From 98143606bf32a15752144d2e0b6af54f91bf3349 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Fri, 1 Mar 2024 10:23:33 +0100 Subject: [PATCH 1/4] Dockerise and move scripts to project root Move scripts out of java jar Fix tests diff by removing absolut path It seems like currently report has been generated inside from container. But the test should work when run from any dev machine Add Dockerfile Include scripts into jar for backward compatibility Remove redundant gitignore for the jar file Use maven:3-eclipse-temurin-2 as jar build image instead Skip tests while building jar file for Dockerfile Install python on java docker image instead of otherwise python is more straightforward to install than java --- .gitignore | 11 +++ Dockerfile | 45 ++++++++++ README.md | 87 +++++++++++++++++++ application.properties.example | 5 ++ pom.xml | 11 +++ .../scripts => scripts}/addCaseList.pl | 0 .../scripts => scripts}/all-breast-su2c.sh | 0 .../all-coadread-public.sh | 0 .../scripts => scripts}/all-gbm-public.sh | 0 .../scripts => scripts}/all-lusc-public.sh | 0 .../scripts => scripts}/all-ovarian-public.sh | 0 .../scripts => scripts}/all-ovarian-su2c.sh | 0 .../scripts => scripts}/all-prostate-broad.sh | 0 .../scripts => scripts}/all-prostate-mich.sh | 0 .../scripts => scripts}/all-prostate-mskcc.sh | 0 .../scripts => scripts}/all-prostate-su2c.sh | 0 .../scripts => scripts}/all-prostate-tcga.sh | 0 .../resources/scripts => scripts}/all-su2c.sh | 0 .../scripts => scripts}/all-ucec-su2c.sh | 0 .../calculateCoExpression.pl | 0 .../calculateMutationFrequencies.py | 0 .../compareDirectAndBulkDBMSload.pl | 0 .../convertCosmicVcfToMaf.pl | 0 .../convertExpressionZscores.pl | 0 .../scripts => scripts}/convertGeneIds.pl | 0 .../scripts => scripts}/convertGeneSymbols.pl | 0 .../scripts => scripts}/convertSvsImages.pl | 0 .../scripts => scripts}/cutInvalidCases.pl | 0 .../scripts => scripts}/deleteAllCaseLists.pl | 0 .../downloadChromosomeSizes.py | 0 .../scripts => scripts}/dumpPortalInfo.pl | 0 .../main/resources/scripts => scripts}/env.pl | 14 +-- .../main/resources/scripts => scripts}/env.sh | 0 .../scripts => scripts}/envSimple.pl | 14 +-- .../scripts => scripts}/exportProfile.pl | 0 .../scripts => scripts}/fetchBCRDataDict.sh | 0 .../scripts => scripts}/filterCases.pl | 0 .../scripts => scripts}/filterCases.sh | 0 .../flagStudyForProductionPortalDeployment.py | 0 .../generateMutationData.pl | 0 .../scripts => scripts}/hot-deploy.sh | 0 .../scripts => scripts}/hotDeploy.py | 0 .../import-portal-users.sh | 0 .../import-prad-su2c-caises-xml.sh | 0 .../scripts => scripts}/importAccessRights.pl | 0 .../scripts => scripts}/importCancerStudy.pl | 0 .../scripts => scripts}/importCaseList.pl | 0 .../scripts => scripts}/importCaseListData.pl | 0 .../scripts => scripts}/importClinicalData.pl | 0 .../importCopyNumberSegmentData.pl | 0 .../scripts => scripts}/importCosmicData.pl | 0 .../scripts => scripts}/importDrugData.pl | 0 .../scripts => scripts}/importGenePanel.pl | 0 .../scripts => scripts}/importGenes.pl | 0 .../scripts => scripts}/importGenesetData.pl | 0 .../importGenesetHierarchy.pl | 0 .../scripts => scripts}/importGistic.pl | 0 .../scripts => scripts}/importHprd.pl | 0 .../scripts => scripts}/importMicroRNAIDs.pl | 0 .../scripts => scripts}/importMicroRna.pl | 0 .../scripts => scripts}/importMutSig.pl | 0 .../scripts => scripts}/importPiHelperData.pl | 0 .../scripts => scripts}/importProfileData.pl | 0 .../importReferenceGenome.pl | 0 .../scripts => scripts}/importSif.pl | 0 .../scripts => scripts}/importTimelineData.pl | 0 .../importTypesOfCancer.pl | 0 .../scripts => scripts}/importUsers.py | 0 .../scripts => scripts}/importer/__init__.py | 0 .../importer/allowed_data_types.txt | 0 .../importer/cbioportalImporter.py | 9 +- .../importer/cbioportal_common.py | 4 +- .../importer/chromosome_sizes.json | 0 .../importer/data_cna_pd_annotations.txt | 0 .../importer/importOncokbDiscreteCNA.py | 0 .../importer/importOncokbMutation.py | 0 .../importer/libImportOncokb.py | 0 .../importer/metaImport.py | 0 .../importer/updateOncokbAnnotations.py | 0 .../importer/validateData.py | 2 +- .../importer/validateStudies.py | 0 .../validation_report_template.html.jinja | 0 .../resources/scripts => scripts}/init.sh | 0 .../scripts => scripts}/loadNetwork.sh | 0 .../scripts => scripts}/loadSampleData.sh | 0 .../massagePortalDataForCancerStudies.pl | 0 .../scripts => scripts}/migrate_db.py | 0 .../scripts => scripts}/mini_load_ova.sh | 0 .../ovarian/preprocess-all.py | 0 .../ovarian/preprocess-mrna.py | 0 .../ovarian/preprocess-rae.py | 0 .../ovarian/removeNullMutations.py | 0 .../scripts => scripts}/portal-client.py | 0 .../prepareBasicPiHelperData.sh | 0 .../scripts => scripts}/prepareCosmicData.sh | 0 .../scripts => scripts}/prepareGeneData.sh | 0 .../preparePathwayCommonsData.sh | 0 .../scripts => scripts}/prepareSangerCGC.sh | 0 .../processPathwayCommonsInteractions.py | 0 .../resources/scripts => scripts}/reload.sh | 0 .../resources/scripts => scripts}/resetDb.pl | 0 .../scripts => scripts}/showAllCaseLists.pl | 0 .../resources/scripts => scripts}/statDb.pl | 0 .../scripts => scripts}/updateGenePanel.pl | 0 .../scripts => scripts}/updateMetaData.pl | 0 .../scripts => scripts}/verifyGeneSets.pl | 0 test_scripts.sh | 1 + 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tests}/test_data/test.xml | 0 .../unit_tests_validate_data.py | 0 466 files changed, 186 insertions(+), 23 deletions(-) create mode 100644 Dockerfile create mode 100644 application.properties.example rename {src/main/resources/scripts => scripts}/addCaseList.pl (100%) rename {src/main/resources/scripts => scripts}/all-breast-su2c.sh (100%) rename {src/main/resources/scripts => scripts}/all-coadread-public.sh (100%) rename {src/main/resources/scripts => scripts}/all-gbm-public.sh (100%) rename {src/main/resources/scripts => scripts}/all-lusc-public.sh (100%) rename {src/main/resources/scripts => scripts}/all-ovarian-public.sh (100%) rename {src/main/resources/scripts => scripts}/all-ovarian-su2c.sh (100%) rename {src/main/resources/scripts => scripts}/all-prostate-broad.sh (100%) rename {src/main/resources/scripts => scripts}/all-prostate-mich.sh (100%) rename {src/main/resources/scripts => scripts}/all-prostate-mskcc.sh (100%) rename {src/main/resources/scripts => 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{src/test/scripts => tests}/test_data/study_wr_clin/data_patients.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/data_samples.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/meta_expression_median.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/meta_patients.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/meta_samples.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/meta_study.txt (100%) rename {src/test/scripts => tests}/test_data/study_wr_clin/result_report.html (100%) rename {src/test/scripts => tests}/test_data/test.xml (100%) rename {src/test/scripts => tests}/unit_tests_validate_data.py (100%) diff --git a/.gitignore b/.gitignore index 9d51d31c..4aadcfa6 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,14 @@ replay_pid* .idea /dependency-reduced-pom.xml + +# python +__pycache__/ +*.pyc +.venv/ + +# test html reports +*.html~ + +# app properties that contains credentials +/application.properties diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..8e850d68 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,45 @@ +FROM maven:3-eclipse-temurin-21 as jar_builder + +# Set the working directory in the Maven image +WORKDIR /app + +# Copy the java source files and the pom.xml file into the image +COPY src ./src +COPY pom.xml . + +# Build the application +RUN mvn clean package -DskipTests + +FROM maven:3-eclipse-temurin-21 + +# download system dependencies first to take advantage of docker caching +RUN apt-get update; apt-get install -y --no-install-recommends \ + build-essential \ + default-mysql-client \ + default-libmysqlclient-dev \ + python3 \ + python3-setuptools \ + python3-dev \ + python3-pip \ + unzip \ + perl \ + && rm -rf /var/lib/apt/lists/* \ + && pip3 install wheel + +# Install any needed packages specified in requirements.txt +COPY requirements.txt ./ +RUN pip install --no-cache-dir -r requirements.txt + +RUN ln -s $(which python3) /usr/local/bin/python || true + +COPY --from=jar_builder /app/core-*.jar / +COPY scripts/ scripts/ +RUN chmod -R a+x /scripts/ + +# Set the working directory in the container +WORKDIR /scripts/ + +ENV PORTAL_HOME=/ + +# This file is empty. It has to be overriden by bind mounting the actual application.properties +RUN touch /application.properties diff --git a/README.md b/README.md index 1a04e860..60433f9c 100644 --- a/README.md +++ b/README.md @@ -44,3 +44,90 @@ Use Maven to run the integration tests. Ensure you are in the root directory of ``` mvn integration-test ``` + +## Development + +### Prerequisites +To contribute to `cbioportal-core`, ensure you have the following tools installed: + +- Python 3: Required for study validation and orchestration scripts. These scripts utilize the underlying loader jar. +- Perl: Specify the version required based on script compatibility. Necessary for data loading scripts interfacing with lookup tables. +- JDK 21: Essential for developing the data loader component. +- Maven 3.8.3: Used to compile and test the loader jar. Review this [issue](https://github.com/cBioPortal/cbioportal-core/issues/15) before starting. + +### Setup + +1. Create a Python virtual environment (first-time setup): +```bash +python -m venv .venv +``` + +2. Activate the virtual environment: +```bash +source .venv/bin/activate +``` + +3. Install required Python dependencies (first-time setup or when dependencies have changed): +```bash +pip install -r requirements.txt +``` + +### Building and Testing + +After you are done with the setup, you can build and test the project. + +1. Execute tests through the provided script: +```bash +source test_scripts.sh +``` + +2. Build the loader jar using Maven (includes testing): +```bash +mvn clean package +``` +*Note:* The Maven configuration is set to place the jar in the project's root directory to ensure consistent paths in both development and production. + +### Configuring Application Properties + +The loader requires specific properties set to establish a connection to