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Changelog

v1.4.7 [2023-01-31]

User visible changes

  • The extensions to CWL that cwltool knows about will no longer results in an error

Operations changes:

  • After we run cwltool, we now try harder to cleanup the process.

Dependecies upgrade:

  • Bump jackson-core from 2.14.1 to 2.14.2
  • Bump mockito-inline from 5.0.0 to 5.1.1

v1.4.6 [2023-01-18]

User visible changes

  • Better identify repository licenses through the Licensee Ruby Gem
  • When processing a directory, the presence of errors will cause a afile to be skipped instead of erroring out the entire process
  • Many user visible error message have been made more helpful; especially in the case of a missing or private repository

Operations changes:

  • Unused RO Bundles and Git repositories are now deleted in case of errors, instead of filling up the disk with unusable files
  • Temporary directories older than 1 day are now cleared via a daily cron job See src/main/resources/application.properties for configuration
  • Error handling and retries are improved for git checkouts

Minor changes:

  • mockito-all was replaced by mockito-inline as it supports mocking static methods

Dependecies upgrade:

  • Bump jackson from 2.13.4 to 2.14.1
  • Bump spring-data-commons from 2.7.3 to 2.7.7
  • Bump hibernate-types-55 from 2.19.2 to 2.21.1
  • Bump liquibase-core from 4.16.1 to 4.19.0
  • Bump snakeyaml-engine from 2.4 to 2.6
  • Bump common-compress from 1.21 to 1.22
  • Bump junit-jupiter from 1.17.4 to 1.17.6
  • Bump postgresql from 1.17.4 to 1.17.6
  • Bump jena-core from 4.6.1 to 4.7.0

Changes related to the migration of view.commonwl.org from Curii, Inc to HPC4AI, University of Turin:

  • Removed Data controller section in the About page
  • Added HPC4AI logo in the page footer
  • Updated docker-compose.yml file to explicitly set ulimit -n to 65536

v1.4.5 [2022-09-30]

User visible changes

  • Switch to snakeyaml-engine (YAML 1.2) from snakeyaml (YAML 1.1) to improve YAML parsing (less errors)
  • Made explicit that only gitlab.com and github.com are supported as shortcuts, and that specifying workflows on other hosts needs an explicit git repo URL + branch + path.
  • Fewer errors due to the use of complex types
  • Support workflows using MultipleInputFeatureRequirement

Minor changes:

  • Always pass --disable-color to cwltool to improve the logs
  • Removed explicit html5lib Python dependency
  • Improvements to container building.
  • Added diagram of operation to the docs

Dependecies upgrade:

  • Bump maven-enforcer-plugin from 3.0.0 to 3.1.0
  • Bump liquibase-core from 4.11.0 to 4.16.1
  • Bump spring-data-commons from 2.7.0 to 2.7.3
  • Bump hibernate-types-55 from 2.16.2 to 2.19.2
  • Bump postgresql from 1.17.2 to 1.17.4
  • Bump junit-jupiter from 1.17.2 to 1.17.3
  • Bump jena-core from 4.5.0 to 4.6.1
  • Bump jackson-core from 2.13.3 to 2.13.4

v1.4.4 [2022-06-08]

Rebuild container to pull in newer version of Python (3.6.9) Use Java 17 LTS Update Docker command java location

Bump postgresql from 1.17.1 to 1.17.2 Bump spring-data-commons from 2.6.3 to 2.7.0 Bump hibernate-types-55 from 2.16.1 to 2.16.2 Bump jena-core from 4.4.0 to 4.5.0 Bump jackson-core from 2.13.2 to 2.13.3 Update spring boot (2.6.1 → 2.6.7), liquibase (unpinned → 4.10.), jgit (5.13 → 6.1) Bump liquibase-core from 4.10.0 to 4.11.0 Bump junit-jupiter from 1.17.1 to 1.17.2

v1.4.3 [2022-04-19]

A few workflows were not rendering correctly after the upgrade from MongoDB to PostgreSQL. The reason was a security update in Thymeleaf that stopped Java static methods from being invoked in templates. Only a few workflows triggered the part of the code with static calls, and the production instance of CWL Viewer, https://view.commonwl.org, was not migrated yet - this issue should only affect users using v1.4.2 locally.

