source: extensions/net.sf.basedb.meludi/trunk/META-INF/extensions.xml @ 5863

Last change on this file since 5863 was 5863, checked in by olle, 23 months ago

Refs #1029. Updates due to version number change to "1.6.0b8".

  1. Version number changed to "1.6.0b8":
    a. Outermost Ant XML build file build.xml in / updated.
    b. Extensions XML configuration file extensions.xml in META-INF/ updated.
    c. Javascript file meludi-2.js in resources/ updated.
    d. Javascript file meludi_quarter_month_report_generator.js in resources/reports/ updated.
    e. Javascript file samplereportgenerator.js in resources/reports/ updated.
    f. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.
File size: 9.1 KB
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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>MeLuDi package</name>
5    <description>
6      A package for simplified registration of biosources
7      and samples.
8    </description>
9    <version>1.6.0b8</version>
10    <min-base-version>3.15.0</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.meludi</url>
14  </about>
15
16<!--
17  <plugin-definition id="CaliperSampleNameExporter">
18    <about>
19      <name>Caliper sample name exporter</name>
20      <description>
21        Plug-in that export the sample names on a bioplate to a
22        CSV file that can be used by the Caliper software. The
23        exported file has one line for each non-empty well with
24        five columns. Only the first two columns are used:
25        Well coordinate, sample name.
26      </description>
27    </about>
28    <plugin-class>net.sf.basedb.meludi.plugins.CaliperSampleNameExporter</plugin-class>
29    <settings>
30      <property name="everyone-use">1</property>
31      <property name="immediate-execution">1</property>
32    </settings>
33  </plugin-definition>
34
35  <plugin-definition id="CaliperRunParametersExporter">
36    <about>
37      <name>Caliper run parameters exporter</name>
38      <description>
39        Plug-in that export run file parameters that can be used by the
40        Caliper software. The run file include information about Assay Type,
41        Plate Name, selected wells, etc.
42      </description>
43    </about>
44    <plugin-class>net.sf.basedb.meludi.plugins.CaliperRunParametersExporter</plugin-class>
45    <settings>
46      <property name="everyone-use">1</property>
47      <property name="immediate-execution">1</property>
48    </settings>
49  </plugin-definition>
50
51  <plugin-definition id="CaliperLibPrepParametersExporter">
52    <about>
53      <name>Caliper library preparation parameters exporter</name>
54      <description>
55        Plug-in that export run file parameters that can be used by the
56        Caliper software. The run file include information about Assay Type,
57        Plate Name, selected wells, etc.
58      </description>
59    </about>
60    <plugin-class>net.sf.basedb.meludi.plugins.CaliperLibPrepParametersExporter</plugin-class>
61    <settings>
62      <property name="everyone-use">1</property>
63      <property name="immediate-execution">1</property>
64    </settings>
65  </plugin-definition>
66
67  <plugin-definition id="QubitSampleNameExporter">
68    <about>
69      <name>Qubit sample name exporter</name>
70      <description>
71        Plug-in that export the sample names on a bioplate to a
72        tab-separated file that the operator can use to fill in
73        concentration measurements from the Qubit. When all data
74        has been filled in, the file can be uploaded to BASE and
75        the concentration values are imported as annotations.
76      </description>
77    </about>
78    <plugin-class>net.sf.basedb.meludi.plugins.QubitSampleNameExporter</plugin-class>
79    <settings>
80      <property name="everyone-use">1</property>
81      <property name="immediate-execution">1</property>
82    </settings>
83  </plugin-definition>
84
85  <plugin-definition id="FlowCellSampleSheetExporter">
86    <about>
87      <name>Flow cell sample sheet exporter</name>
88      <description>
89        Plug-in for exporting information about libraries used in a flow cell.
90        The generated tab-separated text file used used by analysis software
91        to pick up data from the sequencing.
92      </description>
93    </about>
94    <plugin-class>net.sf.basedb.meludi.plugins.FlowCellSampleSheetExporter</plugin-class>
95    <settings>
96      <property name="everyone-use">1</property>
97      <property name="immediate-execution">1</property>
98    </settings>
99  </plugin-definition>
100-->
101
102  <extension
103    id="net.sf.basedb.meludi"
104    extends="net.sf.basedb.clients.web.menu.extensions"
105    >
106    <index>10</index>
107    <about safe-scripts="1">
108      <name>MeLuDi</name>
109      <description>
110        Menu entry for accessing MeLuDi-specific operations.
111      </description>
112    </about>
113    <action-factory>
114      <factory-class>
115        net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
116      </factory-class>
117      <parameters>
118        <title>MeLuDi</title>
119        <tooltip>Access MeLuDi operations</tooltip>
120        <icon>~/images/musical_note.png</icon>
121        <data-url>~/index.jsp?ID=$SESSION-ID$</data-url>
122      </parameters>
123    </action-factory>
124  </extension>
125 
126  <extension
127    id="net.sf.basedb.meludi.toolbar.case-summary"
128    >
129    <extends>
130      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
