From: Patrick Plitzner <p.plitzner@bgbm.org>
Date: Fri, 13 Jan 2017 14:32:31 +0000 (+0100)
Subject: Merge branch 'develop' into LibrAlign
X-Git-Tag: 4.5.0^2~18
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/1c69b0d01165dcae51f1f45667c202e0d15b960d

Merge branch 'develop' into LibrAlign
---

1c69b0d01165dcae51f1f45667c202e0d15b960d
diff --cc .gitignore
index 05274d7b9,ecfb4d5df..a8aaf71ff
--- a/.gitignore
+++ b/.gitignore
@@@ -31,4 -31,5 +31,6 @@@ eu.etaxonomy.taxeditor.webapp/lib/cdmli
  /eu.etaxonomy.taxeditor.webapp/.settings/org.eclipse.m2e.core.prefs
  /eu.etaxonomy.taxeditor.webapp/lib/
  
 +/.ssh
+ eu.etaxonomy.taxeditor.test/src/test/resources/eu/etaxonomy/cdm/database/schema/dataset.xsd
+ eu.etaxonomy.taxeditor.test/src/test/resources/eu/etaxonomy/cdm/database/schema/PUBLIC.xsd
diff --cc eu.etaxonomy.taxeditor.cdmlib/.classpath
index d09ef07c6,658cb9c72..8f6c238b5
--- a/eu.etaxonomy.taxeditor.cdmlib/.classpath
+++ b/eu.etaxonomy.taxeditor.cdmlib/.classpath
@@@ -1,251 -1,251 +1,251 @@@
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 +	<classpathentry exported="true" kind="lib" path="lib/Saxon-HE-9.7.0-2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/servlet-api-2.5.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/slf4j-api-1.7.13.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/slf4j-log4j12-1.7.13.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/slf4j-nop-1.7.13.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/snappy-java-1.0.4.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/solr-analysis-extras-3.6.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/solr-core-3.6.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/solr-solrj-3.6.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-aop-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-aspects-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-beans-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-context-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-context-support-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-core-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-expression-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-jdbc-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-modules-cache-0.7.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-orm-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-oxm-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-plugin-core-1.2.0.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-plugin-metadata-1.2.0.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-security-config-4.0.3.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-security-core-4.0.3.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-security-web-4.0.3.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-test-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-tx-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-web-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/spring-webmvc-4.2.4.RELEASE.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-core-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-schema-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-spi-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-spring-web-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-swagger-common-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/springfox-swagger2-2.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/standard-1.1.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/stax-1.2.0.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/stax-api-1.0.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/stax-ex-1.7.7.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/swagger-annotations-1.5.6.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/swagger-models-1.5.5.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/tools.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/txw2-2.2.11.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-core-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-database-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-dbmaintainer-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-dbunit-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-easymock-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-inject-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-mock-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-orm-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/unitils-spring-3.4.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/usertype.jodatime-2.0.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/usertype.spi-2.0.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/validation-api-1.1.0.Final.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/wsdl4j-1.6.3.