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

Last change on this file was 6428, checked in by Nicklas Nordborg, 2 months ago

Changes for future version Reggie 4.34

File size: 23.4 KB
Line 
1<?xml version="1.0" encoding="UTF-8" ?>
2<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
3  <about safe-resources="1">
4    <name>Reggie package</name>
5    <description>
6      A package for simplified registration of biosources
7      and samples.
8    </description>
9    <version>4.34-dev</version>
10    <min-base-version>3.19.0</min-base-version>
11    <copyright>BASE development team</copyright>
12    <email>basedb-users@lists.sourceforge.net</email>
13    <url>https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie</url>
14  </about>
15
16  <plugin-definition id="CaliperSampleNameExporter">
17    <about>
18      <name>Caliper sample name exporter</name>
19      <description>
20        Plug-in that export the sample names on a bioplate to a
21        CSV file that can be used by the Caliper software. The
22        exported file has one line for each non-empty well with
23        five columns. Only the first two columns are used:
24        Well coordinate, sample name.
25      </description>
26    </about>
27    <plugin-class>net.sf.basedb.reggie.plugins.CaliperSampleNameExporter</plugin-class>
28    <settings>
29      <property name="everyone-use">1</property>
30      <property name="immediate-execution">1</property>
31    </settings>
32  </plugin-definition>
33
34  <plugin-definition id="CaliperRunParametersExporter">
35    <about>
36      <name>Caliper run parameters exporter</name>
37      <description>
38        Plug-in that export run file parameters that can be used by the
39        Caliper software. The run file include information about Assay Type,
40        Plate Name, selected wells, etc.
41      </description>
42    </about>
43    <plugin-class>net.sf.basedb.reggie.plugins.CaliperRunParametersExporter</plugin-class>
44    <settings>
45      <property name="everyone-use">1</property>
46      <property name="immediate-execution">1</property>
47    </settings>
48  </plugin-definition>
49
50  <plugin-definition id="CaliperLibPrepParametersExporter">
51    <about>
52      <name>Caliper library preparation parameters exporter</name>
53      <description>
54        Plug-in that export run file parameters that can be used by the
55        Caliper software. The run file include information about Assay Type,
56        Plate Name, selected wells, etc.
57      </description>
58    </about>
59    <plugin-class>net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter</plugin-class>
60    <settings>
61      <property name="everyone-use">1</property>
62      <property name="immediate-execution">1</property>
63    </settings>
64  </plugin-definition>
65
66  <plugin-definition id="QubitSampleNameExporter">
67    <about>
68      <name>Qubit sample name exporter</name>
69      <description>
70        Plug-in that export the sample names on a bioplate to a
71        tab-separated file that the operator can use to fill in
72        concentration measurements from the Qubit. When all data
73        has been filled in, the file can be uploaded to BASE and
74        the concentration values are imported as annotations.
75      </description>
76    </about>
77    <plugin-class>net.sf.basedb.reggie.plugins.QubitSampleNameExporter</plugin-class>
78    <settings>
79      <property name="everyone-use">1</property>
80      <property name="immediate-execution">1</property>
81    </settings>
82  </plugin-definition>
83  <plugin-definition id="MBafPlotterPlugin">
84    <about>
85      <name>mBAF plotter plug-in</name>
86      <description>
87        Plug-in for extracting and plotting mBAF data from existing
88        VCF files.
89      </description>
90    </about>
91    <plugin-class>net.sf.basedb.reggie.plugins.MBafPlotterPlugin</plugin-class>
92    <settings>
93      <property name="everyone-use">0</property>
94      <property name="immediate-execution">1</property>
95    </settings>
96  </plugin-definition>
97
98  <plugin-definition id="GeneReportPlugin">
99    <about>
100      <name>Report creator</name>
101      <description>
102        Plug-in for generating reports of cufflinks data.
103      </description>
104    </about>
105    <plugin-class>net.sf.basedb.reggie.plugins.GeneReportPlugin</plugin-class>
106    <settings>
107      <property name="everyone-use">0</property>
108      <property name="immediate-execution">1</property>
109    </settings>
110  </plugin-definition>
111  <plugin-definition id="ReportsCombinerPlugin">
112    <about>
113      <name>Report combiner</name>
114      <description>
115        Plug-in for combining multiple existing
116        reports to a single PDF/ZIP file and adding
117        personal information about the patients.
