2021.08_2 Artifact Release

RELEASE DATE: 18 August 2021

Bug Fixes

None

Enhancements (New Features and Functionality)

DE-600 Hanson Research Elite 8 - create parser
  • IDS

    • Slug: No change
    • Version: No change
    • Changes: No change
  • Task Script

    • Slug: common/teledyne-hanson-research-elite8-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
  • Protocol

    • Slug: common/teledyne-hanson-research-elite8-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
DE-1944 Sotax AT70 - create parser
  • IDS

    • Slug: common/dissolution-tester-sotax-at70
    • Version: v3.0.0
    • Changes: No change
  • Task Script

    • Slug: common/sotax-at70-raw-to-ids
    • Version: v2.0.0
    • Changes:
      • Updated logic for input file type change from .xls to .txt
  • Protocol

    • Slug: common/sotax-at70-raw-to-ids
    • Version: v2.0.0
    • Changes:
      • Upgrade to use the latest task script
DE-2131 Malvern MasterSizer 3000 - improve IDS
  • IDS

    • Slug: common/laser-diffraction-particle-size-analyzer-malvern-mastersizer-3000
    • Version: v2.0.0
    • Changes:
      • Predefined the raw data structure in Mastersizer software via report template
      • Updated to IDS convention v1.0.0
      • Modified schema of systems, methods, runs, and results
  • Task Script

    • Slug: To be Updated
    • Version: To be Updated
    • Changes: To be Updated
  • Protocol

    • Slug: To be Updated
    • Version: To be Updated
    • Changes: To be Updated
DE-2162 Fluoroskan SkanIt - improve IDS to support files from SkanIt, DE-2124 Fluoroskan SkanIt - improve parser to support files from SkanIt
  • IDS

    • Slug: common/plate-reader-thermofisher-fluoroskan
    • Version: v4.0.0
    • Changes:
      • Added support for Fluoroskan Excel reports generated by SkanIt, involving several IDS changes to capture additional metadata
      • As well as the newly added fields, these pre-existing IDS fields have moved:
        • methods[*].timepoint_count -> methods[*].kinetic_loop.number_of_readings
        • methods[*].wavelength.excitation -> methods[*].fluorescence.filter_pair.excitation.wavelength
        • methods[*].wavelength.emission -> methods[*].fluorescence.filter_pair.emission.wavelength
        • methods[*].scaling_factor -> methods[*].fluorescence.scaling_factor.string_value, also present as a numerical_value for consistency with data from SkanIt
  • Task Script

    • Slug: common/thermofisher-fluoroskan-raw-to-ids
    • Version: v5.0.0
    • Changes:
      • Add support for Fluoroskan SkanIt Excel reports
      • Modify previous Fluoroskan Excel parser to produce the same format as the SkanIt parser, so that both use the same mapping to IDS
      • Update parser to produce IDS v4.0.0
  • Protocol

    • Slug: common/thermofisher-fluoroskan-raw-to-ids
    • Version: v1.5.0
    • Changes:
      • Updated protocol steps to use thermofisher-fluoroskan-raw-to-ids v5.0.0, which includes support for Fluoroskan reports exported from SkanIt software.
      • Added day_first_date_format optional configuration for date parsing.
DE-2349 Retroactive parser permissive update - NEPHELOstar & FLUOstar
  • IDS

    • Slug: common/plate-reader-bmg-labtech-nephelostar-fluostar
    • Version: v4.0.0
    • Changes:
      • Add @idsConventionVersion property
  • Task Script

    • Slug: common/bmg-labtech-util
    • Version: v5.0.0
    • Changes:
      • Improve permissiveness by handling more cases of unexpected or missing key/value pairs in the input file. Instead of failing the task script in these cases, warnings are logged and null values are used in the output if needed.
      • Make timestamp parsing log a warning if it fails instead of failing the task script, and put the original timestamp into the IDS. This change doesn't apply to time-series data in FLUOstar and NEPHELOstar where timestamps are required to create datacubes - those will still fail on unexpected timestamp formats.
      • For kinetic_windows, parse only: number_of_kinetic_windows, kinetic_windows_mode and windows
      • Add @idsConventionVersion property to IDS output for all instruments.
      • Update to output these IDS versions:
        • plate-reader-bmg-labtech-clariostar v4.0.0
        • plate-reader-bmg-labtech-nephelostar-fluostar v4.0.0
        • plate-reader-bmg-labtech-spectrostar v5.0.0
  • Protocol

    • Slug: common/bmg-labtech-fluostar-raw-to-ids
    • Version: v1.1.0
    • Changes:
  • Protocol

    • Slug: common/bmg-labtech-nephelostar-raw-to-ids
    • Version: v1.1.0
    • Changes:
      • Upgrade to use the latest task script
DE-2350 Retroactive parser permissive update - CLARIOstar
  • IDS

    • Slug: common/plate-reader-bmg-labtech-clariostar
    • Version: v4.0.0
    • Changes:
      • Add @idsConventionVersion property
  • Task Script

