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

Last change on this file was 7005, checked in by Nicklas Nordborg, 11 days ago

Changes for future release Reggie 4.44
File size: 25.6 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>4.44-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      <ref index="1">net.sf.basedb.clients.web.listcolumn.job</ref>
272    </extends>
273    <index>2</index>
274    <about safe-scripts="1">
275      <name>Reggie column</name>
276      <description>
277        Add a column to the list page of samples, extract, derived bioassays,
278        raw bioassays and bioplates for including some reggie-specific links.
279      </description>
280    </about>
281    <action-factory>
282      <factory-class>
283        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
284      </factory-class>
285    </action-factory>
286  </extension>
287 
288  <extension
289    id="net.sf.basedb.reggie.histology-thumbnail-column"
290    extends="net.sf.basedb.clients.web.listcolumn.sample"
291    >
292    <index>3</index>
293    <about safe-scripts="1">
294      <name>Stained image</name>
295      <description>
296        Add a column to the list page of samples that display
297        a thumbnail of the stained histology image.
298      </description>
299    </about>
300    <action-factory>
301      <factory-class>
302        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
303      </factory-class>
304      <parameters>
305        <id>his-image</id>
306        <title>Stained image</title>
307        <link-name>image</link-name>
308        <subtype>STAINED</subtype>
309      </parameters>
310    </action-factory>
311  </extension>
312 
313  <extension
314    id="net.sf.basedb.reggie.ndpi-thumbnail-column"
315    extends="net.sf.basedb.clients.web.listcolumn.bioplate"
316    >
317    <index>3</index>
318    <about safe-scripts="1">
319      <name>NDPI image</name>
320      <description>
321        Add a column to the list page of bioplates that display
322        a thumbnail of the NDPI image for HE glass slides.
323      </description>
324    </about>
325    <action-factory>
326      <factory-class>
327        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
328      </factory-class>
329      <parameters>
330        <id>ndpi-thumbnail</id>
331        <title>NDPI thumbnail</title>
332        <link-name>NDPI Image</link-name>
333        <platetype>HE_GLASS</platetype>
334      </parameters>
335    </action-factory>
336  </extension>
337 
338  <extension
339    id="net.sf.basedb.reggie.genereport-thumbnail-column"
340    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
341    >
342    <index>3</index>
343    <about safe-scripts="1">
344      <name>Gene report PDF</name>
345      <description>
346        Add a column to the list page of raw bioassays that display
347        a thumbnail of the gene report PDF.
348      </description>
349    </about>
350    <action-factory>
351      <factory-class>
352        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
353      </factory-class>
354      <parameters>
355        <id>genereport-pdf</id>
356        <title>Gene report</title>
357        <link-name>genereport.pdf</link-name>
358        <rawdatatype>CUFFLINKS</rawdatatype>
359      </parameters>
360    </action-factory>
361  </extension>
362 
363  <extension
364    id="net.sf.basedb.reggie.pilot-thumbnail-column"
365    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
366    >
367    <index>4</index>
368    <about safe-scripts="1">
369      <name>Pilot report PDF</name>
370      <description>
371        Add a column to the list page of raw bioassays that display
372        a thumbnail of the pilot report PDF.
373      </description>
374    </about>
375    <action-factory>
376      <factory-class>
377        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
378      </factory-class>
379      <parameters>
380        <id>pilotreport-pdf</id>
381        <title>Pilot report</title>
382        <link-name>pilotreport.pdf</link-name>
383        <rawdatatype>CUFFLINKS</rawdatatype>
384      </parameters>
385    </action-factory>
386  </extension>
387 
388  <extension
389    id="net.sf.basedb.reggie.scanbreport-thumbnail-column"
390    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
391    >
392    <index>3</index>
393    <about safe-scripts="1">
394      <name>SCAN-B report PDF</name>
395      <description>
396        Add a column to the list page of raw bioassays that display
397        a thumbnail of the SCAN-B report PDF.
