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 $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -s /data/study_es_0 -p /data/api_json -o
+```
+
diff --git a/application.properties.example b/application.properties.example
new file mode 100644
index 00000000..3cd29cdc
--- /dev/null
+++ b/application.properties.example
@@ -0,0 +1,5 @@
+spring.datasource.url=jdbc:mysql://localhost:3306/cbioportal?useSSL=false
+spring.datasource.username=cbio
+spring.datasource.password=P@ssword1
+spring.datasource.driver-class-name=com.mysql.jdbc.Driver
+spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect
diff --git a/pom.xml b/pom.xml
index 99339126..c71f78a2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -236,7 +236,11 @@
 								<resource>
 									<directory>${project.basedir}</directory>
 									<includes>
+										<!-- FIXME Remove these includes when running loader from the cbioportal docker image is deprecated. Loading should be done from cbioportal-core docker image directly instead. -->
+										<!-- Includes python/perl/shell scripts with the jar to transfer to cbioportal project -->
+										<!-- See here https://github.com/cBioPortal/cbioportal/blob/14e00a6c5580700b96152c45f34baf150e652c89/docker/web-and-data/Dockerfile#L48 -->
 										<include>requirements.txt</include>
+										<include>scripts/</include>
 									</includes>
 								</resource>
 							</resources>
@@ -323,6 +327,13 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<configuration>
+					<outputDirectory>${project.basedir}</outputDirectory>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 
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 100%
rename from src/test/scripts/test_data/data_cancertype_redefining.txt
rename to tests/test_data/data_cancertype_redefining.txt
diff --git a/src/test/scripts/test_data/data_cancertype_undefined_parent.txt b/tests/test_data/data_cancertype_undefined_parent.txt
similarity index 100%
rename from src/test/scripts/test_data/data_cancertype_undefined_parent.txt
rename to tests/test_data/data_cancertype_undefined_parent.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_banned_attribute.txt b/tests/test_data/data_clin_coldefs_banned_attribute.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_banned_attribute.txt
rename to tests/test_data/data_clin_coldefs_banned_attribute.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_correct.txt b/tests/test_data/data_clin_coldefs_correct.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_correct.txt
rename to tests/test_data/data_clin_coldefs_correct.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_hardcoded_attrs.txt b/tests/test_data/data_clin_coldefs_hardcoded_attrs.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_hardcoded_attrs.txt
rename to tests/test_data/data_clin_coldefs_hardcoded_attrs.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_invalid_priority.txt b/tests/test_data/data_clin_coldefs_invalid_priority.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_invalid_priority.txt
rename to tests/test_data/data_clin_coldefs_invalid_priority.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_lowercase_attribute.txt b/tests/test_data/data_clin_coldefs_lowercase_attribute.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_lowercase_attribute.txt
rename to tests/test_data/data_clin_coldefs_lowercase_attribute.txt
diff --git a/src/test/scripts/test_data/data_clin_coldefs_wrong_display_name.txt b/tests/test_data/data_clin_coldefs_wrong_display_name.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_coldefs_wrong_display_name.txt
rename to tests/test_data/data_clin_coldefs_wrong_display_name.txt
diff --git a/src/test/scripts/test_data/data_clin_date_in_nondate_column.txt b/tests/test_data/data_clin_date_in_nondate_column.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_date_in_nondate_column.txt
rename to tests/test_data/data_clin_date_in_nondate_column.txt
diff --git a/src/test/scripts/test_data/data_clin_hardcoded_attr_vals.txt b/tests/test_data/data_clin_hardcoded_attr_vals.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_hardcoded_attr_vals.txt
rename to tests/test_data/data_clin_hardcoded_attr_vals.txt
diff --git a/src/test/scripts/test_data/data_clin_missing_patient.txt b/tests/test_data/data_clin_missing_patient.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_missing_patient.txt
rename to tests/test_data/data_clin_missing_patient.txt
diff --git a/src/test/scripts/test_data/data_clin_order1.txt b/tests/test_data/data_clin_order1.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_order1.txt
rename to tests/test_data/data_clin_order1.txt
diff --git a/src/test/scripts/test_data/data_clin_order2.txt b/tests/test_data/data_clin_order2.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_order2.txt
rename to tests/test_data/data_clin_order2.txt
diff --git a/src/test/scripts/test_data/data_clin_patient_without_samples.txt b/tests/test_data/data_clin_patient_without_samples.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_patient_without_samples.txt
rename to tests/test_data/data_clin_patient_without_samples.txt
diff --git a/src/test/scripts/test_data/data_clin_repeated_sample.txt b/tests/test_data/data_clin_repeated_sample.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_repeated_sample.txt
rename to tests/test_data/data_clin_repeated_sample.txt
diff --git a/src/test/scripts/test_data/data_clin_repeated_tcga_sample.txt b/tests/test_data/data_clin_repeated_tcga_sample.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_repeated_tcga_sample.txt
rename to tests/test_data/data_clin_repeated_tcga_sample.txt
diff --git a/src/test/scripts/test_data/data_clin_wrong_ids.txt b/tests/test_data/data_clin_wrong_ids.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_wrong_ids.txt
rename to tests/test_data/data_clin_wrong_ids.txt
diff --git a/src/test/scripts/test_data/data_clin_wrong_patient_id.txt b/tests/test_data/data_clin_wrong_patient_id.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clin_wrong_patient_id.txt
rename to tests/test_data/data_clin_wrong_patient_id.txt
diff --git a/src/test/scripts/test_data/data_clinical_pat_no_hdr.txt b/tests/test_data/data_clinical_pat_no_hdr.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clinical_pat_no_hdr.txt
rename to tests/test_data/data_clinical_pat_no_hdr.txt
diff --git a/src/test/scripts/test_data/data_clinical_sam_no_hdr.txt b/tests/test_data/data_clinical_sam_no_hdr.txt
similarity index 100%
rename from src/test/scripts/test_data/data_clinical_sam_no_hdr.txt
rename to tests/test_data/data_clinical_sam_no_hdr.txt
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diff --git a/src/test/scripts/test_data/study_es_0/result_report.html b/tests/test_data/study_es_0/result_report.html
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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 @@ <h4 class="panel-title">General</h4>
                 <td><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><span class="sr-only">Debug</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Retrieving chromosome lengths from &#39;/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
+                <td>Retrieving chromosome lengths from &#39;chromosome_sizes.json&#39;</td>
                 <td>&ndash;</td>
                 <td></td>
               </tr>
@@ -150,7 +150,7 @@ <h4 class="panel-title">General</h4>
                 <td><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><span class="sr-only">Debug</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Retrieving chromosome lengths from &#39;/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
+                <td>Retrieving chromosome lengths from &#39;chromosome_sizes.json&#39;</td>
                 <td>&ndash;</td>
                 <td></td>
               </tr>
@@ -3192,4 +3192,4 @@ <h4 class="panel-title">Legend</h4>
     </div>
   </div>
 </body>
-</html>
\ No newline at end of file
+</html>
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