118      </description>
119    </about>
120    <plugin-class>net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin</plugin-class>
121    <settings>
122      <property name="everyone-use">0</property>
123      <property name="immediate-execution">1</property>
124    </settings>
125  </plugin-definition>
126  <plugin-definition id="ReleaseExporterPlugin">
127    <about>
128      <name>Release exporter</name>
129      <description>
130        Plug-in for exporting released data based
131        on raw bioassays in a list.
132      </description>
133    </about>
134    <plugin-class>net.sf.basedb.reggie.plugins.release.ReleaseExporterPlugin</plugin-class>
135    <settings>
136      <property name="everyone-use">0</property>
137    </settings>
138  </plugin-definition>
139  <plugin-definition id="TMASpecimenImporter">
140    <about>
141      <name>TMA Specimen importer</name>
142      <description>
143        Plug-in for importing TMA specimen.
144      </description>
145    </about>
146    <plugin-class>net.sf.basedb.reggie.plugins.TMASpecimenImporter</plugin-class>
147    <settings>
148      <property name="everyone-use">0</property>
149    </settings>
150  </plugin-definition>
151  <plugin-definition id="SingleSamplePredictorPlugin">
152    <about>
153      <name>Single Sample Predictor plug-in</name>
154      <description>
155        Plug-in for running Single Sample Predictor models on raw
156        bioassays with StringTie data.
157      </description>
158    </about>
159    <plugin-class>net.sf.basedb.reggie.ssp.SspPlugin</plugin-class>
160    <settings>
161      <property name="everyone-use">0</property>
162    </settings>
163  </plugin-definition>
164  <plugin-definition id="SetPermissionsForDelivery">
165    <about>
166      <name>Set access permissions for delivery</name>
167      <description>
168        Plug-in for setting access permissions on items that
169        are delivered to sites. This plug-in can't be used
170        interactively. The plug-in gains elevated permissions
171        for setting permissions on items that the user would
172        normally not be allowed to change.
173      </description>
174    </about>
175    <plugin-class>net.sf.basedb.reggie.plugins.SetPermissionsForDeliveryPlugin</plugin-class>
176    <settings>
177      <property name="everyone-use">0</property>
178    </settings>
179  </plugin-definition>
180  <extension
181    id="net.sf.basedb.reggie"
182    extends="net.sf.basedb.clients.web.menu.extensions"
183    >
184    <index>10</index>
185    <about safe-scripts="1">
186      <name>Reggie</name>
187      <description>
188        Menu entry for accessing reggie-specific operations.
189      </description>
190    </about>
191    <action-factory>
192      <factory-class>
193        net.sf.basedb.reggie.extensions.MenuItemFactory
194      </factory-class>
195      <parameters>
196        <title>Reggie</title>
197        <icon>~/images/snake-icon.png</icon>
198        <tooltip>Access reggie operations</tooltip>
199        <data-url>~/index.jsp?ID=$SESSION-ID$</data-url>
200      </parameters>
201    </action-factory>
202  </extension>
203 
204  <extension
205    id="net.sf.basedb.reggie.start-page"
206    extends="net.sf.basedb.clients.web.start-page"
