source: extensions/net.sf.basedb.reggie/branches/4.25-stable/META-INF/extensions.xml @ 5859

Last change on this file since 5859 was 5859, checked in by Nicklas Nordborg, 23 months ago

Preparing to release Reggie 4.25.1

File size: 20.1 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>4.25.1</version>
10    <min-base-version>3.15.2</min-base-version>
11    <copyright>BASE development team</copyright>
12    <email>basedb-users@lists.sourceforge.net</email>
13    <url>http://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  <!--
152  <plugin-definition id="SingleSamplePredictorPlugin">
153    <about>
154      <name>Single Sample Predictor plug-in</name>
155      <description>
156        Plug-in for running Single Sample Predictor models on raw
157        bioassays with StringTie data.
158      </description>
159    </about>
160    <plugin-class>net.sf.basedb.reggie.ssp.SspPlugin</plugin-class>
161    <settings>
162      <property name="everyone-use">0</property>
163    </settings>
164  </plugin-definition>
165  -->
166  <plugin-definition id="SetPermissionsForDelivery">
167    <about>
168      <name>Set access permissions for delivery</name>
169      <description>
170        Plug-in for setting access permissions on items that
171        are delivered to sites. This plug-in can't be used
172        interactively. The plug-in gains elevated permissions
173        for setting permissions on items that the user would
174        normally not be allowed to change.
175      </description>
176    </about>
177    <plugin-class>net.sf.basedb.reggie.plugins.SetPermissionsForDeliveryPlugin</plugin-class>
178    <settings>
179      <property name="everyone-use">0</property>
180    </settings>
181  </plugin-definition>
182  <extension
183    id="net.sf.basedb.reggie"
184    extends="net.sf.basedb.clients.web.menu.extensions"
185    >
186    <index>10</index>
187    <about safe-scripts="1">
188      <name>Reggie</name>
189      <description>
190        Menu entry for accessing reggie-specific operations.
191      </description>
192    </about>
193    <action-factory>
194      <factory-class>
195        net.sf.basedb.reggie.extensions.MenuItemFactory
196      </factory-class>
197      <parameters>
198        <title>Reggie</title>
199        <icon>~/images/snake-icon.png</icon>
200        <tooltip>Access reggie operations</tooltip>
201        <data-url>~/index.jsp?ID=$SESSION-ID$</data-url>
202      </parameters>
203    </action-factory>
204  </extension>
205 
206  <extension
207    id="net.sf.basedb.reggie.start-page"
208    extends="net.sf.basedb.clients.web.start-page"
209    >
210    <index>10</index>
211    <about>
212      <name>Reggie</name>
213      <description>
214        Use the Reggie index page as a start page.
215      </description>
216    </about>
217    <action-factory>
218      <factory-class>
219        net.sf.basedb.reggie.extensions.StartPageFactory
220      </factory-class>
221      <parameters>
222        <name>Extensions › Reggie</name>
223        <url>~/index.jsp?ID=$SESSION-ID$</url>
224        <description>Use Reggie as the start page</description>
225      </parameters>
226    </action-factory>
227  </extension>
228 
229 
230  <extension
231    id="net.sf.basedb.reggie.toolbar.case-summary"
232    >
233    <extends>
234      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
235      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
236      <ref index="1">net.sf.basedb.clients.web.toolbar.item.derivedbioassay</ref>
237      <ref index="1">net.sf.basedb.clients.web.toolbar.item.rawbioassay</ref>
238    </extends>
239    <about safe-scripts="1">
240      <name>Case summary</name>
241      <description>
242        Adds a button to the toolbar of sample, extracts, derived and
243        raw bioassay pages that opens the 'case summary' for the case that the current
244        item is part of. Works for all items that have a name pattern
245        that starts with 7 digits.
246      </description>
247    </about>
248    <action-factory>
249      <factory-class>
250        net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory
251      </factory-class>
252      <parameters>
253        <title>Case summary</title>
254        <clazz>button auto-init</clazz>
255        <data-auto-init>reggie-case-summary-link</data-auto-init>
256        <data-home>$HOME$</data-home>
257        <icon>~/images/case_summary.png</icon>
258        <script>~/scripts/case-summary.js</script>
259        <stylesheet>~/css/reggie-inside-base.css</stylesheet>
260      </parameters>
261    </action-factory>
262  </extension>
263 
264  <extension
265    id="net.sf.basedb.reggie.list-column"
266    >
267    <extends>
268      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
269      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
270      <ref index="1">net.sf.basedb.clients.web.listcolumn.derivedbioassay</ref>
271      <ref index="1">net.sf.basedb.clients.web.listcolumn.rawbioassay</ref>
272      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
273    </extends>
274    <index>2</index>
275    <about safe-scripts="1">
276      <name>Reggie column</name>
277      <description>
278        Add a column to the list page of samples, extract, derived bioassays,
279        raw bioassays and bioplates for including some reggie-specific links.
