From 5def990145464a3dd6e9141aa9255bbf986eb726 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Wed, 21 Sep 2016 14:25:23 +0200 Subject: [PATCH 1/7] Graphtranslator SBGN JSON --- .classpath | 38 +++++++++++++++++++ .project | 36 ++++++++++++++++++ .settings/org.eclipse.jdt.core.prefs | 8 ++++ .settings/org.eclipse.m2e.core.prefs | 4 ++ .settings/org.eclipse.wst.common.component | 7 ++++ ....eclipse.wst.common.project.facet.core.xml | 5 +++ .settings/org.eclipse.wst.validation.prefs | 2 + pom.xml | 6 +++ src/log4j.properties | 6 +++ .../de/unirostock/sems/bives/Executer.java | 15 ++++++++ 10 files changed, 127 insertions(+) create mode 100644 .classpath create mode 100644 .project create mode 100644 .settings/org.eclipse.jdt.core.prefs create mode 100644 .settings/org.eclipse.m2e.core.prefs create mode 100644 .settings/org.eclipse.wst.common.component create mode 100644 .settings/org.eclipse.wst.common.project.facet.core.xml create mode 100644 .settings/org.eclipse.wst.validation.prefs create mode 100644 src/log4j.properties diff --git a/.classpath b/.classpath new file mode 100644 index 0000000..30a32de --- /dev/null +++ b/.classpath @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.project b/.project new file mode 100644 index 0000000..fb4fd5f --- /dev/null +++ b/.project @@ -0,0 +1,36 @@ + + + BiVeS + + + + + + org.eclipse.wst.common.project.facet.core.builder + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.wst.validation.validationbuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jem.workbench.JavaEMFNature + org.eclipse.wst.common.modulecore.ModuleCoreNature + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + org.eclipse.wst.common.project.facet.core.nature + + diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000..69c31cd --- /dev/null +++ b/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,8 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.compliance=1.6 +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.source=1.6 diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 0000000..3e76fb3 --- /dev/null +++ b/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles=release +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component new file mode 100644 index 0000000..aacb13d --- /dev/null +++ b/.settings/org.eclipse.wst.common.component @@ -0,0 +1,7 @@ + + + + + + + diff --git a/.settings/org.eclipse.wst.common.project.facet.core.xml b/.settings/org.eclipse.wst.common.project.facet.core.xml new file mode 100644 index 0000000..c78d932 --- /dev/null +++ b/.settings/org.eclipse.wst.common.project.facet.core.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/.settings/org.eclipse.wst.validation.prefs b/.settings/org.eclipse.wst.validation.prefs new file mode 100644 index 0000000..04cad8c --- /dev/null +++ b/.settings/org.eclipse.wst.validation.prefs @@ -0,0 +1,2 @@ +disabled=06target +eclipse.preferences.version=1 diff --git a/pom.xml b/pom.xml index 3b371c5..04ce2fa 100644 --- a/pom.xml +++ b/pom.xml @@ -58,6 +58,12 @@ log4j 1.2.17 + + de.unirostock.sems + BiVeS + 1.9.1 + provided + http://mvn.sems.uni-rostock.de diff --git a/src/log4j.properties b/src/log4j.properties new file mode 100644 index 0000000..ad20bd5 --- /dev/null +++ b/src/log4j.properties @@ -0,0 +1,6 @@ +log4j.rootLogger=INFO, stdout + +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n \ No newline at end of file diff --git a/src/main/java/de/unirostock/sems/bives/Executer.java b/src/main/java/de/unirostock/sems/bives/Executer.java index 3b329fb..57d8cfa 100644 --- a/src/main/java/de/unirostock/sems/bives/Executer.java +++ b/src/main/java/de/unirostock/sems/bives/Executer.java @@ -81,6 +81,9 @@ public class Executer public static final String REQ_WANT_REACTIONS_DOT = "reactionsDot"; public static final String REQ_WANT_REACTIONS_DOT2 = "crnDot"; + /** The Constant REQ_WANT_REACTIONS_JSON. */ + public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson"; + /** The Constant REQ_WANT_REACTIONS_JSON. */ public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson"; public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson"; @@ -188,6 +191,7 @@ private void fillOptions () options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML).desc ("get the highlighted reaction network encoded in GraphML").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT).desc ("get the highlighted reaction network encoded in DOT language").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON).desc ("get the highlighted reaction network encoded in JSON").build ()); + options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_SBGN_JSON).desc ("get the highlighted reaction network encoded in an SBGN-JSON format").