-
Notifications
You must be signed in to change notification settings - Fork 0
/
pom.xml
353 lines (326 loc) · 13 KB
/
pom.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<packaging>jar</packaging>
<version>1.7.2-SNAPSHOT</version>
<name>MzML Java core API</name>
<url>http://www.ebi.ac.uk/pride</url>
<description>
JAXB implementation of the mzML 1.1 standard as made available from the Proteomics Standards Initiative. This
object model can be used to serialize/deserialize properly formed mzML XML files.
</description>
<!-- License -->
<licenses>
<license>
<name>The Apache Software License 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<!-- Developers -->
<developers>
<developer>
<name>Richard Cote</name>
<id>rcote</id>
<email>rcote@ebi.ac.uk</email>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
</developer>
<developer>
<name>Phil Jones</name>
<id>philip_jones</id>
<email>pjones@ebi.ac.uk</email>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
</developer>
<developer>
<name>Lennart Martens</name>
<id>lennart</id>
<email>lennart.martens@ebi.ac.uk</email>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
</developer>
<developer>
<name>Florian Reisinger</name>
<id>florian</id>
<email>florian@ebi.ac.uk</email>
<organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
</developer>
<developer>
<name>Harald Barsnes</name>
<id>harald</id>
<email>harald.barsnes@biomed.uib.no</email>
<organization>Proteomics Unit, University of Bergen, Norway</organization>
</developer>
</developers>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<!-- Build -->
<build>
<!-- Copy the resources required during building -->
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>jmzML.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>jmzML.properties</exclude>
</excludes>
</resource>
</resources>
<plugins>
<!-- Compiler plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5</version>
<configuration>
<source>1.5</source>
<target>1.5</target>
</configuration>
</plugin>
<!-- Dependency plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/jmzml-${project.version}/lib</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<!-- Resources plugin -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/jmzml-${project.version}</outputDirectory>
<resources>
<resource>
<directory>./</directory>
<includes>
<include>readMe.txt</include>
<include>LICENSE-2.0.txt</include>
</includes>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!--to run the test cases-->
<plugin>
<!-- you can use this plugin to generate the jaxb object model from
the schema and binding files specified below. Note: this will
need an explicit maven goal call, since it is not intergrated
into the standard mvn lifecycle. The goal to use is:
org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.6.3:generate
NOTE: the code generation may overwrite existing classes, so care
should be taken with files that were manually modified. Such
files are in the current version (0.6): CVParam, UserParam,
ParamGroup, BinaryDataArray and ComponentList.
-->
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
<version>0.6.3</version>
<configuration>
<extension>true</extension>
<schemaDirectory>src/main/resources</schemaDirectory>
<schemaIncludes>
<include>mzML1.1.1-idx.xsd</include>
</schemaIncludes>
<bindingDirectory>src/main/resources</bindingDirectory>
<bindingIncludes>
<include>bindings.xjb</include>
</bindingIncludes>
<generateDirectory>src/main/java</generateDirectory>
<removeOldOutput>false</removeOldOutput>
<forceRegenerate>true</forceRegenerate>
<verbose>true</verbose>
<args>
<arg>-no-header</arg>
</args>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.1.2</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.7</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<!-- Dependencies -->
<dependencies>
<!--<dependency>-->
<!--<groupId>hibernate</groupId>-->
<!--<artifactId>hibernate</artifactId>-->
<!--<version>3.1rc2</version>-->
<!--</dependency>-->
<dependency>
<groupId>org.jboss.jsfunit</groupId>
<artifactId>jboss-jsfunit-microdeployer</artifactId>
<version>1.3.0.Final</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.5.10</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.5.8</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.13</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-xjc</artifactId>
<version>2.1.7</version>
</dependency>
<dependency>
<groupId>psidev.psi.tools</groupId>
<artifactId>xxindex</artifactId>
<version>0.14</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.1</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1</version>
</dependency>
<!-- needed for EscapingXMLStreamWriter to cope with ASCII control characters that are not properly escaped in JAXB -->
<dependency>
<groupId>it.unimi.dsi</groupId>
<artifactId>fastutil</artifactId>
<version>6.5.1</version>
</dependency>
</dependencies>
<!-- Repositores -->
<repositories>
<!-- EBI repositories -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>ebi-snapshot-repo</id>
<name>The EBI internal snapshot repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo_snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>JBoss</id>
<name>JBoss repository</name>
<url>https://repository.jboss.org/nexus/content/repositories/releases/</url>
</repository>
</repositories>
<!-- PluginRepositores -->
<pluginRepositories>
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<url>http://download.java.net/maven/2</url>
</pluginRepository>
</pluginRepositories>
<!-- Distribution management -->
<distributionManagement>
<repository>
<id>nexus-ebi-repo</id>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo</url>
</repository>
<!-- EBI SNAPSHOT repo -->
<snapshotRepository>
<id>nexus-ebi-repo-snapshots</id>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots</url>
</snapshotRepository>
</distributionManagement>
</project>