source: trunk/src/core/core-extensions.xml @ 5764

Last change on this file since 5764 was 5764, checked in by Nicklas Nordborg, 10 years ago

Fixes #1624: Create array design (feature) importer for GTF files

  • Created GtfReporterMapImporter and two configurations that uses transcript_id/gene_id for reporter ids. The GTF importer builds on the ReporterMapFlatFileImporter but has less configuration options. Eg. it is locked to use FEATURE_ID for identifying features.
  • Added a new parameter to the regular ReporterMapFlatFileImporter that makes it possible to limit a configuration to certain platforms. This is used to hide genepix, illumina, etc. when using the sequencing platform.
  • Added SEQUENCING platform and SEQUENCING_EXPRESSION variant.
  • Created a GTF validator that hooks into the fileset validation extension point for array designs and extracts the number of unique transcript_id:s from the GTF file.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 6.6 KB
Line 
1<?xml version="1.0" encoding="UTF-8" ?>
2<!--
3  $Id: core-extensions.xml 5764 2011-09-27 12:35:28Z nicklas $
4
5  Copyright (C) Nicklas Nordborg
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License
12  as published by the Free Software Foundation; either version 3
13  of the License, or (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18  GNU General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23<extensions
24  xmlns="http://base.thep.lu.se/extensions.xsd"
25  >
26  <about>
27    <version></version>
28    <name>Core extensions points and extensions</name>
29    <description>
30      This file defines core extension points and extensions.
31      Core extensions are always loaded when BASE starts up and
32      are available in all context, no matter if BASE is running
33      as a job agent, web server, etc.
34    </description>
35    <copyright>BASE development team</copyright>
36    <email>basedb-users@lists.sourceforge.net</email>
37    <url>http://base.thep.lu.se/</url>
38  </about>
39 
40  <extension-point
41    id="net.sf.basedb.core.uri.connection-manager"
42    >
43    <action-class>net.sf.basedb.util.uri.ConnectionManagerFactory</action-class>
44    <name>Connection manager</name>
45    <description>
46      Extension point for external file support. A connection manager is
47      something that knows how to access an external file pointed to by an
48      URI. Actions are ConnectionManagerFactory instances and are typically
49      used in two ways.
50      1) In a single-file context when getting metadata or the contents of
51      a single File item. The ClientContext object is populated with an active
52      DbControl and the current item is the file.
53      2) A standalone context with the external reference as an URI. No
54      DbControl is used and no current item.
55      Extensions to this extension point must not return more than one
56      factory since we need to associate each factory with the id
57      of the extension.
58    </description>
59  </extension-point>
60 
61  <extension-point 
62    id="net.sf.basedb.core.filehandler.validator"
63    >
64    <action-class>net.sf.basedb.util.fileset.ValidationAction</action-class>
65    <name>File set validators</name>
66    <description>
67      Extension point for validating and extracting metadata from files in a FileSet.
68      Extensions can be invoked in three different contexts:
69      1) Validation of a file set: The current item in the context is the owner of
70        the file set (eg. the FileStoreEnabled item).
71      2) Removing a file from a file set: The current item in the context
72        is the owner of the file set (eg. the FileStoreEnabled item). The
73        extension is supposed to remove metadata that was extracted from the
74        given file.
75      3) Checking if a given data file type can be validated or not: The current
76        item in the context is a DataFileType and the core will only check if
77        the action factory returns TRUE from the prepareContext method. The
78        extensions will not actually be invoked.
79    </description>
80  </extension-point>
81 
82  <extension 
83    id="net.sf.basedb.core.uri.http-connection-manager"
84    extends="net.sf.basedb.core.uri.connection-manager"
85    >
86    <about>
87      <name>HTTP(s) connection manager</name>
88      <description>
89        Provides support for regular HTTP and HTTPS including Basic
90        and Digest authentication as well as server- and client-side
91        certificates. Auto-detection matches all URI:s with 'http'
92        or 'https' scheme.
93      </description>
94    </about>
95    <index>1</index>
96    <action-factory>
97      <factory-class>net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory</factory-class>
98    </action-factory>
99  </extension>
100 
101  <extension 
102    id="net.sf.basedb.util.affymetrix.cel-validator"
103    extends="net.sf.basedb.core.filehandler.validator"
104    >
105    <about>
106      <name>CEL file validator</name>
107      <description>
108        Validator and metadata extractor implementation for Affymetrix CEL files.
109        The validation is done by trying to open the file with the Affymetrix
110        Fusion SDK. If this was successful some metadata information is extracted
111        from the headers including chip type and algorithm parameters. The number
112        of spots for the raw bioassay is set to the number of cells in the file.
113      </description>
114    </about>
115    <index>1</index>
116    <action-factory>
117      <factory-class>net.sf.basedb.util.affymetrix.CelValidationFactory</factory-class>
118    </action-factory>
119  </extension>
120
121  <extension 
122    id="net.sf.basedb.util.affymetrix.cdf-validator"
123    extends="net.sf.basedb.core.filehandler.validator"
124    >
125    <about>
126      <name>CDF file validator</name>
127      <description>
128        Validator and metadata extractor implementation for Affymetrix CDF files.
129        The validation is done by trying to open the file with the Affymetrix
130        Fusion SDK. If this was successful some metadata information is extracted
131        from the headers including
132       
133        chip type and algoritm parameters. The number
134        of spots for the raw bioassay is set to the number of cells in the file.
135      </description>
136    </about>
137    <index>1</index>
138    <action-factory>
139      <factory-class>net.sf.basedb.util.affymetrix.CdfValidationFactory</factory-class>
140    </action-factory>
141  </extension>
142
143  <extension 
144    id="net.sf.basedb.util.gtf.gtf-validator"
145    extends="net.sf.basedb.core.filehandler.validator"
146    >
147    <about>
148      <name>GTF file validator</name>
149      <description>
150        Validator for GTF reference files. The validation checks that
151        the first few lines follow the GTF specification.
152        See http://mblab.wustl.edu/GTF22.html
153      </description>
154    </about>
155    <index>1</index>
156    <action-factory>
157      <factory-class>net.sf.basedb.util.gtf.GtfValidationFactory</factory-class>
158    </action-factory>
159  </extension>
160
161  <!--
162  <extension
163    id="net.sf.basedb.core.filehandler.cdf-validator"
164    extends="net.sf.basedb.core.filehandler.affymetrix.cdf"
165    >
166    <about>
167      <name>CDF file validator</name>
168      <description>
169        Validator and metadata extractor implementation for Affymetrix CDF files.
170        The validation is done by trying to open the file with the Affymetrix
171        Fusion SDK. If this was successful the number of features for the array design
172        is set to the number of probesets in the file.
173      </description>
174    </about>
175    <index>1</index>
176    <action-factory>
177      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
178      <parameters>
179        <beanClassName>net.sf.basedb.core.filehandler.CdfFileHandler</beanClassName>
180      </parameters>
181    </action-factory>
182  </extension>
183  -->
184</extensions>
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