source: extensions/net.sf.basedb.reggie/branches/4.27-stable/META-INF/extensions.xml @ 5965

Last change on this file since 5965 was 5965, checked in by Nicklas Nordborg, 2 years ago

Preparing to release Reggie 4.27.2

File size: 20.6 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>4.27.2</version>
10    <min-base-version>3.16.0</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  <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.genereport-thumbnail-column"
314    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
315    >
316    <index>3</index>
317    <about safe-scripts="1">
318      <name>Gene report PDF</name>
319      <description>
320        Add a column to the list page of raw bioassays that display
321        a thumbnail of the gene report PDF.
322      </description>
323    </about>
324    <action-factory>
325      <factory-class>
326        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
327      </factory-class>
328      <parameters>
329        <id>genereport-pdf</id>
330        <title>Gene report</title>
331        <link-name>genereport.pdf</link-name>
332      </parameters>
333    </action-factory>
334  </extension>
335 
336  <extension
337    id="net.sf.basedb.reggie.pilot-thumbnail-column"
338    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
339    >
340    <index>4</index>
341    <about safe-scripts="1">
342      <name>Pilot report PDF</name>
343      <description>
344        Add a column to the list page of raw bioassays that display
345        a thumbnail of the pilot report PDF.
346      </description>
347    </about>
348    <action-factory>
349      <factory-class>
350        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
351      </factory-class>
352      <parameters>
353        <id>pilotreport-pdf</id>
354        <title>Pilot report</title>
355        <link-name>pilotreport.pdf</link-name>
356      </parameters>
357    </action-factory>
358  </extension>
359 
360  <extension
361    id="net.sf.basedb.reggie.mbafplot-thumbnail-column"
362    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
363    >
364    <index>3</index>
365    <about safe-scripts="1">
366      <name>mBAF plot</name>
367      <description>
368        Add a column to the list page of derived bioassays that display
369        a thumbnail of the mBAF plot.
370      </description>
371    </about>
372    <action-factory>
373      <factory-class>
374        net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory
375      </factory-class>
376      <parameters>
377        <id>mbaf-plot</id>
378        <title>mBAF plot</title>
379        <link-name>mbaf_genotype.png</link-name>
380        <subtype>ALIGNED_SEQUENCES</subtype>
381      </parameters>
382    </action-factory>
383  </extension>
384 
385 
386  <extension
387    id="net.sf.basedb.reggie.libplate-column-derivedbioassay"
388    extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay"
389    >
390    <index>2</index>
391    <about safe-scripts="1">
392      <name>LibPlate</name>
393      <description>
394        Add a column to the list page of derived bioassays that display
395        the name of the library plate (assumes that the extract that is
396        linked is a library item).
397      </description>
398    </about>
399    <action-factory>
400      <factory-class>
401        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
402      </factory-class>
403      <parameters>
404        <id>extract.bioPlate</id>
405        <title>LibPlate</title>
406        <property>extract.bioWell.bioPlate</property>
407        <filter-property>extract.bioWell.bioPlate.name</filter-property>
408        <sort-property>extract.bioWell.bioPlate.name</sort-property>
409        <valueType>STRING</valueType>
410        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
411        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
412      </parameters>
413    </action-factory>
414  </extension>
415  <extension
416    id="net.sf.basedb.reggie.libplate-column-rawbioassay"
417    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
418    >
419    <index>2</index>
420    <about safe-scripts="1">
421      <name>LibPlate</name>
422      <description>
423        Add a column to the list page of raw bioassays that display
424        the name of the library plate (assumes that the extract that is
425        linked is a library item).
426      </description>
427    </about>
428    <action-factory>
429      <factory-class>
430        net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
431      </factory-class>
432      <parameters>
433        <id>parentExtract.bioPlate</id>
434        <title>LibPlate</title>
435        <property>parentExtract.bioWell.bioPlate</property>
436        <filter-property>parentExtract.bioWell.bioPlate.name</filter-property>
437        <sort-property>parentExtract.bioWell.bioPlate.name</sort-property>
438        <valueType>STRING</valueType>
439        <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class>
440        <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class>
441      </parameters>
442    </action-factory>
443  </extension>
444  <extension
445    id="net.sf.basedb.reggie.histology-thumbnail-view"
446    extends="net.sf.basedb.clients.web.toolbar.item.sample"
447    >
448    <index>3</index>
449    <about safe-scripts="1">
450      <name>Stained image</name>
451      <description>
452        Add a thumbnail to the sample view page for stained
453        histology samples that has a link to an image file.
454      </description>
455    </about>
456    <action-factory>
457      <factory-class>
458        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
459      </factory-class>
460      <parameters>
461        <link-name>image</link-name>
462        <subtype>STAINED</subtype>
463      </parameters>
464    </action-factory>
465  </extension>
466 
467  <extension
468    id="net.sf.basedb.reggie.genereport-thumbnail-view"
469    extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay"
470    >
471    <index>3</index>
472    <about safe-scripts="1">
473      <name>Gene report PDF</name>
474      <description>
475        Add a thumbnail to the raw bioassay view page for
476        that has a link to "genereport.pdf".
477      </description>
478    </about>