207    >
208    <index>10</index>
209    <about>
210      <name>Reggie</name>
211      <description>
212        Use the Reggie index page as a start page.
213      </description>
214    </about>
215    <action-factory>
216      <factory-class>
217        net.sf.basedb.reggie.extensions.StartPageFactory
218      </factory-class>
219      <parameters>
220        <name>Extensions › Reggie</name>
221        <url>~/index.jsp?ID=$SESSION-ID$</url>
222        <description>Use Reggie as the start page</description>
223      </parameters>
224    </action-factory>
225  </extension>
226 
227 
228  <extension
229    id="net.sf.basedb.reggie.toolbar.case-summary"
230    >
231    <extends>
232      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
233      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
234      <ref index="1">net.sf.basedb.clients.web.toolbar.item.derivedbioassay</ref>
235      <ref index="1">net.sf.basedb.clients.web.toolbar.item.rawbioassay</ref>
236    </extends>
237    <about safe-scripts="1">
238      <name>Case summary</name>
239      <description>
240        Adds a button to the toolbar of sample, extracts, derived and
241        raw bioassay pages that opens the 'case summary' for the case that the current
242        item is part of. Works for all items that have a name pattern
243        that starts with 7 digits.
244      </description>
245    </about>
246    <action-factory>
247      <factory-class>
248        net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory
249      </factory-class>
250      <parameters>
251        <title>Case summary</title>
252        <clazz>button auto-init</clazz>
253        <data-auto-init>reggie-case-summary-link</data-auto-init>
254        <data-home>$HOME$</data-home>
255        <icon>~/images/case_summary.png</icon>
256        <script>~/scripts/case-summary.js</script>
257        <stylesheet>~/css/reggie-inside-base.css</stylesheet>
258      </parameters>
259    </action-factory>
260  </extension>
261 
262  <extension
263    id="net.sf.basedb.reggie.list-column"
264    >
265    <extends>
266      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
267      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
268      <ref index="1">net.sf.basedb.clients.web.listcolumn.derivedbioassay</ref>
269      <ref index="1">net.sf.basedb.clients.web.listcolumn.rawbioassay</ref>
270      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
271    </extends>
272    <index>2</index>
273    <about safe-scripts="1">
274      <name>Reggie column</name>
275      <description>
276        Add a column to the list page of samples, extract, derived bioassays,
277        raw bioassays and bioplates for including some reggie-specific links.
278      </description>
279    </about>
280    <action-factory>
281      <factory-class>
282        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
283      </factory-class>
284    </action-factory>
285  </extension>
286 
287  <extension
288    id="net.sf.basedb.reggie.histology-thumbnail-column"
289    extends="net.sf.basedb.clients.web.listcolumn.sample"
290    >
291    <index>3</index>
292    <about safe-scripts="1">
293      <name>Stained image</name>
294      <description>
295        Add a column to the list page of samples that display
296        a thumbnail of the stained histology image.
297      </description>
298    </about>
299    <action-factory>
300      <factory-class>
301        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
302      </factory-class>
303      <parameters>
304        <id>his-image</id>
305        <title>Stained image</title>
306        <link-name>image</link-name>
307        <subtype>STAINED</subtype>
308      </parameters>
309    </action-factory>
310  </extension>
311 
312  <extension
313    id="net.sf.basedb.reggie.ndpi-thumbnail-column"
314    extends="net.sf.basedb.clients.web.listcolumn.bioplate"
315    >
316    <index>3</index>
317    <about safe-scripts="1">
318      <name>NDPI image</name>
319      <description>
320        Add a column to the list page of bioplates that display
321        a thumbnail of the NDPI image for HE glass slides.
322      </description>
323    </about>
324    <action-factory>
325      <factory-class>
326        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
327      </factory-class>
328      <parameters>
329        <id>ndpi-thumbnail</id>
330        <title>NDPI thumbnail</title>
331        <link-name>NDPI Image</link-name>
332        <platetype>HE_GLASS</platetype>
333      </parameters>
334    </action-factory>
335  </extension>
336 
337  <extension
338    id="net.sf.basedb.reggie.genereport-thumbnail-column"
339    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
340    >
341    <index>3</index>
342    <about safe-scripts="1">
343      <name>Gene report PDF</name>
344      <description>
345        Add a column to the list page of raw bioassays that display
346        a thumbnail of the gene report PDF.
