Merge remote-tracking branch 'remotes/origin/master' into stop-the-madness

# Conflicts:
#	model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
#	model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
#	model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
#	model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
#	model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
#	persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
#	persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
#	persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
#	service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
#	service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
#	service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
#	service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java

Comment: Resolved by "Accept Theirs".
Will fix the comments again via regex rather than manual merging.

.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>

.gitignore

 annotation/minerva-big/
 builds/
-debian/src/
-debian/minerva*
-debian/src/*.sql
 map_images/
 minerva-big/
-*/target/
 web/src/main/webapp/svnversion.txt
 *.war
-/target/
 service/minerva-big/
-npm-debug.log
-converter-sbml/jsbml.log
 
+#log files
+*.log
+
+#IntelliJ files
 .idea/
 *.iml
+
+#eclipse files
+/target/
+.classpath
+.settings
+
+#debian build files
+debian/src/
+debian/minerva*
+debian/src/*.sql
+/bin/

.gitlab-ci.yml

@@ -166,8 +166,8 @@ build_war:
       - minerva.war
   script:
     - apt-get update
-    - apt-get install -y curl gnupg git ant sudo
-    - curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
+    - apt-get install -y curl gnupg git ant
+    - curl -sL https://deb.nodesource.com/setup_9.x | bash -
     - apt-get install -y nodejs
     - ant maven-build
     - cp web/target/web-1.0.war minerva.war
@@ -177,8 +177,8 @@ dependency_conflict_check:
   stage: test
   script:
     - apt-get update
-    - apt-get install -y curl gnupg git ant sudo
-    - curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
+    - apt-get install -y curl gnupg git ant
+    - curl -sL https://deb.nodesource.com/setup_9.x | bash -
     - apt-get install -y nodejs
 
     - mvn clean install -DskipTests=true
@@ -247,7 +247,7 @@ test_upgrade_debian_package:
      - apt-add-repository "deb http://debian-repo/ unstable main"
      - apt-get update
      - apt-get dist-upgrade -y --allow-unauthenticated
-     - mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d 
+     - mv /usr/sbin/policy-rc.d.backup /usr/sbin/policy-rc.d
      - service tomcat8 start
 #we need to wait a bit for tomcat start
      - sleep 15
@@ -325,3 +325,31 @@ rpmlint:
     - yum -y install rpmlint
     - rpmlint rpm/rpmbuildtemp/RPMS/noarch/minerva-*.rpm
 
+test_deploy_with_db_without_superadmin_rights:
+  image: tomcat:7-jre8
+  stage: test
+  services:
+    - postgres:9.6
+  dependencies:
+    - build_war
+  tags:
+    - privileged
+  only:
+    - tags
+  script:
+    - apt-get update
+    - apt-get install -y postgresql-client
+    - mkdir /etc/minerva
+    - echo "database.uri=jdbc:postgresql://postgres:5432/test" > /etc/minerva/db.properties
+    - echo "database.username=test" >> /etc/minerva/db.properties
+    - echo "database.password=test" >> /etc/minerva/db.properties
+    - echo "CREATE DATABASE test;CREATE USER test WITH ENCRYPTED PASSWORD 'test';GRANT ALL PRIVILEGES ON DATABASE test TO test;" >tmp.sql
+    - PGPASSWORD=$POSTGRES_PASSWORD psql -h postgres -U $POSTGRES_USER $POSTGRES_DB < tmp.sql
+    - mv minerva.war /usr/local/tomcat/webapps/minerva.war
+    - /usr/local/tomcat/bin/startup.sh
+    - sleep 15
+    - wget http://localhost:8080/minerva/
+#test if we can login and list projects
+    - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
+    - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null --cookie cookie.txt http://localhost:8080/minerva/api/projects/)
+

.settings/org.eclipse.core.resources.prefs

-eclipse.preferences.version=1
-encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning

.settings/org.eclipse.m2e.core.prefs

-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1

.settings/org.eclipse.wst.validation.prefs

-DELEGATES_PREFERENCE=delegateValidatorList
-USER_BUILD_PREFERENCE=enabledBuildValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
-USER_MANUAL_PREFERENCE=enabledManualValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
-USER_PREFERENCE=overrideGlobalPreferencesfalse
-eclipse.preferences.version=1
-override=false
-suspend=false
-vals/org.eclipse.jst.jsf.facelet.ui.FaceletHTMLValidator/global=FF01
-vals/org.eclipse.jst.jsp.core.JSPBatchValidator/global=FF01
-vals/org.eclipse.jst.jsp.core.JSPContentValidator/global=FF01
-vals/org.eclipse.jst.jsp.core.TLDValidator/global=FF01
-vals/org.eclipse.wst.dtd.core.dtdDTDValidator/global=FF01
-vals/org.eclipse.wst.html.core.HTMLValidator/global=FF01
-vals/org.eclipse.wst.wsdl.validation.wsdl/global=FF02158org.eclipse.wst.wsdl.validation.internal.eclipse.Validator
-vals/org.eclipse.wst.xml.core.xml/global=FF03
-vals/org.eclipse.wst.xsd.core.xsd/global=FF02162org.eclipse.wst.xsd.core.internal.validation.eclipse.Validator
-vals/org.eclipse.wst.xsl.core.xsl/global=FF02
-vf.version=3

CHANGELOG

-minerva (12.1.0~beta.2) experimental; urgency=medium
-  * Bug fix: postgres migration script fixed to work with new docker compose
-  * Bug fix: double click on user add button disabled 
-  * Bug fix: privileges are mirrored correctly across different popups
-  * Bug fix: plugin tab css fixed
-  * Small improvement: all ldap parameters are configurable
+minerva (12.1.1) stable; urgency=medium
+  * Bug fix: lineWidth in data overlays was ignored
+  * Bug fix: legend was blinking after using controls
+  * Bug fix: comment header was missing
+  * Bug fix: click on drug target zooms to the results
+  * Bug fix: export columns return proper value types
+  * Bug fix: partial zooming is disabled
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Oct 2018 11:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 2 Nov 2018 13:00:00 +0200
 