the database. These properties should be defined in the application.properties file within your project. + +#### Creating the Properties File + +1. Begin by creating your application.properties file. This can be done by copying from an example or template provided in the project: +```bash +cp application.properties.example application.properties +``` + +2. Open application.properties in your preferred text editor and modify the properties to match your database configuration and other environment-specific settings. + +#### Setting the PORTAL_HOME Environment Variable + +The PORTAL_HOME environment variable should be set to the directory containing your application.properties file, typically the root of your project: +``` +export PORTAL_HOME=$(pwd) +``` +Ensure this command is run in the root directory of your project, where the application.properties file is located. This setup is crucial for the loader to correctly access the required properties. + +#### maven.properties +TODO: Document role of `maven.properties` file. + +### Script Execution with Loader Jar + +To run scripts that require the loader jar, ensure the jar file is in the project root. +The script will search for `core-*.jar` in the root of the project: +```bash +python scripts/importer/metaImport.py -s tests/test_data/study_es_0 -p tests/test_data/api_json_unit_tests -o +``` + +## Running in docker + +Build docker image with: +```bash +docker build -t cbioportal-core . +``` + +Example of how to start the loading: +```bash +docker run -it -v $(pwd)/data/:/data/ -v $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -s /data/study_es_0 -p /data/api_json -o +``` + diff --git a/application.properties.example b/application.properties.example new file mode 100644 index 00000000..3cd29cdc --- /dev/null +++ b/application.properties.example @@ -0,0 +1,5 @@ +spring.datasource.url=jdbc:mysql://localhost:3306/cbioportal?useSSL=false +spring.datasource.username=cbio +spring.datasource.password=P@ssword1 +spring.datasource.driver-class-name=com.mysql.jdbc.Driver +spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect diff --git a/pom.xml b/pom.xml index 99339126..c71f78a2 100644 --- a/pom.xml +++ b/pom.xml @@ -236,7 +236,11 @@ ${project.basedir} + + + requirements.txt + scripts/ @@ -323,6 +327,13 @@ + + org.apache.maven.plugins + maven-jar-plugin + + ${project.basedir} + + diff --git a/src/main/resources/scripts/addCaseList.pl b/scripts/addCaseList.pl similarity index 100% rename from src/main/resources/scripts/addCaseList.pl rename to scripts/addCaseList.pl diff --git a/src/main/resources/scripts/all-breast-su2c.sh b/scripts/all-breast-su2c.sh similarity index 100% rename from src/main/resources/scripts/all-breast-su2c.sh rename to scripts/all-breast-su2c.sh diff --git a/src/main/resources/scripts/all-coadread-public.sh b/scripts/all-coadread-public.sh similarity index 100% rename from src/main/resources/scripts/all-coadread-public.sh rename to scripts/all-coadread-public.sh diff --git a/src/main/resources/scripts/all-gbm-public.sh b/scripts/all-gbm-public.sh similarity index 100% rename from src/main/resources/scripts/all-gbm-public.sh rename to scripts/all-gbm-public.sh diff --git a/src/main/resources/scripts/all-lusc-public.sh b/scripts/all-lusc-public.sh similarity index 100% rename from src/main/resources/scripts/all-lusc-public.sh rename to scripts/all-lusc-public.sh diff --git a/src/main/resources/scripts/all-ovarian-public.sh b/scripts/all-ovarian-public.sh similarity index 100% rename from src/main/resources/scripts/all-ovarian-public.sh rename to scripts/all-ovarian-public.sh diff --git a/src/main/resources/scripts/all-ovarian-su2c.sh b/scripts/all-ovarian-su2c.sh similarity index 100% rename from src/main/resources/scripts/all-ovarian-su2c.sh rename to scripts/all-ovarian-su2c.sh diff --git a/src/main/resources/scripts/all-prostate-broad.sh b/scripts/all-prostate-broad.sh similarity index 100% rename from src/main/resources/scripts/all-prostate-broad.sh rename to scripts/all-prostate-broad.sh diff --git a/src/main/resources/scripts/all-prostate-mich.sh b/scripts/all-prostate-mich.sh similarity index 100% rename from src/main/resources/scripts/all-prostate-mich.sh rename to scripts/all-prostate-mich.sh diff --git a/src/main/resources/scripts/all-prostate-mskcc.sh b/scripts/all-prostate-mskcc.sh similarity index 100% rename from src/main/resources/scripts/all-prostate-mskcc.sh rename to scripts/all-prostate-mskcc.sh diff --git a/src/main/resources/scripts/all-prostate-su2c.sh b/scripts/all-prostate-su2c.sh similarity index 100% rename from src/main/resources/scripts/all-prostate-su2c.sh rename to scripts/all-prostate-su2c.sh diff --git a/src/main/resources/scripts/all-prostate-tcga.sh b/scripts/all-prostate-tcga.sh similarity index 100% rename from src/main/resources/scripts/all-prostate-tcga.sh rename to scripts/all-prostate-tcga.sh diff --git a/src/main/resources/scripts/all-su2c.sh b/scripts/all-su2c.sh similarity index 100% rename from src/main/resources/scripts/all-su2c.sh rename to scripts/all-su2c.sh diff --git a/src/main/resources/scripts/all-ucec-su2c.sh b/scripts/all-ucec-su2c.sh similarity index 100% rename from src/main/resources/scripts/all-ucec-su2c.sh rename to scripts/all-ucec-su2c.sh diff --git a/src/main/resources/scripts/calculateCoExpression.pl b/scripts/calculateCoExpression.pl similarity index 100% rename from src/main/resources/scripts/calculateCoExpression.pl rename to scripts/calculateCoExpression.pl diff --git a/src/main/resources/scripts/calculateMutationFrequencies.py b/scripts/calculateMutationFrequencies.py similarity index 100% rename from src/main/resources/scripts/calculateMutationFrequencies.py rename to scripts/calculateMutationFrequencies.py diff --git a/src/main/resources/scripts/compareDirectAndBulkDBMSload.pl b/scripts/compareDirectAndBulkDBMSload.pl similarity index 100% rename from src/main/resources/scripts/compareDirectAndBulkDBMSload.pl rename to scripts/compareDirectAndBulkDBMSload.pl diff --git a/src/main/resources/scripts/convertCosmicVcfToMaf.pl b/scripts/convertCosmicVcfToMaf.pl similarity index 100% rename from src/main/resources/scripts/convertCosmicVcfToMaf.pl rename to scripts/convertCosmicVcfToMaf.pl diff --git a/src/main/resources/scripts/convertExpressionZscores.pl b/scripts/convertExpressionZscores.pl similarity index 100% rename from src/main/resources/scripts/convertExpressionZscores.pl rename to scripts/convertExpressionZscores.pl diff --git a/src/main/resources/scripts/convertGeneIds.pl b/scripts/convertGeneIds.pl similarity index 100% rename from src/main/resources/scripts/convertGeneIds.pl rename to scripts/convertGeneIds.pl diff --git a/src/main/resources/scripts/convertGeneSymbols.pl b/scripts/convertGeneSymbols.pl similarity index 100% rename from src/main/resources/scripts/convertGeneSymbols.pl rename to scripts/convertGeneSymbols.pl diff --git a/src/main/resources/scripts/convertSvsImages.pl b/scripts/convertSvsImages.pl similarity index 100% rename from src/main/resources/scripts/convertSvsImages.pl rename to scripts/convertSvsImages.pl diff --git a/src/main/resources/scripts/cutInvalidCases.pl b/scripts/cutInvalidCases.pl similarity index 100% rename from src/main/resources/scripts/cutInvalidCases.pl rename to scripts/cutInvalidCases.pl diff --git a/src/main/resources/scripts/deleteAllCaseLists.pl b/scripts/deleteAllCaseLists.pl similarity index 100% rename from src/main/resources/scripts/deleteAllCaseLists.pl rename to scripts/deleteAllCaseLists.pl diff --git a/src/main/resources/scripts/downloadChromosomeSizes.py b/scripts/downloadChromosomeSizes.py similarity index 100% rename from src/main/resources/scripts/downloadChromosomeSizes.py rename to scripts/downloadChromosomeSizes.py diff --git a/src/main/resources/scripts/dumpPortalInfo.pl b/scripts/dumpPortalInfo.pl similarity index 100% rename from src/main/resources/scripts/dumpPortalInfo.pl rename to scripts/dumpPortalInfo.pl diff --git a/src/main/resources/scripts/env.pl b/scripts/env.pl similarity index 74% rename from src/main/resources/scripts/env.pl rename to scripts/env.pl index c50da9d3..6edff025 100755 --- a/src/main/resources/scripts/env.pl +++ b/scripts/env.pl @@ -39,18 +39,18 @@ } # Set up Classpath to use the scripts jar -sub locate_src_root { +sub locate_root { # isolate the directory this code file is in my ($volume, $script_dir, undef) = File::Spec->splitpath(__FILE__); - # go up from cbioportal/core/src/main/scripts/ to cbioportal/ - my $src_root_dir = File::Spec->catdir($script_dir, (File::Spec->updir()) x 4); + # go up one level + my $root_dir = File::Spec->catdir($script_dir, File::Spec->updir()); # reassamble the path and resolve updirs (/../) - return abs_path(File::Spec->catpath($volume, $src_root_dir)); + return abs_path(File::Spec->catpath($volume, $root_dir)); } -$src_root = locate_src_root(); -@jar_files = glob("$src_root/scripts/target/scripts-*.jar"); +$root_dir = locate_root(); +@jar_files = glob("$root_dir/core-*.jar"); if (scalar @jar_files != 1) { - die "Expected to find 1 scripts-*.jar, but found: " . scalar @jar_files; + die "Expected to find 1 core-*.jar, but found: " . scalar @jar_files; } $cp = pop @jar_files; diff --git a/src/main/resources/scripts/env.sh b/scripts/env.sh similarity index 100% rename from src/main/resources/scripts/env.sh rename to scripts/env.sh diff --git a/src/main/resources/scripts/envSimple.pl b/scripts/envSimple.pl similarity index 72% rename from src/main/resources/scripts/envSimple.pl rename to scripts/envSimple.pl index 92442b8a..f09399e1 100755 --- a/src/main/resources/scripts/envSimple.pl +++ b/scripts/envSimple.pl @@ -34,18 +34,18 @@ } # Set up Classpath to use the scripts jar -sub locate_src_root { +sub locate_root { # isolate the directory this code file is in my ($volume, $script_dir, undef) = File::Spec->splitpath(__FILE__); - # go up from cbioportal/core/src/main/scripts/ to cbioportal/ - my $src_root_dir = File::Spec->catdir($script_dir, (File::Spec->updir()) x 1); + # go up one level + my $root_dir = File::Spec->catdir($script_dir, File::Spec->updir()); # reassamble the path and resolve updirs (/../) - return abs_path(File::Spec->catpath($volume, $src_root_dir)); + return abs_path(File::Spec->catpath($volume, $root_dir)); } -$src_root = locate_src_root(); -@jar_files = glob("$src_root/core-*.jar"); +$root_dir = locate_root(); +@jar_files = glob("$root_dir/core-*.jar"); if (scalar @jar_files != 1) { - die "Expected to find 1 scripts-*.jar, but found: " . scalar @jar_files; + die "Expected to find 1 core-*.jar, but found: " . scalar @jar_files; } $cp = pop @jar_files; diff --git a/src/main/resources/scripts/exportProfile.pl b/scripts/exportProfile.pl similarity index 100% rename from src/main/resources/scripts/exportProfile.pl rename to scripts/exportProfile.pl diff --git a/src/main/resources/scripts/fetchBCRDataDict.sh b/scripts/fetchBCRDataDict.sh similarity index 100% rename from src/main/resources/scripts/fetchBCRDataDict.sh rename to scripts/fetchBCRDataDict.sh diff --git a/src/main/resources/scripts/filterCases.pl b/scripts/filterCases.pl similarity index 100% rename from src/main/resources/scripts/filterCases.pl rename to scripts/filterCases.pl diff --git a/src/main/resources/scripts/filterCases.sh b/scripts/filterCases.sh similarity index 100% rename from src/main/resources/scripts/filterCases.sh rename to scripts/filterCases.sh diff --git a/src/main/resources/scripts/flagStudyForProductionPortalDeployment.py b/scripts/flagStudyForProductionPortalDeployment.py similarity index 100% rename from src/main/resources/scripts/flagStudyForProductionPortalDeployment.py rename to scripts/flagStudyForProductionPortalDeployment.py diff --git a/src/main/resources/scripts/generateMutationData.pl b/scripts/generateMutationData.pl similarity index 100% rename from src/main/resources/scripts/generateMutationData.pl rename to scripts/generateMutationData.pl diff --git a/src/main/resources/scripts/hot-deploy.sh b/scripts/hot-deploy.sh similarity index 100% rename from src/main/resources/scripts/hot-deploy.sh rename to scripts/hot-deploy.sh diff --git a/src/main/resources/scripts/hotDeploy.py b/scripts/hotDeploy.py similarity index 100% rename from src/main/resources/scripts/hotDeploy.py rename to scripts/hotDeploy.py diff --git a/src/main/resources/scripts/import-portal-users.sh b/scripts/import-portal-users.sh similarity index 100% rename from src/main/resources/scripts/import-portal-users.sh rename to scripts/import-portal-users.sh diff --git a/src/main/resources/scripts/import-prad-su2c-caises-xml.sh b/scripts/import-prad-su2c-caises-xml.sh similarity index 100% rename from src/main/resources/scripts/import-prad-su2c-caises-xml.sh rename to scripts/import-prad-su2c-caises-xml.sh diff --git a/src/main/resources/scripts/importAccessRights.pl b/scripts/importAccessRights.pl similarity index 100% rename from src/main/resources/scripts/importAccessRights.pl rename to scripts/importAccessRights.pl diff --git a/src/main/resources/scripts/importCancerStudy.pl b/scripts/importCancerStudy.pl similarity index 100% rename from src/main/resources/scripts/importCancerStudy.pl rename to scripts/importCancerStudy.pl diff --git a/src/main/resources/scripts/importCaseList.pl b/scripts/importCaseList.pl similarity index 100% rename from src/main/resources/scripts/importCaseList.pl rename to scripts/importCaseList.pl diff --git a/src/main/resources/scripts/importCaseListData.pl b/scripts/importCaseListData.pl similarity index 100% rename from src/main/resources/scripts/importCaseListData.pl rename to scripts/importCaseListData.pl diff --git a/src/main/resources/scripts/importClinicalData.pl b/scripts/importClinicalData.pl similarity index 100% rename from src/main/resources/scripts/importClinicalData.pl rename to scripts/importClinicalData.pl diff --git a/src/main/resources/scripts/importCopyNumberSegmentData.pl b/scripts/importCopyNumberSegmentData.pl similarity index 100% rename from src/main/resources/scripts/importCopyNumberSegmentData.pl rename to scripts/importCopyNumberSegmentData.pl diff --git a/src/main/resources/scripts/importCosmicData.pl b/scripts/importCosmicData.pl similarity index 100% rename from src/main/resources/scripts/importCosmicData.pl rename to scripts/importCosmicData.pl diff --git a/src/main/resources/scripts/importDrugData.pl b/scripts/importDrugData.pl similarity index 100% rename from src/main/resources/scripts/importDrugData.pl rename to scripts/importDrugData.pl diff --git a/src/main/resources/scripts/importGenePanel.pl b/scripts/importGenePanel.pl similarity index 100% rename from src/main/resources/scripts/importGenePanel.pl rename to scripts/importGenePanel.pl diff --git a/src/main/resources/scripts/importGenes.pl b/scripts/importGenes.pl similarity index 100% rename from src/main/resources/scripts/importGenes.pl rename to scripts/importGenes.pl diff --git a/src/main/resources/scripts/importGenesetData.pl b/scripts/importGenesetData.pl similarity index 100% rename from src/main/resources/scripts/importGenesetData.pl rename to scripts/importGenesetData.pl diff --git a/src/main/resources/scripts/importGenesetHierarchy.pl b/scripts/importGenesetHierarchy.pl similarity index 100% rename from src/main/resources/scripts/importGenesetHierarchy.pl rename to scripts/importGenesetHierarchy.pl diff --git a/src/main/resources/scripts/importGistic.pl b/scripts/importGistic.pl similarity index 100% rename from src/main/resources/scripts/importGistic.pl rename to scripts/importGistic.pl diff --git a/src/main/resources/scripts/importHprd.pl b/scripts/importHprd.pl similarity index 100% rename from src/main/resources/scripts/importHprd.pl rename to scripts/importHprd.pl diff --git a/src/main/resources/scripts/importMicroRNAIDs.pl b/scripts/importMicroRNAIDs.pl similarity index 100% rename from src/main/resources/scripts/importMicroRNAIDs.pl rename to scripts/importMicroRNAIDs.pl diff --git a/src/main/resources/scripts/importMicroRna.pl b/scripts/importMicroRna.pl similarity index 100% rename from src/main/resources/scripts/importMicroRna.pl rename to scripts/importMicroRna.pl diff --git a/src/main/resources/scripts/importMutSig.pl b/scripts/importMutSig.pl similarity index 100% rename from src/main/resources/scripts/importMutSig.pl rename to scripts/importMutSig.pl diff --git a/src/main/resources/scripts/importPiHelperData.pl b/scripts/importPiHelperData.pl similarity index 100% rename from src/main/resources/scripts/importPiHelperData.pl rename to scripts/importPiHelperData.pl diff --git a/src/main/resources/scripts/importProfileData.pl b/scripts/importProfileData.pl similarity index 100% rename from src/main/resources/scripts/importProfileData.pl rename to scripts/importProfileData.pl diff --git a/src/main/resources/scripts/importReferenceGenome.pl b/scripts/importReferenceGenome.pl similarity index 100% rename from src/main/resources/scripts/importReferenceGenome.pl rename to scripts/importReferenceGenome.pl diff --git a/src/main/resources/scripts/importSif.pl b/scripts/importSif.pl similarity index 100% rename from src/main/resources/scripts/importSif.pl rename to scripts/importSif.pl diff --git a/src/main/resources/scripts/importTimelineData.pl b/scripts/importTimelineData.pl similarity index 100% rename from src/main/resources/scripts/importTimelineData.pl rename to scripts/importTimelineData.pl diff --git a/src/main/resources/scripts/importTypesOfCancer.pl b/scripts/importTypesOfCancer.pl similarity index 100% rename from src/main/resources/scripts/importTypesOfCancer.pl rename to scripts/importTypesOfCancer.pl diff --git a/src/main/resources/scripts/importUsers.py b/scripts/importUsers.py similarity index 100% rename from src/main/resources/scripts/importUsers.py rename to scripts/importUsers.py diff --git a/src/main/resources/scripts/importer/__init__.py b/scripts/importer/__init__.py similarity index 100% rename from src/main/resources/scripts/importer/__init__.py rename to scripts/importer/__init__.py diff --git a/src/main/resources/scripts/importer/allowed_data_types.txt b/scripts/importer/allowed_data_types.txt similarity index 100% rename from src/main/resources/scripts/importer/allowed_data_types.txt rename to scripts/importer/allowed_data_types.txt diff --git a/src/main/resources/scripts/importer/cbioportalImporter.py b/scripts/importer/cbioportalImporter.py similarity index 99% rename from src/main/resources/scripts/importer/cbioportalImporter.py rename to scripts/importer/cbioportalImporter.py index d935e2db..97073ff6 100755 --- a/src/main/resources/scripts/importer/cbioportalImporter.py +++ b/scripts/importer/cbioportalImporter.py @@ -501,10 +501,11 @@ def locate_jar(): """ # get the directory name of the currently running script, # resolving any symlinks - script_dir = Path(__file__).resolve().parent - # go up from core/scripts/importer/ to core/ - src_root = script_dir.parent.parent - jars = list((src_root ).glob('core-*.jar')) + this_file = Path(__file__).resolve() + importer_dir = this_file.parent + scripts_dir = importer_dir.parent + root_dir = scripts_dir.parent + jars = list((root_dir).glob('core-*.jar')) if len(jars) != 1: raise FileNotFoundError( 'Expected to find 1 scripts-*.jar, but found ' + str(len(jars))) diff --git a/src/main/resources/scripts/importer/cbioportal_common.py b/scripts/importer/cbioportal_common.py similarity index 99% rename from src/main/resources/scripts/importer/cbioportal_common.py rename to scripts/importer/cbioportal_common.py index 69275a39..35f71d34 100644 --- a/src/main/resources/scripts/importer/cbioportal_common.py +++ b/scripts/importer/cbioportal_common.py @@ -997,7 +997,9 @@ def run_java(*args): java_command = os.path.join(java_home, 'bin', 'java') else: java_command = 'java' - process = Popen([java_command] + list(args), stdout=PIPE, stderr=STDOUT, + full_cmd = [java_command] + list(args) + print(">", " ".join(full_cmd)) + process = Popen(full_cmd, stdout=PIPE, stderr=STDOUT, universal_newlines=True) ret = [] while process.poll() is None: diff --git a/src/main/resources/scripts/importer/chromosome_sizes.json b/scripts/importer/chromosome_sizes.json similarity index 100% rename from src/main/resources/scripts/importer/chromosome_sizes.json rename to scripts/importer/chromosome_sizes.json diff --git a/src/main/resources/scripts/importer/data_cna_pd_annotations.txt b/scripts/importer/data_cna_pd_annotations.txt similarity index 100% rename from src/main/resources/scripts/importer/data_cna_pd_annotations.txt rename to scripts/importer/data_cna_pd_annotations.txt diff --git a/src/main/resources/scripts/importer/importOncokbDiscreteCNA.py b/scripts/importer/importOncokbDiscreteCNA.py similarity index 100% rename