diff --git a/.gitignore b/.gitignore index 9ea69976..4d5c6784 100644 --- a/.gitignore +++ b/.gitignore @@ -76,7 +76,7 @@ KeyczarTest.java HelperTest.java DownloadPartRequest.java -# collaboratory +# s3 service.jks application-prod.properties diff --git a/CERTS.md b/CERTS.md deleted file mode 100644 index d7402e4c..00000000 --- a/CERTS.md +++ /dev/null @@ -1,7 +0,0 @@ -# ICGC DCC - Storage - Certificates - -First run [gencert.sh](../score-server/bin/gencert.sh): - -```shell -cd score-server -bin/gencert.sh \ No newline at end of file diff --git a/CHANGES.md b/CHANGES.md deleted file mode 100644 index 63bd52b1..00000000 --- a/CHANGES.md +++ /dev/null @@ -1,47 +0,0 @@ -# ICGC DCC - Storage - Change Log - -Change log for the ICGC storage system - -1.0.23 --- - - Updated (default) **``filename``** output layout. Files are no longer written as: -``` - . - └── output-dir - ├── filename-1 - │   └── object-id - └── filename-2 - └── object-id -``` - but instead: -``` - . - └── output-dir - ├── filename-1 - └── filename-2 -``` - - if duplicate filenames (but different object id's) are encountered, warning messages will be displayed/logged - -1.0.22 --- - - Added support for Azure - -1.0.14 --- - - Batch Slicing support in View command - - Validate repository values in download manifest files against client profile - - Remove duplicates in result pagination - - Add client check for correct Java version - -1.0.13 --- - - Fix end-of-stream bug in data channel - -1.0.12 --- - - Fix HTTP timeout settings not being applied - -0.0.20 --- - - Fix `--force` overwrite option diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..8edefa61 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,103 @@ +# Contributing to Overture + +We appreciate your interest in contributing to the Overture project. We are the Genome Informatics Software Engineering team from Ontario Institute for Cancer Research. At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. + +## Code of Conduct + +By participating in this project, you are expected to abide by our [Code of Conduct](https://docs.overture.bio/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed diff --git a/Dockerfile.server b/Dockerfile.server index 45d1e210..8d1f7e12 100644 --- a/Dockerfile.server +++ b/Dockerfile.server @@ -32,6 +32,6 @@ CMD mkdir -p $SCORE_HOME $SCORE_LOGS \ && java -Dlog.path=$SCORE_LOGS \ -jar $JAR_FILE \ --spring.config.location=classpath:/application.yml \ - --spring.profiles.active=amazon,collaboratory,prod,secure + --spring.profiles.active=s3,prod,secure #&& FOR_100_YEARS=$((100*365*24*60*60));while true;do sleep $FOR_100_YEARS;done diff --git a/INSTALL.md b/INSTALL.md deleted file mode 100644 index 2272c632..00000000 --- a/INSTALL.md +++ /dev/null @@ -1,116 +0,0 @@ -# Installation Guide -Installing the ICGC Storage System - - -# Storage System Overview -Backend Components: -- storage-server: allows authenticated users to interact with entities in the storage system -- metadata-server: allows authenticated users to register entities with the storage system -- auth-server: authenticates users by granting access tokens via a REST api - -Client Components: -- metadata-client: registers entities with the storage system -- storage-client: primary client for interaction with storage system - -Each component is a Spring Boot java application packaged in a JAR. Look in src/main/resources/application.yml for default configuration properties, which can be overridden by specifying java system properties when running the jar or by adding an application.properties file via -Dspring.config.location. - - -# Installation -This guide describes setting up the ICGC Storage System on a single Ubuntu EC2 instance. - -Before getting started: -- Ensure you have access to the dcc-auth, Song, and Score source -- Make an S3 bucket to hold the storage system data -- Make a KMS Master Key to encrypt data stored in S3 using the web console (http://docs.aws.amazon.com/kms/latest/developerguide/create-keys.html). -- Make an IAM role with permission to write to s3 (AmazonS3FullAccess). -- Launch an Ubuntu EC2 with the newly created IAM role and a static IP. -- Open ports 8444 and 5431 of the EC2 for anybody who will use the storage system as a client and open port 8443 to anybody who will generate access tokens to be given to end users. - - Also, open ports 8443, 8444, 5431, and 27017 of the EC2 to the ip of the EC2 to ensure the servers can communicate with each other. -- Get a domain and point it towards the new EC2's IP address. The command shown in this guide use the domain storage.ucsc-cgl.org; this should be replaced with the desired domain. -- Install Java 11 on the EC2 instance. - -Add $DCC_HOME environment variable that points to the directory to hold all storage system files. -``` -# set up $DCC_HOME -mkdir ~/dcc -printf "# ICGC Storage System\nexport DCC_HOME=~/dcc\n" >> ~/.bashrc -source ~/.bashrc -# add conf directories -mkdir $DCC_HOME/conf -mkdir $DCC_HOME/conf/ssl -mkdir $DCC_HOME/conf/maven -``` - -Maven version must be between 3.0.3 and 3.2.5 (inclusive). -``` -# install mvnvm (http://mvnvm.org/) -curl -s https://bitbucket.org/mjensen/mvnvm/raw/master/mvn > $DCC_HOME/conf/maven/mvn -chmod 0755 $DCC_HOME/conf/maven/mvn -sudo ln -s $DCC_HOME/conf/maven/mvn /usr/local/bin/mvn -echo "mvn_version=3.2.5" >$DCC_HOME/conf/maven/mvnvm.properties -``` - -Also, install unzip if it's not already installed. -``` -sudo apt-get install -y unzip -``` - -Create an SSL certificate to be used across the storage system. This can be done using the LetsEncrypt certbot client (Note: this will require temporarily opening access to port 443 on the EC2). The root account may need to be used for some of this. -``` -git clone https://github.com/certbot/certbot -cd certbot -./certbot-auto certonly --standalone --email -d storage.ucsc-cgl.org -cd /etc/letsencrypt/archive/storage.ucsc-cgl.org/ # or wherever output from the previous command points you -# convert pem files to pkcs12 -openssl pkcs12 -export -in cert1.pem -inkey privkey1.pem -out ucsc-storage.p12 -name tomcat -CAfile chain1.pem -caname root -chain -# convert pkcs12 to jks -keytool -importkeystore -destkeystore ucsc-storage.jks -deststorepass password -srckeystore ucsc-storage.p12 -srcstoretype PKCS12 -srcstorepass password -chown ubuntu:ubuntu ucsc-storage.p12 -chown ubuntu:ubuntu ucsc-storage.jks -mv ucsc-storage.p12 ucsc-storage.jks $DCC_HOME/conf/ssl -``` - -The LetsEncrypt root CA certificate has to be added to the JVM truststore to tell the JVM to trust our newly generated certificate. To avoid altering the original, a copy is made that can be specified upon invocation of java clients. -``` -# create copy of jvm truststore with LetsEncrypt cert added -cp /usr/lib/jvm/java-8-oracle/jre/lib/security/cacerts $DCC_HOME/conf/ssl/ -keytool -import -file chain1.pem -alias LetsEncryptCA -keystore cacerts -storepass changeit -``` - -Install and configure MongoDB metadata-server dependency (https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/). The commands shown below leave access to mongodb unrestricted. The port that mongod listens on shouldn't be open to external IPs, and in production systems access restriction should be enabled. -``` -sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927 -echo "deb http://repo.mongodb.org/apt/ubuntu trusty/mongodb-org/3.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.2.list -sudo apt-get update -sudo apt-get install -y mongodb-org -# printf 'use admin\ndb.createUser({user:"%s",pwd:"%s", roles:[{role:"userAdminAnyDatabase",db:"admin"}]})' metadata pass | mongo -# printf '\n# Enable auth\nauth=true\n' | sudo tee -a /etc/mongod.conf >/dev/null 2>&1 -# sudo service mongod restart -``` - -Install git. -``` -sudo apt-get install -y git -``` - -Pull in and build the storage system source, linking to the ssl certificate while you're at it. -``` -# clone storage system source -cd $DCC_HOME -git clone git@github.com:overture-stack/score.git -git clone git@github.com:BD2KGenomics/dcc-auth.git -git clone git@github.com:BD2KGenomics/dcc-metadata.git -# link mvnvm.properties and ssl certificate then build -for f in $DCC_HOME/dcc-*; do ln -s $DCC_HOME/conf/maven/mvnvm.properties $f/mvnvm.properties && ln -s $DCC_HOME/conf/ssl/ucsc-storage.jks $f/ucsc-storage.jks && cd $f && mvn; done; -``` - -Run the system. -``` -# run the auth-server (TODO: no description of config properties file) -cd $DCC_HOME/dcc-auth/dcc-auth-server/ && java -Dspring.profiles.active=dev,no_scope_validation -Dserver.ssl.key-store=ucsc-storage.jks -Dserver.ssl.key-store-password=password -Dserver.ssl.key-store-type=JKS -Dlogging.file=/var/log/dcc/auth-server/auth-server.log -Dserver.port=8443 -Dmanagement.port=8543 -jar $DCC_HOME/dcc-auth/dcc-auth-server/target/dcc-auth-server-1.0.13-SNAPSHOT.jar -# run the metadata-server -cd $DCC_HOME/dcc-metadata/dcc-metadata-server && java -Djavax.net.ssl.trustStore=$DCC_HOME/conf/ssl/cacerts -Djavax.net.ssl.trustStorePassword=changeit -Dspring.profiles.active=development,secure -Dserver.port=8444 -Dmanagement.port=8544 -Dlogging.file=/var/log/dcc/metadata-server/metadata-server.log -Dauth.server.url=https://storage.ucsc-cgl.org:8443/oauth/check_token -Dauth.server.clientId=metadata -Dauth.server.clientsecret=pass -Dspring.data.mongodb.uri=mongodb://localhost:27017/dcc-metadata -Dserver.ssl.key-store=ucsc-storage.jks -Dserver.ssl.key-store-password=password -Dserver.ssl.key-store-type=JKS -jar target/dcc-metadata-server-0.0.16-SNAPSHOT.jar -# run the storage-server -cd $DCC_HOME/score/score-server && java -Djavax.net.ssl.trustStore=$DCC_HOME/conf/ssl/cacerts -Djavax.net.ssl.trustStorePassword=changeit -Dspring.profiles.active=secure,default -Dlogging.file=/var/log/dcc/storage-server/storage-server.log -Dserver.port=5431 -Dbucket.name.object= -Dbucket.name.state= -Dauth.server.url=https://storage.ucsc-cgl.org:8443/oauth/check_token -Dauth.server.clientId=storage -Dauth.server.clientsecret=pass -Dmetadata.url=https://storage.ucsc-cgl.org:8444 -Dendpoints.jmx.domain=storage -Ds3.endpoint=https://s3.amazonaws.com -Ds3.accessKey=foo -Ds3.secretKey=bar -Ds3.masterEncryptionKeyId=baz -Ds3.secured=true -Dupload.clean.enabled=false -Dserver.ssl.key-store=ucsc-storage.jks -Dserver.ssl.key-store-password=password -Dserver.ssl.key-store-type=JKS -jar target/score-server-1.0.14-SNAPSHOT.jar -``` -Note: passwords (and ideally all configuration) should be specified in configuration files in production systems. diff --git a/LICENSE b/LICENSE deleted file mode 100644 index dba13ed2..00000000 --- a/LICENSE +++ /dev/null @@ -1,661 +0,0 @@ - GNU AFFERO GENERAL PUBLIC LICENSE - Version 3, 19 November 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU Affero General Public License is a free, copyleft license for -software and other kinds of works, specifically designed to ensure -cooperation with the community in the case of network server software. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Skipping creation..." $(END); \ else \ - $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 mb s3://oicr.icgc.test; \ + $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 mb s3://score.data; \ fi - @$(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 cp /score-data/heliograph s3://oicr.icgc.test/data/heliograph + @$(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 cp /score-data/heliograph s3://score.data/data/heliograph _destroy-object-storage: - @echo $(YELLOW)$(INFO_HEADER) "Removing bucket oicr.icgc.test" $(END) - @if $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 ls s3://oicr.icgc.test ; then \ - $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 rb s3://oicr.icgc.test --force; \ + @echo $(YELLOW)$(INFO_HEADER) "Removing bucket score.data" $(END) + @if $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 ls s3://score.data ; then \ + $(DOCKER_COMPOSE_CMD) run aws-cli --endpoint-url http://object-storage:9000 s3 rb s3://score.data --force; \ else \ echo $(YELLOW)$(INFO_HEADER) "Bucket does not exist. Skipping..." $(END); \ fi diff --git a/README.md b/README.md index 2d79e12f..4967d101 100644 --- a/README.md +++ b/README.md @@ -1,71 +1,71 @@ -# Score - File Transfer & Object Storage +# Score -[](http://slack.overture.bio) -[](https://github.com/overture-stack/score/blob/develop/LICENSE) -[](code_of_conduct.md) - -
-score-logo -
- -Genomics data volume and velocity have increased dramatically, rendering on-premise storage insufficient and demanding specialized software tools to manage data in the cloud. [Score](https://www.overture.bio/documentation/score/) addresses this by facilitating the transfer and storage of genomics data to and from a cloud network. - - +Score is a file transfer service designed to enable large-file upload and download, providing a robust API for secure file transfer and storage operations. It serves as an intermediary between object storage systems and user authorization mechanisms, using pre-signed URLs for efficient and protected data access.
> >
-> +> >
> -> *Score is a core component within the [Overture](https://www.overture.bio/) research software ecosystem. Overture is a toolkit of modular software components made to build into scalable genomics data management systems. See our [related products](#related-products) for more information on what Overture can offer.* +> *Score is part of [Overture](https://www.overture.bio/), a collection of open-source software microservices used to create platforms for researchers to organize and share genomics data.* > -> - -## Technical Specifications +## Key Features -- Written in JAVA -- Supports AWS S3, Azure, Google Cloud, Openstack with Ceph, Minio and all other S3-compliant cloud storage solutions -- Built-in [Samtools](http://www.htslib.org/) functionality including BAM and CRAM file slicing by genomic region -- ACL security using [OAuth 2.0](https://oauth.net/2/) and scopes based on study codes -- Multipart Uploads and Downloads -- REST API with [Swagger UI](https://swagger.io/tools/swagger-ui/) -- [MD5sum](https://www.intel.com/content/www/us/en/support/programmable/articles/000078103.html) validation +- **Multi-cloud Support**: Compatible with AWS S3, Azure Storage, and any object storage with an S3 compliant API (Minio, Ceph, etc.) +- **High-performance Transfers**: Implements multipart uploads and downloads for optimal throughput +- **Genomic Data Handling (SamTools)**: Supports BAM/CRAM file slicing by genomic region and provides built-in samtools operations for BAM file handling +- **Data Integrity**: Ensures file integrity through MD5 checksum validation on uploads and downloads +- **Security**: Implements ACL-based security using OAuth2 with study code-scoped access +- **Metadata Integration**: Integrates with the Song metadata management system for comprehensive data tracking +- **File Bundling**: Enables efficient transfer of multiple files in a single bundle +- **Resumable Downloads**: Supports resuming downloads after network interruptions +- **FUSE Support**: Offers file system in Userspace (FUSE) support for enhanced file operations +- **Interactive API Documentation:** Built-in Swagger UI for easy API interaction and exploration ## Documentation -- :construction: Developer documentation, including instructions for running Score from source can be found in the [Wiki](https://github.com/overture-stack/score/wiki) :construction: -- For user documentation, including installation, configuration and usage guides, see the Overture websites [Score documentation page](https://www.overture.bio/documentation/score/) +Technical resources for those working with or contributing to the project are available from our official documentation site, the following content can also be read and updated within the `/docs` folder of this repository. -## Support & Contributions +- **[Score Overview](https://docs.overture.bio/docs/core-software/Score/overview)** +- [**Setting up the Development Environment**](https://docs.overture.bio/docs/core-software/Score/setup) +- [**Common Usage Docs**](https://docs.overture.bio/docs/core-software/Score/setup) -- Filing an [issue](https://github.com/overture-stack/score/issues) -- Making a [contribution](CONTRIBUTING.md) -- Connect with us on [Slack](https://join.slack.com/t/overture-bio/shared_invite/zt-21tdumtdh-9fP1TFeLepK4~Lc377rOYw) -- Add or Upvote a [feature request](https://github.com/overture-stack/score/issues?q=is%3Aopen+is%3Aissue+label%3Anew-feature+sort%3Areactions-%2B1-desc) +## Development Environment -## Related Software +- [Java 11 (OpenJDK)](https://openjdk.java.net/projects/jdk/11/) +- [Maven 3.5+](https://maven.apache.org/) (or use provided wrapper) +- [VS Code](https://code.visualstudio.com/) or preferred Java IDE +- [Docker](https://www.docker.com/) Container platform -
- Overture overview -
+## Support & Contributions -Score commonly works in tandem with our metadata service, [Song](https://github.com/overture-stack/SONG). While Score handles object storage and file transfer, Song validates and tracks all the associated file metadata. +- For support, feature requests, and bug reports, please see our [Support Guide](https://docs.overture.bio/community/support). +- For detailed information on how to contribute to this project, please see our [Contributing Guide](https://docs.overture.bio/docs/contribution). -All our core microservices are included in the Overture **Data Management System** (DMS). Built from our core collection of microservices, the DMS offers turnkey installation, configuration, and deployment of Overture software. For more information on the DMS, read our [DMS documentation](https://www.overture.bio/documentation/dms/). +## Related Software -See the links below for information on our other research software tools: +The Overture Platform includes the following Overture Components:
|Software|Description| |---|---| -|[Ego](https://github.com/overture-stack/ego)|An authorization and user management service| -|[Ego UI](https://github.com/overture-stack/ego-ui)|A UI for managing Ego authentication and authorization services| -|[Score](https://github.com/overture-stack/score)| Transfer data to and from any cloud-based storage system| -|[Song](https://github.com/overture-stack/song)|Catalog and manage metadata associated to file data spread across cloud storage systems| -|[Maestro](https://github.com/overture-stack/maestro)|Organizing your distributed data into a centralized Elasticsearch index| -|[Arranger](https://github.com/overture-stack/arranger)|A search API with reusable UI components that build into configurable and functional data portals| -|[DMS-UI](https://github.com/overture-stack/dms-ui)|A simple web browser UI that integrates Ego and Arranger| +|[Score](https://github.com/overture-stack/score/)| Transfer data to and from any cloud-based storage system | +|[Song](https://github.com/overture-stack/song/)| Catalog and manage metadata associated to file data spread across cloud storage systems | +|[Maestro](https://github.com/overture-stack/maestro/)| Organizing your distributed data into a centralized Elasticsearch index | +|[Arranger](https://github.com/overture-stack/arranger/)| A search API with reusable search UI components | +|[Stage](https://github.com/overture-stack/stage)| A React-based web portal scaffolding | +|[Lyric](https://github.com/overture-stack/lyric)| A model-agnostic, tabular data submission system | +|[Lectern](https://github.com/overture-stack/lectern)| Schema Manager, designed to validate, store, and manage collections of data dictionaries. | + +If you'd like to get started using our platform [check out our quickstart guides](https://docs.overture.bio/guides/getting-started) + +## Funding Acknowledgement + +Overture is supported by grant #U24CA253529 from the National Cancer Institute at the US National Institutes of Health, and additional funding from Genome Canada, the Canada Foundation for Innovation, the Canadian Institutes of Health Research, Canarie, and the Ontario Institute for Cancer Research. + +#### Powered by +[![JetBrains logo.](https://resources.jetbrains.com/storage/products/company/brand/logos/jetbrains.svg)](https://jb.gg/OpenSourceSupport) diff --git a/code_of_conduct.md b/code_of_conduct.md deleted file mode 100755 index 45d257b2..00000000 --- a/code_of_conduct.md +++ /dev/null @@ -1,133 +0,0 @@ - -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, -nationality, personal appearance, race, caste, color, religion, or sexual -identity and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the overall - community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or advances of - any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email address, - without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -[INSERT CONTACT METHOD]. -All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series of -actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or permanent -ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within the -community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.1, available at -[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. - -Community Impact Guidelines were inspired by -[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. - -For answers to common questions about this code of conduct, see the FAQ at -[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at -[https://www.contributor-covenant.org/translations][translations]. - -[homepage]: https://www.contributor-covenant.org -[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html -[Mozilla CoC]: https://github.com/mozilla/diversity -[FAQ]: https://www.contributor-covenant.org/faq -[translations]: https://www.contributor-covenant.org/translations diff --git a/docker-compose.yml b/docker-compose.yml index 645517f6..cde27bd5 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -53,11 +53,11 @@ services: dockerfile: "$DOCKERFILE_NAME" target: server environment: - SPRING_PROFILES_ACTIVE: amazon,collaboratory,prod,secure + SPRING_PROFILES_ACTIVE: s3,prod,secure SERVER_PORT: 8080 OBJECT_SENTINEL: heliograph - BUCKET_NAME_OBJECT: oicr.icgc.test - BUCKET_NAME_STATE: oicr.icgc.test + BUCKET_NAME_OBJECT: score.data + BUCKET_NAME_STATE: score.data COLLABORATORY_DATA_DIRECTORY: data METADATA_URL: http://song-server:8080 S3_ENDPOINT: http://object-storage:9000 @@ -138,7 +138,7 @@ services: AWS_SECRET_ACCESS_KEY: minio123 AWS_DEFAULT_REGION: us-east-1 volumes: - - "./docker/object-storage-init/data/oicr.icgc.test/data:/score-data:ro" + - "./docker/object-storage-init/data/score.data/data:/score-data:ro" song-server: image: ghcr.io/overture-stack/song-server:438c2c42 environment: diff --git a/docker/object-storage-init/data/oicr.icgc.test/data/heliograph b/docker/object-storage-init/data/score.data/data/heliograph similarity index 100% rename from docker/object-storage-init/data/oicr.icgc.test/data/heliograph rename to docker/object-storage-init/data/score.data/data/heliograph diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 538a98c1..00000000 --- a/docs/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = score -SOURCEDIR = . -CONFDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - 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e
e
Search & Exploration
Search & Exploration
Arranger Configs
Define the structure and formatting of your data
Arranger Configs...


