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RELEASE_NOTES.md

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Release Notes

Version 1.4.1

  • update Globus SDK to globus-sdk==3.62.0

Version 1.4.0

  • update to Python 3.11.13
  • run black on all service and test files, fix most linting complaints (pylint, sonarlint)
  • Added a new KBaseAuth client
  • Modified the bulk_specification endpoint to parse DTS manifest.json files with a dts flag.
  • Added a DTS file watcher that moves a user's files from the DTS dropoff point to the user's subdirectory.
  • Added AUTH_TOKEN, DTS_MANIFEST_SCHEMA, and DTS_STAGING_DIR config values.
    • These are all required.
    • AUTH_TOKEN is a service token used by the service to verify user existence.
  • Added a separate StagingServiceConfig object that manages configurations.
  • Modified the AUTH_URL config to point to the root of the auth service.

Version 1.3.6

  • Fixed a bug that would cause NaN and Inf values in xSV to be returned as JSON barewords, which could cause some JSON parsers to fail. They are now returned as strings.
  • Changed the Excel parser to not consider NaN and Inf as missing values to maintain consistency with the xSV parsers

Version 1.3.5

  • Fixed a bug that under some circumstances could cause incomplete file metadata to be returned.

Version 1.3.4

  • Alter the behavior of the bulk specification file writers to return an error if the input types parameter is empty.
  • Fixed a bug in the csv/tsv bulk specification parser that would case a failure if the first header of a file had trailing separators. This occurs if a csv/tsv file is opened and saved by Excel.

Version 1.3.3

  • Fixed a bug in the csv/tsv bulk specification parser that would include an empty entry for each empty line in the file.

Version 1.3.2

  • Add write_bulk_specification endpoint for writing bulk specifications
  • Add import_filetypes endpoint for getting datatype -> filetype -> extension mappings
  • Fixed a bug in the csv/tsv bulk specification parser that would throw an error on any empty lines in the file, even at the end. The parser now ignores empty lines the same way the Excel parser does.
  • Fixed a bug in the bulk_specification endpoint where a missing header item in a *.?sv file would cause it to be replaced with a strange name.
  • Fixed a bug in the bulk_specification endpoint where a missing header item in an Excel file would cause a duplicate header error rather than a missing header error.
  • As part of the two fixes above, some error message text has changed due to the rewrite of the parsers.

Version 1.3.1

  • added the files key to the returned data from the bulk_specification endpoint.

Version 1.3.0

  • Update to Python 3.9
  • Add bulk_specification endpoint for parsing import specifications

Version 1.2.0

  • BACKWARDS INCOMPATIBILITY: remove the unused apps key from the importer mappings endpoint.
  • added a fileinfo field to the return of the importer mappings endpoint that includes the file prefix, suffix, and file type(s), if any.
  • reverted change to expose dotfiles in the api by default
  • attempting to upload a dotfile will now cause an error

Version 1.1.9

  • Added support for Genbank *.gb and *.gbff extensions
  • Added support for gzipped Reads, Assemblies, Genbank Files, and GFF files.

Version 1.1.8

  • Added new endpoint importer-mappings/ for getting a mapping of importers for file names
  • Updated endpoint to use GET and query_string
  • Ran black
  • BUGFIX: Change head/tail functionality to return 1024 chars to avoid bad cases with really large one line files
  • Update FASTQ/SRA to use their own APP Uis

Version 1.1.7

  • Add a file name check to void user uploading files with name starting with space
  • Update list endpoint so that it only hide .globus_id file by default

Version 1.1.3

  • Add a add-acl-concierge endpoint
  • Added configs for that endpoint
  • Added options to dockerfile/docker-compose

Version 1.1.2

  • Added capability to check 'kbase_session_backup' cookie
  • Added a add-acl and remove-acl endpoint for globus endpoint access
  • Change logging to STDOUT

Version 1.1.0

  • Added a download endpoint for files