from src/main/resources/scripts/importer/importOncokbDiscreteCNA.py rename to scripts/importer/importOncokbDiscreteCNA.py diff --git a/src/main/resources/scripts/importer/importOncokbMutation.py b/scripts/importer/importOncokbMutation.py similarity index 100% rename from src/main/resources/scripts/importer/importOncokbMutation.py rename to scripts/importer/importOncokbMutation.py diff --git a/src/main/resources/scripts/importer/libImportOncokb.py b/scripts/importer/libImportOncokb.py similarity index 100% rename from src/main/resources/scripts/importer/libImportOncokb.py rename to scripts/importer/libImportOncokb.py diff --git a/src/main/resources/scripts/importer/metaImport.py b/scripts/importer/metaImport.py similarity index 100% rename from src/main/resources/scripts/importer/metaImport.py rename to scripts/importer/metaImport.py diff --git a/src/main/resources/scripts/importer/updateOncokbAnnotations.py b/scripts/importer/updateOncokbAnnotations.py similarity index 100% rename from src/main/resources/scripts/importer/updateOncokbAnnotations.py rename to scripts/importer/updateOncokbAnnotations.py diff --git a/src/main/resources/scripts/importer/validateData.py b/scripts/importer/validateData.py similarity index 99% rename from src/main/resources/scripts/importer/validateData.py rename to scripts/importer/validateData.py index 251814fa..1f473abb 100755 --- a/src/main/resources/scripts/importer/validateData.py +++ b/scripts/importer/validateData.py @@ -957,7 +957,7 @@ def load_chromosome_lengths(reference_genome, logger): 'downloadChromosomeSizes.py.') logger.debug("Retrieving chromosome lengths from '%s'", - chrom_size_file) + os.path.basename(chrom_size_file)) try: chrom_size_dict = chrom_sizes[reference_genome] diff --git a/src/main/resources/scripts/importer/validateStudies.py b/scripts/importer/validateStudies.py similarity index 100% rename from src/main/resources/scripts/importer/validateStudies.py rename to scripts/importer/validateStudies.py diff --git a/src/main/resources/scripts/importer/validation_report_template.html.jinja b/scripts/importer/validation_report_template.html.jinja similarity index 100% rename from src/main/resources/scripts/importer/validation_report_template.html.jinja rename to scripts/importer/validation_report_template.html.jinja diff --git a/src/main/resources/scripts/init.sh b/scripts/init.sh similarity index 100% rename from src/main/resources/scripts/init.sh rename to scripts/init.sh diff --git a/src/main/resources/scripts/loadNetwork.sh b/scripts/loadNetwork.sh similarity index 100% rename from src/main/resources/scripts/loadNetwork.sh rename to scripts/loadNetwork.sh diff --git a/src/main/resources/scripts/loadSampleData.sh b/scripts/loadSampleData.sh similarity index 100% rename from src/main/resources/scripts/loadSampleData.sh rename to scripts/loadSampleData.sh diff --git a/src/main/resources/scripts/massagePortalDataForCancerStudies.pl b/scripts/massagePortalDataForCancerStudies.pl similarity index 100% rename from src/main/resources/scripts/massagePortalDataForCancerStudies.pl rename to scripts/massagePortalDataForCancerStudies.pl diff --git a/src/main/resources/scripts/migrate_db.py b/scripts/migrate_db.py similarity index 100% rename from src/main/resources/scripts/migrate_db.py rename to scripts/migrate_db.py diff --git a/src/main/resources/scripts/mini_load_ova.sh b/scripts/mini_load_ova.sh similarity index 100% rename from src/main/resources/scripts/mini_load_ova.sh rename to scripts/mini_load_ova.sh diff --git a/src/main/resources/scripts/ovarian/preprocess-all.py b/scripts/ovarian/preprocess-all.py similarity index 100% rename from src/main/resources/scripts/ovarian/preprocess-all.py rename to scripts/ovarian/preprocess-all.py diff --git a/src/main/resources/scripts/ovarian/preprocess-mrna.py b/scripts/ovarian/preprocess-mrna.py similarity index 100% rename from src/main/resources/scripts/ovarian/preprocess-mrna.py rename to scripts/ovarian/preprocess-mrna.py diff --git a/src/main/resources/scripts/ovarian/preprocess-rae.py b/scripts/ovarian/preprocess-rae.py similarity index 100% rename from src/main/resources/scripts/ovarian/preprocess-rae.py rename to scripts/ovarian/preprocess-rae.py diff --git a/src/main/resources/scripts/ovarian/removeNullMutations.py b/scripts/ovarian/removeNullMutations.py similarity index 100% rename from src/main/resources/scripts/ovarian/removeNullMutations.py rename to scripts/ovarian/removeNullMutations.py diff --git a/src/main/resources/scripts/portal-client.py b/scripts/portal-client.py similarity index 100% rename from src/main/resources/scripts/portal-client.py rename to scripts/portal-client.py diff --git a/src/main/resources/scripts/prepareBasicPiHelperData.sh b/scripts/prepareBasicPiHelperData.sh similarity index 100% rename from src/main/resources/scripts/prepareBasicPiHelperData.sh rename to scripts/prepareBasicPiHelperData.sh diff --git a/src/main/resources/scripts/prepareCosmicData.sh b/scripts/prepareCosmicData.sh similarity index 100% rename from src/main/resources/scripts/prepareCosmicData.sh rename to scripts/prepareCosmicData.sh diff --git a/src/main/resources/scripts/prepareGeneData.sh b/scripts/prepareGeneData.sh similarity index 100% rename from src/main/resources/scripts/prepareGeneData.sh rename to scripts/prepareGeneData.sh diff --git a/src/main/resources/scripts/preparePathwayCommonsData.sh b/scripts/preparePathwayCommonsData.sh similarity index 100% rename from src/main/resources/scripts/preparePathwayCommonsData.sh rename to scripts/preparePathwayCommonsData.sh diff --git a/src/main/resources/scripts/prepareSangerCGC.sh b/scripts/prepareSangerCGC.sh similarity index 100% rename from src/main/resources/scripts/prepareSangerCGC.sh rename to scripts/prepareSangerCGC.sh diff --git a/src/main/resources/scripts/processPathwayCommonsInteractions.py b/scripts/processPathwayCommonsInteractions.py similarity index 100% rename from src/main/resources/scripts/processPathwayCommonsInteractions.py rename to scripts/processPathwayCommonsInteractions.py diff --git a/src/main/resources/scripts/reload.sh b/scripts/reload.sh similarity index 100% rename from src/main/resources/scripts/reload.sh rename to scripts/reload.sh diff --git a/src/main/resources/scripts/resetDb.pl b/scripts/resetDb.pl similarity index 100% rename from src/main/resources/scripts/resetDb.pl rename to scripts/resetDb.pl diff --git a/src/main/resources/scripts/showAllCaseLists.pl b/scripts/showAllCaseLists.pl similarity index 100% rename from src/main/resources/scripts/showAllCaseLists.pl rename to scripts/showAllCaseLists.pl diff --git a/src/main/resources/scripts/statDb.pl b/scripts/statDb.pl similarity index 100% rename from src/main/resources/scripts/statDb.pl rename to scripts/statDb.pl diff --git a/src/main/resources/scripts/updateGenePanel.pl b/scripts/updateGenePanel.pl similarity index 100% rename from src/main/resources/scripts/updateGenePanel.pl rename to scripts/updateGenePanel.pl diff --git a/src/main/resources/scripts/updateMetaData.pl b/scripts/updateMetaData.pl similarity index 100% rename from src/main/resources/scripts/updateMetaData.pl rename to scripts/updateMetaData.pl diff --git a/src/main/resources/scripts/verifyGeneSets.pl b/scripts/verifyGeneSets.pl similarity index 100% rename from src/main/resources/scripts/verifyGeneSets.pl rename to scripts/verifyGeneSets.pl diff --git a/test_scripts.sh b/test_scripts.sh new file mode 100644 index 00000000..807f536e --- /dev/null +++ b/test_scripts.sh @@ -0,0 +1 @@ +pushd tests/; PYTHONPATH=../scripts:$PYTHONPATH python -m unittest *.py; popd diff --git a/src/test/scripts/system_tests_validate_data.py b/tests/system_tests_validate_data.py similarity index 100% rename from src/test/scripts/system_tests_validate_data.py rename to tests/system_tests_validate_data.py diff --git a/src/test/scripts/system_tests_validate_studies.py b/tests/system_tests_validate_studies.py similarity index 100% rename from src/test/scripts/system_tests_validate_studies.py rename to tests/system_tests_validate_studies.py diff --git a/src/test/scripts/test_data/api_json_system_tests/cancer-types.json b/tests/test_data/api_json_system_tests/cancer-types.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/cancer-types.json rename to tests/test_data/api_json_system_tests/cancer-types.json diff --git a/src/test/scripts/test_data/api_json_system_tests/gene-panels.json b/tests/test_data/api_json_system_tests/gene-panels.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/gene-panels.json rename to tests/test_data/api_json_system_tests/gene-panels.json diff --git a/src/test/scripts/test_data/api_json_system_tests/genes.json b/tests/test_data/api_json_system_tests/genes.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/genes.json rename to tests/test_data/api_json_system_tests/genes.json diff --git a/src/test/scripts/test_data/api_json_system_tests/genesaliases.json b/tests/test_data/api_json_system_tests/genesaliases.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/genesaliases.json rename to tests/test_data/api_json_system_tests/genesaliases.json diff --git a/src/test/scripts/test_data/api_json_system_tests/genesets.json b/tests/test_data/api_json_system_tests/genesets.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/genesets.json rename to tests/test_data/api_json_system_tests/genesets.json diff --git a/src/test/scripts/test_data/api_json_system_tests/genesets_version.json b/tests/test_data/api_json_system_tests/genesets_version.json similarity index 100% rename from src/test/scripts/test_data/api_json_system_tests/genesets_version.json rename to tests/test_data/api_json_system_tests/genesets_version.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/cancer-types.json b/tests/test_data/api_json_unit_tests/cancer-types.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/cancer-types.json rename to tests/test_data/api_json_unit_tests/cancer-types.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/gene-panels.json b/tests/test_data/api_json_unit_tests/gene-panels.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/gene-panels.json rename to tests/test_data/api_json_unit_tests/gene-panels.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/genes.json b/tests/test_data/api_json_unit_tests/genes.