347      </description>
348    </about>
349    <action-factory>
350      <factory-class>
351        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
352      </factory-class>
353      <parameters>
354        <id>genereport-pdf</id>
355        <title>Gene report</title>
356        <link-name>genereport.pdf</link-name>
357        <rawdatatype>CUFFLINKS</rawdatatype>
358      </parameters>
359    </action-factory>
360  </extension>
361 
362  <extension
363    id="net.sf.basedb.reggie.pilot-thumbnail-column"
364    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
365    >
366    <index>4</index>
367    <about safe-scripts="1">
368      <name>Pilot report PDF</name>
369      <description>
370        Add a column to the list page of raw bioassays that display
371        a thumbnail of the pilot report PDF.
372      </description>
373    </about>
374    <action-factory>
375      <factory-class>
376        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
377      </factory-class>
378      <parameters>
379        <id>pilotreport-pdf</id>
380        <title>Pilot report</title>
381        <link-name>pilotreport.pdf</link-name>
382        <rawdatatype>CUFFLINKS</rawdatatype>
383      </parameters>
384    </action-factory>
385  </extension>
386 
387  <extension
388    id="net.sf.basedb.reggie.scanbreport-thumbnail-column"
389    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
390    >
391    <index>3</index>
392    <about safe-scripts="1">
393      <name>SCAN-B report PDF</name>
394      <description>
395        Add a column to the list page of raw bioassays that display
396        a thumbnail of the SCAN-B report PDF.
397      </description>
398    </about>
399    <action-factory>
400      <factory-class>
401        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
402      </factory-class>
403      <parameters>
404        <id>scanbreport-pdf</id>
405        <title>SCAN-B report</title>
406        <link-name>scanbreport.pdf</link-name>
407        <rawdatatype>STRINGTIE</rawdatatype>
408      </parameters>
409    </action-factory>
410  </extension>
411 
412 
413  <extension
414    id="net.sf.basedb.reggie.mbafplot-thumbnail-column"
415    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
416    >
417    <index>3</index>
418    <about safe-scripts="1">
419      <name>mBAF plot</name>
420      <description>
421        Add a column to the list page of derived bioassays that display
422        a thumbnail of the mBAF plot.
423      </description>
424    </about>
425    <action-factory>
426      <factory-class>
427        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
428      </factory-class>
429      <parameters>
430        <id>mbaf-plot</id>
431        <title>mBAF plot</title>
432        <link-name>mbaf_genotype.png</link-name>
433        <subtype>ALIGNED_SEQUENCES</subtype>
434      </parameters>
435    </action-factory>
436  </extension>
437 
438 
439  <extension
440    id="net.sf.basedb.reggie.libplate-column-derivedbioassay"
441    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
442    >
443    <index>2</index>
444    <about safe-scripts="1">
445      <name>LibPlate</name>
446      <description>
447        Add a column to the list page of derived bioassays that display
448        the name of the library plate (assumes that the extract that is
449        linked is a library item).
450      </description>
451    </about>
452    <action-factory>
453      <factory-class>
454        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
455      </factory-class>
456      <parameters>
457        <id>extract.bioPlate</id>
458        <title>LibPlate</title>
459        <property>extract.bioWell.bioPlate</property>
460        <filter-property>extract.bioWell.bioPlate.name</filter-property>
461        <sort-property>extract.bioWell.bioPlate.name</sort-property>
462        <valueType>STRING</valueType>
463        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
464        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
465      </parameters>
466    </action-factory>
467  </extension>
468  <extension
469    id="net.sf.basedb.reggie.libplate-column-rawbioassay"
470    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
471    >
472    <index>2</index>
473    <about safe-scripts="1">
474      <name>LibPlate</name>
475      <description>
476        Add a column to the list page of raw bioassays that display
477        the name of the library plate (assumes that the extract that is
478        linked is a library item).