Index Mapping
Define the structure of your index

Index Mapping...
Event Processing
Message queuing of publication events for triggering downstream data indexing 
Event Processing...
Data Management & Storage
Data Management & Storagez

Song Schema
Define input fields with rules, logic and syntax

Song Schema...

Object Storage Providers
Score is compatible with any S3 compliant object storage provider

Object Storage Providers...
Authorization & Authentication
Authorization & Authentication

Overture API Key Provider
Extends Keycloak's functionality to support API authentication

Overture API Key Provider...Text is not SVG - cannot display \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 2185f0c3..00000000 --- a/docs/conf.py +++ /dev/null @@ -1,170 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -# -# score documentation build configuration file, created by -# sphinx-quickstart on Thu Sep 27 15:44:32 2018. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = ['sphinx.ext.mathjax', - 'sphinx.ext.viewcode'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = 'score' -copyright = '2018, andricdu' -author = 'andricdu' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '1.4.0' -# The full version, including alpha/beta/rc tags. -release = '1.4.0' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# This is required for the alabaster theme -# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars -html_sidebars = { - '**': [ - 'relations.html', # needs 'show_related': True theme option to display - 'searchbox.html', - ] -} - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'scoredoc' - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'score.tex', 'score Documentation', - 'andricdu', 'manual'), -] - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'score', 'score Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'score', 'score Documentation', - author, 'score', 'One line description of project.', - 'Miscellaneous'), -] - - - diff --git a/docs/img/azure_policies.png b/docs/img/azure_policies.png deleted file mode 100644 index a06ff45e..00000000 Binary files a/docs/img/azure_policies.png and /dev/null differ diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 34d422c3..00000000 --- a/docs/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -================================= -Score Documentation -================================= - -.. toctree:: - :maxdepth: 4 - - introduction.rst - - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/introduction.rst b/docs/introduction.rst deleted file mode 100644 index 0c55f96c..00000000 --- a/docs/introduction.rst +++ /dev/null @@ -1,89 +0,0 @@ -introduction.rst - -============== -Introduction -============== - - -What is Score? -====================== - -`Score `_ facilitates the transfer and storage of your data seamlessly for cloud-based projects. File bundling, resumable downloads, and BAM/CRAM slicing make data transfer fast and smooth. - -The method with which Score facilitates the transfer of data is through the use of pre-signed URLs. As such, Score can be thought of as a broker between an object storage system and user authorization system, validating user access and generating signed URLs for object access. - - ------------------------------------------ - -.. _introduction_features: - -Features -====================== - -- Multipart Uploads and Downloads (high performance transfers) -- Support for AWS S3, Azure Storage, Google Cloud Storage -- Slicing of BAM and CRAM files by genomic region -- Client includes some samtools functionality such as viewing reads from a BAM -- MD5 validation of uploads and downloads -- ACL security using OAuth2 and scopes based on study codes -- Integrates with the SONG metadata system for data book keeping and consistency -- REST API with swagger docs - - -Projects Using Score -====================== - -1. **Cancer Collaboratory - Toronto**: https://storage.cancercollaboratory.org/swagger-ui.html -2. **AWS - Virginia**: https://virginia.cloud.icgc.org/swagger-ui.html - - -Getting Started -============================ - -Client ---------------- - -The Score Client is available to download as both a docker container or as a Java CLI application. - -The docker container can be pulled from here: - -``docker pull overture/score`` - -For the Java CLI, use the following steps: - -.. code-block:: bash - - wget -O score-client.tar.gz https://artifacts.oicr.on.ca/artifactory/dcc-release/bio/overture/score-client/[RELEASE]/score-client-[RELEASE]-dist.tar.gz - - tar xvzf score-client.tar.gz - - echo export PATH=$(pwd)/score-client-x.x.x/bin:$PATH >> ~/.bashrc - - source ~/.bashrc - - # you will then be able to use it by running the following command anywhere is the system - score-client - - -Server ---------------- - -To be Added... - - -License -============= -Copyright (c) 2018. Ontario Institute for Cancer Research - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU Affero General Public License as -published by the Free Software Foundation, either version 3 of the -License, or (at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU Affero General Public License for more details. - -You should have received a copy of the GNU Affero General Public License -along with this program. If not, see . diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index ff176b65..00000000 --- a/docs/make.bat +++ /dev/null @@ -1,37 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set CONFDIR=source -set BUILDDIR=_build -set SPHINXPROJ=score - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd diff --git a/docs/overview.md b/docs/overview.md new file mode 100644 index 00000000..be0874a8 --- /dev/null +++ b/docs/overview.md @@ -0,0 +1,51 @@ +# Overview + +Score is a file transfer service designed to enable large-file upload and download, providign a robust API for secure file transfer and storage operations. It serves as an intermediary between object storage systems and user authorization mechanisms, using pre-signed URLs for efficient and protected data access. + +## System Architecture + +Score's primary function is to broker authenticated access to your object storage provider. It achieves this by: + +1. Validating user access rights against an authorization system (OAuth) +2. Generating time-limited pre-signed URLs for object access +3. Facilitating secure data transfer between clients and object storage + +![Score Arch](./assets/scoreDev.svg 'Score Architecture Diagram') + +As part of the larger Overture.bio software suite, Score is typically used with multiple other services including: + +- **Song:** A metadata management service made to manage file metadata independently from object storage concerns +- **Score Client:** A command line tool to streamline interactions with Scores REST API endpoints +- **Keycloak:** The authorization and authentication service used to provided OAuth2 authentication for Score + + +## Key Features + +- **Multi-cloud Support**: Compatible with AWS S3, Azure Storage, and any object storage with an S3 compliant API (Minio, Ceph, etc.) +- **High-performance Transfers**: Implements multipart uploads and downloads for optimal throughput +- **Genomic Data Handling (SamTools)**: Supports BAM/CRAM file slicing by genomic region and provides built-in samtools operations for BAM file handling +- **Data Integrity**: Ensures file integrity through MD5 checksum validation on uploads and downloads +- **Security**: Implements ACL-based security using OAuth2 with study code-scoped access +- **Metadata Integration**: Integrates with the Song metadata management system for comprehensive data tracking +- **File Bundling**: Enables efficient transfer of multiple files in a single bundle +- **Resumable Downloads**: Supports resuming downloads after network interruptions +- **FUSE Support**: Offers file system in Userspace (FUSE) support for enhanced file operations +- **Interactive API Documentation:** Built-in Swagger UI for easy API interaction and exploration + + +## Repository Structure +The repository is organized with the following directory structure: +``` +. +├── /score-client +├── /score-core +├── /score-fs +├── /score-server +└── /score-test +``` + +- **score-client:** Command line app for uploading and downloading files, published as a [docker container](https://github.com/overture-stack/score/pkgs/container/score) and availabe as an executable jar from [github releases](https://github.com/overture-stack/score/releases) +- **score-core:** Core library containing shared utilities and data models used by all other packages +- **score-fs:** File system operations module for managing local files +- **score-server:** Main server application that handles object storage and transfers, published as a [docker container](https://github.com/overture-stack/score/pkgs/container/score-server) +- **score-test:** Integration and end-to-end test suite for all packages diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 04c85770..00000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -sphinx -sphinx-autobuild -sphinx_rtd_theme diff --git a/docs/setup.md b/docs/setup.md new file mode 100644 index 00000000..8ce44b81 --- /dev/null +++ b/docs/setup.md @@ -0,0 +1,174 @@ +# Setup + +## Prerequisites + +Before you begin, ensure you have the following installed on your system: + +- [JDK11](https://www.oracle.com/ca-en/java/technologies/downloads/) +- [Docker](https://www.docker.com/products/docker-desktop/) (v4.39.0 or higher) + +## Score-Server Development Setup + +This guide will walk you through setting up a complete development environment, including Score and its complementary services. + +### Setting up supporting services + +We'll use our quickstart service, a flexible Docker Compose setup, to spin up Score's complementary services. + +1. Clone the quickstart repository and move into its directory: + + ```bash + git clone -b quickstart https://github.com/overture-stack/prelude.git + cd prelude + ``` + +2. Run the appropriate start command for your operating system: + + | Operating System | Command | + | ---------------- | --------------------- | + | Unix/macOS | `make scoreDev` | + | Windows | `./make.bat scoreDev` | + +
+ **Click here for a detailed breakdown** + + This command will set up all complementary services for Score development as follows: + + ![ScoreDev](./assets/scoreDev.svg "Score Dev Environment") + + | Service | Port | Description | Purpose in Score Development | + | ----------- | ------ | ----------------------------------------------- | ------------------------------------------- | + | Conductor | `9204` | Orchestrates deployments and environment setups | Manages the overall development environment | + | Keycloak-db | - | Database for Keycloak (no exposed port) | Stores Keycloak data for authentication | + | Keycloak | `8180` | Authorization and authentication service | Provides OAuth2 authentication for Score | + | Song-db | `5433` | Database for Song | Stores metadata managed by Song | + | Song | `8080` | Metadata management service | Manages metadata for files stored by Score | + | Minio | `9000` | Object storage provider | Simulates S3-compatible storage for Score | + + - Ensure these ports are free on your system before starting the environment. + - You may need to adjust the ports in the `docker-compose.yml` file if you have conflicts with existing services. + + For more information, see our [quickstart documentation linked here](https://docs.overture.bio/docs/other-software/quickstart) + +
+ +### Running the Development Server + +1. Clone Score and move into its directory: + + ```bash + git clone https://github.com/overture-stack/score.git + cd score + ``` + +2. Build the application locally: + + ```bash + ./mvnw clean install -DskipTests + ``` + +
+ **Click here for an explaination of command above** + + - `./mvnw`: This is the Maven wrapper script, which ensures you're using the correct version of Maven. + - `clean`: This removes any previously compiled files. + - `install`: This compiles the project, runs tests, and installs the package into your local Maven repository. + - `-DskipTests`: This flag skips running tests during the build process to speed things up. + +
+ + :::tip + Ensure you are running JDK11. To check, you can run `java --version`. You should see something similar to the following: + + ```bash + openjdk version "11.0.18" 2023-01-17 LTS + OpenJDK Runtime Environment Corretto-11.0.18.10.1 (build 11.0.18+10-LTS) + OpenJDK 64-Bit Server VM Corretto-11.0.18.10.1 (build 11.0.18+10-LTS, mixed mode) + ``` + + ::: + +3. Start the Score Server: + + ```bash + ./mvnw spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev -pl score-server + ``` + + :::info + + If you are looking to configure Score for your specific environment, [**the Score-servers configuration file can be found here**](https://github.com/overture-stack/score/blob/develop/score-server/src/main/resources/application.yml). A summary of the available Spring profiles is provided below: + +
+ **Click here for a summary of the Score-server spring profiles** + + **Score Profiles** + | Profile | Description | + | ----------- | ------------------------------------------------------------------------------------------------------------------------------- | + | `default` | Common settings for all environments. Includes server, S3, bucket, object, upload, and authentication configurations. | + | `ssl` | Enables SSL configuration for using a self-signed certificate in production deployments. | + | `azure` | Configuration for Azure blob storage. Includes Azure-specific settings and bucket policies. | + | `s3` | Configuration for Amazon S3 or S3-compatible storage. Includes endpoint, access key, and secret key settings. | + | `prod` | Production environment configuration. Enables secure S3 connections and sets the metadata URL. | + | `secure` | Security configuration for OAuth2 and JWT. Includes settings for resource server, authentication server, and scope definitions. | + | `dev` | Development environment configuration. Uses non-secure S3 connections, local endpoints, and disables upload cleaning. | + | `benchmark` | Configuration for benchmarking purposes. Includes SSL settings and a non-secure S3 endpoint. | + +
+ + ::: + +### Verification + +After installing and configuring Score, verify that the system is functioning correctly: + +1. **Check Server Health** + + ```bash + curl -s -o /dev/null -w "%{http_code}" "http://localhost:8087/download/ping" + ``` + + - Expected result: Status code `200` + - Troubleshooting: + - Ensure Score server is running + - Check you're using the correct port (default is 8087) + - Verify no firewall issues are blocking the connection + +2. **Check the Swagger UI** + - Navigate to `http://localhost:8087/swagger-ui.html` in a web browser + - Expected result: Swagger UI page with a list of available API endpoints + - Troubleshooting: + - Check browser console for error messages + - Verify you're using the correct URL + +:::info Need Help? +If you encounter any issues or have questions about our API, please don't hesitate to reach out through our relevant [**community support channels**](https://docs.overture.bio/community/support). +::: + +## Score-Client Setup + +The `score-client` is a CLI tool used for communicating with a `score-server`. For ease of deployment it can be run using Docker. The client can be configured through environment variables, which take precedence over the `application.yml` config. + +```bash +docker run -d --name score-client \ + -e ACCESSTOKEN=68fb42b4-f1ed-4e8c-beab-3724b99fe528 \ + -e STORAGE_URL=http://localhost:8087 \ + -e METADATA_URL=http://localhost:8080 \ + --network="host" \ + --platform="linux/amd64" \ + --mount type=bind,source=${pwd},target=/output \ + ghcr.io/overture-stack/score:latest +``` + +
+ **Click here for an explaination of command above** + - `-e ACCESSTOKEN=68fb42b4-f1ed-4e8c-beab-3724b99fe528` sets up the score-client with a pre-configured system-wide access token that works with the quickstart service setup. + - `-e STORAGE_URL=http://score:8087` is the url for the Score server that the Score-Client will interact with. + - `-e METADATA_URL=http://song:8080` is the url for the song server that the score-client will interact with. + - `--network="host"` Uses the host network stack inside the container, bypassing the usual network isolation. This means the container shares the network namespace with the host machine. + - `--platform="linux/amd64"` Specifies the platform the container should emulate. In this case, it's set to linux/amd64, indicating the container is intended to run on a Linux system with an AMD64 architecture. + - `--mount type=bind,source={pwd},target=/output` mounts the directory and its contents (volume) from the host machine to the container. In this case, it binds the present working directory from the host to /output inside the container. Any changes made to the files in this directory will be reflected in both locations. +
+ +:::warning +This guide is meant to demonstrate the configuration and usage of Score for development purposes and is not intended for production. If you ignore this warning and use this in any public or production environment, please remember to use Spring profiles accordingly. For production do not use **dev** profile. +::: diff --git a/docs/start-sphinx-server.sh b/docs/start-sphinx-server.sh deleted file mode 100755 index bfaabab6..00000000 --- a/docs/start-sphinx-server.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env bash -sphinx-autobuild \ --b html \ --H localhost \ ---watch source \ ---ignore "*.swp" \ ---ignore "*.pdf" \ ---ignore "*.log" \ ---ignore "*.out" \ ---ignore "*.toc" \ ---ignore "*.aux" \ ---ignore "*.idx" \ ---ignore "*.ind" \ ---ignore "*.ilg" \ ---ignore "*.tex" \ ---ignore "*.pyc" \ ---ignore "*.py_*" \ ---ignore "*.rst_*" \ ---ignore "*4913*" \ --c source source _build/html \ No newline at end of file diff --git a/docs/usage/01-upload.md b/docs/usage/01-upload.md new file mode 100644 index 00000000..7778ad66 --- /dev/null +++ b/docs/usage/01-upload.md @@ -0,0 +1,92 @@ +# File Upload + +Data uploads using the Client or API. + +:::info Data Submission Guide +For detailed step-by-step instructions on using Song and Score clients for data submissions, see our [**platform guide on CLI submissions**](https://docs.overture.bio/guides/user-guides/cli-submissions). +::: + +## Installing Score-Client + +To run the score-client using Docker, provide the following environment variables: +- `STORAGE_URL`: Score server URL +- `METADATA_URL`: Song server URL +- `ACCESSTOKEN`: Valid access token + +Use this command to run a Score Client docker container: + +```bash +docker run -d --name score-client \ + -e ACCESSTOKEN=${token} \ + -e STORAGE_URL=${scoreServerUrl} \ + -e METADATA_URL=${songServerUrl} \ + --network="host" \ + --platform="linux/amd64" \ + --mount type=bind,source="$(pwd)",target=/output \ + ghcr.io/overture-stack/score:latest +``` + +Replace all `${}` placeholders with your environment's values. + +
+ Detailed command breakdown + + - `-d`: Runs container in detached mode (background) + - `-e ACCESSTOKEN=${token}`: Access token from the platform's auth service + - `-e STORAGE_URL=${scoreServerUrl}`: Score server URL + - `-e METADATA_URL=${songServerUrl}`: Song server URL + - `--network="host"`: Uses host network stack + - `--platform="linux/amd64"`: Specifies container platform + - `--mount type=bind,source="$(pwd)",target=/output`: Mounts current directory to container's `/output` + +
+ +## Uploading File Data + +Use the Score Client's `upload` command to upload file data. Main upload methods: + +- `--file`: Upload a specific file by path +- `--manifest`: Upload files based on a manifest file +- `--object-id`: Upload a specific file by object ID + +### Upload Options + +| Option | Description | +|--------|-------------| +| `--force` | Re-upload existing files (overwrite) | +| `--md5` | Specify MD5 checksum of the file | +| `--validate` | Validate file using MD5 checksum | +| `--verify-connection` | Verify object storage connection before upload | + +### Upload Example + +To upload using a manifest file: + +```bash +docker exec score-client sh -c "score-client upload --manifest .//manifest.txt" +``` + +Replace `` with the location of your manifest file. + +A successful upload will produce output similar to: + +```shell +Uploading object: '/home/ubuntu/songdata/input-files/example.vcf.gz.idx' using the object id e98daf88-fdf8-5a89-9803-9ebafb41de94 +100% [##################################################] Parts: 1/1, Checksum: 100%, Write/sec: 1000B/s, Read/sec: 0B/s +Finalizing... +Total execution time: 3.141 s +Total bytes read : 0 +Total bytes written : 24 +Upload completed +Uploading object: '/home/ubuntu/songdata/input-files/example.vcf.gz' using the object id 440f4559-e905-55ec-bdeb-9518f823e287 +100% [##################################################] Parts: 1/1, Checksum: 100%, Write/sec: 7.8K/s, Read/sec: 0B/s +Finalizing... +Total execution time: 3.105 s +Total bytes read : 0 +Total bytes written : 52 +Upload completed +``` + +:::info Support +If you encounter any issues or have questions, please don't hesitate to reach out through our relevant [community support channels](https://docs.overture.bio/community/support) +::: \ No newline at end of file diff --git a/docs/usage/02-download.md b/docs/usage/02-download.md new file mode 100644 index 00000000..d8581134 --- /dev/null +++ b/docs/usage/02-download.md @@ -0,0 +1,80 @@ +# File Download + +Data download using the Score Client. + +:::info Download Guide +For detailed step-by-step instructions on using Song and Score clients for data downloads, see our [**platform guide on CLI downloads**](https://docs.overture.bio/guides/user-guides/cli-downloads). +::: + +## Installing Score-Client + +To run the score-client using Docker, provide the following environment variables: +- `STORAGE_URL`: Score server URL +- `METADATA_URL`: Song server URL +- `ACCESSTOKEN`: Valid access token + +Use this command to run a Score Client docker container: + +```bash +docker run -d --name score-client \ + -e ACCESSTOKEN=${token} \ + -e STORAGE_URL=${scoreServerUrl} \ + -e METADATA_URL=${songServerUrl} \ + --network="host" \ + --platform="linux/amd64" \ + --mount type=bind,source="$(pwd)",target=/output \ + ghcr.io/overture-stack/score:latest +``` + +Replace all `${}` placeholders with your environment's values. + +
+ Detailed command breakdown + + - `-d`: Runs container in detached mode (background) + - `-e ACCESSTOKEN=${token}`: Access token from the platform's auth service + - `-e STORAGE_URL=${scoreServerUrl}`: Score server URL + - `-e METADATA_URL=${songServerUrl}`: Song server URL + - `--network="host"`: Uses host network stack + - `--platform="linux/amd64"`: Specifies container platform + - `--mount type=bind,source="$(pwd)",target=/output`: Mounts current directory to container's `/output` + +