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/genes.json rename to tests/test_data/api_json_unit_tests/genes.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/genesaliases.json b/tests/test_data/api_json_unit_tests/genesaliases.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/genesaliases.json rename to tests/test_data/api_json_unit_tests/genesaliases.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/genesets.json b/tests/test_data/api_json_unit_tests/genesets.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/genesets.json rename to tests/test_data/api_json_unit_tests/genesets.json diff --git a/src/test/scripts/test_data/api_json_unit_tests/genesets_version.json b/tests/test_data/api_json_unit_tests/genesets_version.json similarity index 100% rename from src/test/scripts/test_data/api_json_unit_tests/genesets_version.json rename to tests/test_data/api_json_unit_tests/genesets_version.json diff --git a/src/test/scripts/test_data/case_lists_duplicate_category/cases_test1.txt b/tests/test_data/case_lists_duplicate_category/cases_test1.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_duplicate_category/cases_test1.txt rename to tests/test_data/case_lists_duplicate_category/cases_test1.txt diff --git a/src/test/scripts/test_data/case_lists_duplicate_category/cases_test2.txt b/tests/test_data/case_lists_duplicate_category/cases_test2.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_duplicate_category/cases_test2.txt rename to tests/test_data/case_lists_duplicate_category/cases_test2.txt diff --git a/src/test/scripts/test_data/case_lists_duplicated/cases_all.txt b/tests/test_data/case_lists_duplicated/cases_all.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_duplicated/cases_all.txt rename to tests/test_data/case_lists_duplicated/cases_all.txt diff --git a/src/test/scripts/test_data/case_lists_duplicated/cases_each_and_every.txt b/tests/test_data/case_lists_duplicated/cases_each_and_every.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_duplicated/cases_each_and_every.txt rename to tests/test_data/case_lists_duplicated/cases_each_and_every.txt diff --git a/src/test/scripts/test_data/case_lists_duplicated_sampleid/cases_all.txt b/tests/test_data/case_lists_duplicated_sampleid/cases_all.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_duplicated_sampleid/cases_all.txt rename to tests/test_data/case_lists_duplicated_sampleid/cases_all.txt diff --git a/src/test/scripts/test_data/case_lists_invalid_category/cases_all.txt b/tests/test_data/case_lists_invalid_category/cases_all.txt similarity index 100% rename from src/test/scripts/test_data/case_lists_invalid_category/cases_all.txt rename to tests/test_data/case_lists_invalid_category/cases_all.txt diff --git a/src/test/scripts/test_data/data_cancertype_blank_color_col.txt b/tests/test_data/data_cancertype_blank_color_col.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_blank_color_col.txt rename to tests/test_data/data_cancertype_blank_color_col.txt diff --git a/src/test/scripts/test_data/data_cancertype_confirming_existing.txt b/tests/test_data/data_cancertype_confirming_existing.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_confirming_existing.txt rename to tests/test_data/data_cancertype_confirming_existing.txt diff --git a/src/test/scripts/test_data/data_cancertype_invalid_color.txt b/tests/test_data/data_cancertype_invalid_color.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_invalid_color.txt rename to tests/test_data/data_cancertype_invalid_color.txt diff --git a/src/test/scripts/test_data/data_cancertype_lung.txt b/tests/test_data/data_cancertype_lung.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_lung.txt rename to tests/test_data/data_cancertype_lung.txt diff --git a/src/test/scripts/test_data/data_cancertype_lung_twice.txt b/tests/test_data/data_cancertype_lung_twice.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_lung_twice.txt rename to tests/test_data/data_cancertype_lung_twice.txt diff --git a/src/test/scripts/test_data/data_cancertype_missing_color_col.txt b/tests/test_data/data_cancertype_missing_color_col.txt similarity index 100% rename from src/test/scripts/test_data/data_cancertype_missing_color_col.txt rename to tests/test_data/data_cancertype_missing_color_col.txt diff --git a/src/test/scripts/test_data/data_cancertype_redefining.txt b/tests/test_data/data_cancertype_redefining.txt similarity index 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a/src/test/scripts/test_data/data_cna_genecol_presence_entrez_only.txt b/tests/test_data/data_cna_genecol_presence_entrez_only.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_genecol_presence_entrez_only.txt rename to tests/test_data/data_cna_genecol_presence_entrez_only.txt diff --git a/src/test/scripts/test_data/data_cna_genecol_presence_entrez_only_invalid.txt b/tests/test_data/data_cna_genecol_presence_entrez_only_invalid.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_genecol_presence_entrez_only_invalid.txt rename to tests/test_data/data_cna_genecol_presence_entrez_only_invalid.txt diff --git a/src/test/scripts/test_data/data_cna_genecol_presence_hugo_only.txt b/tests/test_data/data_cna_genecol_presence_hugo_only.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_genecol_presence_hugo_only.txt rename to tests/test_data/data_cna_genecol_presence_hugo_only.txt diff --git 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tests/test_data/data_cna_genecol_presence_hugo_only_possible_alias.txt diff --git a/src/test/scripts/test_data/data_cna_genecol_presence_neither.txt b/tests/test_data/data_cna_genecol_presence_neither.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_genecol_presence_neither.txt rename to tests/test_data/data_cna_genecol_presence_neither.txt diff --git a/src/test/scripts/test_data/data_cna_invalid_values.txt b/tests/test_data/data_cna_invalid_values.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_invalid_values.txt rename to tests/test_data/data_cna_invalid_values.txt diff --git a/src/test/scripts/test_data/data_cna_long_duplicated_entrez.txt b/tests/test_data/data_cna_long_duplicated_entrez.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_duplicated_entrez.txt rename to tests/test_data/data_cna_long_duplicated_entrez.txt diff --git a/src/test/scripts/test_data/data_cna_long_duplicated_gene.txt b/tests/test_data/data_cna_long_duplicated_gene.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_duplicated_gene.txt rename to tests/test_data/data_cna_long_duplicated_gene.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_no_custom_driver.txt b/tests/test_data/data_cna_long_genecol_no_custom_driver.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_no_custom_driver.txt rename to tests/test_data/data_cna_long_genecol_no_custom_driver.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_no_namespace.txt b/tests/test_data/data_cna_long_genecol_no_namespace.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_no_namespace.txt rename to tests/test_data/data_cna_long_genecol_no_namespace.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_no_sample_id.txt b/tests/test_data/data_cna_long_genecol_no_sample_id.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_no_sample_id.txt rename to tests/test_data/data_cna_long_genecol_no_sample_id.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_no_value.txt b/tests/test_data/data_cna_long_genecol_no_value.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_no_value.txt rename to tests/test_data/data_cna_long_genecol_no_value.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_presence_all.txt b/tests/test_data/data_cna_long_genecol_presence_all.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_presence_all.txt rename to tests/test_data/data_cna_long_genecol_presence_all.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_presence_entrez_only.txt b/tests/test_data/data_cna_long_genecol_presence_entrez_only.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_presence_entrez_only.txt rename to tests/test_data/data_cna_long_genecol_presence_entrez_only.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_presence_hugo_only.txt b/tests/test_data/data_cna_long_genecol_presence_hugo_only.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_presence_hugo_only.txt rename to tests/test_data/data_cna_long_genecol_presence_hugo_only.txt diff --git a/src/test/scripts/test_data/data_cna_long_genecol_presence_neither_genic.txt b/tests/test_data/data_cna_long_genecol_presence_neither_genic.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_genecol_presence_neither_genic.txt rename to tests/test_data/data_cna_long_genecol_presence_neither_genic.txt diff --git a/src/test/scripts/test_data/data_cna_long_invalid_values.txt b/tests/test_data/data_cna_long_invalid_values.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_invalid_values.txt rename to tests/test_data/data_cna_long_invalid_values.txt diff --git a/src/test/scripts/test_data/data_cna_long_one_hugo_same_gene.txt b/tests/test_data/data_cna_long_one_hugo_same_gene.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_one_hugo_same_gene.txt rename to tests/test_data/data_cna_long_one_hugo_same_gene.txt diff --git a/src/test/scripts/test_data/data_cna_long_two_hugos_same_gene.txt b/tests/test_data/data_cna_long_two_hugos_same_gene.txt similarity index 100% rename from src/test/scripts/test_data/data_cna_long_two_hugos_same_gene.txt rename to tests/test_data/data_cna_long_two_hugos_same_gene.txt diff --git a/src/test/scripts/test_data/data_gene_matrix_duplicate_sample.txt b/tests/test_data/data_gene_matrix_duplicate_sample.txt similarity index 100% rename from src/test/scripts/test_data/data_gene_matrix_duplicate_sample.txt rename to tests/test_data/data_gene_matrix_duplicate_sample.txt diff --git a/src/test/scripts/test_data/data_generic_assay_categorical_invalid_predefined_data.txt b/tests/test_data/data_generic_assay_categorical_invalid_predefined_data.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_categorical_invalid_predefined_data.txt rename to tests/test_data/data_generic_assay_categorical_invalid_predefined_data.txt diff --git a/src/test/scripts/test_data/data_generic_assay_categorical_valid_predefined_data.txt b/tests/test_data/data_generic_assay_categorical_valid_predefined_data.