479    <action-factory>
480      <factory-class>
481        net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory
482      </factory-class>
483      <parameters>
484        <link-name>genereport.pdf</link-name>
485      </parameters>
486    </action-factory>
487  </extension>
488 
489  <extension
490    id="net.sf.basedb.reggie.overview.case-summary"
491    extends="net.sf.basedb.clients.web.overview.info-details"
492    >
493    <index>1</index>
494    <about safe-scripts="1">
495      <name>Case overview</name>
496      <description>
497        Adds a section to the information pane in the "Item overview"
498        functionality that display a link to the "Case summary"
499        function in Reggie for all items that have a name pattern
500        that starts with 7 digits.
501      </description>
502    </about>
503    <action-factory>
504      <factory-class>
505        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
506      </factory-class>
507      <parameters>
508        <id>reggie.case-summary</id>
509        <title>Reggie</title>
510        <include>~/reports/case_summary_hook.jsp</include>
511      </parameters>
512    </action-factory>
513  </extension>
514 
515  <extension
516    id="net.sf.basedb.reggie.toolbar.histology-score"
517    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
518    >
519    <about safe-scripts="1">
520      <name>Histology score</name>
521      <description>
522        Adds a button to the toolbar of paraffin blocks and
523        HE stain bioplates that start the 'histology scoring wizard'.
524      </description>
525    </about>
526    <action-factory>
527      <factory-class>
528        net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory
529      </factory-class>
530      <parameters>
531        <title>Score HE glass</title>
532        <clazz>button auto-init</clazz>
533        <data-auto-init>reggie-he-score-link</data-auto-init>
534        <data-home>$HOME$</data-home>
535        <icon>~/images/microscope.png</icon>
536        <script>~/scripts/he-score.js</script>
537      </parameters>
538    </action-factory>
539  </extension>
540 
541  <extension
542    id="net.sf.basedb.reggie.grid.job-complete"
543    extends="net.sf.basedb.opengrid.job-complete"
544    >
545    <about>
546      <name>Reggie job completion handler</name>
547      <description>
548        Handles completion of jobs started by Reggie.
549        Depending on the job type it will typically initiate
550        parsing of some result files, etc.
551      </description>
552    </about>
553    <action-factory>
554      <factory-class>
555        net.sf.basedb.reggie.grid.JobCompletionHandlerFactory
556      </factory-class>
557    </action-factory>
558  </extension>
559 
560  <extension
561    id="net.sf.basedb.reggie.extensions.nextseq-signal"
562    extends="net.sf.basedb.core.signal.job"
563    >
564    <about>
565      <name>Reggie signal handler</name>
566      <description>
567        Responds to signals sent from BASE. Support
568        for STATUS signal to get the progress of a
569        NextSeq sequencing run.
570      </description>
571    </about>
572    <action-factory>
573      <factory-class>
574        net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory
575      </factory-class>
576    </action-factory>
577  </extension>
578 
579  <extension
580    id="net.sf.basedb.reggie.auto-confirm-service"
581    extends="net.sf.basedb.clients.web.services"
582    >
583    <about>
584      <name>Reggie auto-confirm service</name>
585      <description>
586        A service that checks for secondary analysis
587        items that has been flagged with AutoProcessing=AutoConfirm.
588        If rules are met, the item is automatically
589        confirmed and the next step in the analysis is started.
590      </description>
591    </about>
592    <action-factory>
593      <factory-class>
594        net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory
595      </factory-class>
596    </action-factory>
597  </extension>
598 
599  <extension
600    id="net.sf.basedb.reggie.counter-service"
601    extends="net.sf.basedb.clients.web.services"
602    >
603    <about>
604      <name>Reggie counter service</name>
605      <description>
606        A service that count the number of items at
607        various stages in the lab and analysis process.
608        The counters are presented on the Reggie index page.
609        If this service is stopped the counter will not
610        be updated.
611      </description>
612    </about>
613    <action-factory>
614      <factory-class>
615        net.sf.basedb.reggie.counter.CounterServiceFactory
616      </factory-class>
617    </action-factory>
618  </extension>
619 
620  <extension
621    id="net.sf.basedb.reggie.project-archive-service"
622    extends="net.sf.basedb.clients.web.services"
623    >
624    <about>
625      <name>Reggie project-archive file permission service</name>
626      <description>
627        Checks and manages file permissions in the project-archive
628        based on the consent information on the related case.
629        Files that belong to a case with Consent=Yes will get
630        group-level read permission, all other files will get
631        private permissions only.
632      </description>
633    </about>
634    <action-factory>
635      <factory-class>
636        net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory
637      </factory-class>
638    </action-factory>
639  </extension>
640 
641  <extension 
642    id="net.sf.basedb.reggie.vcf-actions"
643    extends="net.sf.basedb.clients.web.file-viewer"
644    >
645    <about>
646      <name>Genotype and variant call VCF viewer</name>
647      <description>
648        Add links for viewing the genotype QC VCF (qc_genotype.vcf)
649        file and the filtered variant call VCF file (variants-filtered.vcf).
650      </description>
651    </about>
652    <action-factory>
653      <factory-class>
654        net.sf.basedb.reggie.extensions.VcfViewerActionFactory
655      </factory-class>
656      <parameters>
657        <script>~/scripts/vcf-actions.js</script>
658      </parameters>
659    </action-factory>
660  </extension>
661 
662</extensions>
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