+ +## Downloading File Data + +Use the Score Client's `download` command to retrieve file data using any the following download methods: + +- `--analysis-id`: Download files for a specific Song analysis ID +- `--manifest`: Download files based on a manifest file +- `--object-id`: Download a specific file object +- `--program-id`: Download files for a specific Song program +- `--study-id`: Download files for a specific Song study + +### Download Options + +| Option | Description | +|--------|-------------| +| `--force` | Re-download existing files (overwrite) | +| `--index` | Download file index if available | +| `--length` | Limit download size (bytes) | +| `--offset` | Start download from specific byte position | +| `--output-dir` | Specify download directory | +| `--output-layout` | Set output directory layout (`bundle`, `filename`, or `id`) | +| `--validate` | Validate file using MD5 checksum | +| `--verify-connection` | Verify object storage connection before download | + +### Download Example + +To download using a manifest file: + +```shell +docker exec score-client sh -c "score-client download --manifest .//manifest.txt --output-dir ./" +``` + +- Replace `` with the manifest file location +- Replace `` with your desired download location + +:::info Score Client Reference Doc +For more information see our [**Score Client command reference documentation**](https://docs.overture.bio/docs/core-software/Score/usage/client-reference) +::: \ No newline at end of file diff --git a/docs/usage/03-object-storage.md b/docs/usage/03-object-storage.md new file mode 100644 index 00000000..84c756c4 --- /dev/null +++ b/docs/usage/03-object-storage.md @@ -0,0 +1,151 @@ +# Object Storage Setup + +To set up your object storage for Score: + +1. **Register with an object storage provider** of your choice and follow their instructions for setting up and configuring their service. + + :::info Minio Local Quickstart + If you'd like to quickly spin up a compatible object storage locally, you can run the following command: `docker run --name minIO -p 9000:9000 -e MINIO_ACCESS_KEY=minio -e MINIO_SECRET_KEY=minio123 minio/minio:RELEASE.2018-05-11T00-29-24Z server /data` + ::: + +2. **Create two data buckets for Score** to use: + +- A bucket to store object data +- A bucket to store and maintain state information + + :::tip + After creation, remember the IDs of both buckets, as they will be required later for configuring Score. + ::: + +3. You may need to **create a `/data` sub-folder** in advance for each bucket. This requirement depends on your storage provider and is summarized below: + + | Storage Provider | Data sub-folder required | + |--|--| + | Amazon S3 | No | + | Microsoft Azure | No | + | MinIO | No | + | OpenStack with Ceph | Yes | + +4. **Record the URL, access key, and secret key** used to access your storage service. These credentials will be required later for configuring Score. Record and securely store these values. + + :::info For Amazon S3 buckets + Remember to document the geographical region where you have configured your buckets to be stored, as this will be required when configuring Score. + ::: + +## Environment Variable Setup + +Once your object storage is established, the next step involves configuring Score for connection. The specific configuration settings will vary based on your object storage provider. Below are the detailed setup instructions. + +### AWS, Ceph, or Minio + +To connect Score with AWS, Ceph, or Minio storage, modify your `.env.score` file as follows: + +```bash +# ============================ +# Object Storage Configuration Variables +# ============================ + +SPRING_PROFILES_ACTIVE=prod,aws + +S3_ENDPOINT=http://localhost:9000 +S3_ACCESS_KEY=minio +S3_SECRETKEY=minio123 +S3_SIGV4ENABLED=true + +BUCKET_NAME_OBJECT=object.bucket +BUCKET_NAME_STATE=state.bucket +BUCKET_SIZE_POOL=0 +BUCKET_SIZE_KEY=2 + +UPLOAD_PARTSIZE=1048576 +UPLOAD_RETRY_LIMIT=10 +UPLOAD_CONNECTION_TIMEOUT=60000 +UPLOAD_CLEAN_CRON="0 0 0 * * ?" +UPLOAD_CLEAN_ENABLED=true +``` + +
+**Click here for a summary of these variables** + +**Storage Connection Settings** +* `S3_ENDPOINT`: API endpoint URL of your storage service. Score will communicate with the service via this URL +* `S3_ACCESSKEY`: Access key for your object storage buckets +* `S3_SECRETKEY`: Secret key for your object storage buckets +* `S3_SIGV4ENABLED`: Whether to use AWS S3 Signature Version 4 for authentication (true/false) + +**Bucket Configuration** +* `BUCKET_NAME_OBJECT`: ID of the bucket for storing object data +* `BUCKET_NAME_STATE`: ID of the bucket for storing state information +* `BUCKET_SIZE_POOL`: Used for bucket size pooling +* `BUCKET_SIZE_KEY`: Used for bucket size key configuration + +**Upload Settings** +* `UPLOAD_PARTSIZE`: Byte size of each upload chunk to the object storage (adjust for performance) +* `UPLOAD_RETRY_LIMIT`: Number of retry attempts for failed uploads before aborting +* `UPLOAD_CONNECTION_TIMEOUT`: Timeout duration in milliseconds for idle connections + +**Optional Cleanup Configuration** +* `UPLOAD_CLEAN_CRON`: Schedule for the cleanup cron job (optional) +* `UPLOAD_CLEAN_ENABLED`: Whether to enable the cleanup cron job (optional, true/false) + +
+ +### Azure + +For connecting Score with Azure storage, update `.env.score` as follows: + +```bash +SPRING_PROFILES_ACTIVE=prod,azure + +AZURE_ENDPOINT_PROTOCOL=https +AZURE_ACCOUNT_NAME={storage_account_name} +AZURE_ACCOUNT_KEY={storage_account_secret_key} + +BUCKET_NAME_OBJECT={object_bucket} # Object data storage bucket/container name +BUCKET_POLICY_UPLOAD={write_policy} # Access policy name for write operations +BUCKET_POLICY_DOWNLOAD={read_policy} # Access policy name for read operations + +UPLOAD_PARTSIZE=104587 +DOWNLOAD_PARTSIZE=250000000 # Default part size for downloads + +OBJECT_SENTINEL=heliograph # Required sample object/file name for `ping` operations +``` + +
+**Click here for a summary of these variables** + +**Azure Connection Settings** +* `AZURE_ENDPOINT_PROTOCOL`: Communication protocol for the Azure storage API endpoint (e.g., https) +* `AZURE_ACCOUNT_NAME`: Account name for accessing Azure object storage +* `AZURE_ACCOUNT_KEY`: Account key for accessing Azure object storage + +**Bucket Configuration** +* `BUCKET_NAME_OBJECT`: Bucket ID for storing object data +* `BUCKET_POLICY_UPLOAD`: Access policy name for write operations +* `BUCKET_POLICY_DOWNLOAD`: Access policy name for read operations + +**Performance Settings** +* `UPLOAD_PARTSIZE`: Byte size of each upload chunk (adjust for performance) +* `DOWNLOAD_PARTSIZE`: Byte size of each download chunk (adjust for performance) + +**Monitoring Configuration** +* `OBJECT_SENTINEL`: Default sample object/file name for 'ping' operations + +
+ +#### Access Policy Configuration for Azure + +For Azure storage, you must define a storage access policy for your container. + +1. **Access the Azure dashboard:** Select containers from the left-hand menu. +2. **Locate your container:** Choose `Access Policy` from the dropdown menu. + + ![azure-dash](../assets/azure-dash.png) + +3. **Create `write` and `readonly` access policies:** + + ![azure-policies](../assets/azure-policies.png) + + :::info Azure storage access policies + For more information on Azure storage access policies, visit [the official Azure storage services documentation](https://learn.microsoft.com/en-us/rest/api/storageservices/define-stored-access-policy#create-or-modify-a-stored-access-policy). + ::: \ No newline at end of file diff --git a/docs/usage/04-authentication.md b/docs/usage/04-authentication.md new file mode 100644 index 00000000..7127038d --- /dev/null +++ b/docs/usage/04-authentication.md @@ -0,0 +1,232 @@ +# Configuring Keycloak + +There are multiple methods of deploying Keycloak. Documentation on Keycloak deployment can be found on the [Official Keycloak website](https://www.keycloak.org/guides#getting-started). + +:::info Docker Quickstart +With Docker installed and running on your system you can quickly spin up Keycloak by running: + +```bash +docker run --name keycloak -d \ + -p 8080:8080 \ + -e KEYCLOAK_ADMIN=admin \ + -e KEYCLOAK_ADMIN_PASSWORD=admin \ + quay.io/keycloak/keycloak:22.0 start-dev +``` +If you need to install Docker, visit the [official Docker installation guide](https://docs.docker.com/get-docker/). + +This command starts Keycloak on local port `8080` and creates an initial admin user with the username `admin` and password `admin`. + +::: + +:::warning Development Configuration +This setup is designated for development and testing purposes and should not be used in production settings. For production deployments, please refer to [Configuring Keycloak for Production](https://www.keycloak.org/server/configuration-production). +::: + +## Overture API Key Provider + +The Overture API Key provider extends Keycloak's functionality by adding custom logic that allows Keycloak to interact with Score. The following steps outline how to download and install the Overture API Key provider: + +1. **Download the [Overture API Key Provider](https://github.com/oicr-softeng/keycloak-apikeys/releases/download/1.0.1/keycloak-apikeys-1.0.1.jar)**. +2. **Move the** `keycloak-apikeys.jar` file to the provider's folder within Keycloak (`opt/keycloak/providers/`). +3. **Restart the Keycloak server** for the updated provider to take effect. + +## Realm Configuration + +### Login to the Admin Console + +![Keycloak Login](../assets/KC-Login.png) + +To access the admin console, navigate to `/admin` (e.g., `localhost:8080/admin`) and log in with the credentials created during your Keycloak deployment. + +### Create a Realm + +Keycloak supports the creation of realms for managing isolated groups of applications and users. The default realm is named "master" and is intended solely for Keycloak management. + +![Creating a new realm](../assets/new-realm.png) + +1. Open the **Keycloak Admin Console**. +2. In the top-left corner, **select "master"**, then choose **"Create Realm"**. +3. **Type** `myrealm` in the Realm Name field and select **"Create"**. + +### Creating a Group + +As an example, let's create a `data submitters` group. Afterwards, we will configure and apply the appropriate permissions for this group. + +![Creating a new group](../assets/new-group.png) + +1. From the left-hand panel, select **"Groups"** and click **"Create group"**. +2. **Name the group** `data submitters` and select **"Create"**. + +### Creating a User + +To populate the realm with its first user: + +![Creating a new user](../assets/new-user.png) + +1. From the **Keycloak Admin Console**, under your newly created realm, select **"Users"** from the left-hand menu and click **"Add User"**. +2. **Input your details**, and then click **"Create"**. + + :::info Keycloak User Administration + Various configurations can be applied to new users. Detailed information can be found within [Keycloak's official Server Administration documentation](https://www.keycloak.org/docs/latest/server_admin/). + ::: + +Next, a password must be established: + +1. At the top of the **User details page**, select the **"Credentials" tab**. +2. **Input your Password**. To avoid mandatory password updates upon first login, **set "Temporary" to "Off"**. +3. Using the newly created username and password, **log in to the Keycloak Account Console** accessed at `http://localhost:8080/realms/myrealm/account/`. + + ![Account Profile](../assets/account-profile.png) + +From the Account Console, users can manage their accounts, modify profiles, activate two-factor authentication, and link identity provider accounts. + +## Application Setup + +Before setting up and applying permissions, we must create a "client" for the Score API. + +1. Re-open your Keycloak admin console at `/admin` and confirm you are within your recently created realm. +2. Select **"Clients"** and then **"Create client"** and input the following: + + | Field | Value | + | --------------- | -------------- | + | **Client Type** | OpenID Connect | + | **Client ID** | score-api | + +3. Select **"Next"**, **enable Client Authentication**, confirm **Standard flow is enabled**, **enable authorization**, then click **"Next"** and **"Save"** (Nothing needs to be input for login settings). + + ![Client Configuration](../assets/capability-config.png) + + :::info + Make sure you have enabled both **"Client Authentication"** and **"Authorization"**. + ::: + +### Configuring your Application + +After creating our client, the next step is configuring the resource name, scopes, policies, and permissions. All these settings can be adjusted within the **Authorization tab** of the client you've just created. To access your client, select **"Clients"** from the left-hand navigation menu and from the **"Client list"** select the newly created client. + +![Finding the Client](../assets/finding-client.png) + +#### Scopes + +Scopes represent actions that users can perform on a particular resource. They define the level of access a user has to a resource, such as reading, writing, updating, or deleting. For more details, check out the [Keycloak documentation](https://www.keycloak.org/docs/latest/authorization_services/index.html#scope). + +![New Scope](../assets/auth-scope.png) + +1. Navigate to the **Scopes tab** and select **"Create Authorization Scope"**. +2. **Create two authorization scopes**, one for **READ** and one for **WRITE** access. + +#### Resources + +Resources are objects or entities that users can interact with, such as a database, a file, or an API endpoint. When defining resources, you assign them to specific scopes, indicating what actions can be performed on those resources. For more details, check out the [Keycloak documentation](https://www.keycloak.org/docs/latest/authorization_services/index.html#resource). + +1. From the **Resource tab**, select **"Create Resource"**. +2. Your first resource is generalized and will not be associated with any specific study or program. Name the resource `score`, and from the **authorization scopes field** dropdown select **"READ" and "WRITE"**. +3. **Click Save** and return to the client details page. + + ![New Resource](../assets/new-resource.png) + + :::info Introducing New Studies or Programs + When introducing a new study or program, the creation of an additional resource within Keycloak is required. This includes re-applying the following policies, scopes, and permissions to desired users and groups. + ::: + +#### Policies + +Policies are rules that determine who can access resources based on certain conditions. They encapsulate the logic to decide whether to grant or deny access. Policies can be based on group membership, user attributes, or time-based conditions. For more details, check out the [Keycloak documentation](https://www.keycloak.org/docs/latest/authorization_services/index.html#policy). + +![New Policy](../assets/new-policy.png) + +1. Select the **Policy tab** and click **"Create Client Policy"**. +2. From the popup modal, select **"group policy"**. +3. Name your policy (e.g., `data submission policy`) and select **"Add groups"**. Check the box next to the Data Submitters group and click **"Add"**, then **"Save"**. + +#### Permissions + +Permissions are the final decision-making mechanism connecting resources, scopes, and policies. They define which users or groups can access which resources under what circumstances. Permissions are evaluated based on the evaluation strategy chosen (e.g., Affirmative, Unanimous, or Consensus). For more details, check out the [Keycloak documentation](https://www.keycloak.org/docs/latest/authorization_services/index.html#permission). + +1. Select the **Permissions tab**, click **"Create Permission"**, and from the dropdown select **"Create resource-based permission"**. +2. Assign the newly created resource, scope, and policy. Select `Affirmative strategy`. + +## Creating a New Study + +As mentioned previously, when introducing a new study or program, the creation of an additional resource within Keycloak is required. This includes re-applying policies and permissions to desired users and groups. + +To add a new study, **create a new resource** with the desired name of your study or program (i.e., `score.study123`) and **repeat the steps outlined above**, specifically the Resources, Policies, and Permissions sections of configuring your application. Once complete, you should have the following: + +![Completed](../assets/complete.png) + +## Integration with Score + +Update your `.env.score` file with the required Keycloak variables. The following code block will help you get started: + +```bash +# ============================ +# Keycloak Configurations +# ============================ + +# Profile configuration +SPRING_PROFILES_ACTIVE=aws,prod,secure + +# Server and authentication settings +SERVER_PORT=8087 +SERVER_SSL_ENABLED=false + +# Logging +LOGGING_LEVEL_ORG_SPRINGFRAMEWORK_WEB=INFO +LOGGING_LEVEL_BIO_OVERTURE_SCORE_SERVER=INFO +LOGGING_LEVEL_ROOT=INFO + +# Server Authentication integration +AUTH_SERVER_PROVIDER=keycloak +AUTH_SERVER_KEYCLOAK_HOST=http://localhost:8080 +AUTH_SERVER_KEYCLOAK_REALM=myrealm +AUTH_SERVER_URL=http://localhost:8080/realms/{realmName}/apikey/check_api_key/ +AUTH_SERVER_TOKENNAME=apiKey +AUTH_SERVER_CLIENTID=score-api +AUTH_SERVER_CLIENTSECRET=scoresecret +AUTH_SERVER_SCOPE_STUDY_PREFIX=score. +AUTH_SERVER_SCOPE_UPLOAD_SUFFIX=.WRITE +AUTH_SERVER_SCOPE_DOWNLOAD_SUFFIX=.READ +AUTH_SERVER_SCOPE_DOWNLOAD_SYSTEM=score.WRITE +AUTH_SERVER_SCOPE_DOWNLOAD_SUFFIX=.READ +AUTH_SERVER_SCOPE_UPLOAD_SYSTEM=score.READ +AUTH_SERVER_SCOPE_UPLOAD_SUFFIX=.WRITE +SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_JWKSETURI=http://localhost:8080/realms/{realm-name}/protocol/openid-connect/certs +``` + +Replace any default values with the values specific to your environment. The variables are explained in detail below: + +
+**Click here for details** + +**Profile Configuration** +- `SPRING_PROFILES_ACTIVE`: Defines active Spring profiles for the application (aws,prod,secure) + +**Server and Authentication Settings** +- `SERVER_PORT`: The port number on which the server will listen (default: 8087) +- `SERVER_SSL_ENABLED`: Indicates whether SSL is enabled for the server (default: false) + +**Logging Configuration** +- `LOGGING_LEVEL_ORG_SPRINGFRAMEWORK_WEB`: Sets Spring Framework web components logging level (default: INFO) +- `LOGGING_LEVEL_BIO_OVERTURE_SCORE_SERVER`: Sets Score Server components logging level (default: INFO) +- `LOGGING_LEVEL_ROOT`: Sets the root logging level (default: INFO) + +**Server Authentication Integration** +- `AUTH_SERVER_PROVIDER`: Specifies the authentication server provider (must be keycloak) +- `AUTH_SERVER_KEYCLOAK_HOST`: The host address for the Keycloak server (default: http://localhost:8080) +- `AUTH_SERVER_KEYCLOAK_REALM`: The realm in Keycloak where Score service is registered (example: myrealm) +- `AUTH_SERVER_URL`: Keycloak API endpoint for API key authentication +- `AUTH_SERVER_TOKENNAME`: Token identifier name (keep as default: apiKey) +- `AUTH_SERVER_CLIENTID`: Client ID for Score application in Keycloak (example: score-api) +- `AUTH_SERVER_CLIENTSECRET`: Client secret found under "Client details" → "Credentials tab" + +**Scope Configuration** +- `AUTH_SERVER_SCOPE_STUDY_PREFIX`: Prefix for study-specific scopes (default: score.) +- `AUTH_SERVER_SCOPE_DOWNLOAD_SYSTEM`: System-level download scope (default: score.WRITE) +- `AUTH_SERVER_SCOPE_DOWNLOAD_SUFFIX`: Study-level download scope suffix (default: .READ) +- `AUTH_SERVER_SCOPE_UPLOAD_SYSTEM`: System-level upload scope (default: score.READ) +- `AUTH_SERVER_SCOPE_UPLOAD_SUFFIX`: Study-level upload scope suffix (default: .WRITE) + +**JWT Configuration** +- `SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_JWKSETURI`: URI for JWT JSON Web Key Set for OAuth2 resource server + +
\ No newline at end of file diff --git a/docs/usage/05-hashicorp-vault.md b/docs/usage/05-hashicorp-vault.md new file mode 100644 index 00000000..ce22c7cd --- /dev/null +++ b/docs/usage/05-hashicorp-vault.md @@ -0,0 +1,112 @@ +# Vault Integration + +[HashiCorp's Vault](https://www.vaultproject.io/) provides secure secret management and can be integrated with Score for enhanced security. This section covers how to configure Score to work with Vault. + +:::info Optional Integration +Most deployments do not require Vault integration. The `optional:` prefix means your application will still start even if Vault is unavailable. If you're not explicitly using HashiCorp's Vault, you can skip this configuration. +::: + +## Configuration Options + +### Application YAML Configuration + +The primary way to configure Vault is in your `application.yml`: + +```yaml title="./score-server/src/main/resources/application.yml" +spring: + config: + import: optional:vault:// # Required for Vault integration + cloud: + vault: + # Basic Configuration (Optional) + # host: localhost + # port: 8200 + # scheme: https + + # Authentication (Choose ONE method) + + # Method 1: Token Authentication + # authentication: TOKEN + # token: your-vault-token + + # Method 2: AppRole Authentication + # authentication: APPROLE + # app-role: + # role-id: your-role-id + # secret-id: your-secret-id + # app-auth-path: approle + + # Connection Timeouts (Optional) + # connection-timeout: 5000 + # read-timeout: 15000 +``` + +### Environment Variables + +For Docker deployments, you can configure Vault through environment variables: + +```bash +# ============================ +# Vault Configuration +# ============================ + +# Required - enables Vault integration and configuration import +SPRING_CONFIG_IMPORT=optional:vault:// + +# Basic Configuration (Optional) +SPRING_CLOUD_VAULT_HOST=localhost +SPRING_CLOUD_VAULT_PORT=8200 +SPRING_CLOUD_VAULT_SCHEME=https # Use 'https' for production + +# Authentication (Choose ONE method) + +# Method 1: Token Authentication +SPRING_CLOUD_VAULT_AUTHENTICATION=TOKEN +SPRING_CLOUD_VAULT_TOKEN=your-vault-token + +# Method 2: AppRole Authentication +# SPRING_CLOUD_VAULT_AUTHENTICATION=APPROLE +# SPRING_CLOUD_VAULT_APP_ROLE_ROLE_ID=your-role-id +# SPRING_CLOUD_VAULT_APP_ROLE_SECRET_ID=your-secret-id +# SPRING_CLOUD_VAULT_APP_ROLE_APP_AUTH_PATH=approle + +# Connection Timeouts (Optional) +SPRING_CLOUD_VAULT_CONNECTION_TIMEOUT=5000 +SPRING_CLOUD_VAULT_READ_TIMEOUT=15000 +``` + +## Authentication Methods + +There are two authentication methods with Vault: + +1. **Token Authentication** (simplest, but less secure for production): + ```yaml + authentication: TOKEN + token: your-vault-token + ``` + +2. **AppRole Authentication** (recommended for services): + ```yaml + authentication: APPROLE + app-role: + role-id: your-role-id + secret-id: your-secret-id + app-auth-path: approle + ``` + + :::info AppRole Authentication + AppRole is Vault's recommended authentication method for applications and services. It uses two components: + + - `role-id`: A permanent identifier (like a username) + - `secret-id`: A rotatable credential (like a password) + + AppRole provides enhanced security features like credential rotation, fine-grained access control, and IP restrictions. Contact your Vault administrator to set up AppRole authentication. xwFor details, see [Vault's AppRole documentation](https://developer.hashicorp.com/vault/docs/auth/approle). + ::: + + :::warning Security Notice + Always follow HashiCorp's security guidelines when deploying Vault in production. Never commit sensitive values to version control - use environment variables or secure secret management. + ::: + +For more information about Vault configuration, refer to: +- [Official Vault Documentation](https://www.vaultproject.io/docs) +- [Spring Cloud Vault Documentation](https://docs.spring.io/spring-cloud-vault/docs/current/reference/html/) \ No newline at end of file diff --git a/docs/usage/06-api-reference.mdx b/docs/usage/06-api-reference.mdx new file mode 100644 index 00000000..085011d4 --- /dev/null +++ b/docs/usage/06-api-reference.mdx @@ -0,0 +1,38 @@ +# API Reference + +Scores API is a RESTful API that uses JSON for request and response bodies. It follows standard HTTP methods and status codes, providing a robust interface for managing score-related data in the Overture platform. + +### Access + +Depending on your environment, the Scores Swagger API can be accessed from the following URLs: + +- Development URL: `http://localhost:8087/swagger.html` +- Example production URL: `https://score.demo.overture.bio/swagger-ui.html` + +### Authentication + +In production environments, all requests to the Songs API require authentication using an API key. + +Include your API key in the `Authorization` header of each request as follows: + +``` +Authorization: Bearer YOUR_API_KEY +``` + +:::info API Key Access & Management +For information on accessing an API key from a deployed Overture platform, [**see our platform guide here**](https://docs.overture.bio/guides/user-guides/cli-submissions#generate-an-api-key). + +For information on generating and managing API keys in Overture using Keycloak, [**see our administration guide on identity & access management here**](https://docs.overture.bio/guides/administration-guides). +::: + +### Endpoints + +The following Swagger UI provides an interactive reference for all available Score API endpoints. You can explore the endpoints, request parameters and response schemas from the interface below. + +import SwaggerAPIDoc from '/src/components/SwaggerAPIDoc'; + + + +### Need Help? + +If you