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_categorical_valid_predefined_data.txt rename to tests/test_data/data_generic_assay_categorical_valid_predefined_data.txt diff --git a/src/test/scripts/test_data/data_generic_assay_empty_cell.txt b/tests/test_data/data_generic_assay_empty_cell.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_empty_cell.txt rename to tests/test_data/data_generic_assay_empty_cell.txt diff --git a/src/test/scripts/test_data/data_generic_assay_patient_not_defined.txt b/tests/test_data/data_generic_assay_patient_not_defined.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_patient_not_defined.txt rename to tests/test_data/data_generic_assay_patient_not_defined.txt diff --git a/src/test/scripts/test_data/data_generic_assay_sample_not_defined.txt b/tests/test_data/data_generic_assay_sample_not_defined.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_sample_not_defined.txt rename to tests/test_data/data_generic_assay_sample_not_defined.txt diff --git a/src/test/scripts/test_data/data_generic_assay_valid_binary.txt b/tests/test_data/data_generic_assay_valid_binary.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_valid_binary.txt rename to tests/test_data/data_generic_assay_valid_binary.txt diff --git a/src/test/scripts/test_data/data_generic_assay_valid_categorical.txt b/tests/test_data/data_generic_assay_valid_categorical.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_valid_categorical.txt rename to tests/test_data/data_generic_assay_valid_categorical.txt diff --git a/src/test/scripts/test_data/data_generic_assay_valid_continuous.txt b/tests/test_data/data_generic_assay_valid_continuous.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_valid_continuous.txt rename to tests/test_data/data_generic_assay_valid_continuous.txt diff --git a/src/test/scripts/test_data/data_generic_assay_with_non_numerical_data.txt b/tests/test_data/data_generic_assay_with_non_numerical_data.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_with_non_numerical_data.txt rename to tests/test_data/data_generic_assay_with_non_numerical_data.txt diff --git a/src/test/scripts/test_data/data_generic_assay_with_not_defined_data.txt b/tests/test_data/data_generic_assay_with_not_defined_data.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_with_not_defined_data.txt rename to tests/test_data/data_generic_assay_with_not_defined_data.txt diff --git a/src/test/scripts/test_data/data_generic_assay_without_entity_id_column.txt b/tests/test_data/data_generic_assay_without_entity_id_column.txt similarity index 100% rename from src/test/scripts/test_data/data_generic_assay_without_entity_id_column.txt rename to tests/test_data/data_generic_assay_without_entity_id_column.txt diff --git a/src/test/scripts/test_data/data_gisticgenes_amp_valid.txt b/tests/test_data/data_gisticgenes_amp_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_gisticgenes_amp_valid.txt rename to tests/test_data/data_gisticgenes_amp_valid.txt diff --git a/src/test/scripts/test_data/data_gisticgenes_del_format_errors.txt b/tests/test_data/data_gisticgenes_del_format_errors.txt similarity index 100% rename from src/test/scripts/test_data/data_gisticgenes_del_format_errors.txt rename to tests/test_data/data_gisticgenes_del_format_errors.txt diff --git a/src/test/scripts/test_data/data_gisticgenes_del_region_without_genes.txt b/tests/test_data/data_gisticgenes_del_region_without_genes.txt similarity index 100% rename from src/test/scripts/test_data/data_gisticgenes_del_region_without_genes.txt rename to tests/test_data/data_gisticgenes_del_region_without_genes.txt diff --git a/src/test/scripts/test_data/data_gisticgenes_del_valid.txt b/tests/test_data/data_gisticgenes_del_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_gisticgenes_del_valid.txt rename to tests/test_data/data_gisticgenes_del_valid.txt diff --git a/src/test/scripts/test_data/data_gisticgenes_del_zero_length_peak.txt b/tests/test_data/data_gisticgenes_del_zero_length_peak.txt similarity index 100% rename from src/test/scripts/test_data/data_gisticgenes_del_zero_length_peak.txt rename to tests/test_data/data_gisticgenes_del_zero_length_peak.txt diff --git a/src/test/scripts/test_data/data_gsva_pvalues_missing_column.txt b/tests/test_data/data_gsva_pvalues_missing_column.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_pvalues_missing_column.txt rename to tests/test_data/data_gsva_pvalues_missing_column.txt diff --git a/src/test/scripts/test_data/data_gsva_pvalues_missing_row.txt b/tests/test_data/data_gsva_pvalues_missing_row.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_pvalues_missing_row.txt rename to tests/test_data/data_gsva_pvalues_missing_row.txt diff --git a/src/test/scripts/test_data/data_gsva_pvalues_outrange.txt b/tests/test_data/data_gsva_pvalues_outrange.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_pvalues_outrange.txt rename to tests/test_data/data_gsva_pvalues_outrange.txt diff --git a/src/test/scripts/test_data/data_gsva_scores_geneset_not_in_database.txt b/tests/test_data/data_gsva_scores_geneset_not_in_database.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_scores_geneset_not_in_database.txt rename to tests/test_data/data_gsva_scores_geneset_not_in_database.txt diff --git a/src/test/scripts/test_data/data_gsva_scores_missing_column.txt b/tests/test_data/data_gsva_scores_missing_column.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_scores_missing_column.txt rename to tests/test_data/data_gsva_scores_missing_column.txt diff --git a/src/test/scripts/test_data/data_gsva_scores_missing_row.txt b/tests/test_data/data_gsva_scores_missing_row.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_scores_missing_row.txt rename to tests/test_data/data_gsva_scores_missing_row.txt diff --git a/src/test/scripts/test_data/data_gsva_scores_outrange.txt b/tests/test_data/data_gsva_scores_outrange.txt similarity index 100% rename from src/test/scripts/test_data/data_gsva_scores_outrange.txt rename to tests/test_data/data_gsva_scores_outrange.txt diff --git a/src/test/scripts/test_data/data_methylation_invalid_values.txt b/tests/test_data/data_methylation_invalid_values.txt similarity index 100% rename from src/test/scripts/test_data/data_methylation_invalid_values.txt rename to tests/test_data/data_methylation_invalid_values.txt diff --git a/src/test/scripts/test_data/data_pd_annotation_missing_col_driver.txt b/tests/test_data/data_pd_annotation_missing_col_driver.txt similarity index 100% rename from src/test/scripts/test_data/data_pd_annotation_missing_col_driver.txt rename to tests/test_data/data_pd_annotation_missing_col_driver.txt diff --git a/src/test/scripts/test_data/data_pd_annotation_missing_col_gene_ids.txt b/tests/test_data/data_pd_annotation_missing_col_gene_ids.txt similarity index 100% rename from src/test/scripts/test_data/data_pd_annotation_missing_col_gene_ids.txt rename to tests/test_data/data_pd_annotation_missing_col_gene_ids.txt diff --git a/src/test/scripts/test_data/data_pd_annotation_missing_col_sampleid.txt b/tests/test_data/data_pd_annotation_missing_col_sampleid.txt similarity index 100% rename from src/test/scripts/test_data/data_pd_annotation_missing_col_sampleid.txt rename to tests/test_data/data_pd_annotation_missing_col_sampleid.txt diff --git a/src/test/scripts/test_data/data_pd_annotation_missing_fields.txt b/tests/test_data/data_pd_annotation_missing_fields.txt similarity index 100% rename from src/test/scripts/test_data/data_pd_annotation_missing_fields.txt rename to tests/test_data/data_pd_annotation_missing_fields.txt diff --git a/src/test/scripts/test_data/data_resource_definition_missing_resourceId.txt b/tests/test_data/data_resource_definition_missing_resourceId.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_definition_missing_resourceId.txt rename to tests/test_data/data_resource_definition_missing_resourceId.txt diff --git a/src/test/scripts/test_data/data_resource_is_not_url.txt b/tests/test_data/data_resource_is_not_url.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_is_not_url.txt rename to tests/test_data/data_resource_is_not_url.txt diff --git a/src/test/scripts/test_data/data_resource_patient_duplicate.txt b/tests/test_data/data_resource_patient_duplicate.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_patient_duplicate.txt rename to tests/test_data/data_resource_patient_duplicate.txt diff --git a/src/test/scripts/test_data/data_resource_patient_valid.txt b/tests/test_data/data_resource_patient_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_patient_valid.txt rename to tests/test_data/data_resource_patient_valid.txt diff --git a/src/test/scripts/test_data/data_resource_sample_duplicate.txt b/tests/test_data/data_resource_sample_duplicate.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_sample_duplicate.txt rename to tests/test_data/data_resource_sample_duplicate.txt diff --git a/src/test/scripts/test_data/data_resource_sample_valid.txt b/tests/test_data/data_resource_sample_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_sample_valid.txt rename to tests/test_data/data_resource_sample_valid.txt diff --git a/src/test/scripts/test_data/data_resource_study_duplicate.txt b/tests/test_data/data_resource_study_duplicate.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_study_duplicate.txt rename to tests/test_data/data_resource_study_duplicate.txt diff --git a/src/test/scripts/test_data/data_resource_study_valid.txt b/tests/test_data/data_resource_study_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_resource_study_valid.txt rename to tests/test_data/data_resource_study_valid.txt diff --git a/src/test/scripts/test_data/data_rppa_duplicate_entries.txt b/tests/test_data/data_rppa_duplicate_entries.txt similarity index 100% rename from src/test/scripts/test_data/data_rppa_duplicate_entries.txt rename to tests/test_data/data_rppa_duplicate_entries.txt diff --git a/src/test/scripts/test_data/data_rppa_invalid_values.txt b/tests/test_data/data_rppa_invalid_values.txt similarity index 100% rename from src/test/scripts/test_data/data_rppa_invalid_values.txt rename to tests/test_data/data_rppa_invalid_values.txt diff --git a/src/test/scripts/test_data/data_rppa_na_gene.txt b/tests/test_data/data_rppa_na_gene.txt similarity index 100% rename from src/test/scripts/test_data/data_rppa_na_gene.txt rename to tests/test_data/data_rppa_na_gene.txt diff --git a/src/test/scripts/test_data/data_rppa_valid.txt b/tests/test_data/data_rppa_valid.txt similarity index 100% rename from src/test/scripts/test_data/data_rppa_valid.txt rename to tests/test_data/data_rppa_valid.txt diff --git a/src/test/scripts/test_data/data_seg_blank_line.seg b/tests/test_data/data_seg_blank_line.