Release 0.9.2

• Minimum IRIDA version is now 23.01

Bug Fixes:

• [CRITICAL] Fixed use of deprecated urllib3 method to allowed_methods

Developer Changes:

• Dropped support for Python v3.6 as urllib3 no longer supports it
• Changed api method get_sample_by_name to use new IRIDA endpoint.

Release 0.9.0

Changes:

• Api checks IRIDA version compatibility when initializing a session, throws exception if not compatible.
• Improved GUI error reporting with details of failure to connect on configuration screen.
• Improved GUI error popup when connection error occurs when starting upload.
• Added 2 new config arguments to specify number of retries and backoff time for http/https requests
  • http_max_retries
  • http_backoff_factor
• Uploader no longer has slowdown when uploading to projects with >100,000 samples
• api methods get_sample_details has been replaced by two new methods
  • get_sample_by_id(self, sample_id)
  • get_sample_by_name(self, project_id, sample_name)
  • core code has been switched over to these new methods for performance

Developer Changes:

• [Developer] Fixed minor bugs with object models not handling properties correctly.
• [Developer] Added command make coverage to all tests and collect coverage, exporting results as html
• [Developer] Added automated coverage report generation for PR reviews.
• [Developer] Changed master to main everywhere, including references to irida branches.
• [Developer] Added python 3.10 and 3.11 to unit test matrix
• [Developer] Added get_irida_version(self) to api, returns a string with the irida version

Bug Fixes:

• Fixed config timeout value not being set correctly sometimes.
• Fixed config timeout value division by string issue.
• Fix GUI crash on python >3.9(?) when progress bar is set a float value instead of int
• Fixed edge case where a config default of 0 or False would return an error instead of the default.

Release 0.8.3

Changes:

• [GUI] Partial uploads now display the reason (error) that caused the run to stop.

Bug Fixes:

• Fixed Error's setting run to ERROR when run has uploaded samples. Now sets these runs to PARTIAL to allow continuing from where the Error occurred.

Release 0.8.2

Bug Fixes:

• config file now evaluates any capitalization of True/False and displays errors to the user if unable to parse.
• Fixed command line help text inconsistency
• Catch mixed paired end and single end files in a sequencing run at the validation step and show user which samples are incorrect.

Developer Changes:

• Integration Tests now launch IRIDA with Gradle

Release 0.8.1

Bug Fixes:

• Fixed duplicate / in generated url's

Release 0.8.0

Changes:

• Added GUI option to import config settings from file
  • This writes the settings loaded to the default config file s.t. the settings persist for automated uploads
• Added distinction between "Project does not exist" and "User does not have permission to access project" for error returned to user when trying to upload.

Developer Changes:

• Integration tests now use SQL to add a client and user for tests, instead of selenium and ui navigation.
• Removed the Hateoas links requests and the _get_link function that handles the calls. All REST request URL's are now defined in the functions.
• Added (or updated) both REST error handling and IRIDA exception handling to every api request

Bug Fixes:

• Fixed miniseq/win_10_miseq parser not detecting missing paired end files

Release 0.7.1

Bug fixes:

• Added User-Agent, Accept-Encoding, and Connection headers to API requests which should fix intermittent 10054 errors.

Release 0.7.0

Changes:

• Added --minimum_file_size=[Integer] argument/config option to set the minimum expected file size for files
  • This is checked during the parsing / offline validation step
  • Value in KB
  • Default is 0 KB
• Added minimum_file_size option to the GUI as an ADVANCED option

Bug fixes:

• Fixed directory parser not raising validation errors (to display to user) when samplesheet file is malformed.

Developer Changes:
The following changes have been done to speed up extremely long REST requests, more api improvements should be expected in the future.

• The following api module methods have been changed to accept sample_id instead of sample_name and project_id

  • get_assemblies_files
  • get_metadata
  • send_metadata

• added get_sample_id(self, sample_name, project_id) to fetch the sample_id. This can be used in the modified methods above.

• removed set_irida_id(...) from Sample object, added sample_id property to Sample object

• added get_sample_details(self, sample_id) as an api method to fetch full Sample data from IRIDA

• added sample_identifier as a property to Sample objects

• Dropped support for Python 3.5

Release 0.6.2

Changes:

• Added options for miseq_win10_jun2021 and seqfu parsers (uses existing parsers)
• Added in-depth documentation on using the irida uploader with windows 10 updated miseqs

Bug fixes:

• Fixed missing requirement issue with windows builds

Release 0.6.1

Bug fixes:

• Fixed issue where starting a batch upload from the command line would crash instead of running.