398      </description>
399    </about>
400    <action-factory>
401      <factory-class>
402        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
403      </factory-class>
404      <parameters>
405        <id>scanbreport-pdf</id>
406        <title>SCAN-B report</title>
407        <link-name>scanbreport.pdf</link-name>
408        <rawdatatype>STRINGTIE</rawdatatype>
409      </parameters>
410    </action-factory>
411  </extension>
412 
413 
414  <extension
415    id="net.sf.basedb.reggie.mbafplot-thumbnail-column"
416    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
417    >
418    <index>3</index>
419    <about safe-scripts="1">
420      <name>mBAF plot</name>
421      <description>
422        Add a column to the list page of derived bioassays that display
423        a thumbnail of the mBAF plot.
424      </description>
425    </about>
426    <action-factory>
427      <factory-class>
428        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
429      </factory-class>
430      <parameters>
431        <id>mbaf-plot</id>
432        <title>mBAF plot</title>
433        <link-name>mbaf_genotype.png</link-name>
434        <subtype>ALIGNED_SEQUENCES</subtype>
435      </parameters>
436    </action-factory>
437  </extension>
438 
439 
440  <extension
441    id="net.sf.basedb.reggie.libplate-column-derivedbioassay"
442    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
443    >
444    <index>2</index>
445    <about safe-scripts="1">
446      <name>LibPlate</name>
447      <description>
448        Add a column to the list page of derived bioassays that display
449        the name of the library plate (assumes that the extract that is
450        linked is a library item).
451      </description>
452    </about>
453    <action-factory>
454      <factory-class>
455        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
456      </factory-class>
457      <parameters>
458        <id>extract.bioPlate</id>
459        <title>LibPlate</title>
460        <property>extract.bioWell.bioPlate</property>
461        <filter-property>extract.bioWell.bioPlate.name</filter-property>
462        <sort-property>extract.bioWell.bioPlate.name</sort-property>
463        <valueType>STRING</valueType>
464        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
465        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
466      </parameters>
467    </action-factory>
468  </extension>
469  <extension
470    id="net.sf.basedb.reggie.libplate-column-rawbioassay"
471    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
472    >
473    <index>2</index>
474    <about safe-scripts="1">
475      <name>LibPlate</name>
476      <description>
477        Add a column to the list page of raw bioassays that display
478        the name of the library plate (assumes that the extract that is
479        linked is a library item).
480      </description>
481    </about>
482    <action-factory>
483      <factory-class>
484        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
485      </factory-class>
486      <parameters>
487        <id>parentExtract.bioPlate</id>
488        <title>LibPlate</title>
489        <property>parentExtract.bioWell.bioPlate</property>
490        <filter-property>parentExtract.bioWell.bioPlate.name</filter-property>
491        <sort-property>parentExtract.bioWell.bioPlate.name</sort-property>
492        <valueType>STRING</valueType>
493        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
494        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
495      </parameters>
496    </action-factory>
497  </extension>
498  <extension
499    id="net.sf.basedb.reggie.histology-thumbnail-view"
500    extends="net.sf.basedb.clients.web.toolbar.item.sample"
501    >
502    <index>3</index>
503    <about safe-scripts="1">
504      <name>Stained image</name>
505      <description>
506        Add a thumbnail to the sample view page for stained
507        histology samples that has a link to an image file.
508      </description>
509    </about>
510    <action-factory>
511      <factory-class>
512        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
513      </factory-class>
514      <parameters>
515        <link-name>image</link-name>
516        <subtype>STAINED</subtype>
517      </parameters>
518    </action-factory>
519  </extension>
520  <extension
521    id="net.sf.basedb.reggie.ndpi-thumbnail-view"
522    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
523    >
524    <index>3</index>
525    <about safe-scripts="1">
526      <name>NDPI image</name>
527      <description>
528        Add a thumbnail to the bioplate view page for HE glass
529        has a link to an NDPI image file.
530      </description>
531    </about>
532    <action-factory>
533      <factory-class>
534        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
535      </factory-class>
536      <parameters>
537        <link-name>NDPI Image</link-name>
538        <platetype>HE_GLASS</platetype>
539      </parameters>
540    </action-factory>
541  </extension>
542  <extension
543    id="net.sf.basedb.reggie.genereport-thumbnail-view"
544    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
545    >
546    <index>3</index>
547    <about safe-scripts="1">
548      <name>Gene report PDF</name>
549      <description>
550        Add a thumbnail to the raw bioassay view page for
551        that has a link to "genereport.pdf".
