-B report</title>
        <link-name>scanbreport.pdf</link-name>
        <rawdatatype>STRINGTIE</rawdatatype>
      </parameters>
    </action-factory>
  </extension>
  
  
  <extension
    id="net.sf.basedb.reggie.mbafplot-thumbnail-column"
    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>mBAF plot</name>
      <description>
        Add a column to the list page of derived bioassays that display
        a thumbnail of the mBAF plot.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
      </factory-class>
      <parameters>
        <id>mbaf-plot</id>
        <title>mBAF plot</title>
        <link-name>mbaf_genotype.png</link-name>
        <subtype>ALIGNED_SEQUENCES</subtype>
      </parameters>
    </action-factory>
  </extension>
  
  
  <extension
    id="net.sf.basedb.reggie.libplate-column-derivedbioassay"
    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
    >
    <index>2</index>
    <about safe-scripts="1">
      <name>LibPlate</name>
      <description>
        Add a column to the list page of derived bioassays that display
        the name of the library plate (assumes that the extract that is
        linked is a library item).
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
      </factory-class>
      <parameters>
        <id>extract.bioPlate</id>
        <title>LibPlate</title>
        <property>extract.bioWell.bioPlate</property>
        <filter-property>extract.bioWell.bioPlate.name</filter-property>
        <sort-property>extract.bioWell.bioPlate.name</sort-property>
        <valueType>STRING</valueType>
        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
      </parameters>
    </action-factory>
  </extension>
  <extension
    id="net.sf.basedb.reggie.libplate-column-rawbioassay"
    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
    >
    <index>2</index>
    <about safe-scripts="1">
      <name>LibPlate</name>
      <description>
        Add a column to the list page of raw bioassays that display
        the name of the library plate (assumes that the extract that is
        linked is a library item).
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
      </factory-class>
      <parameters>
        <id>parentExtract.bioPlate</id>
        <title>LibPlate</title>
        <property>parentExtract.bioWell.bioPlate</property>
        <filter-property>parentExtract.bioWell.bioPlate.name</filter-property>
        <sort-property>parentExtract.bioWell.bioPlate.name</sort-property>
        <valueType>STRING</valueType>
        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
      </parameters>
    </action-factory>
  </extension>
  <extension
    id="net.sf.basedb.reggie.histology-thumbnail-view"
    extends="net.sf.basedb.clients.web.toolbar.item.sample"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>Stained image</name>
      <description>
        Add a thumbnail to the sample view page for stained 
        histology samples that has a link to an image file.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
      </factory-class>
      <parameters>
        <link-name>image</link-name>
        <subtype>STAINED</subtype>
      </parameters>
    </action-factory>
  </extension>
  <extension
    id="net.sf.basedb.reggie.ndpi-thumbnail-view"
    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>NDPI image</name>
      <description>
        Add a thumbnail to the bioplate view page for HE glass 
        has a link to an NDPI image file.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
      </factory-class>
      <parameters>
        <link-name>NDPI Image</link-name>
        <platetype>HE_GLASS</platetype>
      </parameters>
    </action-factory>
  </extension>
  <extension
    id="net.sf.basedb.reggie.genereport-thumbnail-view"
    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>Gene report PDF</name>
      <description>
        Add a thumbnail to the raw bioassay view page for 
        that has a link to "genereport.pdf".
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
      </factory-class>
      <parameters>
        <link-name>genereport.pdf</link-name>
        <rawdatatype>CUFFLINKS</rawdatatype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.scanbreport-thumbnail-view"
    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
    >
    <index>3</index>
    <about safe-scripts="1">
      <name>SCAN-B report PDF</name>
      <description>
        Add a thumbnail to the raw bioassay view page for 
        that has a link to "scanbreport.pdf".
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
      </factory-class>
      <parameters>
        <link-name>scanbreport.pdf</link-name>
        <rawdatatype>STRINGTIE</rawdatatype>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.overview.case-summary"
    extends="net.sf.basedb.clients.web.overview.info-details"
    >
    <index>1</index>
    <about safe-scripts="1">
      <name>Case overview</name>
      <description>
        Adds a section to the information pane in the "Item overview"
        functionality that display a link to the "Case summary" 
        function in Reggie for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
      </factory-class>
      <parameters>
        <id>reggie.case-summary</id>
        <title>Reggie</title>
        <include>~/reports/case_summary_hook.jsp</include>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.toolbar.histology-score"
    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
    >
    <about safe-scripts="1">
      <name>Histology score</name>
      <description>
        Adds a button to the toolbar of paraffin blocks and
        HE stain bioplates that start the 'histology scoring wizard'.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
      </factory-class>
      <parameters>
        <title>Score HE glass</title>
        <clazz>button auto-init</clazz>
        <data-auto-init>reggie-he-score-link</data-auto-init>
        <data-home>$HOME$</data-home>
        <icon>~/images/microscope.png</icon>
        <script>~/scripts/he-score.js</script>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.grid.job-complete"
    extends="net.sf.basedb.opengrid.job-complete"
    >
    <about>
      <name>Reggie job completion handler</name>
      <description>
        Handles completion of jobs started by Reggie.
        Depending on the job type it will typically initiate
        parsing of some result files, etc.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.grid.JobCompletionHandlerFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.extensions.nextseq-signal"
    extends="net.sf.basedb.core.signal.job"
    >
    <about>
      <name>Reggie signal handler</name>
      <description>
        Responds to signals sent from BASE. Support
        for STATUS signal to get the progress of a 
        NextSeq sequencing run.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.auto-confirm-service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Reggie auto-confirm service</name>
      <description>
        A service that checks for secondary analysis
        items that has been flagged with AutoProcessing=AutoConfirm.
        If rules are met, the item is automatically
        confirmed and the next step in the analysis is started.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.counter-service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Reggie counter service</name>
      <description>
        A service that count the number of items at
        various stages in the lab and analysis process.
        The counters are presented on the Reggie index page.
        If this service is stopped the counter will not
        be updated.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.counter.CounterServiceFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.reggie.project-archive-service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Reggie project-archive file permission service</name>
      <description>
        Checks and manages file permissions in the project-archive
        based on the consent information on the related case.
        Files that belong to a case with Consent=Yes will get
        group-level read permission, all other files will get
        private permissions only.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension 
    id="net.sf.basedb.reggie.vcf-actions"
    extends="net.sf.basedb.clients.web.file-viewer"
    >
    <about>
      <name>Genotype and variant call VCF viewer</name>
      <description>
        Add links for viewing the genotype QC VCF (qc_genotype.vcf) 
        file and the filtered variant call VCF file (variants-filtered.vcf).
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.reggie.extensions.VcfViewerActionFactory
      </factory-class>
      <parameters>
        <script>~/scripts/vcf-actions.js</script>
      </parameters>
    </action-factory>
  </extension>
  
</extensions>