-minerva (12.1.0~beta.1) experimental; urgency=medium
-  * Bug fix: uploading sbml file with no ids in glyphs returned error that 
-    could not be easily understand
-  * Bug fix: sometimes single variant in genomic view was hidden from initial 
-    view 
-  * Bug fix: ds_store files in subfolders crashed zip upload
-  * Bug fix: when creating new user default privileges were not filled
+minerva (12.1.0) stable; urgency=medium
   * Small improvement: default privilege value for 'Custom overlays' added
   * Small improvement: explicit logging of successful and unsuccessful logins
   * Small improvement: clicking on search result icon (on the map) change tab to 
     the corresponding search results
-  * Bug fix: passwords in the configuration tab are hidden with '*'
-  * Bug fix: user has access to transparency level when creating custom semantic
-    view (without this parametere functionality was very difficult to use)
-  * Bug fix: loading invalid plugin doesn't render empty div anymore
-  * Bug fix: sorting of custom overlays was broken when description of overlay
-    was present
-  * Bug fix: when there is a problem with adjusting font in complexes (because 
-    the font should be smaller than 1pt) description is not drawn anymore
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 18 Sep 2018 20:00:00 +0200
-
-minerva (12.1.0~beta.0) experimental; urgency=medium
   * Small improvement: option to remove additional overlays generated by custom
     semantic zoom
   * Small improvement: 'Reduced modulation' edge was displayed differently in
     CellDesigner and Minerva
   * Small improvement: user-friendly documentation for plugin URL field
   * Small improvement: plugins have to access information about active submap
-  * Small improvement: miriam support for VMH reaction and VMH metabolite
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 05 Sep 2018 17:00:00 +0200
-
-minerva (12.1.0~alpha.0) experimental; urgency=medium
   * Feature: genome browser with gene variants
   * Feature: support of all CellDesigner element modifications
   * Feature: ldap authentication
   * Feature: multicolored anchors for data overlays
   * Feature: minerva is distributed using rpm packages
-  * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
-    weren't provided properly
   * Small improvement: annotations from RHEA are handled
   * Small improvement: changing of Terms of Service url allows admin to reset
     the status of ToS acceptance for all users
   * Small improvement: description of a grouped results in improved
   * Small improvement: selection of required annotation on map upload improved
+  * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
+    weren't provided properly
+  * Bug fix: passwords in the configuration tab are hidden with '*'
+  * Bug fix: user has access to transparency level when creating custom semantic
+    view (without this parametere functionality was very difficult to use)
+  * Bug fix: loading invalid plugin doesn't render empty div anymore
+  * Bug fix: sorting of custom overlays was broken when description of overlay
+    was present
+  * Bug fix: when there is a problem with adjusting font in complexes (because
+    the font should be smaller than 1pt) description is not drawn anymore
+  * Bug fix: going to export page and back was breaking a map
+  * Bug fix: coordinates of selected area wasn't processed properly when they
+    exceeded canvas
+  * Bug fix: postgres migration script fixed to work with new docker compose
+  * Bug fix: double click on user add button disabled
+  * Bug fix: privileges are mirrored correctly across different popups
+  * Bug fix: plugin tab css fixed
+  * Bug fix: uploading sbml file with no ids in glyphs returned error that
+    could not be easily understand
+  * Bug fix: ds_store files in subfolders crashed zip upload
+  * Bug fix: when creating new user default privileges were not filled
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 03 Aug 2018 10:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
 
 minerva (12.0.4) stable; urgency=medium
   * Bug fix: CellDesigner modifications that are drawn as reaction are handled

CellDesigner-plugin/.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>

CellDesigner-plugin/.gitignore

+#eclipse files
+target
+.classpath
+.settings
+/bin/

CellDesigner-plugin/.settings/org.eclipse.core.resources.prefs

-eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/main/resources=UTF-8
-encoding//src/test/java=UTF-8
-encoding//src/test/resources=UTF-8
-encoding/<project>=UTF-8

CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs

-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
-org.eclipse.jdt.core.compiler.compliance=1.8
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.release=disabled
-org.eclipse.jdt.core.compiler.source=1.8

CellDesigner-plugin/.settings/org.eclipse.m2e.core.prefs

-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1

CellDesigner-plugin/pom.xml

@@ -82,6 +82,13 @@
 			<version>${libsbml.version}</version>
 		</dependency>
 
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit.version}</version>
+			<scope>test</scope>
+		</dependency>
+
 	</dependencies>
 
 </project>
\ No newline at end of file

annotation/.classpath

-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>

annotation/.gitignore

+#eclipse files
+target
+.classpath
+.settings
+/bin/

annotation/.settings/org.eclipse.core.resources.prefs

-eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/main/resources=UTF-8
-encoding//src/test/java=UTF-8
-encoding//src/test/resources=UTF-8
-encoding/<project>=UTF-8

annotation/.settings/org.eclipse.jdt.core.prefs

-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.8
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.release=disabled
-org.eclipse.jdt.core.compiler.source=1.8

annotation/.settings/org.eclipse.m2e.core.prefs

-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1

annotation/.settings/org.eclipse.wst.common.component

-<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
-    <wb-module deploy-name="MapViewer-annotation">
-        <wb-resource deploy-path="/" source-path="/src/main/java"/>
-        <wb-resource deploy-path="/" source-path="/src/main/resources"/>
-    </wb-module>
-</project-modules>