2021.10_1 Artifact Release

RELEASE DATE: 13 OCTOBER 2021

Bug Fixes

DE-2683: Sotax DT50 parser missed capturing "Prod No." in the RAW file
  • IDS

    • Slug: common/disintegration-dt50
    • Version: v4.0.0
    • Changes:
      • Add field sample.product_number
  • Task Script

    • Slug: common/sotax-dt50-raw-to-ids
    • Version: v4.0.0
    • Changes:
      • Update jmespath mapping to include sample.product_number
      • Change rearrange_conditions function in src/convert_raw_json.py
  • Protocol

    • Slug: common/sotax-dt50-raw-to-ids
    • Version: v2.2.0
    • Changes:
      • Use the above IDS and task script

Enhancements (New Features and Functionality)

DE-2445: Improve Zeiss .czi parser to extract all images instead of just a thumbnail
  • IDS

    • Slug: common/microscope-zeiss
    • Version: v0.2.0
    • Changes:
      • Forked from ome-confocal-imaging-metadata to capture CZI-specific image tiling
      • Added related_files to store pointers to image tiles in the datalake
  • Task Script

    • Slug: common/zeiss-microscope-raw-to-ids
    • Version: v0.2.0
    • Changes:
      • Add functionality for generating image tiles as PNGs from a CZI image
      • Update to use IDS microscope-zeiss v0.2.0 which includes related_files for pointing to the generated images
      • Add these pipeline configurations related to tile extraction:
        • Default tile size
        • Metadata keys to look for tile size on the input file (takes precedence over defaults if present)
        • Tile filename format, which can depend on the CZI image indices and the tile metadata
        • A boolean of whether or not to extract all files
  • Protocol

    • Slug: common/zeiss-microscope-raw-to-ids
    • Version: v0.2.0
    • Changes:
      • Use the above IDS and task script
DE-1525: Bruker NMR - Create IDS
  • IDS
    • Slug: common/nmr-bruker
    • Version: v1.0.0
    • Changes:
      • First Release
DE-2445: Improve Zeiss .czi parser to extract all images instead of just a thumbnail
  • IDS

    • Slug: common/microscope-zeiss
    • Version: v0.2.0
    • Changes:
      • Forked from ome-confocal-imaging-metadata to capture CZI-specific image tiling
      • Added related_files to store pointers to image tiles in the datalake
  • Task Script

    • Slug: common/zeiss-microscope-raw-to-ids
    • Version: v0.2.0
    • Changes:
      • Add functionality for generating image tiles as PNGs from a CZI image
      • Update to use IDS microscope-zeiss v0.2.0 which includes related_files for pointing to the generated images
      • Add these pipeline configurations related to tile extraction:
        • Default tile size
        • Metadata keys to look for tile size on the input file (takes precedence over defaults if present)
        • Tile filename format, which can depend on the CZI image indices and the tile metadata
        • A boolean of whether or not to extract all files
  • Protocol

    • Slug: common/zeiss-microscope-raw-to-ids
    • Version: v0.2.0
    • Changes:
      • Use the above IDS and task script
DE-2558: Sartorius Octet RED96 - Create Raw to IDS Parser
  • Task Script

    • Slug: common/sartorius-octet-analysis-studio-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First Release
  • Protocol

    • Slug: common/sartorius-octet-analysis-studio-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First Release
DE-2679: Lunatic Parser updates
  • Task Script

    • Slug: common/unchained-labs-lunatic-util/
    • Version: v4.1.0
    • Changes:
      • Update parser to no longer issue warning when a 0 value is detected in a numeric field
      • Update parser to no longer save Lunatic Logo
      • Update parser to save image for Lunatic Protein Concentration experiments as absorbance-spectrum.png
  • Protocol

    • Slug: common/unchained-labs-lunatic-util
    • Version: v2.3.1
    • Changes:
      • Use above task script

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