552      </description>
553    </about>
554    <action-factory>
555      <factory-class>
556        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
557      </factory-class>
558      <parameters>
559        <link-name>genereport.pdf</link-name>
560        <rawdatatype>CUFFLINKS</rawdatatype>
561      </parameters>
562    </action-factory>
563  </extension>
564 
565  <extension
566    id="net.sf.basedb.reggie.scanbreport-thumbnail-view"
567    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
568    >
569    <index>3</index>
570    <about safe-scripts="1">
571      <name>SCAN-B report PDF</name>
572      <description>
573        Add a thumbnail to the raw bioassay view page for
574        that has a link to "scanbreport.pdf".
575      </description>
576    </about>
577    <action-factory>
578      <factory-class>
579        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
580      </factory-class>
581      <parameters>
582        <link-name>scanbreport.pdf</link-name>
583        <rawdatatype>STRINGTIE</rawdatatype>
584      </parameters>
585    </action-factory>
586  </extension>
587 
588  <extension
589    id="net.sf.basedb.reggie.methylation-thumbnail-view"
590    extends="net.sf.basedb.clients.web.toolbar.item.derivedbioassay"
591    >
592    <index>3</index>
593    <about safe-scripts="1">
594      <name>Methylation beta adjustment plot</name>
595      <description>
596        Add a thumbnail to the Methylation derived bioassay
597        view page that has a link to "adjustmentPlots.pdf".
598      </description>
599    </about>
600    <action-factory>
601      <factory-class>
602        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
603      </factory-class>
604      <parameters>
605        <link-name>adjustmentPlots.pdf</link-name>
606        <subtype>METHYLATION</subtype>
607      </parameters>
608    </action-factory>
609  </extension>
610 
611  <extension
612    id="net.sf.basedb.reggie.methylation-thumbnail-column"
613    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
614    >
615    <index>3</index>
616    <about safe-scripts="1">
617      <name>Methylation beta adjustment plot</name>
618      <description>
619        Add a column to the list page of derived bioassays that display
620        a thumbnail of the Methylation beta adjustment plot.
621      </description>
622    </about>
623    <action-factory>
624      <factory-class>
625        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
626      </factory-class>
627      <parameters>
628        <id>beta-plot</id>
629        <title>Beta plot</title>
630        <link-name>adjustmentPlots.pdf</link-name>
631        <subtype>METHYLATION</subtype>
632      </parameters>
633    </action-factory>
634  </extension>
635 
636  <extension
637    id="net.sf.basedb.reggie.overview.case-summary"
638    extends="net.sf.basedb.clients.web.overview.info-details"
639    >
640    <index>1</index>
641    <about safe-scripts="1">
642      <name>Case overview</name>
643      <description>
644        Adds a section to the information pane in the "Item overview"
645        functionality that display a link to the "Case summary"
646        function in Reggie for all items that have a name pattern
647        that starts with 7 digits.
648      </description>
649    </about>
650    <action-factory>
651      <factory-class>
652        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
653      </factory-class>
654      <parameters>
655        <id>reggie.case-summary</id>
656        <title>Reggie</title>
657        <include>~/reports/case_summary_hook.jsp</include>
658      </parameters>
659    </action-factory>
660  </extension>
661 
662  <extension
663    id="net.sf.basedb.reggie.toolbar.histology-score"
664    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
665    >
666    <about safe-scripts="1">
667      <name>Histology score</name>
668      <description>
669        Adds a button to the toolbar of paraffin blocks and
670        HE stain bioplates that start the 'histology scoring wizard'.
671      </description>
672    </about>
673    <action-factory>
674      <factory-class>
675        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
676      </factory-class>
677      <parameters>
678        <title>Score HE glass</title>
679        <clazz>button auto-init</clazz>
680        <data-auto-init>reggie-he-score-link</data-auto-init>
681        <data-home>$HOME$</data-home>
682        <icon>~/images/microscope.png</icon>
683        <script>~/scripts/he-score.js</script>
684      </parameters>
685    </action-factory>
686  </extension>
687 
688  <extension
689    id="net.sf.basedb.reggie.grid.job-complete"
690    extends="net.sf.basedb.opengrid.job-complete"
691    >
692    <about>
693      <name>Reggie job completion handler</name>
694      <description>
695        Handles completion of jobs started by Reggie.
696        Depending on the job type it will typically initiate
697        parsing of some result files, etc.
