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runConfigurations/Repo template_ Cromwell server Terra TES.run.xml
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| <component name="ProjectRunConfigurationManager"> | ||
| <configuration default="false" name="Repo template: Cromwell server Terra TES" type="Application" factoryName="Application"> | ||
| <option name="ALTERNATIVE_JRE_PATH" value="$PROJECT_DIR$/../.sdkman/candidates/java/current" /> | ||
| <envs> | ||
| <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" /> | ||
| <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" /> | ||
| <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC&useInformationSchema=true" /> | ||
| <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" /> | ||
| <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" /> | ||
| <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" /> | ||
| <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" /> | ||
| </envs> | ||
| <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" /> | ||
| <module name="cromwell" /> | ||
| <option name="PROGRAM_PARAMETERS" value="server" /> | ||
| <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/terra_tes_application.conf" /> | ||
| <method v="2"> | ||
| <option name="Make" enabled="true" /> | ||
| <option name="ToolBeforeRunTask" enabled="true" actionId="Tool_External Tools_Acquire Google B2C Token" /> | ||
| <option name="RunConfigurationTask" enabled="true" run_configuration_name="renderCiResources" run_configuration_type="SbtRunConfiguration" /> | ||
| </method> | ||
| </configuration> | ||
| </component> |
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| #!/bin/bash | ||
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| # This script acquires a b2c token using gcloud auth and writes it to a file. | ||
| # This file is used by renderCiResources to populate the CROMWELL_B2C_TOKEN in tes_application.conf. | ||
| # It should be run as a "Before Launch" task in IntelliJ so the token is refreshed regularly. | ||
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| ### Setting up this script for the first time in IntelliJ? | ||
| ### 1. Open the "Run/Debug Configurations" dialog for the TES repo template. | ||
| ### 2. Add a new "Before Launch" task, selecting "Run External Tool". | ||
| ### This task should run BEFORE the renderCiResources task. | ||
| ### 3. Configure the new task: | ||
| ### - Name: "Acquire b2c token" | ||
| ### - Program: /full/path/to/src/ci/resources/acquire_b2c_token.sh | ||
| ### - Arguments: ./env.temp | ||
| ### - Working directory: /full/path/to/src/ci/resources | ||
| ### - Advanced Options > Uncheck "Synchronize files after execution" | ||
| ### 4. Click "OK" to save the new task. Apply and close the "Run/Debug Configurations" dialog. | ||
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| # User must provide an output file path as an argument. | ||
| # This can be provided by IntelliJ as a program argument in the run configuration. | ||
| if [ -z "$1" ]; then | ||
| echo "Error: Must specify an output file path for the environment file." | ||
| exit 1 | ||
| fi | ||
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| # Acquire a b2c token using gcloud auth. | ||
| # Send stderr to /dev/null so that any gcloud auth errors/update prompts don't pollute the token output. | ||
| echo "Using local gcloud auth to acquire a b2c token..." | ||
| B2C_TOKEN=$(gcloud auth print-access-token 2>/dev/null) | ||
| if [ $? -eq 0 ]; then | ||
| echo "Acquired b2c token: ${B2C_TOKEN:0:4}****" | ||
| else | ||
| echo "Failed to acquire b2c token. Is your local shell logged into gcloud?" | ||
| fi | ||
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| # Create the output directory if it doesn't exist | ||
| output_dir=$(dirname "$1") | ||
| mkdir -p "$output_dir" | ||
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| # Write the token to the output file. dsde-toolbox will call `source` on this file that we're writing, | ||
| # so it's expected that this file contains valid bash syntax for setting an environment variable. | ||
| echo "export CROMWELL_B2C_TOKEN=${B2C_TOKEN}" > "$1" |
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| include required(classpath("application.conf")) | ||
| include "build_application.inc.conf" | ||
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| filesystems { | ||
| blob { | ||
| class = "cromwell.filesystems.blob.BlobPathBuilderFactory" | ||
| global { | ||
| class = "cromwell.filesystems.blob.BlobFileSystemManager" | ||
| config { | ||
| workspace-manager: { | ||
| # static: Where is WSM Endpoint | ||
| url: "https://workspace.dsde-dev.broadinstitute.org" | ||
| # See comment in src/ci/resources/acquire_b2c_token.sh for the one-time setup required to automatically acquire this. | ||
| # This token can also be manually acquired with gcloud auth print-access-token myAccount@gmail.com | ||
| b2cToken: "{{ env "CROMWELL_B2C_TOKEN" }}" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| engine { | ||
| filesystems { | ||
| local { | ||
| enabled: true | ||
| } | ||
| http { | ||
| enabled: true | ||
| } | ||
| blob { | ||
| enabled: true | ||
| } | ||
| } | ||
| } | ||
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| backend { | ||
| default = "TES" | ||
| providers { | ||
| TES { | ||
| actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory" | ||
| config { | ||
| # Root of a blob storage container to use | ||
| # Might look something like: https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/some/path/" | ||
| root = "" | ||
| dockerRoot = "/cromwell-executions" | ||
| # TES Endpoint for cromwell to use. Might look something like: "https://lz7388ada396994bb48ea5c87a02eed673689c82c2af423d03.servicebus.windows.net/something/tes/v1/tasks | ||
| endpoint = "" | ||
| concurrent-job-limit = 1000 | ||
| # Identity to execute the workflow as. Might look something like: "pet-2676571657071603a9eab" | ||
| workflow-execution-identity = "" | ||
| # See comment in src/ci/resources/acquire_b2c_token.sh for the one-time setup required to automatically acquire this. | ||
| # This token can also be manually acquired with gcloud auth print-access-token myAccount@gmail.com | ||
| bearer-token="Bearer {{ env "CROMWELL_B2C_TOKEN" }}" | ||
| # Override default polling to make it faster for speedy tests | ||
| poll-backoff { | ||
| min: "10 seconds" | ||
| max: "5 minutes" | ||
| multiplier: 1.1 | ||
| randomization-factor: 0.5 | ||
| } | ||
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| filesystems { | ||
| blob { | ||
| enabled: true | ||
| } | ||
| local { | ||
| enabled: false | ||
| } | ||
| http { | ||
| enabled: true | ||
| } | ||
| } | ||
| } | ||
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| # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info. | ||
| include "dockerhub_provider_config_v1.inc.conf" | ||
| } | ||
| } | ||
| } |
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