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xalan-2.7.0.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xercesImpl-2.11.0.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xml-apis-1.0.b2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xml-apis-ext-1.3.04.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xml-resolver-1.2.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xmlbeans-2.6.0.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xmlgraphics-commons-1.5.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xmlpull-1.1.3.1.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xmlunit-1.6.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xom-1.2.5.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xpp3_min-1.1.4c.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xpp3-1.1.4c.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xsom-20140925.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/xstream-1.4.8.jar"/>
 +	<classpathentry exported="true" kind="lib" path="lib/yjp-controller-api-redist-9.0.8.jar"/>
- 	<classpathentry exported="true" kind="lib" path="lib/spring-security-oauth2-2.0.11.RELEASE.jar"/>
 +	<classpathentry kind="output" path="target/classes"/>
 +</classpath>
diff --cc eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
index 29336904c,22f8923e1..543d4e02e
--- a/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
@@@ -2,25 -2,19 +2,25 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
- Bundle-Version: 4.4.0.qualifier
+ Bundle-Version: 4.5.0.qualifier
  Bundle-ClassPath: .,
 - lib/bioinfweb-commons-bio-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-core-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-swing-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-swt-2.0.0-preview-1.jar,
 - lib/core-1.9.2-SNAPSHOT.jar,
 - lib/libralign-biojava1-0.4.0-preview-1.jar,
 - lib/libralign-core-0.4.0-preview-1.jar,
 - lib/libralign-swt-0.4.0-preview-1.jar,
 - lib/sequencing-1.9.2-SNAPSHOT.jar,
 - lib/tic-core-2.0.0-preview-1.jar,
 - lib/tic-swt-2.0.0-preview-1.jar
 + lib/owlapi-xmlutils-4.1.4.jar,
 + lib/commons-collections4-4.1.jar,
 + lib/core-1.9.2.jar,
 + lib/sequencing-1.9.2.jar,
 + lib/commons-lang3-3.5.jar,
 + lib/commons-beanutils-1.9.2.jar,
 + lib/bioinfweb-commons-java-bio-2.0.0.jar,
 + lib/bioinfweb-commons-java-core-2.2.0.jar,
 + lib/bioinfweb-commons-java-swing-2.2.0.jar,
 + lib/bioinfweb-commons-java-swt-2.0.0.jar,
 + lib/jphyloio-core-0.3.0.jar,
 + lib/libralign-biojava1-0.4.0-preview-2.jar,
 + lib/libralign-core-0.4.0-preview-2.jar,
 + lib/libralign-io-0.4.0-preview-2.jar,
 + lib/libralign-swt-0.4.0-preview-2.jar,
 + lib/tic-core-2.0.0-preview-2.jar,
 + lib/tic-swt-2.0.0-preview-2.jar
  Export-Package: info.bioinfweb.commons,
   info.bioinfweb.commons.appversion,
   info.bioinfweb.commons.beans,
diff --cc eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
index da122384a,c1023e1c6..41a6b82e1
--- a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
@@@ -755,14 -761,4 +754,14 @@@ public class AlignmentEditor extends Ed
  		}
  		return id;
  	}
 +
 +
 +    public static URI getPherogramURI(SingleRead pherogramInfo) {
 +        if (pherogramInfo.getPherogram() != null) {
 +            return MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
 +        }
 +        else {
 +            return null;
 +        }
 +    }
- }
+ }
diff --cc eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
index 41c429529,e193176ec..fd6c1f29c
--- a/eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
+++ b/eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
@@@ -1,58 -1,39 +1,39 @@@
 -<?xml version="1.0" encoding="UTF-8"?>
 -<?pde version="3.5"?><product application="eu.etaxonomy.taxeditor.application.application" id="eu.etaxonomy.taxeditor.application.eu_etaxonomy_taxeditor_product" includeLaunchers="true" name="EDIT Taxonomic Editor" uid="eu.etaxonomy.taxeditor.product" useFeatures="true" version="4.5.0.qualifier">
 -  <aboutInfo>
 -    <image path="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
 -    <text>
 -         %productBlurb
 -      </text>
 -  </aboutInfo>
 -  <configIni use="default"></configIni>
 -  <launcherArgs>
 -    <programArgs>-data @user.home/.cdmLibrary -Dserver_port=58080
 -      </programArgs>
 -    <vmArgs>-Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
 -      </vmArgs>
 -    <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
 -      </vmArgsMac>
 -  </launcherArgs>
 -  <windowImages i16="/eu.etaxonomy.taxeditor.application/icons/256color_16x16.gif" i32="/eu.etaxonomy.taxeditor.application/icons/256color_32x32.gif" i48="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
 -  <splash location="eu.etaxonomy.taxeditor.application" startupForegroundColor="000000" startupMessageRect="7,432,360,20" startupProgressRect="5,447,366,15"/>