698      </description>
699    </about>
700    <action-factory>
701      <factory-class>
702        net.sf.basedb.reggie.grid.JobCompletionHandlerFactory
703      </factory-class>
704    </action-factory>
705  </extension>
706 
707  <extension
708    id="net.sf.basedb.reggie.extensions.nextseq-signal"
709    extends="net.sf.basedb.core.signal.job"
710    >
711    <about>
712      <name>Reggie signal handler</name>
713      <description>
714        Responds to signals sent from BASE. Support
715        for STATUS signal to get the progress of a
716        NextSeq sequencing run.
717      </description>
718    </about>
719    <action-factory>
720      <factory-class>
721        net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory
722      </factory-class>
723    </action-factory>
724  </extension>
725 
726  <extension
727    id="net.sf.basedb.reggie.auto-confirm-service"
728    extends="net.sf.basedb.clients.web.services"
729    >
730    <about>
731      <name>Reggie auto-confirm service</name>
732      <description>
733        A service that checks for secondary analysis
734        items that has been flagged with AutoProcessing=AutoConfirm.
735        If rules are met, the item is automatically
736        confirmed and the next step in the analysis is started.
737      </description>
738    </about>
739    <action-factory>
740      <factory-class>
741        net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory
742      </factory-class>
743    </action-factory>
744  </extension>
745 
746  <extension
747    id="net.sf.basedb.reggie.counter-service"
748    extends="net.sf.basedb.clients.web.services"
749    >
750    <about>
751      <name>Reggie counter service</name>
752      <description>
753        A service that count the number of items at
754        various stages in the lab and analysis process.
755        The counters are presented on the Reggie index page.
756        If this service is stopped the counter will not
757        be updated.
758      </description>
759    </about>
760    <action-factory>
761      <factory-class>
762        net.sf.basedb.reggie.counter.CounterServiceFactory
763      </factory-class>
764    </action-factory>
765  </extension>
766 
767  <extension
768    id="net.sf.basedb.reggie.project-archive-service"
769    extends="net.sf.basedb.clients.web.services"
770    >
771    <about>
772      <name>Reggie project-archive file permission service</name>
773      <description>
774        Checks and manages file permissions in the project-archive
775        based on the consent information on the related case.
776        Files that belong to a case with Consent=Yes will get
777        group-level read permission, all other files will get
778        private permissions only.
779      </description>
780    </about>
781    <action-factory>
782      <factory-class>
783        net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory
784      </factory-class>
785    </action-factory>
786  </extension>
787 
788  <extension 
789    id="net.sf.basedb.reggie.vcf-actions"
790    extends="net.sf.basedb.clients.web.file-viewer"
791    >
792    <about>
793      <name>Genotype and variant call VCF viewer</name>
794      <description>
795        Add links for viewing the genotype QC VCF (qc_genotype.vcf)
796        file and the filtered variant call VCF file (variants-filtered.vcf).
797      </description>
798    </about>
799    <action-factory>
800      <factory-class>
801        net.sf.basedb.reggie.extensions.VcfViewerActionFactory
802      </factory-class>
803      <parameters>
804        <script>~/scripts/vcf-actions.js</script>
805      </parameters>
806    </action-factory>
807  </extension>
808 
809  <extension
810    id="net.sf.basedb.reggie.toolbar.download-as-zip"
811    extends="net.sf.basedb.clients.web.file-viewer"
812    >
813    <about safe-scripts="1">
814      <name>Download file as ZIP</name>
815      <description>
816        Implements an action that can be used on files to download
817        them as a ZIP file. The ZIP file is created on the fly and
818        has support for encryption with AES256.
819       
820        The action is currently only enabled CSV files inside
821        the /home/SCANB/ReferralIdLogs directory.
822      </description>
823    </about>
824    <action-factory>
825      <factory-class>
826        net.sf.basedb.reggie.extensions.DownloadAsZipActionFactory
827      </factory-class>
828      <parameters>
829        <script>~/download-as-zip.js</script>
830      </parameters>
831    </action-factory>
832  </extension>
833 
834</extensions>
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