131      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
132    </extends>
133    <about safe-scripts="1">
134      <name>Case summary</name>
135      <description>
136        Adds a button to the toolbar of sample and extracts pages
137        that opens the 'case summary' for the case that the current
138        item is part of. Works for all items that have a name pattern
139        that starts with 7 digits.
140      </description>
141    </about>
142    <action-factory>
143      <factory-class>
144        net.sf.basedb.meludi.extensions.CaseSummaryButtonFactory
145      </factory-class>
146      <parameters>
147        <title>Case summary</title>
148        <clazz>button auto-init</clazz>
149        <data-auto-init>meludi-case-summary-link</data-auto-init>
150        <data-home>$HOME$</data-home>
151        <icon>~/images/case_summary.png</icon>
152        <script>~/scripts/case-summary.js</script>
153      </parameters>
154    </action-factory>
155  </extension>
156 
157  <extension
158    id="net.sf.basedb.meludi.list-column"
159    >
160    <extends>
161      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
162      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
163      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
164    </extends>
165    <index>2</index>
166    <about safe-scripts="1">
167      <name>MeLuDi column</name>
168      <description>
169        Add a column to the list page of samples, extract and bioplates
170        for including some MeLuDi-specific links.
171      </description>
172    </about>
173    <action-factory>
174      <factory-class>
175        net.sf.basedb.meludi.extensions.MeludiListColumnsFactory
176      </factory-class>
177    </action-factory>
178  </extension>
179 
180 
181  <extension
182    id="net.sf.basedb.meludi.overview.case-summary"
183    extends="net.sf.basedb.clients.web.overview.info-details"
184    >
185    <index>1</index>
186    <about safe-scripts="1">
187      <name>Case overview</name>
188      <description>
189        Adds a section to the information pane in the "Item overview"
190        functionality that display a link to the "Case summary"
191        function in MeLuDi for all items that have a name pattern
192        that starts with 7 digits.
193      </description>
194    </about>
195    <action-factory>
196      <factory-class>
197        net.sf.basedb.meludi.extensions.CaseSummarySectionFactory
198      </factory-class>
199      <parameters>
200        <id>meludi.case-summary</id>
201        <title>MeLuDi</title>
202        <include>~/reports/case_summary_hook.jsp</include>
203      </parameters>
204    </action-factory>
205  </extension>
206
207<!-- 
208  <extension
209    id="net.sf.basedb.meludi.toolbar.histology-score"
210    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
211    >
212    <about safe-scripts="1">
213      <name>Histology score</name>
214      <description>
215        Adds a button to the toolbar of paraffin blocks and
216        HE stain bioplates that start the 'histology scoring wizard'.
217      </description>
218    </about>
219    <action-factory>
220      <factory-class>
221        net.sf.basedb.meludi.extensions.HistologyScoreButtonFactory
222      </factory-class>
223      <parameters>
224        <title>Score HE glass</title>
225        <clazz>button auto-init</clazz>
226        <data-auto-init>meludi-he-score-link</data-auto-init>
227        <data-home>$HOME$</data-home>
228        <icon>~/images/microscope.png</icon>
229        <script>~/scripts/he-score.js</script>
230      </parameters>
231    </action-factory>
232  </extension>
233-->
234
235<!--
236  <extension
237    id="net.sf.basedb.meludi.grid.ogs-service"
238    extends="net.sf.basedb.clients.web.services"
239    >
240    <about>
241      <name>Open Grid Scheduler service</name>
242      <description>
243        A service for managing Open Grid Scheduler hosts
244        which makes it possible to connect to, execute commands,
245        control jobs, etc. on configured hosts.
246      </description>
247    </about>
248    <action-factory>
249      <factory-class>
250        net.sf.basedb.meludi.grid.OpenGridServiceFactory
251      </factory-class>
252    </action-factory>
253  </extension>
254 
255  <extension
256    id="net.sf.basedb.meludi.grid.job-signal"
257    extends="net.sf.basedb.core.signal.job"
258    >
259    <about>
260      <name>Open Grid Scheduler signal handler</name>
261      <description>
262        Responds to signals sent from BASE. Support
263        for ABORT and STATUS signals.
264      </description>
265    </about>
266    <action-factory>
267      <factory-class>
268        net.sf.basedb.meludi.grid.OpenGridSignalHandlerFactory
269      </factory-class>
270    </action-factory>
271  </extension>
272-->
273
274  <extension
275    id="net.sf.basedb.meludi.counter-service"
276    extends="net.sf.basedb.clients.web.services"
277    >
278    <about>
279      <name>Auto-confirm service</name>
280      <description>
281        A service that count the number of items at
282        various stages in the lab and analysis process.
283        The counters are presented on the MeLuDi index page.
284        If this service is stopped the counter will not
285        be updated.
286      </description>
287    </about>
288    <action-factory>
289      <factory-class>
290        net.sf.basedb.meludi.counter.CounterServiceFactory
291      </factory-class>
292    </action-factory>
293  </extension>
294 
295</extensions>
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