From c2dfa27b6703c844b872ac494f910b1289d33d62 Mon Sep 17 00:00:00 2001 From: Marco Brandizi Date: Thu, 29 Aug 2019 11:00:57 +0100 Subject: [PATCH 1/5] Bugfixing change of test dir in aratiny. --- common/quickstart/runtime-helper.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/common/quickstart/runtime-helper.sh b/common/quickstart/runtime-helper.sh index 51b54a8eb..74ac0865b 100755 --- a/common/quickstart/runtime-helper.sh +++ b/common/quickstart/runtime-helper.sh @@ -112,10 +112,10 @@ rm -Rf /tmp/aratiny-ws common/aratiny/aratiny-ws/target cp -Rf common/aratiny/aratiny-ws /tmp # We don't need the test queries used for aratiny, let's remove them from the build location -rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-config/neo4j/*.cypher +rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j/*.cypher # And then copy the dataset-specific config to the build place (in /tmp) -cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-config +cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config # Eventually, go to the build place and do mvn test-compile. This creates interpolated config files (ie, # all the placeholders are instantiated with the values in maven settings or in ancestor POMS). @@ -125,7 +125,7 @@ cd /tmp/aratiny-ws mvn $MAVEN_ARGS --settings "$knet_dataset_dir/config/actual-maven-settings.xml" clean test-compile # End eventually, deploy the instantiated config files -cp -Rf target/test-classes/knetminer-config/* "$knet_dataset_dir/config" +cp -Rf target/test-classes/knetminer-dataset/knetminer-config/* "$knet_dataset_dir/config" From 11237d18a9d9b5af4b4bbce507c50c2e36d1a4f5 Mon Sep 17 00:00:00 2001 From: Marco Brandizi Date: Thu, 29 Aug 2019 11:17:29 +0100 Subject: [PATCH 2/5] Bugfixing change of test dir in aratiny. --- common/aratiny/README.md | 4 ++-- common/quickstart/runtime-helper.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/common/aratiny/README.md b/common/aratiny/README.md index 9e89b4b98..14db340b0 100644 --- a/common/aratiny/README.md +++ b/common/aratiny/README.md @@ -91,7 +91,7 @@ is at ## Using the `aratinty` project for Cypher-based semantic motif queries. The neo4j mode uses Cypher-based queries for finding paths between genes to other entities. The queries are -at [aratiny-ws/src/test/resources/knetminer-config/neo4j](aratiny-ws/src/test/resources/knetminer-config/neo4j). Any +in the [test folder](aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j). Any addition of .cypher files to this folder will be used by the `./run-ws-neo4j.sh` above to initially scan the test data and find the paths specified by the queries. @@ -103,7 +103,7 @@ UI). ### Rules for valid semantic motif queries -Let's look at [an example](aratiny-ws/src/test/resources/knetminer-config/neo4j/simple-protein-publication.cypher): +Let's look at [an example](aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j/simple-protein-publication.cypher): ```sql MATCH path = diff --git a/common/quickstart/runtime-helper.sh b/common/quickstart/runtime-helper.sh index 74ac0865b..2f8d7a6df 100755 --- a/common/quickstart/runtime-helper.sh +++ b/common/quickstart/runtime-helper.sh @@ -172,7 +172,7 @@ cp target/knetminer-aratiny.war "$knet_tomcat_home/webapps/client.war" # --- And eventually run the server, which will have the ws.war (from the Docker build), the new client .war and the server config. #  -if [ "$is_deploy_only" != '' ]; then +if [ "$is_deploy_only" != '' ]; then echo -e "\n\n\tFiles deployed at '$knet_tomcat_home/webapps/', not running Tomcat because of --deploy-only\n" exit fi From d5fed36696dfa2b6cdfa00ce429426323767587b Mon Sep 17 00:00:00 2001 From: Marco Brandizi Date: Thu, 29 Aug 2019 11:29:51 +0100 Subject: [PATCH 3/5] Bugfixing change of test dir in aratiny, again. --- common/aratiny/README.md | 4 ++-- common/quickstart/runtime-helper.sh | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/common/aratiny/README.md b/common/aratiny/README.md index 14db340b0..11933c579 100644 --- a/common/aratiny/README.md +++ b/common/aratiny/README.md @@ -91,7 +91,7 @@ is at ## Using the `aratinty` project for Cypher-based semantic motif queries. The neo4j mode uses Cypher-based queries for finding paths between genes to other entities. The queries are -in the [test folder](aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j). Any +in the [test folder](aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j). Any addition of .cypher files to this folder will be used by the `./run-ws-neo4j.sh` above to initially scan the test data and find the paths specified by the queries. @@ -103,7 +103,7 @@ UI). ### Rules for valid semantic motif queries -Let's look at [an example](aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j/simple-protein-publication.cypher): +Let's look at [an example](aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j/simple-protein-publication.cypher): ```sql MATCH path = diff --git a/common/quickstart/runtime-helper.sh b/common/quickstart/runtime-helper.sh index 2f8d7a6df..8b834a1c6 100755 --- a/common/quickstart/runtime-helper.sh +++ b/common/quickstart/runtime-helper.sh @@ -112,10 +112,10 @@ rm -Rf /tmp/aratiny-ws common/aratiny/aratiny-ws/target cp -Rf common/aratiny/aratiny-ws /tmp # We don't need the test queries used for aratiny, let's remove them from the build location -rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config/neo4j/*.cypher +rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j/*.cypher # And then copy the dataset-specific config to the build place (in /tmp) -cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-dataset/knetminer-config +cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-dataset/config # Eventually, go to the build place and do mvn test-compile. This creates interpolated config files (ie, # all the placeholders are instantiated with the values in maven settings or in ancestor POMS). @@ -125,7 +125,7 @@ cd /tmp/aratiny-ws mvn $MAVEN_ARGS --settings "$knet_dataset_dir/config/actual-maven-settings.xml" clean test-compile # End eventually, deploy the instantiated config files -cp -Rf target/test-classes/knetminer-dataset/knetminer-config/* "$knet_dataset_dir/config" +cp -Rf target/test-classes/knetminer-dataset/config/* "$knet_dataset_dir/config" From b97a159b89b80963f71dbabd14a6a6b33494256e Mon Sep 17 00:00:00 2001 From: root Date: Thu, 29 Aug 2019 12:07:54 +0100 Subject: [PATCH 4/5] Fixing cleanup-volume.sh --- common/quickstart/cleanup-volume.sh | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/common/quickstart/cleanup-volume.sh b/common/quickstart/cleanup-volume.sh index 10a7bc978..22dc846f6 100755 --- a/common/quickstart/cleanup-volume.sh +++ b/common/quickstart/cleanup-volume.sh @@ -34,8 +34,13 @@ cd "$dataset_dir" cd config rm -Rf * -echo -e "\tCleaning config" +echo -e "\tCleaning data" cd ../data rm -Rf *.tab index map* +echo -e "\tCleaning client-src" +cd .. +rm -Rf client-src + +echo -e "\t" echo -e "\n\tThe end\n" From 0e37b43c74aa71f5a127ae454f43420c98073b45 Mon Sep 17 00:00:00 2001 From: Keywan Hassani-Pak Date: Thu, 29 Aug 2019 15:55:09 +0100 Subject: [PATCH 5/5] Fixed Lucene accession search issue #345 The Lucene field is called ConceptAccession_DSID --- .../knetminer/datasource/ondexlocal/OndexServiceProvider.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java b/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java index 49d7eeedd..b6620478b 100644 --- a/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java +++ b/common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java @@ -698,7 +698,7 @@ public HashMap searchLucene(String keywords, Collection