encounter any issues or have questions about our API, please don't hesitate to reach out through our relevant [community support channels](https://docs.overture.bio/community/support) \ No newline at end of file diff --git a/docs/usage/07-client-reference.md b/docs/usage/07-client-reference.md new file mode 100644 index 00000000..33c8c7ea --- /dev/null +++ b/docs/usage/07-client-reference.md @@ -0,0 +1,135 @@ +# Client Reference + +Commands and options supported by the Score client. + +## Download + +- The `download` command retrieves file object(s) from the remote storage repository. + +- **Usage:** `score-client download [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--analysis-id` | Download files for a specific Song analysis ID | + | `--force` | Force re-download of existing file (overrides local file) | + | `--index` | Also download file index if available | + | `--length` | Limit number of bytes to download (default: entire file) | + | `--manifest` | Download files based on manifest file ID, URL, or path | + | `--object-id` | Download a specific file object ID | + | `--offset` | Starting byte position for download (default: 0) | + | `--output-dir` | Path to download directory | + | `--output-layout` | Layout of output directory (bundle, filename, or id) | + | `--program-id` | Download files for a specific Song program ID | + | `--study-id` | Download files for a specific Song study ID | + | `--validate` | Perform MD5 checksum validation if available | + | `--verify-connection` | Verify connection to object storage repository first | + +## Help + +- The `help` command displays detailed information about Score client commands and options. + +## Info + +- The `info` command shows active configuration details of the Score client. + +- **Usage:** `score-client info [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--verbose` | Display all Score client configuration properties | + +## Manifest + +- The `manifest` command shows entries of a specific Score manifest file. + +- **Usage:** `score-client manifest [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--manifest` | Manifest file ID, URL, or path to display | + +## Mount + +- The `mount` command provides a read-only FUSE filesystem view of the object storage repository. + +- **Usage:** `score-client mount [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--cache-metadata` | Cache metadata on local disk for faster load times | + | `--daemonize` | Run mount point in background | + | `--layout` | Mount point directory layout (bundle or object-id) | + | `--manifest` | Manifest file to mount contents for | + | `--mount-point` | FUSE file system mount point | + | `--options` | Additional file system mount options | + | `--verify-connection` | Verify connection to object storage repository first | + +## Upload + +- The `upload` command sends file object(s) to the remote storage repository. + +- **Usage:** `score-client upload [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--file` | Path to specific file for upload | + | `--force` | Force re-upload of existing file (overrides repository file) | + | `--manifest` | Upload files using manifest file ID, URL, or path | + | `--md5` | MD5 checksum of file to upload | + | `--object-id` | Upload specific file by object ID | + | `--validate` | Perform MD5 checksum validation if available | + | `--verify-connection` | Verify connection to object storage repository first | + +## Url + +- The `url` command reveals the URL of a specific file object in the storage repository. + +- **Usage:** `score-client url [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--object-id` | Object ID of file to display URL for | + +## Version + +- The `version` command provides current version details of the Score client. + +## View + +- The `view` command stores locally and showcases a SAM or BAM file. + +- **Usage:** `score-client view [OPTIONS]` + + | Option | Description | + |--------|-------------| + | `--bed-query` | BED format file with ranges to query (overrides --query) | + | `--contained` | Output alignments completely contained in specified region | + | `--header-only` | Output only the SAM/BAM file header | + | `--input-file` | Local path to BAM file for querying | + | `--input-file-index` | Local path to index file (requires --input-file) | + | `--manifest` | Manifest file for querying object IDs and ranges | + | `--object-id` | Specific object ID to download slice from | + | `--output-file` | Name of output file | + | `--output-format` | Output file format (SAM or BAM) | + | `--output-dir` | Path to output directory (with --manifest) | + | `--output-index` | Write index files to output (with --manifest) | + | `--output-original-header` | Output entire original header | + | `--output-type` | Structure of output file (CROSS, MERGED, or TRIMMED) | + | `--query` | Query for BAM file content extraction (coordinate format) | + | `--reference-file` | Local path to FASTA file for CRAM decoding | + | `--stdout` | Send output to stdout (forces SAM format) | + | `--verify-connection` | Verify connection to object storage repository first | + +## Additional Options + +Additional option flags available for the `score-client` executable: + +| Option | Description | +|--------|-------------| +| `--profile` | Define specific environment profile for configuration | +| `--quiet` | Run client in quiet mode with minimal info messages | +| `--silent` | Run client in silent mode without any info messages | + +## Need Help? + +If you encounter any issues or have questions, please don't hesitate to reach out through our relevant [community support channels](https://docs.overture.bio/community/support) \ No newline at end of file diff --git a/docs/usage/usage.mdx b/docs/usage/usage.mdx new file mode 100644 index 00000000..09bee5d4 --- /dev/null +++ b/docs/usage/usage.mdx @@ -0,0 +1,21 @@ +# Usage + + + +The following usage docs provide instructions for common tasks and workflows in Score: + +

+ + + +### Score Terminology + +Whether you're new to these tools or looking to refresh your understanding, this glossary is here as a reference of key terms and concepts. + +- **Score Client**: A command-line tool used to interact with the Score server for uploading and downloading data files. + +- **Manifest**: A file that establishes a link between an analysis ID and the data files on your local system, used by Score for file uploads and downloads. + +- **Object ID**: A unique identifier assigned to each file object stored in object storage. + +- **MD5 Checksum**: A cryptographic hash function used to verify the integrity of files during upload and download processes. diff --git a/license.md b/license.md new file mode 100644 index 00000000..8b259447 --- /dev/null +++ b/license.md @@ -0,0 +1,660 @@ +# GNU AFFERO GENERAL PUBLIC LICENSE + +Version 3, 19 November 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. +https://fsf.org/ + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders +of that material) supplement the terms of this License with terms: + +- a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or +- b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or +- c) Prohibiting misrepresentation of the origin of that material, + or requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or +- d) Limiting the use for publicity purposes of names of licensors + or authors of the material; or +- e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or +- f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions + of it) with contractual assumptions of liability to the recipient, + for any liability that these contractual assumptions directly + impose on those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; the +above requirements apply either way. + +### 8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your license +from a particular copyright holder is reinstated (a) provisionally, +unless and until the copyright holder explicitly and finally +terminates your license, and (b) permanently, if the copyright holder +fails to notify you of the violation by some reasonable means prior to +60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run +a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + +An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +### 11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims owned +or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on +the non-exercise of one or more of the rights that are specifically +granted under this License. You may not convey a covered work if you +are a party to an arrangement with a third party that is in the +business of distributing software, under which you make payment to the +third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties +who would receive the covered work from you, a discriminatory patent +license (a) in connection with copies of the covered work conveyed by +you (or copies made from those copies), or (b) primarily for and in +connection with specific products or compilations that contain the +covered work, unless you entered into that arrangement, or that patent +license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under +this License and any other pertinent obligations, then as a +consequence you may not convey it at all. For example, if you agree to +terms that obligate you to collect a royalty for further conveying +from those to whom you convey the Program, the only way you could +satisfy both those terms and this License would be to refrain entirely +from conveying the Program. + +### 13. Remote Network Interaction; Use with the GNU General Public License. + +Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your +version supports such interaction) an opportunity to receive the +Corresponding Source of your version by providing access to the +Corresponding Source from a network server at no charge, through some +standard or customary means of facilitating copying of software. This +Corresponding Source shall include the Corresponding Source for any +work covered by version 3 of the GNU General Public License that is +incorporated pursuant to the following paragraph. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + +### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions +of the GNU Affero General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever +published by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future versions +of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +### 15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT +WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND +PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively state +the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + one line to give the program's name and a brief idea of what it does. + Copyright (C) year name of author + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as + published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see https://www.gnu.org/licenses/. + +Also add information on how to contact you by electronic and paper +mail. + +If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for +the specific requirements. + +You should also get your employer (if you work as a programmer) or +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. For more information on this, and how to apply and follow +the GNU AGPL, see https://www.gnu.org/licenses/. \ No newline at end of file diff --git a/pom.xml b/pom.xml index 22b99150..4194bc43 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 pom ${project.artifactId} ${project.name} diff --git a/score-client/.settings/org.eclipse.jdt.core.prefs b/score-client/.settings/org.eclipse.jdt.core.prefs deleted file mode 100644 index 137ddfa9..00000000 --- a/score-client/.settings/org.eclipse.jdt.core.prefs +++ /dev/null @@ -1,369 +0,0 @@ -eclipse.preferences.version=1 -org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore -org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull -org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault 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-org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=true -org.eclipse.jdt.core.formatter.lineSplit=120 -org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false -org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false -org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0 -org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1 -org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true -org.eclipse.jdt.core.formatter.tabulation.char=space -org.eclipse.jdt.core.formatter.tabulation.size=2 -org.eclipse.jdt.core.formatter.use_on_off_tags=true -org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false -org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true -org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true -org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true diff --git a/score-client/.settings/org.eclipse.jdt.ui.prefs b/score-client/.settings/org.eclipse.jdt.ui.prefs deleted file mode 100644 index ea44eba1..00000000 --- a/score-client/.settings/org.eclipse.jdt.ui.prefs +++ /dev/null @@ -1,58 +0,0 @@ -eclipse.preferences.version=1 -editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true -formatter_profile=_DCC -formatter_settings_version=12 -org.eclipse.jdt.ui.javadoc=true -org.eclipse.jdt.ui.text.custom_code_templates= -sp_cleanup.add_default_serial_version_id=true -sp_cleanup.add_generated_serial_version_id=false -sp_cleanup.add_missing_annotations=true -sp_cleanup.add_missing_deprecated_annotations=true -sp_cleanup.add_missing_methods=false -sp_cleanup.add_missing_nls_tags=false -sp_cleanup.add_missing_override_annotations=true -sp_cleanup.add_missing_override_annotations_interface_methods=true -sp_cleanup.add_serial_version_id=false -sp_cleanup.always_use_blocks=true -sp_cleanup.always_use_parentheses_in_expressions=false -sp_cleanup.always_use_this_for_non_static_field_access=false -sp_cleanup.always_use_this_for_non_static_method_access=false -sp_cleanup.convert_to_enhanced_for_loop=false -sp_cleanup.correct_indentation=false -sp_cleanup.format_source_code=true -sp_cleanup.format_source_code_changes_only=false -sp_cleanup.make_local_variable_final=false -sp_cleanup.make_parameters_final=false -sp_cleanup.make_private_fields_final=true -sp_cleanup.make_type_abstract_if_missing_method=false -sp_cleanup.make_variable_declarations_final=false -sp_cleanup.never_use_blocks=false -sp_cleanup.never_use_parentheses_in_expressions=true -sp_cleanup.on_save_use_additional_actions=true -sp_cleanup.organize_imports=true -sp_cleanup.qualify_static_field_accesses_with_declaring_class=false -sp_cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true -sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true -sp_cleanup.qualify_static_member_accesses_with_declaring_class=false -sp_cleanup.qualify_static_method_accesses_with_declaring_class=false -sp_cleanup.remove_private_constructors=true -sp_cleanup.remove_trailing_whitespaces=false -sp_cleanup.remove_trailing_whitespaces_all=true -sp_cleanup.remove_trailing_whitespaces_ignore_empty=false -sp_cleanup.remove_unnecessary_casts=true -sp_cleanup.remove_unnecessary_nls_tags=false -sp_cleanup.remove_unused_imports=false -sp_cleanup.remove_unused_local_variables=false -sp_cleanup.remove_unused_private_fields=true -sp_cleanup.remove_unused_private_members=false -sp_cleanup.remove_unused_private_methods=true -sp_cleanup.remove_unused_private_types=true -sp_cleanup.sort_members=false -sp_cleanup.sort_members_all=false -sp_cleanup.use_blocks=false -sp_cleanup.use_blocks_only_for_return_and_throw=false -sp_cleanup.use_parentheses_in_expressions=false -sp_cleanup.use_this_for_non_static_field_access=false -sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true -sp_cleanup.use_this_for_non_static_method_access=false -sp_cleanup.use_this_for_non_static_method_access_only_if_necessary=true diff --git a/score-client/.settings/org.eclipse.m2e.core.prefs b/score-client/.settings/org.eclipse.m2e.core.prefs deleted file mode 100644 index f897a7f1..00000000 --- a/score-client/.settings/org.eclipse.m2e.core.prefs +++ /dev/null @@ -1,4 +0,0 @@ -activeProfiles= -eclipse.preferences.version=1 -resolveWorkspaceProjects=true -version=1 diff --git a/score-client/Dockerfile b/score-client/Dockerfile index 7b4323e7..c39bb487 100644 --- a/score-client/Dockerfile +++ b/score-client/Dockerfile @@ -8,7 +8,6 @@ # Banner @ https://goo.gl/Yyoc6R FROM ubuntu:16.04 -MAINTAINER ICGC # # Update apt, add FUSE support and basic command line tools diff --git a/score-client/README.md b/score-client/README.md index fedec157..fd9795fe 100644 --- a/score-client/README.md +++ b/score-client/README.md @@ -35,13 +35,13 @@ An example usage of the container which will download a remote file (with associ pull overture/score # Publish token -export ACCESSTOKEN= +export ACCESSTOKEN= # Make life easy for usage alias score-client="docker run -it --rm -u $(id -u):$(id -g) -e ACCESSTOKEN -v /tmp:/data score-client bin/score-client" -# Usage with an example object-id from https://dcc.icgc.org +# Usage with an example object-id score-client download --object-id 5b845b9a-3dcd-59ef-9f56-9a99396e988f --output-dir /data --output-layout bundle ``` diff --git a/score-client/integration/bash_colors.sh b/score-client/integration/bash_colors.sh deleted file mode 100755 index 931ca91f..00000000 --- a/score-client/integration/bash_colors.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env sh - -Bold="$(tput bold)" -Black="$(tput setaf 0)" -BlackBG="$(tput setab 0)" -DarkGrey="$(tput bold ; tput setaf 0)" -LightGrey="$(tput setaf 7)" -LightGreyBG="$(tput setab 7)" -White="$(tput bold ; tput setaf 7)" -Red="$(tput setaf 1)" -RedBG="$(tput setab 1)" -LightRed="$(tput bold ; tput setaf 1)" -Green="$(tput setaf 2)" -GreenBG="$(tput setab 2)" -LightGreen="$(tput bold ; tput setaf 2)" -Brown="$(tput setaf 3)" -BrownBG="$(tput setab 3)" -Yellow="$(tput bold ; tput setaf 3)" -Blue="$(tput setaf 4)" -BlueBG="$(tput setab 4)" -LightBlue="$(tput bold ; tput setaf 4)" -Purple="$(tput setaf 5)" -PurpleBG="$(tput setab 5)" -Pink="$(tput bold ; tput setaf 5)" -Cyan="$(tput setaf 6)" -CyanBG="$(tput setab 6)" -LightCyan="$(tput bold ; tput setaf 6)" -NC="$(tput sgr0)" # No Colo -Color_Off="$(tput sgr0)" # No Colo diff --git a/score-client/integration/expected1 b/score-client/integration/expected1 deleted file mode 100644 index 8dda4873..00000000 --- a/score-client/integration/expected1 +++ /dev/null @@ -1,5 +0,0 @@ - Active Configuration: - Profile: default - Storage URL: https://example.score.org - Metadata URL: https://example.song.org - Access Token: myToken diff --git a/score-client/integration/expected2 b/score-client/integration/expected2 deleted file mode 100644 index 15ed5481..00000000 --- a/score-client/integration/expected2 +++ /dev/null @@ -1,5 +0,0 @@ -Active Configuration: - Profile: default - Storage URL: https://something.org - Metadata URL: https://example.song.org - Access Token: myToken diff --git a/score-client/integration/expected3 b/score-client/integration/expected3 deleted file mode 100644 index debab2d7..00000000 --- a/score-client/integration/expected3 +++ /dev/null @@ -1,5 +0,0 @@ - Active Configuration: - Profile: collab - Storage URL: https://storage.cancercollaboratory.org - Metadata URL:https://song.cancercollaboratory.org - Access Token: myToken diff --git a/score-client/integration/expected4 b/score-client/integration/expected4 deleted file mode 100644 index c19d8a02..00000000 --- a/score-client/integration/expected4 +++ /dev/null @@ -1,5 +0,0 @@ - Active Configuration: - Profile: aws - Storage URL: https://virginia.cloud.icgc.org - Metadata URL:https://virginia.song.icgc.org - Access Token: myToken diff --git a/score-client/integration/expected5 b/score-client/integration/expected5 deleted file mode 100644 index 29bfdf6f..00000000 --- a/score-client/integration/expected5 +++ /dev/null @@ -1,5 +0,0 @@ - Active Configuration: - Profile: aws - Storage URL: https://something.org - Metadata URL: https://virginia.song.icgc.org - Access Token: myToken diff --git a/score-client/integration/header b/score-client/integration/header deleted file mode 100644 index 8c721073..00000000 --- a/score-client/integration/header +++ /dev/null @@ -1,2 +0,0 @@ ->ICGC Storage Client - diff --git a/score-client/integration/test.sh b/score-client/integration/test.sh deleted file mode 100755 index f4f4a05e..00000000 --- a/score-client/integration/test.sh +++ /dev/null @@ -1,51 +0,0 @@ -#!/bin/bash -#HERE=$(dirname $0) -#RUN_DIR=$HERE -#cd $HERE -RUN_DIR=$(pwd) -expected=$RUN_DIR/expected -result=$RUN_DIR/result -actual=$RUN_DIR/actual - -eval . $RUN_DIR/bash_colors.sh - -#set -x -cd ../target - -echo "Extracting client from tarball" -tar xf score-client-2.2.1-SNAPSHOT-dist.tar.gz - -cd score-client-2.2.1-SNAPSHOT -echo "Setting up configuration files" - -echo "metadata.url=https://example.song.org" >> ./conf/application.properties -echo "storage.url=https://example.score.org" >> ./conf/application.properties -echo "accessToken=myToken" >> ./conf/application.properties - -export PATH=$PATH:`pwd`/bin - -function validate { - local test - test=$1 - echo -n Test test${test}... - want=${expected}${test} - have=${result}${test} - config=${actual}${test} - grep -A 10 Configuration $have > $config - diff -w $config $want && echo "${Green}OK${NC}"|| echo "${Red}FAILED${NC}" -} - -score-client info >& ${result}1 -validate 1 - -STORAGE_URL=https://something.org score-client info >& ${result}2 -validate 2 - -score-client --profile collab info >& ${result}3 -validate 3 - -score-client --profile aws info >& ${result}4 -validate 4 - -STORAGE_URL=https://something.org score-client --profile aws info >& ${result}5 -validate 5 diff --git a/score-client/pom.xml b/score-client/pom.xml index 677908bf..d465ff3b 100644 --- a/score-client/pom.xml +++ b/score-client/pom.xml @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 ../pom.xml @@ -147,13 +147,6 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S ${guava.version} - - - com.fasterxml.jackson.dataformat - jackson-dataformat-csv - ${fasterxml-jackson.version} - - org.bouncycastle diff --git a/score-client/src/main/java/bio/overture/score/client/command/AbstractClientCommand.java b/score-client/src/main/java/bio/overture/score/client/command/AbstractClientCommand.java index 3be0915a..e429d369 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/AbstractClientCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/AbstractClientCommand.java @@ -19,9 +19,6 @@ import bio.overture.score.client.cli.Terminal; import bio.overture.score.client.config.ClientProperties; -import bio.overture.score.client.manifest.DownloadManifest; -import bio.overture.score.client.util.ProfileRepoValidator; -import lombok.val; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; @@ -39,22 +36,4 @@ public abstract class AbstractClientCommand implements ClientCommand { protected void printTitle() { terminal.printStatus("\n" + terminal.label("> ") + terminal.value("SCORE ") + "Client\n\n"); } - - protected void validateManifest(final DownloadManifest manifest) { - for (val entry : manifest.getEntries()) { - try { - if (!ProfileRepoValidator.validateRepoAgainstProfile(storageProfile, entry.getRepoCode())) { - terminal.printWarn( - "Manifest entry %s - %s (%s) exists in the '%s' repository. However, this SCORe Client instance is using the '%s' profile.", - entry.getFileId(), - entry.getFileName(), - entry.getFileUuid(), - entry.getRepoCode(), - storageProfile); - } - } catch (IllegalArgumentException iae) { - terminal.printWarn(iae.getMessage()); - } - } - } } diff --git a/score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java b/score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java index 0f637a1f..cd5d28fa 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/DownloadCommand.java @@ -167,14 +167,11 @@ private List getIdsFromManifest(ManifestResource manifestResource) if (manifestResource.isGnosManifest()) { throw new BadManifestException( format( - "Manifest '%s' looks like a GNOS-format manifest file. Please ensure you are using a tab-delimited text file" - + " manifest from https://dcc.icgc.org/repositories", + "Manifest '%s' looks like a GNOS-format manifest file. Please ensure you are using a tab-delimited text file manifest", manifestResource.getValue())); } val manifest = manifestService.getDownloadManifest(manifestResource); - validateManifest(manifest); - val entries = manifest.getEntries(); if (entries.isEmpty()) { throw new BadManifestException(format("Manifest '%s' is empty", manifestResource)); diff --git a/score-client/src/main/java/bio/overture/score/client/command/InfoCommand.java b/score-client/src/main/java/bio/overture/score/client/command/InfoCommand.java index 468c35b7..997fed13 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/InfoCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/InfoCommand.java @@ -64,6 +64,11 @@ private void version() { } private void active() { + if ((storageUrl == null || storageUrl.isEmpty()) + && (metadataUrl == null || metadataUrl.isEmpty())) { + throw new IllegalArgumentException( + "Error: Storage URL or Metadata URL is not configured. Please provide a valid URL."); + } terminal.println(terminal.label(" Active Configuration: ")); terminal.println(" Profile: " + storageProfile); terminal.println(" Storage URL: " + terminal.url(storageUrl)); diff --git a/score-client/src/main/java/bio/overture/score/client/command/MountCommand.java b/score-client/src/main/java/bio/overture/score/client/command/MountCommand.java index 66e1724b..03469d34 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/MountCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/MountCommand.java @@ -59,7 +59,6 @@ import lombok.extern.slf4j.Slf4j; import lombok.val; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; import org.springframework.stereotype.Component; @Slf4j @@ -67,7 +66,6 @@ @Parameters( separators = "=", commandDescription = "Mount a read-only FUSE file system view of the remote storage repository") -@Profile("!kf") public class MountCommand extends RepositoryAccessCommand { /** Constants. */ @@ -112,7 +110,7 @@ public class MountCommand extends RepositoryAccessCommand { @Parameter( names = "--options", description = - "The mount options of the file system (e.g. --options user_allow_other,allow_other,fsname=icgc,debug) " + "The mount options of the file system (e.g. --options user_allow_other,allow_other,fsname=score,debug) " + "in addition to those specified internally: " + INTERNAL_MOUNT_OPTIONS + ". See " @@ -394,8 +392,6 @@ private boolean hasManifest() { private List filterManifestObjects(List objects) { val manifest = manifestService.getDownloadManifest(manifestResource); - validateManifest(manifest); - val objectIds = manifest.getEntries().stream() .flatMap(entry -> Stream.of(entry.getFileUuid(), entry.getIndexFileUuid())) diff --git a/score-client/src/main/java/bio/overture/score/client/command/UploadCommand.java b/score-client/src/main/java/bio/overture/score/client/command/UploadCommand.java index 1e35e00d..9b17ede9 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/UploadCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/UploadCommand.java @@ -36,7 +36,6 @@ import lombok.val; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; -import org.springframework.context.annotation.Profile; import org.springframework.stereotype.Component; @Slf4j @@ -44,7 +43,6 @@ @Parameters( separators = "=", commandDescription = "Upload file object(s) to the remote storage repository") -@Profile("!kf") public class UploadCommand extends RepositoryAccessCommand { /** Options. */ diff --git a/score-client/src/main/java/bio/overture/score/client/command/VersionCommand.java b/score-client/src/main/java/bio/overture/score/client/command/VersionCommand.java index 072bd19c..3daf3f06 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/VersionCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/VersionCommand.java @@ -28,8 +28,6 @@ public class VersionCommand extends AbstractClientCommand { /** Constants. */ - private static final String SUPPORT_EMAIL = "dcc-support@icgc.org"; - @Override public int execute() throws Exception { printTitle(); @@ -40,7 +38,6 @@ public int execute() throws Exception { private void version() { terminal.println(terminal.label(" Version: ") + getVersion()); terminal.println(terminal.label(" Built: ") + getScmInfo().get("git.build.time")); - terminal.println(terminal.label(" Contact: ") + terminal.email(SUPPORT_EMAIL)); } private String getVersion() { diff --git a/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java b/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java index 1b4b0040..216b5b12 100644 --- a/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java +++ b/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java @@ -57,7 +57,6 @@ import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.ApplicationArguments; -import org.springframework.context.annotation.Profile; import org.springframework.stereotype.Component; @Slf4j @@ -65,7 +64,6 @@ @Parameters( separators = "=", commandDescription = "Locally store/display some or all of a remote SAM/BAM file object") -@Profile("!kf") public class ViewCommand extends RepositoryAccessCommand { public enum OutputFormat { @@ -84,7 +82,7 @@ public enum OutputType { public static final int MAX_FILENAME_LENGTH = 120; public static final String PROGRAM_NAME = "Score Client"; - public static final String ICGC = "ICGC"; + public static final String SCORE = "score"; /** Options. */ @Parameter( @@ -274,7 +272,7 @@ public SamFileBuilder configureBuilder(SamFileBuilder builder) { builder .programName(PROGRAM_NAME) .version(VersionUtils.getScmInfo().get("git.commit.id.describe")) - .programId(ICGC) + .programId(SCORE) .commandLine(getCommandLine()) .containedOnly(containedOnly) .useOriginalHeader(useOriginalHeader) diff --git a/score-client/src/main/java/bio/overture/score/client/config/ClientConfig.java b/score-client/src/main/java/bio/overture/score/client/config/ClientConfig.java index 648a7955..c18636ce 100644 --- a/score-client/src/main/java/bio/overture/score/client/config/ClientConfig.java +++ b/score-client/src/main/java/bio/overture/score/client/config/ClientConfig.java @@ -29,9 +29,7 @@ import bio.overture.score.client.exception.NotRetryableException; import bio.overture.score.client.exception.RetryableException; import bio.overture.score.client.exception.ServiceRetryableResponseErrorHandler; -import bio.overture.score.client.manifest.kf.KFFileBean; import bio.overture.score.client.upload.UploadStateStore; -import bio.overture.score.client.util.CsvParser; import com.google.common.collect.ImmutableMap; import java.io.IOException; import javax.net.ssl.HostnameVerifier; @@ -68,8 +66,6 @@ @Import(PropertyPlaceholderAutoConfiguration.class) public class ClientConfig { - private static final Character TAB_SEP = '\t'; - /** Configuration. */ @Autowired private ClientProperties properties; @@ -84,11 +80,6 @@ public String clientVersion() { ClientConfig.class.getPackage().getImplementationVersion(), "[unknown version]"); } - @Bean - public CsvParser kfFileBeanCsvParser() { - return new CsvParser<>(KFFileBean.class, TAB_SEP); - } - @Bean public TemplateEngine textTemplateEngine() { val templateEngine = new TemplateEngine(); diff --git a/score-client/src/main/java/bio/overture/score/client/config/ClientProperties.java b/score-client/src/main/java/bio/overture/score/client/config/ClientProperties.java index 41c4c437..69675c2a 100644 --- a/score-client/src/main/java/bio/overture/score/client/config/ClientProperties.java +++ b/score-client/src/main/java/bio/overture/score/client/config/ClientProperties.java @@ -14,7 +14,7 @@ public class ClientProperties { /** Constants. */ private static final int DEFAULT_LIMIT = 10; - /** OAuth2 access token for ICGC authorization server */ + /** OAuth2 access token for SCORe authorization server */ private String accessToken; private String encryptedAccessToken; diff --git a/score-client/src/main/java/bio/overture/score/client/config/ProfileConfig.java b/score-client/src/main/java/bio/overture/score/client/config/ProfileConfig.java index f47e19a3..b2b42c75 100644 --- a/score-client/src/main/java/bio/overture/score/client/config/ProfileConfig.java +++ b/score-client/src/main/java/bio/overture/score/client/config/ProfileConfig.java @@ -27,7 +27,7 @@ public class ProfileConfig { private String endpoint; @Autowired - @Value("${defaultProfile:collaboratory}") + @Value("${defaultProfile:s3}") private String defaultProfile; @Autowired diff --git a/score-client/src/main/java/bio/overture/score/client/config/StorageConfig.java b/score-client/src/main/java/bio/overture/score/client/config/StorageConfig.java index 6d8388ac..9b8e6c20 100644 --- a/score-client/src/main/java/bio/overture/score/client/config/StorageConfig.java +++ b/score-client/src/main/java/bio/overture/score/client/config/StorageConfig.java @@ -18,7 +18,7 @@ public class StorageConfig { @Value("${storage.url}") private String endpoint; - @Value("${kf.download.partSize}") + @Value("${download.partSize}") private int partSize; @Autowired private DownloadStateStore downloadStateStore; diff --git a/score-client/src/main/java/bio/overture/score/client/exception/ConnectivityResponseHandler.java b/score-client/src/main/java/bio/overture/score/client/exception/ConnectivityResponseHandler.java index 6af33412..a615f2f2 100644 --- a/score-client/src/main/java/bio/overture/score/client/exception/ConnectivityResponseHandler.java +++ b/score-client/src/main/java/bio/overture/score/client/exception/ConnectivityResponseHandler.java @@ -34,16 +34,16 @@ public void handleError(ClientHttpResponse response) throws IOException { switch (status) { case FORBIDDEN: log.warn( - "FORBIDDEN response code received. If you are trying to connect to the AWS S3 Repository, you need to be running ths ICGC client on an EC2 VM instance."); + "Connection to object storage refused, received response code FORBIDDEN."); throw notRetryableException( - "Amazon S3 error: FORBIDDEN: If you are trying to connect to the AWS S3 Repository, you need to be running ths ICGC client on an EC2 VM instance", + "Connection to object storage refused, received response code FORBIDDEN.", response); case REQUEST_TIMEOUT: log.warn( - "Unable to connect to repository endpoint. You need to be running on a compute node within the repository cloud. Or else your network connection is hinky."); + "Connection to object storage failed, request timed out."); throw notRetryableException( - "Cloud error: Access refused by object store. Confirm request host is on permitted list", + "Connection to object storage failed, request timed out.", response); default: diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifest.java b/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifest.java index a5104197..a48c330d 100644 --- a/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifest.java +++ b/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifest.java @@ -22,12 +22,6 @@ import lombok.Builder; import lombok.NonNull; import lombok.Value; - -/** - * See - * https://wiki.oicr.on.ca/display/DCCSOFT/Uniform+metadata+JSON+document+for+ICGC+Data+Repositories# - * UniformmetadataJSONdocumentforICGCDataRepositories-Manifestfileformatfordownloader - */ @Value public class DownloadManifest { @NonNull private final List entries; diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/DownloadManifestReader.java b/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifestReader.java similarity index 97% rename from score-client/src/main/java/bio/overture/score/client/manifest/icgc/DownloadManifestReader.java rename to score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifestReader.java index 12909b48..3dc6c050 100644 --- a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/DownloadManifestReader.java +++ b/score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifestReader.java @@ -15,12 +15,11 @@ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -package bio.overture.score.client.manifest.icgc; +package bio.overture.score.client.manifest; import static com.google.common.base.Preconditions.checkState; import static java.nio.charset.StandardCharsets.UTF_8; -import bio.overture.score.client.manifest.DownloadManifest; import bio.overture.score.client.manifest.DownloadManifest.ManifestEntry; import com.google.common.base.Splitter; import com.google.common.collect.ImmutableList; diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/IcgcManifestService.java b/score-client/src/main/java/bio/overture/score/client/manifest/ManifestServiceImpl.java similarity index 93% rename from score-client/src/main/java/bio/overture/score/client/manifest/icgc/IcgcManifestService.java rename to score-client/src/main/java/bio/overture/score/client/manifest/ManifestServiceImpl.java index 8fbc4c87..61b95aa8 100644 --- a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/IcgcManifestService.java +++ b/score-client/src/main/java/bio/overture/score/client/manifest/ManifestServiceImpl.java @@ -15,14 +15,10 @@ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -package bio.overture.score.client.manifest.icgc; +package bio.overture.score.client.manifest; import static java.nio.charset.StandardCharsets.UTF_8; -import bio.overture.score.client.manifest.DownloadManifest; -import bio.overture.score.client.manifest.ManifestResource; -import bio.overture.score.client.manifest.ManifestService; -import bio.overture.score.client.manifest.UploadManifest; import com.google.common.io.Resources; import java.io.File; import java.net.MalformedURLException; @@ -35,7 +31,7 @@ @Service @Profile("!kf") -public class IcgcManifestService implements ManifestService { +public class ManifestServiceImpl implements ManifestService { /** Constants */ private static final DownloadManifestReader DOWNLOAD_READER = new DownloadManifestReader(); diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/UploadManifestReader.java b/score-client/src/main/java/bio/overture/score/client/manifest/UploadManifestReader.java similarity index 96% rename from score-client/src/main/java/bio/overture/score/client/manifest/icgc/UploadManifestReader.java rename to score-client/src/main/java/bio/overture/score/client/manifest/UploadManifestReader.java index f576265e..4a086141 100644 --- a/score-client/src/main/java/bio/overture/score/client/manifest/icgc/UploadManifestReader.java +++ b/score-client/src/main/java/bio/overture/score/client/manifest/UploadManifestReader.java @@ -15,12 +15,11 @@ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -package bio.overture.score.client.manifest.icgc; +package bio.overture.score.client.manifest; import static com.google.common.base.Preconditions.checkState; import static java.nio.charset.StandardCharsets.UTF_8; -import bio.overture.score.client.manifest.UploadManifest; import bio.overture.score.client.manifest.UploadManifest.ManifestEntry; import com.google.common.base.Splitter; import com.google.common.collect.ImmutableList; diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFDownloadManifestReader.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFDownloadManifestReader.java deleted file mode 100644 index 6f5b030b..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFDownloadManifestReader.java +++ /dev/null @@ -1,50 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import static bio.overture.score.core.util.Collectors.toImmutableList; - -import bio.overture.score.client.manifest.DownloadManifest; -import bio.overture.score.client.manifest.DownloadManifest.ManifestEntry; -import bio.overture.score.client.util.CsvParser; -import java.io.File; -import lombok.NonNull; -import lombok.SneakyThrows; -import lombok.val; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Component; - -@Component -public class KFDownloadManifestReader { - - private final CsvParser kfFileBeanCsvParser; - - @Autowired - public KFDownloadManifestReader(@NonNull CsvParser kfFileBeanCsvParser) { - this.kfFileBeanCsvParser = kfFileBeanCsvParser; - } - - @SneakyThrows - public DownloadManifest readManifest(@NonNull File manifestFile) { - val entries = - kfFileBeanCsvParser.parseFile(manifestFile).stream() - .map(KFDownloadManifestReader::convertToManifestEntry) - .collect(toImmutableList()); - return new DownloadManifest(entries); - } - - private static ManifestEntry convertToManifestEntry(KFFileBean bean) { - return ManifestEntry.builder() - .projectId(null) - .donorId(bean.getParticipantsId()) - .fileFormat(bean.getFileFormat()) - .fileId(bean.getFileId()) - .fileMd5sum(null) - .fileName(bean.getFileName()) - .fileSize(null) - .fileUuid(bean.getLatestDid()) - .indexFileUuid(null) - .indexFileUuid(null) - .repoCode(null) - .study(null) - .build(); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileBean.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileBean.java deleted file mode 100644 index cd7253ab..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileBean.java +++ /dev/null @@ -1,55 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import com.fasterxml.jackson.annotation.JsonProperty; -import com.fasterxml.jackson.annotation.JsonPropertyOrder; -import lombok.Data; - -@Data -@JsonPropertyOrder({ - "File ID", - "Latest Did", - "File Name", - "Data Type", - "File Format", - "Experiment Strategy", - "Participants ID", - "Proband", - "Family ID", - "External Sample Id", - "External Aliquot Id" -}) -public class KFFileBean { - - @JsonProperty("File ID") - private String fileId; - - @JsonProperty("Latest Did") - private String latestDid; - - @JsonProperty("File Name") - private String fileName; - - @JsonProperty("Data Type") - private String dataType; - - @JsonProperty("File Format") - private String fileFormat; - - @JsonProperty("Experiment Strategy") - private String experimentStrategy; - - @JsonProperty("Participants ID") - private String participantsId; - - @JsonProperty("Proband") - private String proband; - - @JsonProperty("Family ID") - private String familyId; - - @JsonProperty("External Sample Id") - private String externalSampleId; - - @JsonProperty("External Aliquot Id") - private String externalAliquotId; -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileEntity.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileEntity.java deleted file mode 100644 index a48fcf7a..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFFileEntity.java +++ /dev/null @@ -1,23 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import java.util.Set; -import lombok.AllArgsConstructor; -import lombok.Builder; -import lombok.Data; -import lombok.NoArgsConstructor; - -@Data -@Builder -@AllArgsConstructor -@NoArgsConstructor -public class KFFileEntity { - private boolean controlledAccess; - private Set participants; - private String fileId; - private String fileName; - private String dataType; - private String fileFormat; - private long size; - private String latestDid; - private String id; -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFManifestService.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFManifestService.java deleted file mode 100644 index 10070fa2..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFManifestService.java +++ /dev/null @@ -1,79 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import static bio.overture.score.core.util.Collectors.toImmutableList; -import static java.lang.String.format; - -import bio.overture.score.client.manifest.DownloadManifest; -import bio.overture.score.client.manifest.DownloadManifest.ManifestEntry; -import bio.overture.score.client.manifest.ManifestResource; -import bio.overture.score.client.manifest.ManifestService; -import bio.overture.score.client.manifest.UploadManifest; -import java.io.File; -import java.util.Set; -import lombok.NonNull; -import lombok.val; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; -import org.springframework.stereotype.Service; - -@Service -@Profile("kf") -public class KFManifestService implements ManifestService { - - private final KFPortalClient kfPortalClient; - private final KFDownloadManifestReader kfDownloadManifestReader; - - @Autowired - public KFManifestService( - @NonNull KFPortalClient kfPortalClient, - @NonNull KFDownloadManifestReader kfDownloadManifestReader) { - this.kfPortalClient = kfPortalClient; - this.kfDownloadManifestReader = kfDownloadManifestReader; - } - - @Override - public String getManifestContent(ManifestResource resource) { - return getDownloadManifest(resource).toString(); - } - - @Override - public DownloadManifest getDownloadManifest(ManifestResource resource) { - if (resource.getType() == ManifestResource.Type.ID) { - val entities = kfPortalClient.findEntitiesFromManifest(resource.getValue()); - return convertToDownloadManifest(entities); - } else if (resource.getType() == ManifestResource.Type.FILE) { - return kfDownloadManifestReader.readManifest(new File(resource.getValue())); - } else { - throw new IllegalStateException( - format("The ManifestResource type '%s' is not supported", resource.getType())); - } - } - - @Override - public UploadManifest getUploadManifest(ManifestResource resource) { - throw new IllegalStateException("Not implemented for KF mode"); - } - - private DownloadManifest convertToDownloadManifest(Set entities) { - val manifestEntries = - entities.stream().map(this::convertToManifestEntry).collect(toImmutableList()); - return new DownloadManifest(manifestEntries); - } - - private ManifestEntry convertToManifestEntry(KFFileEntity entity) { - return entity.getParticipants().stream() - .findFirst() - .map(x -> ManifestEntry.builder().donorId(x.getParticipantId()).projectId(x.getStudyId())) - .orElse(ManifestEntry.builder()) - .fileFormat(entity.getFileFormat()) - .fileId(entity.getFileId()) - .fileMd5sum(null) - .fileName(entity.getFileName()) - .fileUuid(entity.getLatestDid()) - .fileSize(Long.toString(entity.getSize())) - .indexFileUuid(null) - .repoCode(null) - .study(null) - .build(); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParser.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParser.java deleted file mode 100644 index 5ffc1529..