Smaller changes:

  • Small fixes for issues found during dev/prod deployment (includes Thymeleaf fix) #391 @kinow

Misc fixes:

  • Add mongo_to_pg Python script and notebook, replace dump.sh by dump.py (supports pagination) #396 @kinow

Dependencies upgrade:

  • Bump junit-jupiter from 1.16.2 to 1.16.3 #387 @mr-c
  • Bump postgresql from 1.16.2 to 1.16.3 #386 @mr-c
  • Bump jackson-core from 2.13.1 to 2.13.2 #390 @kinow
  • Bump spring-data-commons from 2.6.2 to 2.6.3 #392 @kinow
  • Bump hibernate-types-55 from 2.14.0 to 2.14.1 #393 @kinow
  • Bump hibernate-types-55 from 2.14.0 to 2.14.1 #393 @kinow
  • Bump hibernate-types-55 from 2.14.1 to 2.15.2 #400 @kinow
  • Bump postgresql from 1.16.3 to 1.17.0 #401 @kinow
  • Bump hibernate-types-55 from 2.15.2 to 2.16.0 #403 @kinow
  • Bump junit-jupiter from 1.16.3 to 1.17.0 #402 @kinow
  • Bump postgresql from 1.17.0 to 1.17.1 #404 @kinow
  • Bump junit-jupiter from 1.17.0 to 1.17.1 #405 @kinow
  • Bump hibernate-types-55 from 2.16.0 to 2.16.1 #406 @kinow

v1.4.2 [2022-02-25]

The database model has been migrated from MongoDB to PostgreSQL. README instructions and Docker images updated. New version will be deployed to https://view.commonwl.org soon.

Smaller changes:

  • Added Maven default build goal #377 @kinow

Misc fixes:

  • Document Git, GitHub, Docker Hub, and Quay.io release process #360 @mr-c
  • Migrate from MongoDB to PostgreSQL #378 @kinow

Dependencies upgrade:

  • Bump spring-data-commons from 2.6.0 to 2.6.1 #383 @mr-c
  • Bump jena-core from 4.3.2 to 4.4.0 #382 @mr-c
  • Bump hibernate-validator from 7.0.1.Final to 7.0.2.Final #381 @kinow
  • Bump spring-data-commons from 2.6.1 to 2.6.2 #380 @mr-c

v1.4.1 [2021-12-21]

This version started using SpringBoot 2.6.1, and had other small code changes, and many dependencies upgraded.

Smaller changes:

  • Convert label-schema to OCI annotations #361 @mr-c

Misc fixes:

  • Added plug-in configuration for avoiding any usages of outdated log4j2 versions, some of which are subject to the RCE CVE-2021-44228 ("Log4Shell") and CVE-2021-45046 20c58b9d782802de04cdce3e975198940900a504 @mr-c

Dependencies upgrade:

  • Upgrade to SpringBoot 2.6.1 #284 @mr-c @etzanis @kinow
  • update pip & setuptools #364 @mr-c
  • Dependency updates, courtesy of @dependabot-bot
    • Bump jackson-core from 2.12.5 to 2.13.0 #358
    • Bump jsonld-java from 0.13.3 to 0.13.4 #365
    • Bump snakeyaml from 1.29 to 1.30 #366
    • Bump hibernate-validator from 6.0.13.Final to 6.0.20.Final #370
    • Bump jena-core from 4.3.1 to 4.3.2 #372
    • Bump hibernate-validator from 6.0.20.Final to 7.0.1.Final #373
    • Bump jackson-core from 2.13.0 to 2.13.1 #374

v1.4.0 [2021-10-04]

Many updates since 2018, but the most important is the fix (#355) for CVE-2021-41110 courtesy of @kinow

New features:

  • Streamable CWL graph images #240 @stain
  • Schedule recurrent CWL Viewer maintained cron-job for purging of old queued workflows from database #326 @obasekiosa

Smaller changes:

  • Separate workflow URL from repository URL in "retrieved from" column of workflows page #316 @obasekiosa
  • Fix replace non working deleteByRetrievedFrom function with working delete function #321 @obasekiosa

Documentation updates:

  • Update README.md to explain better how to get started #308 @Anushka-shukla
  • README.d: correct example URL to use port 8080 #311 @yichiehc
  • Add links to the 2017 Video overview & Mark's report 612f5b4 b83b4fd 3380d44 @mr-c @stain
  • Notes on running Mongo/Jena in Docker, and spring boot on host #334 @tetron
  • Typos in README.md #349 @kinow

Misc fixes:

  • Update jena & switch to Turtle syntax for SPARQL connection #213 @stain
  • fix reversed class & id attributes #235 @mr-c & fixed by @kinow in #352 #353
  • Use HTTPS instead of HTTP to resolve dependencies #250 [security update!] @JLLeitschuh
  • Indexing retrievedOn in mongo to fix "Clicking 'Last' on the Explore page gives ISE" (#270) 922b434 @stain
  • Update copyright year (#286) @stain
  • add skip-schemas to the cwltool invocation so we are more lenient

Changes related to the migration of view.commonwl.org from University of Manchester to Curii, Inc (Many thanks to @stain and UNIMAN for their years of service to the public!)

  • Add restart:always in docker-compose.yml #294 @cure
  • Update the data controller for the https://view.commonwl.org instance. #297 @cure
  • Tweaks for the docker-compose.yml file & set a larger internalQueryExecMaxBlockingSortBytes value for mongod #298 @cure
  • Remove mention of dev instance 51a7d38 @tetron

Dependencies upgrade:

CI updates:

  • stop double testing PRs with Travis (#234) @mr-c
  • speed up Travis by caching maven ea47b4a76fb9072f8aa4d2847edfc48a4f11d825 @mr-c
  • Install codeql-analysis.yml #268 @mr-c (this helped @kinow and I find CVE-2021-41110; thanks https://github.com/github/codeql-action !)
  • Update primary branch name to main 3e3865c3f5b779458f8395f1cfc6c0589e89cb59 @mr-c
  • Mergify: configuration update a867bd3 1178ed2 @mr-c
  • Upgrade to GitHub-native Dependabot 0a5b427 @mr-c
  • Update codeql-analysis.yml to run less often 50401a5 @mr-c
  • codeql: git checkout HEAD^2 is no longer necessary 2502986 @mr-c

v1.3.0 [2018-07-06]

Added

Fixed

v1.2.2 [2017-08-24]

Fixed

  • Fix for invalid branch names being accepted in some circumstances
  • Fix regression in supporting slashes in branch names
  • References

v1.2.1 [2017-08-22]

Added

  • Adds directory listing functionality

Fixed

  • Better support for packed workflows
    • Use %26 (#) in the URL to view individual workflows as per cwltool
    • Links to subworkflows within a packed file now function correctly
  • Improved error reporting
  • Fix for array and optional types not being parsed correctly
  • Fix for twitter meta tags not containing the correct image URL
  • Fix for a concurrency issue
  • Brings API documentation up to date with the current state of the JSON API

v1.2.0 [2017-08-22]

v1.1.1 [2017-08-11]

Fixed

  • This patch release of CWL Viewer fixes documentation and a potential git checkout issue.
  • References

v.1.1.0 [2017-08-11]

  • Support for any workflow stored in a Git repository
    • Specific additional features eg linking directly to files for Github, Gitlab, Bitbucket
  • Adds cwltool use for parsing - uses RDF representation with triple store
  • Intermediate loading screen
  • Research Object enhancements
    • Add visualisation images as bundled aggregates
    • RDF representation as annotation
    • Packed version of workflow files as annotation
    • Git2prov link for the repository as history
    • Schema.org support for author attribution in CWL descriptions
  • API and documentation backing current features
  • Visualisation improvements
    • Intermediate value names
  • Ontology information linked and name given for format fields on inputs and outputs
  • "About" page with best practices for writing CWL for parsing by the viewer
  • Label and description searching on the explore page
  • Various bug fixes
  • References

v1.0.1 [2017-08-11]

Fixed

v1.0 [2017-07-06]