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML2).desc ("get the highlighted reaction network encoded in GraphML (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT2).desc ("get the highlighted reaction network encoded in DOT language (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON2).desc ("get the highlighted reaction network encoded in JSON (deprecated version)").build ()); @@ -509,6 +513,17 @@ else if ((type & DocumentClassifier.XML) != 0) errors.add (e); } + if (line.hasOption (REQ_WANT_REACTIONS_SBGN_JSON)) + try + { + hasOption = true; + toReturn.put (Executer.REQ_WANT_REACTIONS_SBGN_JSON, result (diff.getReactionsSbgnJsonGraph ())); + } + catch (Exception e) + { + errors.add (e); + } + if (line.hasOption (REQ_WANT_COMP_HIERARCHY_DOT)) try { From 8b58adbecb4c69ba6ac39e950b195d667ddde9e5 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Thu, 12 Jan 2017 12:40:59 +0100 Subject: [PATCH 2/7] updatet dependencies --- pom.xml | 8 ++++---- .../java/de/unirostock/sems/bives/Executer.java | 15 +++++++++++++++ 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 4eaaa66..6e2e1bd 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ de.unirostock.sems BiVeS jar - 1.9.2 + 1.10.0 BiVeS BiVeS - BioModel Version Control System @@ -36,17 +36,17 @@ de.unirostock.sems BiVeS-SBML - 1.7.5 + 1.8.0 de.unirostock.sems BiVeS-CellML - 1.6.6 + 1.7.0 de.unirostock.sems BiVeS-Core - 1.7.2 + 1.8.0 commons-cli diff --git a/src/main/java/de/unirostock/sems/bives/Executer.java b/src/main/java/de/unirostock/sems/bives/Executer.java index 3b329fb..eceba57 100644 --- a/src/main/java/de/unirostock/sems/bives/Executer.java +++ b/src/main/java/de/unirostock/sems/bives/Executer.java @@ -81,6 +81,9 @@ public class Executer public static final String REQ_WANT_REACTIONS_DOT = "reactionsDot"; public static final String REQ_WANT_REACTIONS_DOT2 = "crnDot"; + /** The Constant REQ_WANT_REACTIONS_SBGN_JSON. */ + public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson"; + /** The Constant REQ_WANT_REACTIONS_JSON. */ public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson"; public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson"; @@ -188,6 +191,7 @@ private void fillOptions () options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML).desc ("get the highlighted reaction network encoded in GraphML").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT).desc ("get the highlighted reaction network encoded in DOT language").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON).desc ("get the highlighted reaction network encoded in JSON").build ()); + options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_SBGN_JSON).desc ("get the highlighted reaction network encoded in an SBGN-JSON format").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML2).desc ("get the highlighted reaction network encoded in GraphML (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT2).desc ("get the highlighted reaction network encoded in DOT language (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON2).desc ("get the highlighted reaction network encoded in JSON (deprecated version)").build ()); @@ -509,6 +513,17 @@ else if ((type & DocumentClassifier.XML) != 0) errors.add (e); } + if (line.hasOption (REQ_WANT_REACTIONS_SBGN_JSON)) + try + { + hasOption = true; + toReturn.put (Executer.REQ_WANT_REACTIONS_SBGN_JSON, result (diff.getReactionsSbgnJsonGraph ())); + } + catch (Exception e) + { + errors.add (e); + } + if (line.hasOption (REQ_WANT_COMP_HIERARCHY_DOT)) try { From cc387bbc0207f83fed4f342a9b2c8ca06df26cb1 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Thu, 12 Jan 2017 12:46:14 +0100 Subject: [PATCH 3/7] deleted unnecassary files --- .classpath | 38 ------------------- .project | 36 ------------------ .settings/org.eclipse.jdt.core.prefs | 8 ---- .settings/org.eclipse.m2e.core.prefs | 4 -- .settings/org.eclipse.wst.common.component | 7 ---- ....eclipse.wst.common.project.facet.core.xml | 5 --- .settings/org.eclipse.wst.validation.prefs | 2 - 7 files changed, 100 deletions(-) delete mode 100644 .classpath delete mode 100644 .project delete mode 100644 .settings/org.eclipse.jdt.core.prefs delete mode 100644 .settings/org.eclipse.m2e.core.prefs delete mode 100644 .settings/org.eclipse.wst.common.component delete mode 100644 .settings/org.eclipse.wst.common.project.facet.core.xml delete mode 100644 .settings/org.eclipse.wst.validation.prefs