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParser.java +++ /dev/null @@ -1,168 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import static bio.overture.score.core.util.Collectors.toImmutableSet; -import static bio.overture.score.core.util.Streams.stream; -import static com.google.common.base.Preconditions.checkArgument; -import static lombok.AccessLevel.PRIVATE; - -import com.fasterxml.jackson.databind.JsonNode; -import com.google.common.collect.ImmutableSet; -import java.util.Set; -import lombok.NoArgsConstructor; -import lombok.val; - -@NoArgsConstructor(access = PRIVATE) -public class KFParser { - - private static final String DATA = "data"; - private static final String FILE = "file"; - private static final String HITS = "hits"; - private static final String EDGES = "edges"; - private static final String NODE = "node"; - private static final String KF_ID = "kf_id"; - private static final String DATA_TYPE = "data_type"; - private static final String FILE_FORMAT = "file_format"; - private static final String SIZE = "size"; - private static final String LATEST_DID = "latest_did"; - private static final String ID = "id"; - private static final String PARTICIPANTS = "participants"; - private static final String IS_PROBAND = "is_proband"; - private static final String STUDY = "study"; - private static final String SHORT_NAME = "short_name"; - private static final String CONTROLLED_ACCESS = "controlled_access"; - private static final String EXTERNAL_ID = "external_id"; - private static final String FILE_NAME = "file_name"; - private static final String TOTAL = "total"; - private static final Set EMPTY_KF_ENTITY_SET = ImmutableSet.of(); - - public static Set readEntries(JsonNode root) { - val fileNode = getFileNode(getDataNode(root)); - val totalHits = readFileTotal(fileNode); - if (totalHits > 0) { - val edgesNode = getEdgesNode(getHitsNode(fileNode)); - return stream(edgesNode) - .map(KFParser::getNodeNode) - .map( - x -> - KFFileEntity.builder() - .controlledAccess(isControlledAccess(x)) - .participants(readParticipants(getParticipantsNode(x))) - .fileId(readFileId(x)) - .fileName(readFileName(x)) - .dataType(readDataType(x)) - .fileFormat(readFileFormat(x)) - .size(readSize(x)) - .latestDid(readLatestDid(x)) - .id(readId(x)) - .build()) - .collect(toImmutableSet()); - } else { - return EMPTY_KF_ENTITY_SET; - } - } - - private static JsonNode getDataNode(JsonNode root) { - return requiredGet(root, DATA); - } - - private static JsonNode getFileNode(JsonNode root) { - return requiredGet(root, FILE); - } - - private static JsonNode getHitsNode(JsonNode root) { - return requiredGet(root, HITS); - } - - private static JsonNode getHitsTotal(JsonNode hits) { - return requiredGet(hits, TOTAL); - } - - private static JsonNode getEdgesNode(JsonNode root) { - return requiredGet(root, EDGES); - } - - private static boolean isControlledAccess(JsonNode root) { - return requiredGet(root, CONTROLLED_ACCESS).booleanValue(); - } - - private static JsonNode getNodeNode(JsonNode root) { - return requiredGet(root, NODE); - } - - private static String readFileId(JsonNode node) { - return requiredGet(node, KF_ID).textValue(); - } - - private static long readFileTotal(JsonNode file) { - return getHitsTotal(getHitsNode(file)).longValue(); - } - - private static String readFileName(JsonNode node) { - return requiredGet(node, FILE_NAME).textValue(); - } - - private static String readDataType(JsonNode node) { - return requiredGet(node, DATA_TYPE).textValue(); - } - - private static String readFileFormat(JsonNode node) { - return requiredGet(node, FILE_FORMAT).textValue(); - } - - private static long readSize(JsonNode node) { - return requiredGet(node, SIZE).longValue(); - } - - private static String readLatestDid(JsonNode node) { - return requiredGet(node, LATEST_DID).textValue(); - } - - private static String readId(JsonNode node) { - return requiredGet(node, ID).textValue(); - } - - private static String readParticipantId(JsonNode node) { - return requiredGet(node, KF_ID).textValue(); - } - - private static boolean isProband(JsonNode node) { - return requiredGet(node, IS_PROBAND).booleanValue(); - } - - private static JsonNode getStudyNode(JsonNode node) { - return requiredGet(node, STUDY); - } - - private static String readStudyShortName(JsonNode node) { - return requiredGet(node, SHORT_NAME).textValue(); - } - - private static String readStudyStudyId(JsonNode node) { - return requiredGet(node, EXTERNAL_ID).textValue(); - } - - private static JsonNode getParticipantsNode(JsonNode node) { - return requiredGet(node, PARTICIPANTS); - } - - private static Set readParticipants(JsonNode participantsNode) { - val edgesNode = getEdgesNode(getHitsNode(participantsNode)); - return stream(edgesNode) - .map(KFParser::getNodeNode) - .map( - x -> - KFParticipantEntity.builder() - .participantId(readParticipantId(x)) - .proband(isProband(x)) - .studyShortName(readStudyShortName(getStudyNode(x))) - .studyId(readStudyStudyId(getStudyNode(x))) - .build()) - .collect(toImmutableSet()); - } - - private static JsonNode requiredGet(JsonNode root, String key) { - checkArgument( - root.has(key), "The following root element doesnt have the key '%s': %s", key, root); - return root.path(key); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParticipantEntity.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParticipantEntity.java deleted file mode 100644 index aa787cd9..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFParticipantEntity.java +++ /dev/null @@ -1,17 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import lombok.AllArgsConstructor; -import lombok.Builder; -import lombok.Data; -import lombok.NoArgsConstructor; - -@Data -@Builder -@AllArgsConstructor -@NoArgsConstructor -public class KFParticipantEntity { - private String participantId; - private boolean proband; - private String studyShortName; - private String studyId; -} diff --git a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFPortalClient.java b/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFPortalClient.java deleted file mode 100644 index 7d80204b..00000000 --- a/score-client/src/main/java/bio/overture/score/client/manifest/kf/KFPortalClient.java +++ /dev/null @@ -1,122 +0,0 @@ -package bio.overture.score.client.manifest.kf; - -import static bio.overture.score.client.manifest.kf.KFParser.readEntries; -import static com.google.common.base.Preconditions.checkState; -import static org.springframework.http.HttpMethod.POST; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.ImmutableSet; -import java.net.URI; -import java.util.Optional; -import java.util.Set; -import lombok.NonNull; -import lombok.SneakyThrows; -import lombok.val; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.beans.factory.annotation.Qualifier; -import org.springframework.beans.factory.annotation.Value; -import org.springframework.http.HttpEntity; -import org.springframework.http.HttpHeaders; -import org.springframework.http.ResponseEntity; -import org.springframework.retry.support.RetryTemplate; -import org.springframework.stereotype.Component; -import org.springframework.web.client.RestTemplate; -import org.thymeleaf.TemplateEngine; -import org.thymeleaf.context.Context; - -@Component -public class KFPortalClient { - - private static final String MANIFEST_ID_SEARCH_QUERY_TEMPLATE_NAME = "manifest_id_query"; - private static final String OBJECT_ID_SEARCH_QUERY_TEMPLATE_NAME = "object_id_search_query"; - private static final String MANIFEST_ID = "manifestId"; - private static final String OBJECT_ID = "objectId"; - private static final String OFFSET = "offset"; - private static final String FIRST = "first"; - private static final int MAX_SIZE = 10000; - private final String kfPortalUrl; - private final RestTemplate serviceTemplate; - private final RetryTemplate retry; - private final TemplateEngine textTemplateEngine; - - @Autowired - public KFPortalClient( - @Value("${kfportal.url}") @NonNull String kfportalUrl, - @Qualifier("serviceTemplate") @NonNull RestTemplate serviceTemplate, - @NonNull RetryTemplate retry, - @NonNull TemplateEngine textTemplateEngine) { - this.kfPortalUrl = kfportalUrl; - this.serviceTemplate = serviceTemplate; - this.retry = retry; - this.textTemplateEngine = textTemplateEngine; - } - - /** Page through all entities belonging to a manifestId, MAX_SIZE at a time */ - public Set findEntitiesFromManifest(String manifestId) { - int currentOffset = 0; - val allEntities = ImmutableSet.builder(); - val pageSize = MAX_SIZE; - while (true) { - val query = createManifestIdQuery(manifestId, currentOffset, pageSize); - val response = post(String.class, kfPortalUrl, query); - val entities = parseManifestEntityResponse(response); - if (entities.isEmpty()) { - return allEntities.build(); - } - allEntities.addAll(entities); - currentOffset += pageSize; - } - } - - public Optional findEntity(@NonNull String objectId) { - val query = createObjectIdQuery(objectId); - val response = post(String.class, kfPortalUrl, query); - val entities = parseManifestEntityResponse(response); - checkState( - entities.size() < 2, - "There was more than 1 (%s) result for the objectId '%s': %s", - entities.size(), - objectId, - entities); - return entities.stream().findFirst(); - } - - private String createObjectIdQuery(String objectId) { - val context = new Context(); - context.setVariable(OBJECT_ID, objectId); - context.setVariable(OFFSET, 0); - context.setVariable(FIRST, 1); - return textTemplateEngine.process(OBJECT_ID_SEARCH_QUERY_TEMPLATE_NAME, context); - } - - private String createManifestIdQuery(String manifestId, int offset, int size) { - val context = new Context(); - context.setVariable(MANIFEST_ID, manifestId); - context.setVariable(OFFSET, offset); - context.setVariable(FIRST, size); - return textTemplateEngine.process(MANIFEST_ID_SEARCH_QUERY_TEMPLATE_NAME, context); - } - - @SneakyThrows - private Set parseManifestEntityResponse(ResponseEntity response) { - val mapper = new ObjectMapper(); - val root = mapper.readTree(response.getBody()); - return readEntries(root); - } - - @SneakyThrows - private ResponseEntity post(Class responseType, String url, T body) { - return retry.execute( - ctx -> serviceTemplate.exchange(new URI(url), POST, defaultEntity(body), responseType)); - } - - private static HttpEntity defaultEntity(T body) { - return new HttpEntity<>(body, defaultHeaders()); - } - - private static HttpHeaders defaultHeaders() { - val h = new HttpHeaders(); - h.add(HttpHeaders.CONTENT_TYPE, "application/json"); - return h; - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/metadata/kf/KFMetadataService.java b/score-client/src/main/java/bio/overture/score/client/metadata/kf/KFMetadataService.java deleted file mode 100644 index 3e1a2843..00000000 --- a/score-client/src/main/java/bio/overture/score/client/metadata/kf/KFMetadataService.java +++ /dev/null @@ -1,83 +0,0 @@ -package bio.overture.score.client.metadata.kf; - -import static java.lang.String.format; - -import bio.overture.score.client.manifest.kf.KFFileEntity; -import bio.overture.score.client.manifest.kf.KFParticipantEntity; -import bio.overture.score.client.manifest.kf.KFPortalClient; -import bio.overture.score.client.metadata.Entity; -import bio.overture.score.client.metadata.EntityNotFoundException; -import bio.overture.score.client.metadata.MetadataService; -import com.google.common.collect.ImmutableList; -import java.util.List; -import java.util.Optional; -import lombok.NonNull; -import lombok.extern.slf4j.Slf4j; -import lombok.val; -import org.apache.commons.lang.NotImplementedException; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; -import org.springframework.stereotype.Service; - -@Slf4j -@Service -@Profile("kf") -public class KFMetadataService implements MetadataService { - private static final List EMPTY_LIST = ImmutableList.of(); - private static final String CONTROLLED = "controlled"; - private static final String OPEN = "open"; - private static final String DEFAULT_BUNDLE = "unknown_bundle"; - - private final KFPortalClient kfPortalClient; - - @Autowired - public KFMetadataService(@NonNull KFPortalClient kfPortalClient) { - this.kfPortalClient = kfPortalClient; - } - - @Override - public List getEntities(String... fields) { - return EMPTY_LIST; - } - - @Override - public Entity getEntity(String objectId) { - val result = kfPortalClient.findEntity(objectId); - val kfEntity = - result.orElseThrow( - () -> - new EntityNotFoundException( - format("The KF entity with objectId '%s' does not exist", objectId))); - return Entity.builder() - .gnosId( - kfEntity.getParticipants().stream() - .map(KFParticipantEntity::getParticipantId) - .findFirst() - .orElse(DEFAULT_BUNDLE)) - .access(resolveAccess(kfEntity)) - .createdTime(System.currentTimeMillis()) - .fileName(kfEntity.getFileName()) - .id(objectId) - .projectCode( - kfEntity.getParticipants().stream() - .findFirst() - .map(KFParticipantEntity::getStudyId) - .orElse(null)) - .build(); - } - - private static String resolveAccess(KFFileEntity kfFileEntity) { - return kfFileEntity.isControlledAccess() ? CONTROLLED : OPEN; - } - - @Override - public Optional getIndexEntity(Entity entity) { - return Optional.empty(); - } - - @Override - public List getObjectIdsByAnalysisId( - @NonNull String programId, @NonNull String analysisId) { - throw new NotImplementedException(); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataService.java b/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataService.java index 47944ab9..dbc946ea 100644 --- a/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataService.java +++ b/score-client/src/main/java/bio/overture/score/client/metadata/legacy/LegacyMetadataService.java @@ -24,11 +24,9 @@ import lombok.NonNull; import lombok.val; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; import org.springframework.stereotype.Service; @Service -@Profile("!kf") public class LegacyMetadataService implements MetadataService { @Autowired private LegacyMetadataClient legacyMetadataClient; diff --git a/score-client/src/main/java/bio/overture/score/client/slicing/SamFileBuilder.java b/score-client/src/main/java/bio/overture/score/client/slicing/SamFileBuilder.java index ac455b12..4d8dbd7b 100644 --- a/score-client/src/main/java/bio/overture/score/client/slicing/SamFileBuilder.java +++ b/score-client/src/main/java/bio/overture/score/client/slicing/SamFileBuilder.java @@ -408,21 +408,21 @@ private List updateProgramRecords(List pgRec new ArrayList(pgRecords); // get returns an unmodifiable collection String id = programId == null ? "unknown" : programId; - val count = getIcgcProgramRecordCount(pgRecords); + val count = getProgramRecordCount(pgRecords); if (count > 0) { id = String.format("%s.%d", id, count + 1); } - SAMProgramRecord icgcClientRecord = new SAMProgramRecord(id); - if (programName != null) icgcClientRecord.setProgramName(programName); - if (commandLine != null) icgcClientRecord.setCommandLine(commandLine); - if (description != null) icgcClientRecord.setAttribute("DS", description); - if (version != null) icgcClientRecord.setAttribute("VN", version); - if (commandLine != null) icgcClientRecord.setCommandLine(commandLine); - newPgRecords.add(icgcClientRecord); + SAMProgramRecord clientRecord = new SAMProgramRecord(id); + if (programName != null) clientRecord.setProgramName(programName); + if (commandLine != null) clientRecord.setCommandLine(commandLine); + if (description != null) clientRecord.setAttribute("DS", description); + if (version != null) clientRecord.setAttribute("VN", version); + if (commandLine != null) clientRecord.setCommandLine(commandLine); + newPgRecords.add(clientRecord); return newPgRecords; } - private int getIcgcProgramRecordCount(List pgRecords) { + private int getProgramRecordCount(List pgRecords) { int count = 0; for (val pg : pgRecords) { if (pg.getId().substring(0, programId.length() - 1).equalsIgnoreCase(programId)) { diff --git a/score-client/src/main/java/bio/overture/score/client/storage/AbstractStorageService.java b/score-client/src/main/java/bio/overture/score/client/storage/AbstractStorageService.java index 5e4c6b09..0075abe4 100644 --- a/score-client/src/main/java/bio/overture/score/client/storage/AbstractStorageService.java +++ b/score-client/src/main/java/bio/overture/score/client/storage/AbstractStorageService.java @@ -28,7 +28,7 @@ @RequiredArgsConstructor public abstract class AbstractStorageService implements StorageService { - private static final String ICGC_TOKEN_KEY = "X-ICGC-TOKEN"; + private static final String SCORE_TOKEN_KEY = "X-SCORE-TOKEN"; private final DownloadStateStore downloadStateStore; private final RestTemplate dataTemplate; private final RetryTemplate retry; @@ -54,7 +54,7 @@ public Void doWithRetry(RetryContext ctx) throws IOException { request -> { request.getHeaders().set(HttpHeaders.RANGE, Parts.getHttpRangeValue(part)); String token = getEncryptedAccessToken().orElse(""); - request.getHeaders().set(ICGC_TOKEN_KEY, token); + request.getHeaders().set(SCORE_TOKEN_KEY, token); }, response -> { try (HashingInputStream his = diff --git a/score-client/src/main/java/bio/overture/score/client/storage/score/ScoreStorageService.java b/score-client/src/main/java/bio/overture/score/client/storage/ScoreStorageService.java similarity index 98% rename from score-client/src/main/java/bio/overture/score/client/storage/score/ScoreStorageService.java rename to score-client/src/main/java/bio/overture/score/client/storage/ScoreStorageService.java index a237f9b9..d0a6793d 100644 --- a/score-client/src/main/java/bio/overture/score/client/storage/score/ScoreStorageService.java +++ b/score-client/src/main/java/bio/overture/score/client/storage/ScoreStorageService.java @@ -15,7 +15,7 @@ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -package bio.overture.score.client.storage.score; +package bio.overture.score.client.storage; import static org.springframework.http.HttpMethod.DELETE; import static org.springframework.http.HttpMethod.GET; @@ -27,7 +27,6 @@ import bio.overture.score.client.exception.NotResumableException; import bio.overture.score.client.exception.NotRetryableException; import bio.overture.score.client.exception.RetryableException; -import bio.overture.score.client.storage.AbstractStorageService; import bio.overture.score.core.model.DataChannel; import bio.overture.score.core.model.ObjectInfo; import bio.overture.score.core.model.ObjectSpecification; @@ -66,7 +65,7 @@ /** Service responsible for interacting with the remote upload service. */ @Slf4j @Service -@Profile({"dev", "collab", "aws", "default", "!kf"}) +@Profile({"dev", "collab", "aws", "default"}) public class ScoreStorageService extends AbstractStorageService { /** Configuration. */ diff --git a/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageClient.java b/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageClient.java deleted file mode 100644 index ca073c22..00000000 --- a/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageClient.java +++ /dev/null @@ -1,129 +0,0 @@ -package bio.overture.score.client.storage.kf; - -import static com.google.common.base.Preconditions.checkState; -import static java.lang.String.format; -import static java.util.Objects.isNull; -import static org.springframework.http.HttpHeaders.AUTHORIZATION; -import static org.springframework.http.HttpHeaders.CONTENT_LENGTH; - -import com.fasterxml.jackson.annotation.JsonProperty; -import java.net.HttpURLConnection; -import java.net.URI; -import java.net.URL; -import lombok.Builder; -import lombok.Data; -import lombok.NonNull; -import lombok.SneakyThrows; -import lombok.val; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.beans.factory.annotation.Value; -import org.springframework.context.annotation.Profile; -import org.springframework.http.HttpEntity; -import org.springframework.http.HttpHeaders; -import org.springframework.http.HttpMethod; -import org.springframework.http.ResponseEntity; -import org.springframework.retry.support.RetryTemplate; -import org.springframework.stereotype.Component; -import org.springframework.web.client.RestTemplate; - -@Builder -@Component -@Profile("kf") -public class KFStorageClient { - - private static final long MIN_EXPIRATION = 3600; - private final String jwt; - private final String tokenUrl; - private final String apiUrl; - private final long urlExpiration; - private final RetryTemplate retry; - private final RestTemplate restTemplate = new RestTemplate(); - - public KFStorageClient( - @Value("${client.accessToken}") @NonNull String jwt, - @Value("${kf.token.url}") @NonNull String tokenUrl, - @Value("${kf.download.url}") @NonNull String apiUrl, - @Value("${kf.download.expiration}") long urlExpiration, - @Autowired RetryTemplate retry) { - this.jwt = jwt; - this.apiUrl = apiUrl; - this.urlExpiration = Math.max(urlExpiration, MIN_EXPIRATION); - this.tokenUrl = tokenUrl; - this.retry = retry; - } - - public String generateAccessToken() { - val accessTokenResponse = getObject(AccessTokenResponse.class, jwt, tokenUrl); - return accessTokenResponse.getAccessToken(); - } - - public PresignedUrl generatePresignedUrl(@NonNull String objectId) { - val accessToken = generateAccessToken(); - val response = getResponse(UrlResponse.class, accessToken, getKFDownloadEndpoint(objectId)); - val url = response.getBody().getUrl(); - val size = peekResponseContentSize(url); - return PresignedUrl.builder().size(size).url(url).build(); - } - - private String getKFDownloadEndpoint(String objectId) { - return format("%s/user/data/download/%s?expires_in=%s", apiUrl, objectId, urlExpiration); - } - - @SneakyThrows - private ResponseEntity getResponse(Class responseType, String accessToken, String url) { - val entity = new HttpEntity(null, buildAuthHeader(accessToken)); - return retry.execute( - ctx -> restTemplate.exchange(new URI(url), HttpMethod.GET, entity, responseType)); - } - - @SneakyThrows - private T getObject(Class responseType, String accessToken, String url) { - return getResponse(responseType, accessToken, url).getBody(); - } - - @SneakyThrows - private static long peekResponseContentSize(String url) { - val u = new URL(url); - val conn = (HttpURLConnection) u.openConnection(); - val contentLength = conn.getContentLengthLong(); - checkState( - contentLength != -1, - "The following response does not contain the '%s' header: %s", - CONTENT_LENGTH, - conn.getHeaderFields()); - checkState( - contentLength > 0, - "The following response contains a content length of 0: %s", - conn.getHeaderFields()); - return contentLength; - } - - private static HttpHeaders buildAuthHeader(String accessToken) { - val headers = new HttpHeaders(); - if (!isNull(accessToken)) { - headers.set(AUTHORIZATION, "Bearer " + accessToken); - } - return headers; - } - - @lombok.Value - @Builder - public static class PresignedUrl { - @NonNull private final String url; - private final long size; - } - - @Data - public static class AccessTokenResponse { - @JsonProperty("access_token") - private String accessToken; - - @JsonProperty("refresh_token") - private String refreshToken; - } - - @Data - public static class UrlResponse { - private String url; - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageService.java b/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageService.java deleted file mode 100644 index f5f49d32..00000000 --- a/score-client/src/main/java/bio/overture/score/client/storage/kf/KFStorageService.java +++ /dev/null @@ -1,170 +0,0 @@ -package bio.overture.score.client.storage.kf; - -import static com.google.common.base.Preconditions.checkArgument; -import static java.lang.String.format; - -import bio.overture.score.client.download.DownloadStateStore; -import bio.overture.score.client.storage.AbstractStorageService; -import bio.overture.score.client.storage.kf.KFStorageClient.PresignedUrl; -import bio.overture.score.core.model.DataChannel; -import bio.overture.score.core.model.ObjectInfo; -import bio.overture.score.core.model.ObjectSpecification; -import bio.overture.score.core.model.Part; -import bio.overture.score.core.model.UploadProgress; -import bio.overture.score.core.util.SimplePartCalculator; -import com.google.common.collect.ImmutableList; -import java.io.IOException; -import java.util.List; -import java.util.Optional; -import lombok.NonNull; -import lombok.SneakyThrows; -import lombok.extern.slf4j.Slf4j; -import lombok.val; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.beans.factory.annotation.Qualifier; -import org.springframework.context.annotation.Profile; -import org.springframework.retry.support.RetryTemplate; -import org.springframework.stereotype.Service; -import org.springframework.web.client.RestTemplate; - -@Slf4j -@Service -@Profile("kf") -public class KFStorageService extends AbstractStorageService { - - /** Dependencies. */ - private final KFStorageClient kfStorageClient; - - private final SimplePartCalculator partCalculator; - - @Autowired - public KFStorageService( - @NonNull DownloadStateStore downloadStateStore, - @Qualifier("pingTemplate") @NonNull RestTemplate dataTemplate, - @NonNull RetryTemplate retry, - SimplePartCalculator partCalculator, - @NonNull KFStorageClient kfStorageClient) { - super(downloadStateStore, dataTemplate, retry); - this.kfStorageClient = kfStorageClient; - this.partCalculator = partCalculator; - } - - @Override - public ObjectSpecification getDownloadSpecification(String objectId, long offset, long length) - throws IOException { - val presignedUrl = kfStorageClient.generatePresignedUrl(objectId); - val parts = generateParts(presignedUrl, offset, length); - return ObjectSpecification.builder() - .objectId(objectId) - .objectMd5(null) // useless, since we do not have the md5 values of the initial part uploads - .objectSize(presignedUrl.getSize()) - .parts(parts) - .objectKey(null) - .relocated(false) - .build(); - } - - @Override - public ObjectSpecification getExternalDownloadSpecification( - String objectId, long offset, long length) throws IOException { - return getDownloadSpecification(objectId); - } - - @Override - protected Optional getEncryptedAccessToken() { - return Optional.empty(); - } - - @SneakyThrows - private List generateParts(PresignedUrl presignedUrl, long offset, long length) { - val url = presignedUrl.getUrl(); - val totalSize = presignedUrl.getSize(); - checkArgument( - offset + length < totalSize, - "The sum of: offset(%s) + length(%s) = %s must be less than the total size (%s)", - offset, - length, - offset + length, - totalSize); - List parts; - if (offset == 0 && length < 0) { - parts = partCalculator.divide(totalSize); - } else { - parts = partCalculator.divide(offset, length); - } - parts.forEach( - x -> { - x.setMd5(null); // Unobtainable - x.setSourceMd5( - null); // useless, since we do not have the md5 values of the initial part uploads - x.setUrl(url); - }); - return ImmutableList.copyOf(parts); - } - - private static String getNonImplementedMessage() { - val calledMethod = Thread.currentThread().getStackTrace()[2].getMethodName(); - return format("The method '%s' is not implemented for KF", calledMethod); - } - - /** Not implemented for KF */ - @Override - public String ping() { - log.warn("The 'ping' method is not implemented properly in KF. This is a bypass"); - return "bypass ping"; - } - - @Override - public boolean isUploadDataRecoverable(String objectId, long fileSize) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public void deleteUploadPart(String objectId, String uploadId, Part part) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public void finalizeUpload(String objectId, String uploadId) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public void finalizeUploadPart( - String objectId, - String uploadId, - int partNumber, - String md5, - String etag, - boolean disableChecksum) - throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public boolean isObjectExist(String objectId) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public void uploadPart(DataChannel channel, Part part, String objectId, String uploadId) - throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public List listObjects() { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public UploadProgress getProgress(String objectId, long fileSize) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } - - @Override - public ObjectSpecification initiateUpload( - String objectId, long length, boolean overwrite, String md5) throws IOException { - throw new IllegalStateException(getNonImplementedMessage()); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/util/CsvParser.java b/score-client/src/main/java/bio/overture/score/client/util/CsvParser.java deleted file mode 100644 index 51da6983..00000000 --- a/score-client/src/main/java/bio/overture/score/client/util/CsvParser.java +++ /dev/null @@ -1,24 +0,0 @@ -package bio.overture.score.client.util; - -import com.fasterxml.jackson.dataformat.csv.CsvMapper; -import java.io.File; -import java.util.List; -import lombok.RequiredArgsConstructor; -import lombok.SneakyThrows; -import lombok.val; - -@RequiredArgsConstructor -public class CsvParser { - - private final Class type; - private final Character columnSep; - - @SneakyThrows - public List parseFile(File file) { - val mapper = new CsvMapper(); - mapper.addMixIn(type, type); - val schema = mapper.schemaFor(type).withHeader().withColumnSeparator(columnSep); - - return mapper.readerFor(type).with(schema).readValues(file).readAll(); - } -} diff --git a/score-client/src/main/java/bio/overture/score/client/util/ProfileRepoValidator.java b/score-client/src/main/java/bio/overture/score/client/util/ProfileRepoValidator.java deleted file mode 100644 index e70b5265..00000000 --- a/score-client/src/main/java/bio/overture/score/client/util/ProfileRepoValidator.java +++ /dev/null @@ -1,50 +0,0 @@ -/* - * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved. - * - * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0. - * You should have received a copy of the GNU General Public License along with - * this program. If not, see . - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY - * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES - * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT - * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, - * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED - * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; - * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER - * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN - * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ -package bio.overture.score.client.util; - -public class ProfileRepoValidator { - - /* - * values found in DCC Portal manifest downloads - */ - public static final String COLLABORATORY_REPO = "collaboratory"; - public static final String AWS_VIRGINIA_REPO = "aws-virginia"; - public static final String AZURE_REPO = "azure"; - - public static final String COLLABORATORY_PROFILE = "collab"; - public static final String AWS_PROFILE = "aws"; - public static final String AZURE_PROFILE = "azure"; - - public static boolean validateRepoAgainstProfile(String profile, String repoCode) { - if (profile.equalsIgnoreCase(COLLABORATORY_PROFILE)) { - return repoCode.equalsIgnoreCase(COLLABORATORY_REPO); - } - - if (profile.equalsIgnoreCase(AWS_PROFILE)) { - return repoCode.equalsIgnoreCase(AWS_VIRGINIA_REPO); - } - - if (profile.equalsIgnoreCase(AZURE_PROFILE)) { - return repoCode.equalsIgnoreCase(AZURE_REPO); - } - - throw new IllegalArgumentException( - String.format( - "Didn't recognize Client Profile/Repository combination '%s'/'%s'", profile, repoCode)); - } -} diff --git a/score-client/src/main/resources/application.yml b/score-client/src/main/resources/application.yml index dfb27361..2ac3a7bd 100644 --- a/score-client/src/main/resources/application.yml +++ b/score-client/src/main/resources/application.yml @@ -36,16 +36,9 @@ client: ssl: custom: false -kfportal: - url: https://arranger.kids-first.io/june_13/graphql -kf: - token: - url: https://v2i1r42t6d.execute-api.us-east-1.amazonaws.com/beta/token - download: - url: https://data.kidsfirstdrc.org - partSize: 1073741824 - expiration: 86400 +download: + partSize: 1073741824 transport: fileFrom: memory @@ -54,13 +47,13 @@ transport: storage: # default for backwards compatibility - url: https://virginia.cloud.icgc.org +# url: retryNumber: 10 retryTimeout: 1 metadata: # default for backwards compatibility - url: https://virginia.song.icgc.org +# url: ssl: enabled: true @@ -78,41 +71,7 @@ token: isTest: false -defaultProfile: collaboratory - ---- - -############################################################################### -# Profile - "kf" -############################################################################### - -spring: - config: - activate: - on-profile: kf - -# Storage server -storage: - url: https://kf.com - - -client: - ssl: - custom: false - ---- - -############################################################################### -# Profile - "oicr" -############################################################################### - -spring: - config: - activate: - on-profile: oicr - -# uses storage.url and client.ssl.custom define in common - +defaultProfile: s3 --- @@ -132,7 +91,3 @@ logging: springframework.web: DEBUG com.amazonaws.services: DEBUG ---- -############################################################################### -# Profile - "debug" -############################################################################### diff --git a/score-client/src/main/resources/templates/manifest_id_query.txt b/score-client/src/main/resources/templates/manifest_id_query.txt deleted file mode 100644 index f4922bfa..00000000 --- a/score-client/src/main/resources/templates/manifest_id_query.txt +++ /dev/null @@ -1,29 +0,0 @@ -{ - "fields": "controlled_access\nkf_id\nfile_name\nparticipants {\n hits {\n edges {\n node {\n kf_id\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n is_proband\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n short_name\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n external_id\n }\n }\n }\n }\n }\ndata_type\nfile_format\nsize\nparticipants {\n hits {\n edges {\n node {\n diagnoses {\n hits {\n edges {\n node {\n icd_id_diagnosis\n }\n }\n }\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n family_id\n }\n }\n }\n }\nlatest_did\nkf_id\nid", - "query": "\n query($sort: [Sort], $first: Int, $offset: Int, $score: String, $sqon: JSON) {\n file {\n hits(first: $first, offset: $offset, sort: $sort, score: $score, filters: $sqon) {\n total\n edges {\n node {\n controlled_access\nkf_id\nfile_name\nparticipants {\n hits {\n edges {\n node {\n kf_id\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n is_proband\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n short_name\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n external_id\n }\n }\n }\n }\n }\ndata_type\nfile_format\nsize\nparticipants {\n hits {\n edges {\n node {\n diagnoses {\n hits {\n edges {\n node {\n icd_id_diagnosis\n }\n }\n }\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n family_id\n }\n }\n }\n }\nlatest_did\nkf_id\nid\n }\n }\n }\n }\n }\n ", - "variables": { - "sqon": { - "op": "and", - "content": [ - { - "op": "in", - "content": { - "field": "kf_id", - "value": [ - "set_id:[(${manifestId})]" - ] - } - } - ] - }, - "sort": [ - { - "field": "size", - "order": "asc" - } - ], - "score": null, - "offset": [(${offset})], - "first": [(${first})] - } -} diff --git a/score-client/src/main/resources/templates/object_id_search_query.txt b/score-client/src/main/resources/templates/object_id_search_query.txt deleted file mode 100644 index 4271ec3c..00000000 --- a/score-client/src/main/resources/templates/object_id_search_query.txt +++ /dev/null @@ -1,38 +0,0 @@ -{ - "fields": "controlled_access\nkf_id\nfile_name\nparticipants {\n hits {\n edges {\n node {\n kf_id\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n is_proband\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n short_name\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n external_id\n }\n }\n }\n }\n }\ndata_type\nfile_format\nsize\nparticipants {\n hits {\n edges {\n node {\n diagnoses {\n hits {\n edges {\n node {\n icd_id_diagnosis\n }\n }\n }\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n family_id\n }\n }\n }\n }\nlatest_did\nkf_id\nid", - "query": "\n query($sort: [Sort], $first: Int, $offset: Int, $score: String, $sqon: JSON) {\n file {\n hits(first: $first, offset: $offset, sort: $sort, score: $score, filters: $sqon) {\n total\n edges {\n node {\n controlled_access\nkf_id\nfile_name\nparticipants {\n hits {\n edges {\n node {\n kf_id\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n is_proband\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n short_name\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n study {\n external_id\n }\n }\n }\n }\n }\ndata_type\nfile_format\nsize\nparticipants {\n hits {\n edges {\n node {\n diagnoses {\n hits {\n edges {\n node {\n icd_id_diagnosis\n }\n }\n }\n }\n }\n }\n }\n }\nparticipants {\n hits {\n edges {\n node {\n family_id\n }\n }\n }\n }\nlatest_did\nkf_id\nid\n }\n }\n }\n }\n }\n ", - "variables": { - "sqon": { - "op": "and", - "content": [ - { - "op": "filter", - "content": { - "fields": [ - "kf_id", - "file_name", - "participants.kf_id", - "participants.study.short_name", - "participants.study.external_id", - "data_type", - "file_format", - - "participants.family_id", - "latest_did" - ], - "value": "[(${objectId})]" - } - } - ] - }, - "sort": [ - { - "field": "size", - "order": "asc" - } - ], - "score": null, - "offset": [(${offset})], - "first": [(${first})] - } -} \ No newline at end of file diff --git a/score-client/src/test/java/bio/overture/score/client/config/TestProfileConfig.java b/score-client/src/test/java/bio/overture/score/client/config/TestProfileConfig.java index 04cbd9e9..5238a6fd 100644 --- a/score-client/src/test/java/bio/overture/score/client/config/TestProfileConfig.java +++ b/score-client/src/test/java/bio/overture/score/client/config/TestProfileConfig.java @@ -10,7 +10,7 @@ public class TestProfileConfig { @Autowired - @Value("${defaultProfile:collaboratory}") + @Value("${defaultProfile:s3}") private String defaultProfile; @Bean diff --git a/score-client/src/test/java/bio/overture/score/client/manifest/DownloadManifestReaderTest.java b/score-client/src/test/java/bio/overture/score/client/manifest/DownloadManifestReaderTest.java index e7573827..f8e7dd28 100644 --- a/score-client/src/test/java/bio/overture/score/client/manifest/DownloadManifestReaderTest.java +++ b/score-client/src/test/java/bio/overture/score/client/manifest/DownloadManifestReaderTest.java @@ -22,7 +22,6 @@ import static org.junit.Assert.assertThat; import bio.overture.score.client.manifest.DownloadManifest.ManifestEntry; -import bio.overture.score.client.manifest.icgc.DownloadManifestReader; import java.io.File; import lombok.val; import org.junit.Test; diff --git a/score-client/src/test/java/bio/overture/score/client/manifest/UploadManifestReaderTest.java b/score-client/src/test/java/bio/overture/score/client/manifest/UploadManifestReaderTest.java index 95ca054e..c95e1314 100644 --- a/score-client/src/test/java/bio/overture/score/client/manifest/UploadManifestReaderTest.java +++ b/score-client/src/test/java/bio/overture/score/client/manifest/UploadManifestReaderTest.java @@ -22,7 +22,6 @@ import static org.junit.Assert.assertThat; import bio.overture.score.client.manifest.UploadManifest.ManifestEntry; -import bio.overture.score.client.manifest.icgc.UploadManifestReader; import java.io.File; import lombok.val; import org.junit.Test; diff --git a/score-client/src/test/resources/application.yml b/score-client/src/test/resources/application.yml index bed661c5..962bbc31 100644 --- a/score-client/src/test/resources/application.yml +++ b/score-client/src/test/resources/application.yml @@ -36,16 +36,8 @@ client: ssl: custom: false -kfportal: - url: https://arranger.kids-first.io/june_13/graphql - -kf: - token: - url: https://v2i1r42t6d.execute-api.us-east-1.amazonaws.com/beta/token - download: - url: https://data.kidsfirstdrc.org - partSize: 1073741824 - expiration: 86400 +download: + partSize: 1073741824 transport: fileFrom: memory @@ -54,13 +46,13 @@ transport: storage: # default for backwards compatibility - url: https://virginia.cloud.icgc.org + url: https://teststorageurl retryNumber: 10 retryTimeout: 1 metadata: # default for backwards compatibility - url: https://virginia.song.icgc.org + url: https://testmetadataurl ssl: enabled: true @@ -69,7 +61,7 @@ portal: logging: file: target/logs/client.log - + mount: logging: false @@ -78,38 +70,9 @@ token: isTest: true -defaultProfile: collaboratory - ---- - -############################################################################### -# Profile - "kf" -############################################################################### - -spring.profiles: kf - -# Storage server -storage: - url: https://kf.com - - -client: - ssl: - custom: false - ---- - -############################################################################### -# Profile - "oicr" -############################################################################### - -spring.profiles: oicr - -# uses storage.url and client.ssl.custom define in common - +defaultProfile: s3 --- - ############################################################################### # Profile - "debug" ############################################################################### diff --git a/score-core/README.md b/score-core/README.md index b75111df..d96cfe4f 100644 --- a/score-core/README.md +++ b/score-core/README.md @@ -1,6 +1,6 @@ -# ICGC DCC - Storage Core +# SCORe - Storage Core -Core library / shared classes for ICGC storage system. +Core library / shared classes for SCORe. ## Build diff --git a/score-core/pom.xml b/score-core/pom.xml index d1bd5a68..1e7a8091 100644 --- a/score-core/pom.xml +++ b/score-core/pom.xml @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 ../pom.xml diff --git a/score-core/src/main/java/bio/overture/score/core/model/StorageProfiles.java b/score-core/src/main/java/bio/overture/score/core/model/StorageProfiles.java index 0fd86d2a..93cbe713 100644 --- a/score-core/src/main/java/bio/overture/score/core/model/StorageProfiles.java +++ b/score-core/src/main/java/bio/overture/score/core/model/StorageProfiles.java @@ -5,7 +5,7 @@ public enum StorageProfiles { AZURE("azure", "az"), - COLLABORATORY("collaboratory", "s3"); + S3("s3", "s3"); private final String profileKey; private final String profileValue; diff --git a/score-core/src/test/resources/legacy.meta b/score-core/src/test/resources/legacy.meta index 2a2dba4d..2889b5ee 100644 --- a/score-core/src/test/resources/legacy.meta +++ b/score-core/src/test/resources/legacy.meta @@ -1 +1 @@ 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\ No newline at end of file +{"objectKey":"data/000ebcb8-e753-58e3-bc3a-319f7b4c525c","objectId":"000ebcb8-e753-58e3-bc3a-319f7b4c525c","uploadId":"01Ody8tJlM5hiBiSw8GfJCM6HeCbIbuNKq1f_nCdeVxj..8U0lsUioSNyfSdmTBnaheBB8Q5E58VOBjEBuP137G3BLKwJaQyoh4TPSfEyMHDgVOEbUs_ugjiiuTvvvLI","parts":[{"partNumber":1,"partSize":50153,"offset":0,"url":"https://s3-external-1.amazonaws.com/overture.example.score/data/000ebcb8-e753-58e3-bc3a-319f7b4c525c?uploadId=01Ody8tJlM5hiBiSw8GfJCM6HeCbIbuNKq1f_nCdeVxj..8U0lsUioSNyfSdmTBnaheBB8Q5E58VOBjEBuP137G3BLKwJaQyoh4TPSfEyMHDgVOEbUs_ugjiiuTvvvLI&partNumber=1&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20160302T081320Z&X-Amz-SignedHeaders=host&X-Amz-Expires=604800&X-Amz-Credential=AKIAJKP4PCJDQ7DT55OA%2F20160302%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=fccc71da37d5a04d7167f104e24bce6b8c38a1e475cf654c8006ca683c4a6efa","md5":"some_md5_value"},{"partNumber":2,"partSize":50153,"offset":50153,"url":"https://s3-external-1.amazonaws.com/overture.example.score/data/000ebcb8-e753-58e3-bc3a-319f7b4c525c?uploadId=01Ody8tJlM5hiBiSw8GfJCM6HeCbIbuNKq1f_nCdeVxj..8U0lsUioSNyfSdmTBnaheBB8Q5E58VOBjEBuP137G3BLKwJaQyoh4TPSfEyMHDgVOEbUs_ugjiiuTvvvLI&partNumber=1&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20160302T081320Z&X-Amz-SignedHeaders=host&X-Amz-Expires=604800&X-Amz-Credential=AKIAJKP4PCJDQ7DT55OA%2F20160302%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=fccc71da37d5a04d7167f104e24bce6b8c38a1e475cf654c8006ca683c4a6efa","md5":null}],"objectSize":50153,"relocated":false} \ No newline at end of file diff --git a/score-fs/README.md b/score-fs/README.md index e1db3aae..bcb88845 100644 --- a/score-fs/README.md +++ b/score-fs/README.md @@ -1,7 +1,7 @@ -ICGC DCC - Storage File System +SCORe - Storage File System === -ICGC storage file system for the ICGC storage system. +SCORe storage file system for the SCORe. ## Build diff --git a/score-fs/pom.xml b/score-fs/pom.xml index 7320fc7c..0cfa164b 100644 --- a/score-fs/pom.xml +++ b/score-fs/pom.xml @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 ../pom.xml diff --git a/score-fs/src/main/java/bio/overture/score/fs/StorageFileStore.java b/score-fs/src/main/java/bio/overture/score/fs/StorageFileStore.java index 4b3129ee..b8aa5c7c 100644 --- a/score-fs/src/main/java/bio/overture/score/fs/StorageFileStore.java +++ b/score-fs/src/main/java/bio/overture/score/fs/StorageFileStore.java @@ -24,11 +24,11 @@ public class StorageFileStore extends FileStore { - public static final String ICGCFS = "icgcfs"; + public static final String SCOREFS = "scorefs"; @Override public String type() { - return ICGCFS; + return SCOREFS; } @Override @@ -43,7 +43,7 @@ public boolean supportsFileAttributeView(Class type @Override public String name() { - return "icgc"; + return "score"; } @Override diff --git a/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystemProvider.java b/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystemProvider.java index 1ff5bf0a..998a8ba2 100644 --- a/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystemProvider.java +++ b/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystemProvider.java @@ -70,7 +70,7 @@ public class StorageFileSystemProvider extends ReadOnlyFileSystemProvider { @Override public String getScheme() { - return "icgc"; + return "score"; } @Override diff --git a/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystems.java b/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystems.java index e853cde4..127111ca 100644 --- a/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystems.java +++ b/score-fs/src/main/java/bio/overture/score/fs/StorageFileSystems.java @@ -38,7 +38,7 @@ public StorageFileSystem newFileSystem(@NonNull StorageContext context) public StorageFileSystem newFileSystem(@NonNull StorageContext context, Map env) throws IOException, URISyntaxException { val provider = new StorageFileSystemProvider(context); - val uri = new URI("icgc://storage"); + val uri = new URI("score://storage"); return (StorageFileSystem) provider.newFileSystem(uri, env); } diff --git a/score-server/README.md b/score-server/README.md index eb773e04..21034c46 100644 --- a/score-server/README.md +++ b/score-server/README.md @@ -1,6 +1,4 @@ -# ICGC DCC - Storage Server - -Storage server for ICGC storage system. +# SCORe - Storage Server ## Libraries @@ -46,7 +44,42 @@ bucket: download: partsize: 250000000 # 250 MB ``` -At this time, only a single Azure Blob Storage account (and container) is used. However, since Azure Storage can only store 500 TB per account, the Storage Server will need to manage multiple account/key credentials in the near future. It may also make sense to have multiple containers per account as well. There are suggestions that having many objects in a single container can impose a performance penalty on some operations. +### S3 Configuration +To configure SCORe to use an S3-compatible object storage service, the s3 Spring profile must be activated. This profile is designed to work with services like AWS S3, MinIO, or any other compatible service. Below are the configuration properties available under the s3 section in application.yml, along with their descriptions: + +Profile Name: ``s3`` + +## Configuration + +### Operating Profiles + +| Profile Name | Description | +| ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| azure | Enable connection to Azure Blob storage for file storage, instead of default S3. | +| secure | Enables Authorization validation for all protected routes. Either `secure` or `noSecurityDev` profile must be set for Score to operate. **ALWAYS USE THIS IN PRODUCTION** | +| | | +| benchmark | _Development Profile_ Enables tooling to help with benchmark testing. | +| dev | Disables application level SSL verfication, if configured. | +| noSecurityDev | Disable Authorization check for all routes. **DO NOT USE THIS PRODUCTION** | +| test | Used to configure app when running unit test suite. | + +### S3 Configuration Properties + +| Property | Description | +| -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `s3.secured` | Determines whether the connection to the S3 service should use HTTPS (true) or HTTP (false). Set to true to secure the connection. | +| `s3.endpoint` | The URL of the S3-compatible service. This is the endpoint where the service is hosted. This property should be provided based on the service you're using. | +| `s3.accessKey` | The access key for authenticating with the S3 service. It's required for secure access and should be kept confidential. | +| `s3.secretKey` | The secret key paired with the access key for secure authentication to the S3 service. It must also be kept confidential. | +| `s3.masterEncryptionKeyId` | The ID of the encryption key used for server-side encryption of files stored in S3. If provided, this key ensures that all data at rest is encrypted using the specified key. | +| `s3.customMd5Property` | A custom metadata property that stores an MD5 checksum of the uploaded files. This is useful for validating the integrity of the files. | +| `s3.connectionTimeout` | The maximum amount of time (in milliseconds) the client will wait to establish a connection to the S3 service before timing out. This helps manage delays in the network or service availability. | +| `s3.retryLimit` | The number of retries the client will attempt if an operation fails (e.g., an upload). This helps ensure robustness in case of transient issues. | +| `s3.sigV4Enabled` | Enables AWS Signature Version 4 for request signing. This is required for certain regions or when using advanced features like server-side encryption with AWS KMS. | + + +> [!NOTE] +> At this time, only a single Azure Blob Storage account (and container) is used. However, since Azure Storage can only store 500 TB per account, the Storage Server will need to manage multiple account/key credentials in the near future. It may also make sense to have multiple containers per