v0.21.1

• Fix stub submission wdl to include analysis_file_version parameter

v0.21.0

• Fix the order of stage and confirm tasks
• Pass Cromwell automated retries parameter to analysis wdl
• Add support for changes to HCA metadata schema
  • Update the analysis json file to follow the "process" to "protocol" schema changes
  • Update getting the sample id from links_json

v0.20.0

• The Python codes in adapter workflows are not using buffering now, so the stdouts won’t run into some intermittent-empty problems.
• The stub submit workflow now uses a slim version of Python docker image for efficiency.
• All the requests to Ingest now will retry on ReadTimeout exception by default, in case Ingest is unavailable.
• Submit workflow now has separate stage_files and confirm_submission tasks, this decoupled structure helps debugging and workflow management.
• Some documentation style fixes.

v0.19.0

Added the ability to optionally record HTTP requests and responses made by pipeline-tools code.

Retry logic has been centralized and all retry parameters like timeout and max interval are now exposed as workflow parameters in the Smart-seq2 WDL. A timeout for individual requests has been added and exposed as a workflow parameter for Smart-seq2.

ConnectionErrors are now retried. 4xx errors are no longer retried.

v0.18.0

This release covers:

1. Set up monitor scripts for the workflows started by Lira as Cromwell option files.
2. Fix the dcp-integration test by upgrading the hca cli the pipeline-tools is using.

v0.17.0

• Add retries when making requests to the HCA data storage service and ingestion service, using the tenacity python library to add exponential wait times and timeouts.
• Simplify the retry logic for getting the staging urn and checking if the submission status is valid.
• Add auto-build documentation with Sphinx and hook up to readthedocs.io

v0.16.0

Update submit.wdl to work with Cromwell-as-a-Service

v0.15.0

• Move embedded python code from get_metadata task into a python script
• Use the retry decorator from the tenacity python library to retry the request to get metadata from Cromwell, with exponentially larger wait times in between requests.
• Add unit tests for get_analysis_metadata.py
• Freeze package versions in requirements.txt

v0.14.0

Update submit.wdl to follow the v5.1.0 metadata schema.

v0.13.0

Remove environment-specific urls for the HCA data storage service and ingestion service from the static input files.