479      </description>
480    </about>
481    <action-factory>
482      <factory-class>
483        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
484      </factory-class>
485      <parameters>
486        <id>parentExtract.bioPlate</id>
487        <title>LibPlate</title>
488        <property>parentExtract.bioWell.bioPlate</property>
489        <filter-property>parentExtract.bioWell.bioPlate.name</filter-property>
490        <sort-property>parentExtract.bioWell.bioPlate.name</sort-property>
491        <valueType>STRING</valueType>
492        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
493        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
494      </parameters>
495    </action-factory>
496  </extension>
497  <extension
498    id="net.sf.basedb.reggie.histology-thumbnail-view"
499    extends="net.sf.basedb.clients.web.toolbar.item.sample"
500    >
501    <index>3</index>
502    <about safe-scripts="1">
503      <name>Stained image</name>
504      <description>
505        Add a thumbnail to the sample view page for stained
506        histology samples that has a link to an image file.
507      </description>
508    </about>
509    <action-factory>
510      <factory-class>
511        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
512      </factory-class>
513      <parameters>
514        <link-name>image</link-name>
515        <subtype>STAINED</subtype>
516      </parameters>
517    </action-factory>
518  </extension>
519  <extension
520    id="net.sf.basedb.reggie.ndpi-thumbnail-view"
521    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
522    >
523    <index>3</index>
524    <about safe-scripts="1">
525      <name>NDPI image</name>
526      <description>
527        Add a thumbnail to the bioplate view page for HE glass
528        has a link to an NDPI image file.
529      </description>
530    </about>
531    <action-factory>
532      <factory-class>
533        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
534      </factory-class>
535      <parameters>
536        <link-name>NDPI Image</link-name>
537        <platetype>HE_GLASS</platetype>
538      </parameters>
539    </action-factory>
540  </extension>
541  <extension
542    id="net.sf.basedb.reggie.genereport-thumbnail-view"
543    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
544    >
545    <index>3</index>
546    <about safe-scripts="1">
547      <name>Gene report PDF</name>
548      <description>
549        Add a thumbnail to the raw bioassay view page for
550        that has a link to "genereport.pdf".
551      </description>
552    </about>
553    <action-factory>
554      <factory-class>
555        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
556      </factory-class>
557      <parameters>
558        <link-name>genereport.pdf</link-name>
559        <rawdatatype>CUFFLINKS</rawdatatype>
560      </parameters>
561    </action-factory>
562  </extension>
563 
564  <extension
565    id="net.sf.basedb.reggie.scanbreport-thumbnail-view"
566    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
567    >
568    <index>3</index>
569    <about safe-scripts="1">
570      <name>SCAN-B report PDF</name>
571      <description>
572        Add a thumbnail to the raw bioassay view page for
573        that has a link to "scanbreport.pdf".
574      </description>
575    </about>
576    <action-factory>
577      <factory-class>
578        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
579      </factory-class>
580      <parameters>
581        <link-name>scanbreport.pdf</link-name>
582        <rawdatatype>STRINGTIE</rawdatatype>
583      </parameters>
584    </action-factory>
585  </extension>
586 
587  <extension
588    id="net.sf.basedb.reggie.overview.case-summary"
589    extends="net.sf.basedb.clients.web.overview.info-details"
590    >
591    <index>1</index>
592    <about safe-scripts="1">
593      <name>Case overview</name>
594      <description>
595        Adds a section to the information pane in the "Item overview"
596        functionality that display a link to the "Case summary"
597        function in Reggie for all items that have a name pattern
598        that starts with 7 digits.
599      </description>
600    </about>
601    <action-factory>
602      <factory-class>
603        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
604      </factory-class>
605      <parameters>
606        <id>reggie.case-summary</id>
607        <title>Reggie</title>
608        <include>~/reports/case_summary_hook.jsp</include>
609      </parameters>
610    </action-factory>
611  </extension>
612 
613  <extension
614    id="net.sf.basedb.reggie.toolbar.histology-score"