account as well. There are suggestions that having many objects in a single container can impose a performance penalty on some operations. The Storage Server no longer uses ``.meta`` files to track state in the repository. Object Specifications are dynamically generated on the fly for use on the client (to allow downloads to be resumed). Also, the block upload implementation supplied by Microsoft in the Azure Java SDK supercedes the use of this file. diff --git a/score-server/pom.xml b/score-server/pom.xml index 244dbac7..f0781ddf 100644 --- a/score-server/pom.xml +++ b/score-server/pom.xml @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 ../pom.xml diff --git a/score-server/src/main/conf/application.properties b/score-server/src/main/conf/application.properties index 720c51d3..7b331d4e 100644 --- a/score-server/src/main/conf/application.properties +++ b/score-server/src/main/conf/application.properties @@ -22,4 +22,4 @@ # s3.secretKey= # server.ssl.key-store-password= # s3.masterEncryptionKeyId= -# collaboratory.bucket.name= \ No newline at end of file +# s3.bucket.name= \ No newline at end of file diff --git a/score-server/src/main/java/bio/overture/score/server/config/NoSecurityConfig.java b/score-server/src/main/java/bio/overture/score/server/config/NoSecurityConfig.java new file mode 100644 index 00000000..182071f5 --- /dev/null +++ b/score-server/src/main/java/bio/overture/score/server/config/NoSecurityConfig.java @@ -0,0 +1,68 @@ +package bio.overture.score.server.config; + +import bio.overture.score.server.metadata.MetadataService; +import lombok.Getter; +import lombok.NonNull; +import lombok.Setter; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Profile; +import org.springframework.context.annotation.Scope; +import org.springframework.security.config.annotation.web.builders.HttpSecurity; +import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity; +import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter; +import org.springframework.security.core.Authentication; + +@Profile("noSecurityDev") +@Configuration +@Getter +@Setter +@EnableWebSecurity +public class NoSecurityConfig extends WebSecurityConfigurerAdapter { + + private String provider; + + @Override + protected void configure(HttpSecurity http) throws Exception { + // Disable cors and csrf to avoid 403 forbidden for local development. + http.cors().and().csrf().disable().authorizeRequests().antMatchers("/").permitAll(); + } + + /* + * In order to mirror the security provisions in SecurityConfig.java: we need to define projectSecurity, and + * accessSecurity, which are used for method level authorization in the DownloadController and UploadController. These + * need to return a ScopeAuthorizationStrategy, which we do here by returning an anonymous class version of the + * expected return class, and these anonymous implementations override the authorize() function call to always return + * true. + */ + public interface AnonymousScopeAuthorizationStategy { + + boolean authorize(@NonNull Authentication authentication, @NonNull String objectId); + } + + @Bean + public AnonymousScopeAuthorizationStategy projectSecurity( + @Autowired MetadataService metadataService) { + return new AnonymousScopeAuthorizationStategy() { + + @Override + public boolean authorize(@NonNull Authentication authentication, @NonNull String objectId) { + return true; + } + }; + } + + @Bean + @Scope("prototype") + public AnonymousScopeAuthorizationStategy accessSecurity( + @Autowired MetadataService metadataService) { + return new AnonymousScopeAuthorizationStategy() { + + @Override + public boolean authorize(@NonNull Authentication authentication, @NonNull String objectId) { + return true; + } + }; + } +} diff --git a/score-server/src/main/java/bio/overture/score/server/config/S3Config.java b/score-server/src/main/java/bio/overture/score/server/config/S3Config.java index 927e19ab..310b8b8c 100644 --- a/score-server/src/main/java/bio/overture/score/server/config/S3Config.java +++ b/score-server/src/main/java/bio/overture/score/server/config/S3Config.java @@ -19,13 +19,11 @@ import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Profile; /** S3/Ceph Object Gateway configuration. */ @Data @Slf4j @Configuration -@Profile({"aws", "collaboratory", "default"}) @ConfigurationProperties(prefix = "s3") public class S3Config { diff --git a/score-server/src/main/java/bio/overture/score/server/config/ServerConfig.java b/score-server/src/main/java/bio/overture/score/server/config/ServerConfig.java index 4e8f6d6c..29bcc411 100644 --- a/score-server/src/main/java/bio/overture/score/server/config/ServerConfig.java +++ b/score-server/src/main/java/bio/overture/score/server/config/ServerConfig.java @@ -29,11 +29,9 @@ import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Profile; /** Server level configuration */ @Configuration -@Profile({"aws", "collaboratory", "default"}) public class ServerConfig { @Value("${upload.partsize}") diff --git a/score-server/src/main/java/bio/overture/score/server/controller/DownloadController.java b/score-server/src/main/java/bio/overture/score/server/controller/DownloadController.java index 22decc8c..38ad5478 100644 --- a/score-server/src/main/java/bio/overture/score/server/controller/DownloadController.java +++ b/score-server/src/main/java/bio/overture/score/server/controller/DownloadController.java @@ -26,7 +26,6 @@ import lombok.extern.slf4j.Slf4j; import lombok.val; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; @@ -46,7 +45,6 @@ @RestController @RequestMapping("/download") @Slf4j -@Profile({"prod", "default", "debug"}) public class DownloadController { @Autowired DownloadService downloadService; diff --git a/score-server/src/main/java/bio/overture/score/server/controller/UploadController.java b/score-server/src/main/java/bio/overture/score/server/controller/UploadController.java index c77b9891..2dd556a0 100644 --- a/score-server/src/main/java/bio/overture/score/server/controller/UploadController.java +++ b/score-server/src/main/java/bio/overture/score/server/controller/UploadController.java @@ -31,7 +31,6 @@ import lombok.extern.slf4j.Slf4j; import lombok.val; import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.context.annotation.Profile; import org.springframework.http.HttpHeaders; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; @@ -52,7 +51,6 @@ @RestController @RequestMapping("/upload") @Slf4j -@Profile({"prod", "default", "debug"}) public class UploadController { @Autowired UploadService uploadService; diff --git a/score-server/src/main/java/bio/overture/score/server/health/BackendHealth.java b/score-server/src/main/java/bio/overture/score/server/health/BackendHealth.java index 22b26a81..b92268fa 100644 --- a/score-server/src/main/java/bio/overture/score/server/health/BackendHealth.java +++ b/score-server/src/main/java/bio/overture/score/server/health/BackendHealth.java @@ -22,12 +22,10 @@ import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.actuate.health.Health; import org.springframework.boot.actuate.health.HealthIndicator; -import org.springframework.context.annotation.Profile; import org.springframework.stereotype.Component; /** check health for object upload service */ @Component -@Profile({"aws", "collaboratory", "default"}) public class BackendHealth implements HealthIndicator { @Autowired AmazonS3 s3; diff --git a/score-server/src/main/java/bio/overture/score/server/repository/UploadCleanupService.java b/score-server/src/main/java/bio/overture/score/server/repository/UploadCleanupService.java index b7c47d82..940db9f8 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/UploadCleanupService.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/UploadCleanupService.java @@ -40,10 +40,10 @@ public class UploadCleanupService { /** Configuration. */ - @Value("${collaboratory.data.directory}") + @Value("${s3.data.directory}") private String dataDir; - @Value("${collaboratory.upload.expiration}") + @Value("${s3.upload.expiration}") private int expiration; /** Dependencies. */ diff --git a/score-server/src/main/java/bio/overture/score/server/repository/azure/AzureURLGenerator.java b/score-server/src/main/java/bio/overture/score/server/repository/azure/AzureURLGenerator.java index e68f0c51..cf308381 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/azure/AzureURLGenerator.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/azure/AzureURLGenerator.java @@ -49,7 +49,7 @@ public class AzureURLGenerator implements URLGenerator { @Value("${bucket.policy.download}") private String downloadPolicy; - @Value("${collaboratory.download.expiration}") + @Value("${s3.download.expiration}") private int expiration; @Autowired private CloudBlobContainer azureContainer; diff --git a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3DownloadService.java b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3DownloadService.java index bf8ceb7e..f93894af 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3DownloadService.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3DownloadService.java @@ -55,7 +55,6 @@ import lombok.val; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; -import org.springframework.context.annotation.Profile; import org.springframework.http.HttpStatus; import org.springframework.stereotype.Service; @@ -63,7 +62,6 @@ @Slf4j @Setter @Service -@Profile({"aws", "collaboratory", "default"}) public class S3DownloadService implements DownloadService { /** Constants. */ @@ -72,10 +70,10 @@ public class S3DownloadService implements DownloadService { private static final String PUBLISHED_ANALYSIS_STATE = "PUBLISHED"; /** Configuration. */ - @Value("${collaboratory.data.directory}") + @Value("${s3.data.directory}") private String dataDir; - @Value("${collaboratory.download.expiration}") + @Value("${s3.download.expiration}") private int expiration; @Value("${object.sentinel}") @@ -212,7 +210,7 @@ public ObjectSpecification download( private String getObjectMd5(ObjectMetadata metadata) { val contentMd5 = metadata.getContentMD5(); if (contentMd5 != null) { - return MD5s.toHex(contentMd5); + return MD5s.toHex(contentMd5); } val userMetadataMd5 = metadata.getUserMetaDataOf(s3config.getCustomMd5Property()); // get literal from config diff --git a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3ListingService.java b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3ListingService.java index 8e357056..93ee7b40 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3ListingService.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3ListingService.java @@ -36,28 +36,21 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.cache.annotation.Cacheable; -import org.springframework.context.annotation.Profile; import org.springframework.http.HttpStatus; import org.springframework.stereotype.Service; @Slf4j @Setter @Service -@Profile({"aws", "collaboratory", "default"}) public class S3ListingService implements ListingService { /** Configuration. */ @Value("${bucket.name.object}") private String bucketName; - @Value("${collaboratory.data.directory}") + @Value("${s3.data.directory}") private String dataDir; - // @Value("${collaboratory.bucket.poolsize}") - // private int bucketPoolSize; - // @Value("${collaboratory.bucket.keysize}") - // private int bucketKeySize; - /** Dependencies. */ @Autowired private AmazonS3 s3; @@ -109,8 +102,10 @@ private List listBucketContents(String bucket) { } private void readBucket(String bucketName, String prefix, Consumer callback) { - val request = prefix.isBlank() ? new ListObjectsRequest().withBucketName(bucketName) : - new ListObjectsRequest().withBucketName(bucketName).withPrefix(prefix); + val request = + prefix.isBlank() + ? new ListObjectsRequest().withBucketName(bucketName) + : new ListObjectsRequest().withBucketName(bucketName).withPrefix(prefix); log.debug("Reading summaries from '{}/{}'...", bucketName, prefix); ObjectListing listing; diff --git a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadService.java b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadService.java index 85178fa1..7cbad788 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadService.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadService.java @@ -46,7 +46,6 @@ import lombok.val; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; -import org.springframework.context.annotation.Profile; import org.springframework.http.HttpStatus; import org.springframework.stereotype.Service; import org.springframework.web.client.RestClientException; @@ -55,7 +54,6 @@ @Slf4j @Setter @Service -@Profile({"aws", "collaboratory", "default"}) public class S3UploadService implements UploadService { /** Constants. */ @@ -64,10 +62,10 @@ public class S3UploadService implements UploadService { private static final String UNPUBLISHED_ANALYSIS_STATE = "UNPUBLISHED"; /** Configuration. */ - @Value("${collaboratory.data.directory}") + @Value("${s3.data.directory}") private String dataDir; - @Value("${collaboratory.upload.expiration}") + @Value("${s3.upload.expiration}") private int expiration; @Value("${metadata.useLegacyMode:false}") diff --git a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadStateStore.java b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadStateStore.java index b4cf2840..16f9e972 100644 --- a/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadStateStore.java +++ b/score-server/src/main/java/bio/overture/score/server/repository/s3/S3UploadStateStore.java @@ -76,10 +76,10 @@ public class S3UploadStateStore implements UploadStateStore { private static final ObjectMapper MAPPER = new ObjectMapper(); /** Configuration. */ - @Value("${collaboratory.data.directory}") + @Value("${s3.data.directory}") private String dataDir; - @Value("${collaboratory.upload.directory}") + @Value("${s3.upload.directory}") private String uploadDir; /** Dependencies. */ diff --git a/score-server/src/main/resources/application.yml b/score-server/src/main/resources/application.yml index 47587ca1..05ae8499 100644 --- a/score-server/src/main/resources/application.yml +++ b/score-server/src/main/resources/application.yml @@ -33,6 +33,11 @@ server: s3: secured: true sigV4Enabled: true + upload.directory: upload + upload.expiration: 6 + data.directory: data + # COL-131: Change pre-signed URLs TTL to 1 day max + download.expiration: 1 # custom meta property with md5 hash, unused when upload state files are available (default behaviour) # customMd5Property: md5chksum @@ -57,14 +62,6 @@ bucket: object: sentinel: heliograph -collaboratory: - upload.directory: upload - upload.expiration: 6 - data.directory: data - - # COL-131: Change pre-signed URLs TTL to 1 day max - download.expiration: 1 - upload: retry.limit: 5 partsize: 20000000 @@ -101,13 +98,11 @@ spring: pathmatch: matching-strategy: ant_path_matcher - logging: level: root: INFO org.springframework.web: INFO --- - ############################################################################### # Profile - "ssl" # this is the configuration for the service using the self-signed cert created @@ -128,73 +123,67 @@ server: key-alias: object-store-service --- - ############################################################################### -# Profile - "amazon" +# Profile - "azure" ############################################################################### spring: config: activate: - on-profile: amazon + on-profile: azure -s3: - endpoint: s3-external-1.amazonaws.com - masterEncryptionKeyId: af628f04-ac12-4b11-bf83-6545fd44ad18 +azure: + endpointProtocol: https + accountName: oicricgc + accountKey: bucket: - name.object: oicr.icgc - name.state: oicr.icgc + name.object: data + policy.upload: UploadPolicy + policy.download: DownloadPolicy -metadata: - url: https://virginia.song.icgc.org - useLegacyMode: false +download: + partsize: 250000000 --- - ############################################################################### -# Profile - "collaboratory" +# Profile - "s3" ############################################################################### spring: config: activate: - on-profile: collaboratory + on-profile: s3 s3: - endpoint: https://object.cancercollaboratory.org:9080 - masterEncryptionKeyId: + # Whether the connection should use HTTPS (true) or HTTP (false) + secured: true -metadata: - url: https://song.cancercollaboratory.org - useLegacyMode: false + # Endpoint URL for the S3-compatible service + # endpoint: your-s3-endpoint ---- + # Access key for authentication + # accessKey: your-access-key -############################################################################### -# Profile - "azure" -############################################################################### + # Secret key for authentication + # secretKey: your-secret-key -spring: - config: - activate: - on-profile: azure + # Master encryption key ID for server-side encryption + # masterEncryptionKeyId: your-encryption-key-id -azure: - endpointProtocol: https - accountName: oicricgc - accountKey: + # Custom MD5 checksum property (if needed) + customMd5Property: md5chksum -bucket: - name.object: data - policy.upload: UploadPolicy - policy.download: DownloadPolicy + # Connection timeout in milliseconds + connectionTimeout: 15000 -download: - partsize: 250000000 + # Retry limit for failed operations + retryLimit: 5 ---- + # Whether to use Signature Version 4 + sigV4Enabled: true +--- ############################################################################### # Profile - "prod" ############################################################################### @@ -212,7 +201,6 @@ metadata: url: https://meta.icgc.org --- - ############################################################################### # Profile - "secure" ############################################################################### @@ -257,7 +245,6 @@ auth: suffix: .WRITE --- - ############################################################################### # Profile - "dev" ############################################################################### @@ -288,7 +275,6 @@ metadata: url: http://localhost:8080 --- - ############################################################################### # Profile - "benchmark" ############################################################################### @@ -305,5 +291,4 @@ server: s3: secured: false - # Sinai Center - endpoint: http://www.cancercollaboratory.org:9081 + endpoint: diff --git a/score-server/src/main/resources/favicon.ico b/score-server/src/main/resources/favicon.ico deleted file mode 100644 index 06996cdd..00000000 Binary files a/score-server/src/main/resources/favicon.ico and /dev/null differ diff --git a/score-server/src/main/resources/static/index.html b/score-server/src/main/resources/static/index.html deleted file mode 100644 index 783b10f9..00000000 --- a/score-server/src/main/resources/static/index.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - ICGC DCC | Storage Server - - - -
- -
-
-

Storage Server

-

This is the ICGC DCC Storage server

- Contact DCC Support - Contact the ICGC -
-
- - - - diff --git a/score-server/src/main/scripts/crontab b/score-server/src/main/scripts/crontab deleted file mode 100644 index 45a5723c..00000000 --- a/score-server/src/main/scripts/crontab +++ /dev/null @@ -1,35 +0,0 @@ -# -# Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved. -# -# This program and the accompanying materials are made available under the terms of the GNU Public License v3.0. -# You should have received a copy of the GNU General Public License along with -# this program. If not, see . -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY -# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES -# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT -# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, -# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED -# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER -# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN -# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# - -SHELL=/bin/bash -PATH=/sbin:/bin:/usr/sbin:/usr/bin -MAILTO=ayang@oicr.on.ca -HOME=/ - -# For details see man 4 crontabs - -# Example of job definition: -# .---------------- minute (0 - 59) -# | .------------- hour (0 - 23) -# | | .---------- day of month (1 - 31) -# | | | .------- month (1 - 12) OR jan,feb,mar,apr ... -# | | | | .---- day of week (0 - 6) (Sunday=0 or 7) OR sun,mon,tue,wed,thu,fri,sat -# | | | | | -# * * * * * user-name command to be executed -1 1 * * * ec2-user /home/ec2-user/harvest.sh &>/tmp/harvest.log - diff --git a/score-server/src/main/scripts/harvest.py b/score-server/src/main/scripts/harvest.py deleted file mode 100644 index f31fe1a9..00000000 --- a/score-server/src/main/scripts/harvest.py +++ /dev/null @@ -1,60 +0,0 @@ -# -# Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved. -# -# This program and the accompanying materials are made available under the terms of the GNU Public License v3.0. -# You should have received a copy of the GNU General Public License along with -# this program. If not, see . -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY -# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES -# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT -# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, -# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED -# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER -# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN -# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# - -import boto3 -import os -import fnmatch -import shutil - -source = '/icgc/object-store-service-0.0.17/logs' - -def all_files(root, patterns='*', single_level=False, yield_folders=False): - # Expand patterns from semicolon-separated string to list - patterns = patterns.split(';') - for path, subdirs, files in os.walk(root): - if yield_folders: - files.extend(subdirs) - files.sort( ) - for name in files: - for pattern in patterns: - if fnmatch.fnmatch(name, pattern): - yield os.path.join(path, name) - break - if single_level: - break - -s3 = boto3.resource('s3') - -instance = os.getenv('OBJECTSTORE_INSTANCE', 'default') -print 'Instance: ' + instance - -for p in all_files(source, 'objectstore.*.log', True): - fname = os.path.basename(p) - # print p - # print fname - - # Upload a new file - data = open(p, 'rb') - keyval = instance + '/' + fname - s3.Bucket('oicr.icgc.audit').put_object(Key=keyval, Body=data) - - # to be replaced with operation to just delete audit logs instead of keeping them - backup = source + '/archive/' + fname - shutil.move(p, backup) - - # os.remove(p) diff --git a/score-server/src/main/scripts/harvest.sh b/score-server/src/main/scripts/harvest.sh deleted file mode 100755 index b74c3a7d..00000000 --- a/score-server/src/main/scripts/harvest.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash -# -# Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved. -# -# This program and the accompanying materials are made available under the terms of the GNU Public License v3.0. -# You should have received a copy of the GNU General Public License along with -# this program. If not, see . -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY -# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES -# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT -# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, -# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED -# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER -# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN -# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# - -#cd /home/ec2-user -export OBJECTSTORE_INSTANCE=objectstore.cancercollaboratory.org -export AWS_ACCESS_KEY_ID= -export AWS_SECRET_ACCESS_KEY= -export AWS_DEFAULT_REGION=us-east-1 -/usr/bin/python /home/ec2-user/harvest.py - diff --git a/score-test/README.md b/score-test/README.md index 8ff1395b..0ba48e90 100644 --- a/score-test/README.md +++ b/score-test/README.md @@ -1,4 +1,4 @@ -# ICGC DCC - Storage Test +# SCORe - Storage Test Module used for integration testing. diff --git a/score-test/pom.xml b/score-test/pom.xml index 178181b6..7b93c925 100644 --- a/score-test/pom.xml +++ b/score-test/pom.xml @@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S bio.overture score - 5.11.0 + 5.12.0 ../pom.xml