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2021.09_2 Artifact Release

RELEASE DATE: 29 SEPTEMBER 2021 EST

Bug Fixes

DE-2616 Sotax DT50 - update parser to work with the RAW file from IoT model IE Pro
  • IDS
    • Slug: same
    • Version: same
    • Changes: N/A
  • Task Script
    • Slug: common/sotax-dt50-raw-to-ids
    • Version: v3.0.1
    • Changes:
      • Update to support files collected by Tetra IoT Agent with DT50 driver v1.0.3
  • Protocol
    • Slug: common/sotax-dt50-raw-to-ids
    • Version: v2.1.1
    • Changes:
      • Update to use task script common/sotax-dt50-raw-to-ids v3.0.1
DE-2589 Charles River Endosafe Nexus - investigate why the parser failed
  • IDS
    • Slug: common/endotoxin-software-charles-river-endoscan-v
    • Version: v3.0.0
    • Changes:
      • Add nullable_boolean object to definitions
      • Update several fields to nullable_number, nullable_string, and nullable_boolean
      • Add @idsConventionVersion to schema base requirements as a string constant “v1.0.0”
      • Add serial_number and last_updated_timestamp to systems[*].software object
      • Add firmware object to systems object
      • Add id, name, firmware to systems object
      • Add id and type to users object
      • Remove serial_number and software from systems requirements
      • Remove related_files object and move the name field to the runs[*].source_file
      • Remove enum restriction on results[*].optical_density, results[*].reaction_time, results[*].endotoxin, results[*].processing.reaction_time, and results[*].processing.endotoxin fields
      • Update RAW to IDS mapping table to reflect changes to IDS
      • Move contents of example-files into supporting-files as the contents are manually annotated examples of sample data
  • Task Script
    • Slug: common/charles-river-endoscan-v-util
    • Version: v2.0.0
    • Changes:
      • Update to use IDS version v3.0.0
      • Generalize casting of data from CSV to appropriate types for IDS with new cast_or_default function
      • Add function to remove non-number characters from numbers to be cast to floats and check for multiple decimals and hyphens, and that what remains is a valid number string (Examples. 1.2.0 is not valid, but 2.3 is; .1-2 and -1-2 are invalid, but -5.123 is)
      • Add id and type to ids["users"] object
      • Remove logic for ids["related_files"] object and move filename to runs[*).source_name
      • Improve boolean parsing so only strings cast to lowercase equal to "true" and "1" parse to True
      • Update unit tests to accommodate IDS changes
      • Reorder construction of output dictionary parts to mimic order of IDS
  • Protocol
    • Slug: common/charles-river-endosafe-nexus-raw-to-ids
    • Version: v2.3.0
    • Changes:
      • Update to use task script common/charles-river-endoscan-v-util v2.0.0
DE-2567 Bruker Sierra SPR32 - parser errors
  • IDS
    • Slug: same
    • Version: same
    • Changes: N/A
  • Task Script
    • Slug: common/bruker-sierra-spr32-util
    • Version: v2.2.1
    • Changes:
      • Allow un-mapped units to be parsed as-is
      • Allow injection to run without Rack information
      • Capture all injections in a Cycle
  • Protocol
    • Slug: common/bruker-sierra-spr32-util
    • Version: v2.2.1
    • Changes:
      • Update to use task script common/bruker-sierra-spr32-util v2.2.1
PIPE-381 Waters Empower - Update task script base memory
  • IDS
    • Slug: same
    • Version: same
    • Changes: N/A
  • Task Script
    • Slug: same
    • Version: same
    • Changes: N/A
  • Protocol
    • Slug: common/empower-raw-to-ids
    • Version: v3.7.1
    • Changes:
      • Update empower-raw-to-ids step to start with 4GB base memory instead of 500MB

Enhancements (New Features and Functionality)

DE-2558 Sartorius Octet RED96 - create Raw to IDS Parser
  • IDS
    • Slug: common/plate-reader-sartorius-octet-analysis-studio
    • Version: v1.0.0
    • Changes: no change. Previously released
  • 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

Zeiss Microscope - prototype IDS and parser DE-2445 Improve Zeiss .czi parser to extract all images instead of just a thumbnail DE-2557 Add file pointer links to images for common OME microscopy IDS

  • 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:
      • Update to use task script common/zeiss-microscope-raw-to-ids v0.2.0

Updated about 1 month ago