615    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
616    >
617    <about safe-scripts="1">
618      <name>Histology score</name>
619      <description>
620        Adds a button to the toolbar of paraffin blocks and
621        HE stain bioplates that start the 'histology scoring wizard'.
622      </description>
623    </about>
624    <action-factory>
625      <factory-class>
626        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
627      </factory-class>
628      <parameters>
629        <title>Score HE glass</title>
630        <clazz>button auto-init</clazz>
631        <data-auto-init>reggie-he-score-link</data-auto-init>
632        <data-home>$HOME$</data-home>
633        <icon>~/images/microscope.png</icon>
634        <script>~/scripts/he-score.js</script>
635      </parameters>
636    </action-factory>
637  </extension>
638 
639  <extension
640    id="net.sf.basedb.reggie.grid.job-complete"
641    extends="net.sf.basedb.opengrid.job-complete"
642    >
643    <about>
644      <name>Reggie job completion handler</name>
645      <description>
646        Handles completion of jobs started by Reggie.
647        Depending on the job type it will typically initiate
648        parsing of some result files, etc.
649      </description>
650    </about>
651    <action-factory>
652      <factory-class>
653        net.sf.basedb.reggie.grid.JobCompletionHandlerFactory
654      </factory-class>
655    </action-factory>
656  </extension>
657 
658  <extension
659    id="net.sf.basedb.reggie.extensions.nextseq-signal"
660    extends="net.sf.basedb.core.signal.job"
661    >
662    <about>
663      <name>Reggie signal handler</name>
664      <description>
665        Responds to signals sent from BASE. Support
666        for STATUS signal to get the progress of a
667        NextSeq sequencing run.
668      </description>
669    </about>
670    <action-factory>
671      <factory-class>
672        net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory
673      </factory-class>
674    </action-factory>
675  </extension>
676 
677  <extension
678    id="net.sf.basedb.reggie.auto-confirm-service"
679    extends="net.sf.basedb.clients.web.services"
680    >
681    <about>
682      <name>Reggie auto-confirm service</name>
683      <description>
684        A service that checks for secondary analysis
685        items that has been flagged with AutoProcessing=AutoConfirm.
686        If rules are met, the item is automatically
687        confirmed and the next step in the analysis is started.
688      </description>
689    </about>
690    <action-factory>
691      <factory-class>
692        net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory
693      </factory-class>
694    </action-factory>
695  </extension>
696 
697  <extension
698    id="net.sf.basedb.reggie.counter-service"
699    extends="net.sf.basedb.clients.web.services"
700    >
701    <about>
702      <name>Reggie counter service</name>
703      <description>
704        A service that count the number of items at
705        various stages in the lab and analysis process.
706        The counters are presented on the Reggie index page.
707        If this service is stopped the counter will not
708        be updated.
709      </description>
710    </about>
711    <action-factory>
712      <factory-class>
713        net.sf.basedb.reggie.counter.CounterServiceFactory
714      </factory-class>
715    </action-factory>
716  </extension>
717 
718  <extension
719    id="net.sf.basedb.reggie.project-archive-service"
720    extends="net.sf.basedb.clients.web.services"
721    >
722    <about>
723      <name>Reggie project-archive file permission service</name>
724      <description>
725        Checks and manages file permissions in the project-archive
726        based on the consent information on the related case.
727        Files that belong to a case with Consent=Yes will get
728        group-level read permission, all other files will get
729        private permissions only.
730      </description>
731    </about>
732    <action-factory>
733      <factory-class>
734        net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory
735      </factory-class>
736    </action-factory>
737  </extension>
738 
739  <extension 
740    id="net.sf.basedb.reggie.vcf-actions"
741    extends="net.sf.basedb.clients.web.file-viewer"
742    >
743    <about>
744      <name>Genotype and variant call VCF viewer</name>
745      <description>
746        Add links for viewing the genotype QC VCF (qc_genotype.vcf)
747        file and the filtered variant call VCF file (variants-filtered.vcf).
748      </description>
749    </about>
750    <action-factory>
751      <factory-class>
752        net.sf.basedb.reggie.extensions.VcfViewerActionFactory
753      </factory-class>
754      <parameters>
755        <script>~/scripts/vcf-actions.js</script>
756      </parameters>
757    </action-factory>
758  </extension>
759 
760</extensions>
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