280      </description>
281    </about>
282    <action-factory>
283      <factory-class>
284        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
285      </factory-class>
286    </action-factory>
287  </extension>
288 
289  <extension
290    id="net.sf.basedb.reggie.histology-thumbnail-column"
291    extends="net.sf.basedb.clients.web.listcolumn.sample"
292    >
293    <index>3</index>
294    <about safe-scripts="1">
295      <name>Stained image</name>
296      <description>
297        Add a column to the list page of samples that display
298        a thumbnail of the stained histology image.
299      </description>
300    </about>
301    <action-factory>
302      <factory-class>
303        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
304      </factory-class>
305      <parameters>
306        <id>his-image</id>
307        <title>Stained image</title>
308        <link-name>image</link-name>
309        <subtype>STAINED</subtype>
310      </parameters>
311    </action-factory>
312  </extension>
313 
314  <extension
315    id="net.sf.basedb.reggie.genereport-thumbnail-column"
316    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
317    >
318    <index>3</index>
319    <about safe-scripts="1">
320      <name>Gene report PDF</name>
321      <description>
322        Add a column to the list page of raw bioassays that display
323        a thumbnail of the gene report PDF.
324      </description>
325    </about>
326    <action-factory>
327      <factory-class>
328        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
329      </factory-class>
330      <parameters>
331        <id>genereport-pdf</id>
332        <title>Gene report</title>
333        <link-name>genereport.pdf</link-name>
334      </parameters>
335    </action-factory>
336  </extension>
337 
338  <extension
339    id="net.sf.basedb.reggie.pilot-thumbnail-column"
340    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
341    >
342    <index>4</index>
343    <about safe-scripts="1">
344      <name>Pilot report PDF</name>
345      <description>
346        Add a column to the list page of raw bioassays that display
347        a thumbnail of the pilot 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>pilotreport-pdf</id>
356        <title>Pilot report</title>
357        <link-name>pilotreport.pdf</link-name>
358      </parameters>
359    </action-factory>
360  </extension>
361 
362  <extension
363    id="net.sf.basedb.reggie.mbafplot-thumbnail-column"
364    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
365    >
366    <index>3</index>
367    <about safe-scripts="1">
368      <name>mBAF plot</name>
369      <description>
370        Add a column to the list page of derived bioassays that display
371        a thumbnail of the mBAF plot.
372      </description>
373    </about>
374    <action-factory>
375      <factory-class>
376        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
377      </factory-class>
378      <parameters>
379        <id>mbaf-plot</id>
380        <title>mBAF plot</title>
381        <link-name>mbaf_genotype.png</link-name>
382        <subtype>ALIGNED_SEQUENCES</subtype>
383      </parameters>
384    </action-factory>
385  </extension>
386 
387 
388  <extension
389    id="net.sf.basedb.reggie.libplate-column-derivedbioassay"
390    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
391    >
392    <index>2</index>
393    <about safe-scripts="1">
394      <name>LibPlate</name>
395      <description>
396        Add a column to the list page of derived bioassays that display
397        the name of the library plate (assumes that the extract that is
398        linked is a library item).
399      </description>
400    </about>
401    <action-factory>
402      <factory-class>
403        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
404      </factory-class>
405      <parameters>
406        <id>extract.bioPlate</id>
407        <title>LibPlate</title>
408        <property>extract.bioWell.bioPlate</property>
409        <filter-property>extract.bioWell.bioPlate.name</filter-property>
410        <sort-property>extract.bioWell.bioPlate.name</sort-property>
411        <valueType>STRING</valueType>
412        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
413        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
414      </parameters>
415    </action-factory>
416  </extension>
417  <extension
418    id="net.sf.basedb.reggie.libplate-column-rawbioassay"
419    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
420    >
421    <index>2</index>
422    <about safe-scripts="1">
423      <name>LibPlate</name>
424      <description>
425        Add a column to the list page of raw bioassays that display
426        the name of the library plate (assumes that the extract that is
427        linked is a library item).
428      </description>
429    </about>
430    <action-factory>
431      <factory-class>
432        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
433      </factory-class>
434      <parameters>
435        <id>parentExtract.bioPlate</id>
436        <title>LibPlate</title>
437        <property>parentExtract.bioWell.bioPlate</property>
438        <filter-property>parentExtract.bioWell.bioPlate.name</filter-property>
439        <sort-property>parentExtract.bioWell.bioPlate.name</sort-property>
440        <valueType>STRING</valueType>
441        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
442        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
443      </parameters>
444    </action-factory>
445  </extension>
446  <extension
447    id="net.sf.basedb.reggie.histology-thumbnail-view"
448    extends="net.sf.basedb.clients.web.toolbar.item.sample"
449    >
450    <index>3</index>
451    <about safe-scripts="1">
452      <name>Stained image</name>
453      <description>
454        Add a thumbnail to the sample view page for stained
455        histology samples that has a link to an image file.
