POM update

PGB-LIV · Oct 19, 2015 · e650472 · e650472
1 parent 83e4f47
commit e650472
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Showing 10 changed files with 62 additions and 59 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
 
     <groupId>uk.ac.liv</groupId>
     <artifactId>mzidlib</artifactId>
-    <version>1.6.12-SNAPSHOT</version>
+    <version>1.7</version>
     <packaging>jar</packaging>
 
     <name>mzidlib</name>
@@ -31,7 +31,8 @@
         <connection>scm:git:git://github.com/fghali/mzidlib.git</connection>
         <developerConnection>scm:git:git@github.com:fghali/mzidlib.git</developerConnection>
         <url>https://github.com/fghali/mzidlib</url>
-    </scm>
+      <tag>mzidlib-1.7</tag>
+  </scm>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

diff --git a/pom.xml.releaseBackup b/pom.xml.releaseBackup
@@ -351,38 +351,36 @@
             <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
         </repository>
     </distributionManagement>
-
+    <profiles>
+        <profile>
+            <id>release-sign-artifacts</id>
+            <activation>
+                <property>
+                    <name>performRelease</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-gpg-plugin</artifactId>
+                        <version>1.4</version>
+                        <configuration>
+                            <passphrase>${gpg.passphrase}</passphrase>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <id>sign-artifacts</id>
+                                <phase>verify</phase>
+                                <goals>
+                                    <goal>sign</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
 </project>
-
-<profiles>
-    <profile>
-        <id>release-sign-artifacts</id>
-        <activation>
-            <property>
-                <name>performRelease</name>
-                <value>true</value>
-            </property>
-        </activation>
-        <build>
-            <plugins>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-gpg-plugin</artifactId>
-                    <version>1.4</version>
-                    <configuration>
-                        <passphrase>${gpg.passphrase}</passphrase>
-                    </configuration>
-                    <executions>
-                        <execution>
-                            <id>sign-artifacts</id>
-                            <phase>verify</phase>
-                            <goals>
-                                <goal>sign</goal>
-                            </goals>
-                        </execution>
-                    </executions>
-                </plugin>
-            </plugins>
-        </build>
-    </profile>
-</profiles>
diff --git a/release.properties b/release.properties
@@ -1,14 +1,18 @@
 #release configuration
-#Mon Oct 19 15:58:23 BST 2015
+#Mon Oct 19 16:03:44 BST 2015
 project.rel.uk.ac.liv\:mzidlib=1.7
+project.scm.uk.ac.liv\:mzidlib.connection=scm\:git\:git\://github.com/fghali/mzidlib.git
 scm.tagNameFormat=@{project.artifactId}-@{project.version}
 scm.tag=mzidlib-1.7
 pushChanges=true
 scm.url=scm\:git\:git@github.com\:fghali/mzidlib.git
 preparationGoals=clean verify
 project.dev.uk.ac.liv\:mzidlib=1.7.1
+project.scm.uk.ac.liv\:mzidlib.developerConnection=scm\:git\:git@github.com\:fghali/mzidlib.git
 remoteTagging=true
 scm.commentPrefix=[maven-release-plugin] 
+project.scm.uk.ac.liv\:mzidlib.tag=HEAD
+project.scm.uk.ac.liv\:mzidlib.url=https\://github.com/fghali/mzidlib
 exec.additionalArguments=-Dgpg.passphrase\=fwzliv2014 -P sign
 exec.snapshotReleasePluginAllowed=false
-completedPhase=map-development-versions
+completedPhase=generate-release-poms
diff --git a/src/test/data/20091015_spiking_0_05fmol_CytC_MSMS_XTANDEM.out.mzid b/src/test/data/20091015_spiking_0_05fmol_CytC_MSMS_XTANDEM.out.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:51" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:50" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-51" name="Tandem2mzid_2015-10-19 15-59-51">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-50" name="Tandem2mzid_2015-10-19 16-03-50">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/55merge_tandem.xml.mzid b/src/test/data/55merge_tandem.xml.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:53" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:52" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-53" name="Tandem2mzid_2015-10-19 15-59-53">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-52" name="Tandem2mzid_2015-10-19 16-03-52">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/55merge_tandem_WITH_SUBSTITUTIONS.xml.mzid b/src/test/data/55merge_tandem_WITH_SUBSTITUTIONS.xml.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:52" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:51" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-52" name="Tandem2mzid_2015-10-19 15-59-52">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-51" name="Tandem2mzid_2015-10-19 16-03-51">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/DEBUG_MSMS_XTANDEM.bioml.mzid b/src/test/data/DEBUG_MSMS_XTANDEM.bioml.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:53" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:52" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-53" name="Tandem2mzid_2015-10-19 15-59-53">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-52" name="Tandem2mzid_2015-10-19 16-03-52">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/DEBUG_MSMS_XTANDEM.bioml_REGEX_TEST.mzid b/src/test/data/DEBUG_MSMS_XTANDEM.bioml_REGEX_TEST.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:51" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:50" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-51" name="Tandem2mzid_2015-10-19 15-59-51">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-50" name="Tandem2mzid_2015-10-19 16-03-50">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/Galaxy-[X_Tandem_on_data_N].bioml.mzid b/src/test/data/Galaxy-[X_Tandem_on_data_N].bioml.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:53" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:52" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-53" name="Tandem2mzid_2015-10-19 15-59-53">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-52" name="Tandem2mzid_2015-10-19 16-03-52">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>

diff --git a/src/test/data/S2_depl_spiked_6.mzML_xtandemOut.bioml.mzid b/src/test/data/S2_depl_spiked_6.mzML_xtandemOut.bioml.mzid
@@ -1,5 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T15:59:52" >
+<?xml version="1.0" encoding="Cp1252"?>
+<MzIdentML id="12345" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2015-10-19T16:03:51" >
 <cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
   <cv fullName="PSI-MS" version="2.25.0" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="PSI-MS"></cv>
   <cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"></cv>
@@ -11,7 +11,7 @@
       <cvParam cvRef="PSI-MS" accession="MS:1001476" name="X\!Tandem"></cvParam>
     </SoftwareName>
   </AnalysisSoftware>
-  <AnalysisSoftware id="Tandem2mzid_2015-10-19 15-59-52" name="Tandem2mzid_2015-10-19 15-59-52">
+  <AnalysisSoftware id="Tandem2mzid_2015-10-19 16-03-51" name="Tandem2mzid_2015-10-19 16-03-51">
     <SoftwareName>
       <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
     </SoftwareName>