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_blank_line.seg rename to tests/test_data/data_seg_blank_line.seg diff --git a/src/test/scripts/test_data/data_seg_end_before_start.seg b/tests/test_data/data_seg_end_before_start.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_end_before_start.seg rename to tests/test_data/data_seg_end_before_start.seg diff --git a/src/test/scripts/test_data/data_seg_invalid_hg18.seg b/tests/test_data/data_seg_invalid_hg18.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_invalid_hg18.seg rename to tests/test_data/data_seg_invalid_hg18.seg diff --git a/src/test/scripts/test_data/data_seg_nonsense_values.seg b/tests/test_data/data_seg_nonsense_values.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_nonsense_values.seg rename to tests/test_data/data_seg_nonsense_values.seg diff --git a/src/test/scripts/test_data/data_seg_out_of_bounds.seg b/tests/test_data/data_seg_out_of_bounds.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_out_of_bounds.seg rename to tests/test_data/data_seg_out_of_bounds.seg diff --git a/src/test/scripts/test_data/data_seg_valid.seg b/tests/test_data/data_seg_valid.seg similarity index 100% rename from src/test/scripts/test_data/data_seg_valid.seg rename to tests/test_data/data_seg_valid.seg diff --git a/src/test/scripts/test_data/data_seg_wrong_order.txt b/tests/test_data/data_seg_wrong_order.txt similarity index 100% rename from src/test/scripts/test_data/data_seg_wrong_order.txt rename to tests/test_data/data_seg_wrong_order.txt diff --git a/src/test/scripts/test_data/data_structural_variants_duplicate_entry.txt b/tests/test_data/data_structural_variants_duplicate_entry.txt similarity index 100% rename from src/test/scripts/test_data/data_structural_variants_duplicate_entry.txt rename to tests/test_data/data_structural_variants_duplicate_entry.txt diff --git a/src/test/scripts/test_data/data_structural_variants_missing_columns.txt b/tests/test_data/data_structural_variants_missing_columns.txt similarity index 100% rename from src/test/scripts/test_data/data_structural_variants_missing_columns.txt rename to tests/test_data/data_structural_variants_missing_columns.txt diff --git a/src/test/scripts/test_data/data_structural_variants_missing_values.txt b/tests/test_data/data_structural_variants_missing_values.txt similarity index 100% rename from src/test/scripts/test_data/data_structural_variants_missing_values.txt rename to tests/test_data/data_structural_variants_missing_values.txt diff --git a/src/test/scripts/test_data/data_timeline_invalid_start_date.txt b/tests/test_data/data_timeline_invalid_start_date.txt similarity index 100% rename from src/test/scripts/test_data/data_timeline_invalid_start_date.txt rename to tests/test_data/data_timeline_invalid_start_date.txt diff --git a/src/test/scripts/test_data/data_unique_column_test.txt b/tests/test_data/data_unique_column_test.txt similarity index 100% rename from src/test/scripts/test_data/data_unique_column_test.txt rename to tests/test_data/data_unique_column_test.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_pmid_values/meta_study.txt b/tests/test_data/meta_study/invalid_pmid_values/meta_study.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_pmid_values/meta_study.txt rename to tests/test_data/meta_study/invalid_pmid_values/meta_study.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/case_lists/cases_cna.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/case_lists/cases_cna.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/case_lists/cases_cna.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/case_lists/cases_cna.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_patients.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_patients.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_patients.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_patients.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_samples.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_samples.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_samples.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/data_clinical_samples.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_cna_log2.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/data_cna_log2.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/data_cna_log2.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/data_cna_log2.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_patients.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_patients.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_patients.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_patients.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_samples.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_samples.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_samples.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_clinical_samples.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_cna_log2.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_cna_log2.txt similarity index 100% rename from src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_cna_log2.txt rename to tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_cna_log2.txt diff --git a/src/test/scripts/test_data/meta_study/invalid_show_profile_setting_cna/meta_study.txt b/tests/test_data/meta_study/invalid_show_profile_setting_cna/meta_study.txt similarity index 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src/test/scripts/test_data/study_es_0/meta_treatment_ec50.txt rename to tests/test_data/study_es_0/meta_treatment_ec50.txt diff --git a/src/test/scripts/test_data/study_es_0/meta_treatment_ic50.txt b/tests/test_data/study_es_0/meta_treatment_ic50.txt similarity index 100% rename from src/test/scripts/test_data/study_es_0/meta_treatment_ic50.txt rename to tests/test_data/study_es_0/meta_treatment_ic50.txt diff --git a/src/test/scripts/test_data/study_es_0/result_report.html b/tests/test_data/study_es_0/result_report.html similarity index 99% rename from src/test/scripts/test_data/study_es_0/result_report.html rename to tests/test_data/study_es_0/result_report.html index 0def1eae..e5ab1c19 100644 --- a/src/test/scripts/test_data/study_es_0/result_report.html +++ b/tests/test_data/study_es_0/result_report.html @@ -142,7 +142,7 @@

General

Debug – – - Retrieving chromosome lengths from '/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json' + Retrieving chromosome lengths from 'chromosome_sizes.json' – @@ -150,7 +150,7 @@

General

Debug – – - Retrieving chromosome lengths from '/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json' + Retrieving chromosome lengths from 'chromosome_sizes.json' – @@ -3192,4 +3192,4 @@

Legend

- \ No newline at end of file + diff --git a/src/test/scripts/test_data/study_es_0/study_tags.yml b/tests/test_data/study_es_0/study_tags.yml similarity index 100% rename from src/test/scripts/test_data/study_es_0/study_tags.yml rename to tests/test_data/study_es_0/study_tags.yml diff --git a/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cna.txt b/tests/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cna.txt similarity index 100% rename from src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cna.txt rename to tests/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cna.txt diff --git a/src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cnaseq.txt b/tests/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cnaseq.txt similarity index 100% rename from src/test/scripts/test_data/study_es_0_legacy_cna_discrete/case_lists/cases_cnaseq.txt rename to 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diff --git a/src/test/scripts/test_data/study_es_3/cancer_type.txt b/tests/test_data/study_es_3/cancer_type.txt similarity index 100% rename from src/test/scripts/test_data/study_es_3/cancer_type.txt rename to tests/test_data/study_es_3/cancer_type.txt diff --git a/src/test/scripts/test_data/study_es_3/case_lists/cases_all.txt b/tests/test_data/study_es_3/case_lists/cases_all.txt similarity index 100% rename from src/test/scripts/test_data/study_es_3/case_lists/cases_all.txt rename to tests/test_data/study_es_3/case_lists/cases_all.txt diff --git a/src/test/scripts/test_data/study_es_3/data_gistic_genes_amp.txt b/tests/test_data/study_es_3/data_gistic_genes_amp.txt similarity index 100% rename from src/test/scripts/test_data/study_es_3/data_gistic_genes_amp.txt rename to tests/test_data/study_es_3/data_gistic_genes_amp.txt diff --git a/src/test/scripts/test_data/study_es_3/data_samples.txt b/tests/test_data/study_es_3/data_samples.txt similarity index 100% rename from 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diff --git a/src/test/scripts/test_data/study_quotes/brca_tcga_pub.maf b/tests/test_data/study_quotes/brca_tcga_pub.maf similarity index 100% rename from src/test/scripts/test_data/study_quotes/brca_tcga_pub.maf rename to tests/test_data/study_quotes/brca_tcga_pub.maf diff --git a/src/test/scripts/test_data/study_quotes/case_lists/cases_cna.txt b/tests/test_data/study_quotes/case_lists/cases_cna.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/case_lists/cases_cna.txt rename to tests/test_data/study_quotes/case_lists/cases_cna.txt diff --git a/src/test/scripts/test_data/study_quotes/case_lists/cases_cnaseq.txt b/tests/test_data/study_quotes/case_lists/cases_cnaseq.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/case_lists/cases_cnaseq.txt rename to tests/test_data/study_quotes/case_lists/cases_cnaseq.txt diff --git a/src/test/scripts/test_data/study_quotes/case_lists/cases_custom.txt b/tests/test_data/study_quotes/case_lists/cases_custom.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/case_lists/cases_custom.txt rename to tests/test_data/study_quotes/case_lists/cases_custom.txt diff --git a/src/test/scripts/test_data/study_quotes/case_lists/cases_sequenced.txt b/tests/test_data/study_quotes/case_lists/cases_sequenced.