    • Slug: common/bmg-labtech-util
    • Version: v5.0.0
    • Changes:
      • Improve permissiveness by handling more cases of unexpected or missing key/value pairs in the input file. Instead of failing the task script in these cases, warnings are logged and null values are used in the output if needed.
      • Make timestamp parsing log a warning if it fails instead of failing the task script, and put the original timestamp into the IDS. This change doesn't apply to time-series data in FLUOstar and NEPHELOstar where timestamps are required to create datacubes - those will still fail on unexpected timestamp formats.
      • For kinetic_windows, parse only: number_of_kinetic_windows, kinetic_windows_mode and windows
      • Add @idsConventionVersion property to IDS output for all instruments.
      • Update to output these IDS versions:
        • plate-reader-bmg-labtech-clariostar v4.0.0
        • plate-reader-bmg-labtech-nephelostar-fluostar v4.0.0
        • plate-reader-bmg-labtech-spectrostar v5.0.0
  • Protocol

    • Slug: common/bmg-labtech-clariostar-raw-to-ids
    • Version: v2.2.0
    • Changes:
      • Upgrade to use the latest task script
DE-2351 Retroactive parser permissive update - SPECTROstar
  • IDS

    • Slug: common/plate-reader-bmg-labtech-spectrostar
    • Version: v5.0.0
    • Changes:
      • Add @idsConventionVersion property
  • Task Script

    • Slug: common/bmg-labtech-util
    • Version: v5.0.0
    • Changes:
      • Improve permissiveness by handling more cases of unexpected or missing key/value pairs in the input file. Instead of failing the task script in these cases, warnings are logged and null values are used in the output if needed.
      • Make timestamp parsing log a warning if it fails instead of failing the task script, and put the original timestamp into the IDS. This change doesn't apply to time-series data in FLUOstar and NEPHELOstar where timestamps are required to create datacubes - those will still fail on unexpected timestamp formats.
      • For kinetic_windows, parse only: number_of_kinetic_windows, kinetic_windows_mode and windows
      • Add @idsConventionVersion property to IDS output for all instruments.
      • Update to output these IDS versions:
        • plate-reader-bmg-labtech-clariostar v4.0.0
        • plate-reader-bmg-labtech-nephelostar-fluostar v4.0.0
        • plate-reader-bmg-labtech-spectrostar v5.0.0
  • Protocol

    • Slug: common/bmg-labtech-spectrostar-raw-to-ids
    • Version: v2.3.0
    • Changes:
      • Upgrade to use the latest task script
DE-2361 Renishaw InVia - improve parser
  • IDS

    • Slug: common/raman-microscope-renishaw-invia
    • Version: v1.0.0
    • Changes: No change
  • Task Script

    • Slug: common/renishaw-invia-raw-to-ids
    • Version: v1.1.1
    • Changes:
      • Added a patching logic to handle the out-dated parameter mapping in the py-wdf-reader library.
  • Protocol

    • Slug: common/renishaw-invia-raw-to-ids
    • Version: v1.1.1
    • Changes:
      • Upgrade to use the latest task script
DE-2369 Beckman Coulter Vi-Cell - improve IDS/parser
  • IDS

    • Slug: common/cell-counter
    • Version: v4.0.0
    • Changes:
      • Add @idsConventionVersion field
      • Move system field to systems array
      • Move run field to runs array
      • Move top level time field into runs sub-field
      • Move sample field to samples array
      • Move sample.file_name to runs.file_name because samples cannot contain the field file_name by IDS convention v1.0.0
      • Move sample.local_image_path.directory to runs.local_image_directory because samples cannot contain the field local_image_path by IDS convention v1.0.0
      • Move sample.local_image_path.base_name to runs.local_image_basename because samples cannot contain the field local_image_path by IDS convention v1.0.0
      • Move method field to methods array
      • Create users[*].name field
      • Remove sample subfields batch.id and batch.number because this metadata is not present in the raw file
      • Move run.comment field to array runs[*].comments array
      • Rename images top level field to related_files
      • Remove images[*].id field as it does not fit IDS convention v1.0.0.
      • Add related_files[*].name field
      • Add field results[*].cell.diameter.sum.value
      • Add field results[*].cell.diameter.sum.unit
      • Add field results[*].cell.circularity.sum
      • Add field results[*].cell.background_intensity_sum
      • Add field methods[*].aspirate_cycles found in exports from newer software versions
      • Add field methods[*].sharpness found in exports from newer software versions
      • Add field methods[*].viable_spot_area found in exports from newer software versions
      • Add field methods[*].brightness.total found in exports from newer software versions
      • Add field methods[*].brightness.viable_spot found in exports from newer software versions
  • Task Script

    • Slug: common/beckmancoulter-vicell-raw-to-ids
    • Version: v2.0.0
    • Changes:
      • Update parser output to use IDS version 2.0.0
      • Add logging support
      • Add check for known and expected RAW file keys
      • Update data-time parser to no longer assume US-Eastern time zone
        • No longer converts to UTC
      • Output numeric data in the same format as ingested
        • Integers stay integers and are no longer auto-converted to floating-point values
      • Maintain consistent output structure with values null when key or value are missing
  • Protocol

    • Slug: common/beckmancoulter-vicell-raw-to-ids
    • Version: v1.1.0
    • Changes:
      • Upgrade to use the latest task script
DE-2395 Metrohm 874 KFC - improve IDS
  • IDS

    • Slug: common/kf-coulometer-metrohm-titrino
    • Version: v3.0.0
    • Changes:
      • Design based on the CSV exported form Tiamo system (both v2.5 and v3.0)
      • Add data exporting guidance
      • Update to IDS convention v1.0.0
  • Task Script

    • Slug: To be Updated
    • Version: To be Updated
    • Changes: To be Updated
  • Protocol

    • Slug: To be Updated
    • Version: To be Updated
    • Changes: To be Updated

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