456      </description>
457    </about>
458    <action-factory>
459      <factory-class>
460        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
461      </factory-class>
462      <parameters>
463        <link-name>image</link-name>
464        <subtype>STAINED</subtype>
465      </parameters>
466    </action-factory>
467  </extension>
468 
469  <extension
470    id="net.sf.basedb.reggie.genereport-thumbnail-view"
471    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
472    >
473    <index>3</index>
474    <about safe-scripts="1">
475      <name>Gene report PDF</name>
476      <description>
477        Add a thumbnail to the raw bioassay view page for
478        that has a link to "genereport.pdf".
479      </description>
480    </about>
481    <action-factory>
482      <factory-class>
483        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
484      </factory-class>
485      <parameters>
486        <link-name>genereport.pdf</link-name>
487      </parameters>
488    </action-factory>
489  </extension>
490 
491  <extension
492    id="net.sf.basedb.reggie.overview.case-summary"
493    extends="net.sf.basedb.clients.web.overview.info-details"
494    >
495    <index>1</index>
496    <about safe-scripts="1">
497      <name>Case overview</name>
498      <description>
499        Adds a section to the information pane in the "Item overview"
500        functionality that display a link to the "Case summary"
501        function in Reggie for all items that have a name pattern
502        that starts with 7 digits.
503      </description>
504    </about>
505    <action-factory>
506      <factory-class>
507        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
508      </factory-class>
509      <parameters>
510        <id>reggie.case-summary</id>
511        <title>Reggie</title>
512        <include>~/reports/case_summary_hook.jsp</include>
513      </parameters>
514    </action-factory>
515  </extension>
516 
517  <extension
518    id="net.sf.basedb.reggie.toolbar.histology-score"
519    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
520    >
521    <about safe-scripts="1">
522      <name>Histology score</name>
523      <description>
524        Adds a button to the toolbar of paraffin blocks and
525        HE stain bioplates that start the 'histology scoring wizard'.
526      </description>
527    </about>
528    <action-factory>
529      <factory-class>
530        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
531      </factory-class>
532      <parameters>
533        <title>Score HE glass</title>
534        <clazz>button auto-init</clazz>
535        <data-auto-init>reggie-he-score-link</data-auto-init>
536        <data-home>$HOME$</data-home>
537        <icon>~/images/microscope.png</icon>
538        <script>~/scripts/he-score.js</script>
539      </parameters>
540    </action-factory>
541  </extension>
542 
543  <extension
544    id="net.sf.basedb.reggie.grid.job-complete"
545    extends="net.sf.basedb.opengrid.job-complete"
546    >
547    <about>
548      <name>Reggie job completion handler</name>
549      <description>
550        Handles completion of jobs started by Reggie.
551        Depending on the job type it will typically initiate
552        parsing of some result files, etc.
553      </description>
554    </about>
555    <action-factory>
556      <factory-class>
557        net.sf.basedb.reggie.grid.JobCompletionHandlerFactory
558      </factory-class>
559    </action-factory>
560  </extension>
561 
562  <extension
563    id="net.sf.basedb.reggie.extensions.nextseq-signal"
564    extends="net.sf.basedb.core.signal.job"
565    >
566    <about>
567      <name>Reggie signal handler</name>
568      <description>
569        Responds to signals sent from BASE. Support
570        for STATUS signal to get the progress of a
571        NextSeq sequencing run.
572      </description>
573    </about>
574    <action-factory>
575      <factory-class>
576        net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory
577      </factory-class>
578    </action-factory>
579  </extension>
580 
581  <extension
582    id="net.sf.basedb.reggie.auto-confirm-service"
583    extends="net.sf.basedb.clients.web.services"
584    >
585    <about>
586      <name>Reggie auto-confirm service</name>
587      <description>
588        A service that checks for secondary analysis
589        items that has been flagged with AutoProcessing=AutoConfirm.
590        If rules are met, the item is automatically
591        confirmed and the next step in the analysis is started.
592      </description>
593    </about>
594    <action-factory>
595      <factory-class>
596        net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory
597      </factory-class>
598    </action-factory>
599  </extension>
600 
601  <extension
602    id="net.sf.basedb.reggie.counter-service"
603    extends="net.sf.basedb.clients.web.services"
604    >
605    <about>
606      <name>Reggie counter service</name>
607      <description>
608        A service that count the number of items at
609        various stages in the lab and analysis process.
610        The counters are presented on the Reggie index page.
611        If this service is stopped the counter will not
612        be updated.
613      </description>
614    </about>
615    <action-factory>
616      <factory-class>
617        net.sf.basedb.reggie.counter.CounterServiceFactory
618      </factory-class>
619    </action-factory>
620  </extension>
621 
622  <extension
623    id="net.sf.basedb.reggie.project-archive-service"
624    extends="net.sf.basedb.clients.web.services"
625    >
626    <about>
627      <name>Reggie project-archive file permission service</name>
628      <description>
629        Checks and manages file permissions in the project-archive
630        based on the consent information on the related case.
631        Files that belong to a case with Consent=Yes will get
632        group-level read permission, all other files will get
633        private permissions only.
634      </description>
635    </about>
636    <action-factory>
637      <factory-class>
638        net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory
639      </factory-class>
640    </action-factory>
641  </extension>
642 
643</extensions>
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