diff --git a/README.md b/README.md
index 319d939..a0b5a63 100644
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@ This QA check requires additional config settings in `auth.properties` to connec
### Running the code
You can run the checks like this:
```
-java -Xmx8G -jar release-qa-0.1.0-jar-with-dependencies.jar
+java -Xmx8G -jar release-qa-0.1.0-exec
```
This will run a set of QAs for release. Before running the above, make sure you have edited
`resources/auth.properties` to provide required database connection information. All outputs
@@ -31,7 +31,7 @@ will be generated in the output folder.
You can run a specific check like this:
```
-java -Xmx8G -jar release-qa-0.1.0-jar-with-dependencies.jar [CHECK]
+java -Xmx8G -jar release-qa-0.1.0-exec [CHECK]
```
where `CHECK` is the QA check simple class name without file extension.
diff --git a/pom.xml b/pom.xml
index 6983664..aa62aa9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,255 +1,269 @@
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-
- reactome-release-qa
- org.reactome
-
- UTF-8
- 4.2
- 2.11.0
- 1.4
- 2.1.0-SNAPSHOT
-
+
+ reactome-release-qa
+ org.reactome
+
+ UTF-8
+ 4.2
+ 2.17.1
+ 1.4
+ 5.7.2
+ 2.1.0-SNAPSHOT
+ 11
+
- 4.0.0
- org.reactome
- release-qa
- 0.1.0
- ${bundle.symbolicName}
- jar
+ 4.0.0
+ org.reactome
+ release-qa
+ 0.1.0
+ ${bundle.symbolicName}
+ jar
-
-
-
- org.apache.maven.plugins
- maven-compiler-plugin
- 3.5.1
-
-
- default-testCompile
- test-compile
-
- testCompile
-
-
-
- default-compile
- compile
-
- compile
-
-
-
-
- 1.8
- 1.8
- true
- true
- true
-
- 10000
- 10000
-
-
-
-
- org.apache.maven.plugins
- maven-surefire-plugin
- 2.7.1
-
- true
- true
-
-
-
- org.apache.maven.plugins
- maven-assembly-plugin
- 2.6
-
-
-
- org.reactome.release.qa.Main
-
-
-
- jar-with-dependencies
-
-
-
-
- make-assembly
- package
-
- single
-
-
-
-
-
- maven-resources-plugin
- 3.0.2
-
-
- copy-resources
- validate
-
- copy-resources
-
-
- ${basedir}/target/resources
-
-
- src/main/resources
- true
-
- *.properties
- *.txt
- *.xml
-
-
-
-
-
-
- copy-skiplists
- validate
-
- copy-resources
-
-
- ${basedir}/target/QA_SkipList
-
-
- QA_SkipList
- true
-
- *.txt
-
-
-
-
-
-
-
-
-
+
+
+
+ org.apache.maven.plugins
+ maven-compiler-plugin
+ 3.8.1
+
+
+ default-testCompile
+ test-compile
+
+ testCompile
+
+
+
+ default-compile
+ compile
+
+ compile
+
+
+
+
+ ${java.version}
+ ${java.version}
+ true
+ true
+ true
+
+ 10000
+ 10000
+
+
+
+
+ org.apache.maven.plugins
+ maven-surefire-plugin
+ 2.12.4
+
+ true
+ true
+
+
+
+ org.springframework.boot
+ spring-boot-maven-plugin
+ 2.7.5
+
+ exec
+ org.reactome.release.qa.Main
+
+
+
+ repackage
+ package
+
+ repackage
+
+
+
+
+
+ org.apache.maven.plugins
+ maven-resources-plugin
+ 2.6
+
+
+ copy-resources
+ validate
+
+ copy-resources
+
+
+ ${basedir}/target/resources
+
+
+ src/main/resources
+ true
+
+ *.properties
+ *.txt
+ *.xml
+
+
+
+
+
+
+ copy-skiplists
+ validate
+
+ copy-resources
+
+
+ ${basedir}/target/QA_SkipList
+
+
+ QA_SkipList
+ true
+
+ *.txt
+
+
+
+
+
+
+
+
+
-
-
-
- oss.sonatype.org-snapshot
- https://oss.sonatype.org/content/repositories/snapshots
-
- false
-
-
- true
-
-
-
+
+
+
+ oss.sonatype.org-snapshot
+ https://oss.sonatype.org/content/repositories/snapshots
+
+ false
+
+
+ true
+
+
+
+ nexus-ebi-repo
+ The EBI internal repository
+ https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/
+
+ true
+
+
+ false
+
+
+
-
-
- javax.json
- javax.json-api
- 1.1
-
-
- org.glassfish
- javax.json
- 1.1
-
-
- org.reactome.release
- release-common-lib
- 1.2.0
-
-
- junit
- junit
- 4.12
- test
-
-
-
- com.opencsv
- opencsv
- ${opencsv.version}
-
-
-
- org.reflections
- reflections
- 0.9.11
-
-
-
- org.apache.logging.log4j
- log4j-api
- ${log4j2.version}
-
-
- org.apache.logging.log4j
- log4j-core
- ${log4j2.version}
-
-
-
- org.apache.logging.log4j
- log4j-1.2-api
- ${log4j2.version}
-
-
-
- javax.mail
- mail
- ${javax.mail.version}
-
-
-
- org.reactome.base
- reactome-base
- ${reactome.base.version}
-
-
-
- log4j
- log4j
-
