source: extensions/net.sf.basedb.reggie/trunk/META-INF/extensions.xml @ 2021

Last change on this file since 2021 was 2021, checked in by Nicklas Nordborg, 8 years ago

References #499: Export sample sheet for flow cell

First implementation of an export plug-in. It is yet a bit uncertain were some information should be coming from. Eg. the ReadString? is now configuration parameter for the plug-in, but it may be better to store this as an annotation on the flow cell (as is done for 'operator' and 'flow cell id'). Some information is still hard-coded in the plug-in (eg. concentration = 12pM).

File size: 6.3 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>
4    <name>Reggie package</name>
5    <description>
6      A package for simplified registration of biosources
7      and samples.
8    </description>
9    <version>2.13-dev</version>
10    <min-base-version>3.2.2</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
84  <plugin-definition id="FlowCellSampleSheetExporter">
85    <about>
86      <name>Flow cell sample sheet exporter</name>
87      <description>
88        Plug-in for exporting information about libraries used in a flow cell.
89        The generated tab-separated text file used used by analysis software
90        to pick up data from the sequencing.
91      </description>
92    </about>
93    <plugin-class>net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter</plugin-class>
94    <settings>
95      <property name="everyone-use">1</property>
96      <property name="immediate-execution">1</property>
97    </settings>
98  </plugin-definition>
99
100  <extension
101    id="net.sf.basedb.reggie"
102    extends="net.sf.basedb.clients.web.menu.extensions"
103    >
104    <index>10</index>
105    <about>
106      <name>Reggie</name>
107      <description>
108        Menu entry for accessing reggie-specific operations.
109      </description>
110    </about>
111    <action-factory>
112      <factory-class>
113        net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
114      </factory-class>
115      <parameters>
116        <title>Reggie</title>
117        <tooltip>Access reggie operations</tooltip>
118        <onClick>Menu.openUrl('$HOME$/index.jsp?ID='+getSessionId())</onClick>
119        <icon>/images/padding.gif</icon>
120      </parameters>
121    </action-factory>
122  </extension>
123 
124  <extension
125    id="net.sf.basedb.reggie.toolbar.case-summary"
126    >
127    <extends>
128      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
129      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
130    </extends>
131    <about>
132      <name>Case summary</name>
133      <description>
134        Adds a button to the toolbar of sample and extracts pages
135        that opens the 'case summary' for the case that the current
136        item is part of. Works for all items that have a name pattern
137        that starts with 7 digits.
138      </description>
139    </about>
140    <action-factory>
141      <factory-class>
142        net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory
143      </factory-class>
144    </action-factory>
145  </extension>
146 
147  <extension
148    id="net.sf.basedb.reggie.list-column"
149    >
150    <extends>
151      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
152      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
153    </extends>
154    <index>2</index>
155    <about>
156      <name>Reggie column</name>
157      <description>
158        Add a column to the list page of samples and extract for
159        including some reggie-specific links.
160      </description>
161    </about>
162    <action-factory>
163      <factory-class>
164        net.sf.basedb.reggie.extensions.ReggieListColumnsFactory
165      </factory-class>
166    </action-factory>
167  </extension>
168 
169 
170  <extension
171    id="net.sf.basedb.reggie.overview.case-summary"
172    extends="net.sf.basedb.clients.web.overview.info-details"
173    >
174    <index>1</index>
175    <about>
176      <name>Case overview</name>
177      <description>
178        Adds a section to the information pane in the "Item overview"
179        functionality that display a link to the "Case summary"
180        function in Reggie for all items that have a name pattern
181        that starts with 7 digits.
182      </description>
183    </about>
184    <action-factory>
185      <factory-class>
186        net.sf.basedb.reggie.extensions.CaseSummarySectionFactory
187      </factory-class>
188      <parameters>
189        <id>reggie.case-summary</id>
190        <title>Reggie</title>
191        <include>~/reports/case_summary_hook.jsp</include>
192      </parameters>
193    </action-factory>
194  </extension>
195 
196 
197</extensions>
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