diff --git a/.classpath b/.classpath deleted file mode 100644 index 30a32de..0000000 --- a/.classpath +++ /dev/null @@ -1,38 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/.project b/.project deleted file mode 100644 index fb4fd5f..0000000 --- a/.project +++ /dev/null @@ -1,36 +0,0 @@ - - - BiVeS - - - - - - org.eclipse.wst.common.project.facet.core.builder - - - - - org.eclipse.jdt.core.javabuilder - - - - - org.eclipse.wst.validation.validationbuilder - - - - - org.eclipse.m2e.core.maven2Builder - - - - - - org.eclipse.jem.workbench.JavaEMFNature - org.eclipse.wst.common.modulecore.ModuleCoreNature - org.eclipse.jdt.core.javanature - org.eclipse.m2e.core.maven2Nature - org.eclipse.wst.common.project.facet.core.nature - - diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs deleted file mode 100644 index 69c31cd..0000000 --- a/.settings/org.eclipse.jdt.core.prefs +++ /dev/null @@ -1,8 +0,0 @@ -eclipse.preferences.version=1 -org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 -org.eclipse.jdt.core.compiler.compliance=1.6 -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.source=1.6 diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs deleted file mode 100644 index 3e76fb3..0000000 --- a/.settings/org.eclipse.m2e.core.prefs +++ /dev/null @@ -1,4 +0,0 @@ -activeProfiles=release -eclipse.preferences.version=1 -resolveWorkspaceProjects=true -version=1 diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component deleted file mode 100644 index aacb13d..0000000 --- a/.settings/org.eclipse.wst.common.component +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/.settings/org.eclipse.wst.common.project.facet.core.xml b/.settings/org.eclipse.wst.common.project.facet.core.xml deleted file mode 100644 index c78d932..0000000 --- a/.settings/org.eclipse.wst.common.project.facet.core.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/.settings/org.eclipse.wst.validation.prefs b/.settings/org.eclipse.wst.validation.prefs deleted file mode 100644 index 04cad8c..0000000 --- a/.settings/org.eclipse.wst.validation.prefs +++ /dev/null @@ -1,2 +0,0 @@ -disabled=06target -eclipse.preferences.version=1 From 5a58d46bef43f8c60d276a399e395733e70e9809 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Thu, 12 Jan 2017 12:47:30 +0100 Subject: [PATCH 4/7] delets --- src/log4j.properties | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 src/log4j.properties diff --git a/src/log4j.properties b/src/log4j.properties deleted file mode 100644 index ad20bd5..0000000 --- a/src/log4j.properties +++ /dev/null @@ -1,6 +0,0 @@ -log4j.rootLogger=INFO, stdout - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.Target=System.out -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n \ No newline at end of file From d8b4010d125876e1c795b500695f9cb3abdffe71 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Thu, 12 Jan 2017 12:49:36 +0100 Subject: [PATCH 5/7] gitihnore update --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index 3cb3963..3bbfb9d 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,7 @@ dist testfiles target lib +.settings +src/log4j.properties +.project +.classpath \ No newline at end of file From 1cf26cfa0af967acb3115becd12131c1fa411e7b Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Fri, 13 Jan 2017 10:36:42 +0100 Subject: [PATCH 6/7] removed double line in Executer --- src/main/java/de/unirostock/sems/bives/Executer.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/main/java/de/unirostock/sems/bives/Executer.java b/src/main/java/de/unirostock/sems/bives/Executer.java index e8df3f1..012b147 100644 --- a/src/main/java/de/unirostock/sems/bives/Executer.java +++ b/src/main/java/de/unirostock/sems/bives/Executer.java @@ -83,10 +83,7 @@ public class Executer /** The Constant REQ_WANT_REACTIONS_SBGN_JSON. */ public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson"; - - /** The Constant REQ_WANT_REACTIONS_JSON. */ - public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson"; - + /** The Constant REQ_WANT_REACTIONS_JSON. */ public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson"; public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson"; From ee7626b781bac2117cc602222fe3415c5e4c3e06 Mon Sep 17 00:00:00 2001 From: Tom_Laptop Date: Thu, 19 Jan 2017 08:43:27 +0100 Subject: [PATCH 7/7] dependencies update --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 005935c..ba08d03 100644 --- a/pom.xml +++ b/pom.xml @@ -41,12 +41,12 @@ de.unirostock.sems BiVeS-CellML - 1.7.0 + 1.7.1 de.unirostock.sems BiVeS-Core - 1.8.0 + 1.8.1 commons-cli