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/case_lists/cases_sequenced.txt rename to tests/test_data/study_quotes/case_lists/cases_sequenced.txt diff --git a/src/test/scripts/test_data/study_quotes/data_CNA.txt b/tests/test_data/study_quotes/data_CNA.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/data_CNA.txt rename to tests/test_data/study_quotes/data_CNA.txt diff --git a/src/test/scripts/test_data/study_quotes/data_patients.txt b/tests/test_data/study_quotes/data_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/data_patients.txt rename to tests/test_data/study_quotes/data_patients.txt diff --git a/src/test/scripts/test_data/study_quotes/data_samples.txt b/tests/test_data/study_quotes/data_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/data_samples.txt rename to tests/test_data/study_quotes/data_samples.txt diff --git a/src/test/scripts/test_data/study_quotes/meta_CNA.txt b/tests/test_data/study_quotes/meta_CNA.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/meta_CNA.txt rename to tests/test_data/study_quotes/meta_CNA.txt diff --git a/src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt b/tests/test_data/study_quotes/meta_mutations_extended.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt rename to tests/test_data/study_quotes/meta_mutations_extended.txt diff --git a/src/test/scripts/test_data/study_quotes/meta_patients.txt b/tests/test_data/study_quotes/meta_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/meta_patients.txt rename to tests/test_data/study_quotes/meta_patients.txt diff --git a/src/test/scripts/test_data/study_quotes/meta_samples.txt b/tests/test_data/study_quotes/meta_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/meta_samples.txt rename to tests/test_data/study_quotes/meta_samples.txt diff --git a/src/test/scripts/test_data/study_quotes/meta_study.txt b/tests/test_data/study_quotes/meta_study.txt similarity index 100% rename from src/test/scripts/test_data/study_quotes/meta_study.txt rename to tests/test_data/study_quotes/meta_study.txt diff --git a/src/test/scripts/test_data/study_quotes/result_report.html b/tests/test_data/study_quotes/result_report.html similarity index 100% rename from src/test/scripts/test_data/study_quotes/result_report.html rename to tests/test_data/study_quotes/result_report.html diff --git a/src/test/scripts/test_data/study_various_issues/brca_tcga_pub.maf b/tests/test_data/study_various_issues/brca_tcga_pub.maf similarity index 100% rename from src/test/scripts/test_data/study_various_issues/brca_tcga_pub.maf rename to tests/test_data/study_various_issues/brca_tcga_pub.maf diff --git a/src/test/scripts/test_data/study_various_issues/case_lists/cases_custom.txt b/tests/test_data/study_various_issues/case_lists/cases_custom.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/case_lists/cases_custom.txt rename to tests/test_data/study_various_issues/case_lists/cases_custom.txt diff --git a/src/test/scripts/test_data/study_various_issues/case_lists/cases_sequenced.txt b/tests/test_data/study_various_issues/case_lists/cases_sequenced.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/case_lists/cases_sequenced.txt rename to tests/test_data/study_various_issues/case_lists/cases_sequenced.txt diff --git a/src/test/scripts/test_data/study_various_issues/data_patients.txt b/tests/test_data/study_various_issues/data_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/data_patients.txt rename to tests/test_data/study_various_issues/data_patients.txt diff --git a/src/test/scripts/test_data/study_various_issues/data_samples.txt b/tests/test_data/study_various_issues/data_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/data_samples.txt rename to tests/test_data/study_various_issues/data_samples.txt diff --git a/src/test/scripts/test_data/study_various_issues/error_file.txt b/tests/test_data/study_various_issues/error_file.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/error_file.txt rename to tests/test_data/study_various_issues/error_file.txt diff --git a/src/test/scripts/test_data/study_various_issues/meta_mutations_extended.txt b/tests/test_data/study_various_issues/meta_mutations_extended.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/meta_mutations_extended.txt rename to tests/test_data/study_various_issues/meta_mutations_extended.txt diff --git a/src/test/scripts/test_data/study_various_issues/meta_patients.txt b/tests/test_data/study_various_issues/meta_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/meta_patients.txt rename to tests/test_data/study_various_issues/meta_patients.txt diff --git a/src/test/scripts/test_data/study_various_issues/meta_samples.txt b/tests/test_data/study_various_issues/meta_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/meta_samples.txt rename to tests/test_data/study_various_issues/meta_samples.txt diff --git a/src/test/scripts/test_data/study_various_issues/meta_study.txt b/tests/test_data/study_various_issues/meta_study.txt similarity index 100% rename from src/test/scripts/test_data/study_various_issues/meta_study.txt rename to tests/test_data/study_various_issues/meta_study.txt diff --git a/src/test/scripts/test_data/study_various_issues/result_report.html b/tests/test_data/study_various_issues/result_report.html similarity index 100% rename from src/test/scripts/test_data/study_various_issues/result_report.html rename to tests/test_data/study_various_issues/result_report.html diff --git a/src/test/scripts/test_data/study_wr_clin/cancer_type.txt b/tests/test_data/study_wr_clin/cancer_type.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/cancer_type.txt rename to tests/test_data/study_wr_clin/cancer_type.txt diff --git a/src/test/scripts/test_data/study_wr_clin/data_expression_median.txt b/tests/test_data/study_wr_clin/data_expression_median.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/data_expression_median.txt rename to tests/test_data/study_wr_clin/data_expression_median.txt diff --git a/src/test/scripts/test_data/study_wr_clin/data_patients.txt b/tests/test_data/study_wr_clin/data_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/data_patients.txt rename to tests/test_data/study_wr_clin/data_patients.txt diff --git a/src/test/scripts/test_data/study_wr_clin/data_samples.txt b/tests/test_data/study_wr_clin/data_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/data_samples.txt rename to tests/test_data/study_wr_clin/data_samples.txt diff --git a/src/test/scripts/test_data/study_wr_clin/meta_expression_median.txt b/tests/test_data/study_wr_clin/meta_expression_median.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/meta_expression_median.txt rename to tests/test_data/study_wr_clin/meta_expression_median.txt diff --git a/src/test/scripts/test_data/study_wr_clin/meta_patients.txt b/tests/test_data/study_wr_clin/meta_patients.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/meta_patients.txt rename to tests/test_data/study_wr_clin/meta_patients.txt diff --git a/src/test/scripts/test_data/study_wr_clin/meta_samples.txt b/tests/test_data/study_wr_clin/meta_samples.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/meta_samples.txt rename to tests/test_data/study_wr_clin/meta_samples.txt diff --git a/src/test/scripts/test_data/study_wr_clin/meta_study.txt b/tests/test_data/study_wr_clin/meta_study.txt similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/meta_study.txt rename to tests/test_data/study_wr_clin/meta_study.txt diff --git a/src/test/scripts/test_data/study_wr_clin/result_report.html b/tests/test_data/study_wr_clin/result_report.html similarity index 100% rename from src/test/scripts/test_data/study_wr_clin/result_report.html rename to tests/test_data/study_wr_clin/result_report.html diff --git a/src/test/scripts/test_data/test.xml b/tests/test_data/test.xml similarity index 100% rename from src/test/scripts/test_data/test.xml rename to tests/test_data/test.xml diff --git a/src/test/scripts/unit_tests_validate_data.py b/tests/unit_tests_validate_data.py similarity index 100% rename from src/test/scripts/unit_tests_validate_data.py rename to tests/unit_tests_validate_data.py From 92963a1e55a533f553804995bd51d093d24bc57a Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Fri, 12 Apr 2024 06:47:19 +0200 Subject: [PATCH 2/4] Fix python gh action paths --- .github/workflows/validate-python.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 058ccb65..f209680f 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -17,8 +17,8 @@ jobs: docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/sh -c ' cd cbioportal-core && pip install -r requirements.txt && - export PYTHONPATH=/cbioportal-core/src/main/resources/scripts && - cd src/test/scripts/ && + export PYTHONPATH=/cbioportal-core/scripts && + cd tests/ && python unit_tests_validate_data.py && python system_tests_validate_data.py && python system_tests_validate_studies.py' From 89a0ee85cc302f9cbf8fbba7b3831ab303610904 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Fri, 12 Apr 2024 07:12:56 +0200 Subject: [PATCH 3/4] Fix diff tests by removing newline at the end of the file It seems like jinja2 started to remove newline character since recent version? --- tests/test_data/study_es_0/result_report.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_data/study_es_0/result_report.html b/tests/test_data/study_es_0/result_report.html index e5ab1c19..c983adc6 100644 --- a/tests/test_data/study_es_0/result_report.html +++ b/tests/test_data/study_es_0/result_report.html @@ -3192,4 +3192,4 @@

Legend

- + \ No newline at end of file From d7386fa6335563deeaf64ece47038b91d6bb8ddc Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Fri, 12 Apr 2024 07:15:35 +0200 Subject: [PATCH 4/4] Reuse test script wrapper in python gh action --- .github/workflows/validate-python.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index f209680f..ccf67a61 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -14,11 +14,7 @@ jobs: - name: 'Validate tests' working-directory: ./cbioportal-core run: | - docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/sh -c ' + docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/bash -c ' cd cbioportal-core && pip install -r requirements.txt && - export PYTHONPATH=/cbioportal-core/scripts && - cd tests/ && - python unit_tests_validate_data.py && - python system_tests_validate_data.py && - python system_tests_validate_studies.py' + source test_scripts.sh'