From 2a86508e6e4bc04cb0ae10f1a59a18c6a8d1153e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Igor=20Kupczy=C5=84ski?= Date: Wed, 27 Jul 2016 18:30:27 +0200 Subject: [PATCH 1/4] Workarounds for building the project --- build.sh | 11 +++++++++++ isa-graphparser/pom.xml | 5 +++-- linkedISA-core/pom.xml | 4 ++-- .../linkedISA/converter/Assay2linkedConverter.java | 2 +- 4 files changed, 17 insertions(+), 5 deletions(-) create mode 100755 build.sh diff --git a/build.sh b/build.sh new file mode 100755 index 0000000..be256c6 --- /dev/null +++ b/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash -ex + +# FIXME: this is a workaround for out-of-date transitive dependencies +# See: https://github.com/ISA-tools/linkedISA/issues/11 +mvn dependency:get -Dartifact=xalan:xalan:2.4.0 + +mvn install:install-file -Dfile="$HOME/.m2/repository/xalan/xalan/2.4.0/xalan-2.4.0.jar" -DgroupId=xalan -DartifactId=xalan -Dversion=2.4 -Dpackaging=jar + +# FIXME: some tests are failing +# See: https://github.com/ISA-tools/linkedISA/issues/12 +mvn clean install -DskipTests=true diff --git a/isa-graphparser/pom.xml b/isa-graphparser/pom.xml index 04d11d8..decc55d 100644 --- a/isa-graphparser/pom.xml +++ b/isa-graphparser/pom.xml @@ -41,12 +41,13 @@ - + + org.isatools ISAcreator - 1.7.8 + 1.7.7 org.slf4j diff --git a/linkedISA-core/pom.xml b/linkedISA-core/pom.xml index 7c06625..8e078a1 100644 --- a/linkedISA-core/pom.xml +++ b/linkedISA-core/pom.xml @@ -77,7 +77,7 @@ org.isatools ISacreator - 1.7.8 + 1.7.7 @@ -289,4 +289,4 @@ - \ No newline at end of file + diff --git a/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java b/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java index 232cf40..c875190 100644 --- a/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java +++ b/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java @@ -1095,4 +1095,4 @@ private void addComments(NodeWithComments nodeWithComments, int row, OWLNamedInd } -} \ No newline at end of file +} From f72523f2954ee8745040951bb0e616954b2a1d9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Igor=20Kupczy=C5=84ski?= Date: Wed, 27 Jul 2016 18:57:49 +0200 Subject: [PATCH 2/4] Fixed the source paths in graph pom --- isa-graphparser/pom.xml | 2 -- 1 file changed, 2 deletions(-) diff --git a/isa-graphparser/pom.xml b/isa-graphparser/pom.xml index decc55d..544c185 100644 --- a/isa-graphparser/pom.xml +++ b/isa-graphparser/pom.xml @@ -12,8 +12,6 @@ isa-graphparser - src/main - src/test org.apache.maven.plugins From 6dd5361b07b867d6c33616185b417b68980d8d36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Igor=20Kupczy=C5=84ski?= Date: Wed, 27 Jul 2016 19:42:03 +0200 Subject: [PATCH 3/4] Filename case fix --- .../{Assay2linkedConverter.java => Assay2LinkedConverter.java} | 0 .../{ISAtab2linkedConverter.java => ISAtab2LinkedConverter.java} | 0 ...nkedFolderConverter.java => ISAtab2LinkedFolderConverter.java} | 0 ...b2linkedConverterTest.java => ISAtab2LinkedConverterTest.java} | 0 ...erConverterTest.java => ISAtab2LinkedFolderConverterTest.java} | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename linkedISA-core/src/main/java/org/isatools/linkedISA/converter/{Assay2linkedConverter.java => Assay2LinkedConverter.java} (100%) rename linkedISA-core/src/main/java/org/isatools/linkedISA/converter/{ISAtab2linkedConverter.java => ISAtab2LinkedConverter.java} (100%) rename linkedISA-core/src/main/java/org/isatools/linkedISA/converter/{ISAtab2linkedFolderConverter.java => ISAtab2LinkedFolderConverter.java} (100%) rename linkedISA-core/src/test/java/org/isatools/linkedISA/converter/{ISAtab2linkedConverterTest.java => ISAtab2LinkedConverterTest.java} (100%) rename linkedISA-core/src/test/java/org/isatools/linkedISA/converter/{ISAtab2linkedFolderConverterTest.java => ISAtab2LinkedFolderConverterTest.java} (100%) diff --git a/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java b/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2LinkedConverter.java similarity index 100% rename from linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2linkedConverter.java rename to linkedISA-core/src/main/java/org/isatools/linkedISA/converter/Assay2LinkedConverter.java diff --git a/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2linkedConverter.java b/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2LinkedConverter.java similarity index 100% rename from linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2linkedConverter.java rename to linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2LinkedConverter.java diff --git a/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2linkedFolderConverter.java b/linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2LinkedFolderConverter.java similarity index 100% rename from linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2linkedFolderConverter.java rename to linkedISA-core/src/main/java/org/isatools/linkedISA/converter/ISAtab2LinkedFolderConverter.java diff --git a/linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2linkedConverterTest.java b/linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2LinkedConverterTest.java similarity index 100% rename from linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2linkedConverterTest.java rename to linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2LinkedConverterTest.java diff --git a/linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2linkedFolderConverterTest.java b/linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2LinkedFolderConverterTest.java similarity index 100% rename from linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2linkedFolderConverterTest.java rename to linkedISA-core/src/test/java/org/isatools/linkedISA/converter/ISAtab2LinkedFolderConverterTest.java From 5936a9f3dba586196c0b33ac806255e8375ace9b Mon Sep 17 00:00:00 2001 From: hcwi Date: Wed, 27 Jul 2016 19:51:09 +0200 Subject: [PATCH 4/4] Cleaned dependencies in linkedISA-core --- linkedISA-core/pom.xml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/linkedISA-core/pom.xml b/linkedISA-core/pom.xml index 8e078a1..bf5fa19 100644 --- a/linkedISA-core/pom.xml +++ b/linkedISA-core/pom.xml @@ -57,13 +57,6 @@ Apaches's Maven repository https://repository.apache.org/content/repositories/releases/ - - - Aduna repository - Sesame's Maven repository - http://repo.aduna-software.org/maven2/releases/ - - @@ -76,7 +69,7 @@ org.isatools - ISacreator + ISAcreator 1.7.7