-
-
+
+
+ javax.json
+ javax.json-api
+ 1.1
+
+
+ org.glassfish
+ javax.json
+ 1.1
+
+
+ org.reactome.release
+ release-common-lib
+ 1.2.0
+
+
+ org.junit.jupiter
+ junit-jupiter-api
+ ${junit.version}
+ test
+
+
+ org.junit.jupiter
+ junit-jupiter-engine
+ ${junit.version}
+ test
+
+
+
+ com.opencsv
+ opencsv
+ ${opencsv.version}
+
+
+
+ org.reflections
+ reflections
+ 0.9.11
+
+
+
+ org.apache.logging.log4j
+ log4j-api
+ ${log4j2.version}
+
+
+ org.apache.logging.log4j
+ log4j-core
+ ${log4j2.version}
+
+
+
+ org.apache.logging.log4j
+ log4j-1.2-api
+ ${log4j2.version}
+
+
+
+ javax.mail
+ mail
+ ${javax.mail.version}
+
+
+
+ org.reactome.base
+ reactome-base
+ ${reactome.base.version}
+
+
+
+ log4j
+ log4j
+
+
+
-
- mysql
- mysql-connector-java
- 5.1.28
-
+
+ mysql
+ mysql-connector-java
+ 5.1.28
+
-
- org.jdom
- jdom
- 1.1.3
-
+
+ org.jdom
+ jdom
+ 1.1.3
+
-
- org.mockito
- mockito-core
- 3.8.0
- test
-
-
- org.mockito
- mockito-inline
- 3.8.0
- test
-
-
+
+ org.mockito
+ mockito-core
+ 3.8.0
+ test
+
+
+ org.mockito
+ mockito-inline
+ 3.8.0
+ test
+
+
diff --git a/src/main/java/org/reactome/release/qa/check/EHLDSubpathwayChangeCheck.java b/src/main/java/org/reactome/release/qa/check/EHLDSubpathwayChangeCheck.java
index 60df43c..1196caa 100644
--- a/src/main/java/org/reactome/release/qa/check/EHLDSubpathwayChangeCheck.java
+++ b/src/main/java/org/reactome/release/qa/check/EHLDSubpathwayChangeCheck.java
@@ -120,7 +120,7 @@ private List parsePathwayIds(BufferedReader ehldWebSource) throws IOExcept
}
private Pattern getSVGFileNamePattern() {
- return Pattern.compile("\"(\\d+)\\.svg\"");
+ return Pattern.compile("\"R\\-HSA\\-(\\d+)\\.svg\"");
}
private List getEHLDPathways(Collection dbIds, MySQLAdaptor database) {
@@ -336,4 +336,4 @@ private Integer getReactomeVersionOfPathway(GKInstance pathway) {
}
}
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/org/reactome/release/qa/package-info.java b/src/main/java/org/reactome/release/qa/package-info.java
index 7e00dad..012f61f 100644
--- a/src/main/java/org/reactome/release/qa/package-info.java
+++ b/src/main/java/org/reactome/release/qa/package-info.java
@@ -6,5 +6,4 @@
// Eclipse error. This can also cause a problem with Maven
// (cf. https://stackoverflow.com/questions/6770455/maven-compiling-package-info-java-to-package-info-class).
// The work-around is to add an extraneous Deprecated annotation.
-@Deprecated
package org.reactome.release.qa;
\ No newline at end of file
diff --git a/src/main/scripts/qa-check-weeky.sh b/src/main/scripts/qa-check-weeky.sh
index bd9b083..32a1532 100644
--- a/src/main/scripts/qa-check-weeky.sh
+++ b/src/main/scripts/qa-check-weeky.sh
@@ -28,7 +28,7 @@ echo "Starting the $date_hyphenated weekly QA checks..."
# The Slicing Tool location.
slicing_dir="$share/SlicingTool"
# The Slicing Tool jar file.
-slicing_jar="$share/lib/SlicingTool-jar-with-dependencies.jar"
+slicing_jar="$share/lib/SlicingTool-exec"
# The slice database name.
slice_db="test_slice_$date"
@@ -62,7 +62,7 @@ if [ ! -e "$curator_qa_dir" ]; then
exit 1
fi
# The Curator QA jar file.
-curator_qa_jar="$share/lib/CuratorQA-jar-with-dependencies.jar"
+curator_qa_jar="$share/lib/CuratorQA-exec"
# The Curator QA output area.
curator_qa_out_dir="$curator_qa_dir/QA_Output"
[ -e "$curator_qa_out_dir" ] || mkdir $curator_qa_out_dir
@@ -94,7 +94,7 @@ rls_qa_out_dir="$rls_qa_dir/output"
[ -n "$(ls -A $rls_qa_out_dir)" ] && rm -f $rls_qa_out_dir/*
# Run the Release QA.
-rls_qa_jar="$share/lib/ReleaseQA-jar-with-dependencies.jar"
+rls_qa_jar="$share/lib/ReleaseQA-exec"
echo "Running the Release QA checks..."
(cd $rls_qa_dir; java -Xmx8G -jar $rls_qa_jar $db_opt)
rc=$?
@@ -122,7 +122,7 @@ if [ ! -e "$notify_dir" ]; then
fi
# Run the notifier.
-notify_jar="$share/lib/Notify-jar-with-dependencies.jar"
+notify_jar="$share/lib/Notify-exec"
# For some reason, the log config is not picked up in the
# notifier. Work around this by specifying it in an option.
java_opts="-Dlog4j.configurationFile=resources/log4j2.properties"