 -  <launcher name="TaxonomicEditor">
 -    <solaris/>
 -    <win useIco="false">
 -      <bmp/>
 -    </win>
 -  </launcher>
 -  <vm></vm>
 -  <plugins></plugins>
 -  <features>
 -    <feature id="eu.etaxonomy.taxeditor.feature"/>
 -  </features>
 -  <configurations>
 -    <plugin autoStart="true" id="eu.etaxonomy.taxeditor.application" startLevel="5"/>
 -    <plugin autoStart="true" id="org.eclipse.core.runtime" startLevel="4"/>
 -    <plugin autoStart="true" id="org.eclipse.equinox.common" startLevel="2"/>
 -    <plugin autoStart="true" id="org.eclipse.equinox.ds" startLevel="2"/>
 -    <plugin autoStart="true" id="org.eclipse.equinox.p2.transport.ecf" startLevel="4"/>
 -    <plugin autoStart="true" id="org.eclipse.equinox.simpleconfigurator" startLevel="1"/>
 -  </configurations>
 -</product>
 +<?xml version="1.0" encoding="UTF-8"?>
- <?pde version="3.5"?>
- 
- <product name="EDIT Taxonomic Editor" uid="eu.etaxonomy.taxeditor.product" id="eu.etaxonomy.taxeditor.application.eu_etaxonomy_taxeditor_product" application="eu.etaxonomy.taxeditor.application.application" version="4.4.0.qualifier" useFeatures="true" includeLaunchers="true">
- 
-    <aboutInfo>
-       <image path="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
-       <text>
++<?pde version="3.5"?><product application="eu.etaxonomy.taxeditor.application.application" id="eu.etaxonomy.taxeditor.application.eu_etaxonomy_taxeditor_product" includeLaunchers="true" name="EDIT Taxonomic Editor" uid="eu.etaxonomy.taxeditor.product" useFeatures="true" version="4.5.0.qualifier">
++  <aboutInfo>
++    <image path="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
++    <text>
 +         %productBlurb
 +      </text>
-    </aboutInfo>
- 
-    <configIni use="default">
-    </configIni>
- 
-    <launcherArgs>
-       <programArgs>-data @user.home/.cdmLibrary -Dserver_port=58080
++  </aboutInfo>
++  <configIni use="default"></configIni>
++  <launcherArgs>
++    <programArgs>-data @user.home/.cdmLibrary -Dserver_port=58080
 +      </programArgs>
-       <vmArgs>-Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
++    <vmArgs>-Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
 +      </vmArgs>
-       <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
++    <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
 +      </vmArgsMac>
-    </launcherArgs>
- 
-    <windowImages i16="/eu.etaxonomy.taxeditor.application/icons/256color_16x16.gif" i32="/eu.etaxonomy.taxeditor.application/icons/256color_32x32.gif" i48="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
- 
-    <splash
-       location="eu.etaxonomy.taxeditor.application"
-       startupProgressRect="5,447,366,15"
-       startupMessageRect="7,432,360,20"
-       startupForegroundColor="000000" />
-    <launcher name="TaxonomicEditor">
-       <solaris/>
-       <win useIco="false">
-          <bmp/>
-       </win>
-    </launcher>
- 
-    <vm>
-    </vm>
- 
-    <plugins>
-    </plugins>
- 
-    <features>
-       <feature id="eu.etaxonomy.taxeditor.feature"/>
-    </features>
- 
-    <configurations>
-       <plugin id="eu.etaxonomy.taxeditor.application" autoStart="true" startLevel="5" />
-       <plugin id="org.eclipse.core.runtime" autoStart="true" startLevel="4" />
-       <plugin id="org.eclipse.equinox.common" autoStart="true" startLevel="2" />
-       <plugin id="org.eclipse.equinox.ds" autoStart="true" startLevel="2" />
-       <plugin id="org.eclipse.equinox.p2.transport.ecf" autoStart="true" startLevel="4" />
-       <plugin id="org.eclipse.equinox.simpleconfigurator" autoStart="true" startLevel="1" />
-    </configurations>
- 
++  </launcherArgs>
++  <windowImages i16="/eu.etaxonomy.taxeditor.application/icons/256color_16x16.gif" i32="/eu.etaxonomy.taxeditor.application/icons/256color_32x32.gif" i48="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
++  <splash location="eu.etaxonomy.taxeditor.application" startupForegroundColor="000000" startupMessageRect="7,432,360,20" startupProgressRect="5,447,366,15"/>
++  <launcher name="TaxonomicEditor">
++    <solaris/>
++    <win useIco="false">
++      <bmp/>
++    </win>
++  </launcher>
++  <vm></vm>
++  <plugins></plugins>
++  <features>
++    <feature id="eu.etaxonomy.taxeditor.feature"/>
++  </features>
++  <configurations>
++    <plugin autoStart="true" id="eu.etaxonomy.taxeditor.application" startLevel="5"/>
++    <plugin autoStart="true" id="org.eclipse.core.runtime" startLevel="4"/>
++    <plugin autoStart="true" id="org.eclipse.equinox.common" startLevel="2"/>
++    <plugin autoStart="true" id="org.eclipse.equinox.ds" startLevel="2"/>
++    <plugin autoStart="true" id="org.eclipse.equinox.p2.transport.ecf" startLevel="4"/>
++    <plugin autoStart="true" id="org.eclipse.equinox.simpleconfigurator" startLevel="1"/>
++  </configurations>
 +</product>