2021.11_2 Artifact Release

RELEASE DATE: 24 NOVEMBER 2021

Bugs

DE-2905 AKTA parser should not parse "null" to "0"
  • Protocol

    • namespace: common
    • slug: akta-raw-to-ids
    • version: v3.0.1
    • changelog:
      • Update to use task script akta-raw-to-ids v3.0.1
  • task-script

    • namespace: common
    • slug: akta-raw-to-ids
    • version: v3.0.1
    • changelog:
      • Fix a datacubes parser bug that will parse string with only spaces or empty string value to 0
DE-2839 NanoTemper raw-to-IDS pipeline - null sample position
  • Protocol

    • namespace: common
    • slug: nanotemper-prometheus-raw-to-ids
    • version: v3.2.1
    • changelog:
      • Update to use task script nanotemper-prometheus-raw-to-ids v4.0.1
  • Task Script

    • namespace: common
    • slug: nanotemper-prometheus-raw-to-ids
    • version: v4.0.1
    • changelog:
      • Update regex pattern for extracting samples[*].location.position from MeltingControlExperiment.ExperimentName, the first part of the name can now be any non-empty string instead of being required to be "plate #"
DE-2832 plate-reader-perkinelmer-envision/DE-2814 Perkinelmer-Envision parser fails on wrong extension of inputfile
  • IDS

    • namespace: common
    • slug: plate-reader-perkinelmer-envision
    • version: v5.0.1
    • changelog:
      • Fix differences with IDS Design Conventions
        • Set additionalProperties false at the root level of the IDS, and for the datacubes, datacubes[*].measures and datacubes[*].dimensions objects
        • Require name, measures, and dimensions fields within the datacubes object
        • Permit null values for systems[*].vendor, systems[*].model, and systems[*].type
  • Protocol

    • namespace: common
    • slug: perkinelmer-envision-raw-to-ids
    • version: v2.5.1
    • changelog:
      • Update to use task script perkinelmer-envision-raw-to-ids v5.0.1
  • Task Script

    • namespace: common
    • slug: perkinelmer-envision-raw-to-ids
    • version: v5.0.1
    • changelog:
      • Update to use IDS v5.0.1
      • Convert file extension check to raise a warning instead of an error
DE-2690 Waters MassLynx - raw-to-IDS pipeline failures with Protocol v2.2.0
  • Protocol

    • namespace: common
    • slug: waters-masslynx-raw-to-ids
    • version: v2.2.1
    • changelog:
      • Update to use task script masslynx-util v4.0.1
  • Task Script

    • namespace: common
    • slug: masslynx-util
    • version: v4.0.1
    • changelog:
      • Remove the requirement for the file _extern.inf to be present in the Raw folder because this format can be read by the MassLynx SDK
        • Other inputs are not affected by this change - the IDS used is still ms-masslynx v4.0.0
        • Raw files not containing _extern.inf will be parsed the same as other inputs, except:
          • methods[1].raw_string will be null
          • methods[1].parameters won't contain any extern_inf sections

Enhancements (New Features and Functionality)

DE-2639 [Hamilton STAR REGN Log] IDS/DE-2853 [Hamilton Generic Log] IDS update/DE-2854 [Hamilton Generic Log] Pipeline update
  • IDS

    • namespace: common
    • slug: liquid-handler-hamilton-star-log
    • version: v1.0.0
    • changelog:
      • Make each IDS file stores multiple logs (e.g. 100 - 1000) instead of one log
  • Protocol

    • namespace: common
    • slug: hamilton-star-log-raw-to-ids
    • version: v1.0.0
    • changelog:
      • Update to use task script hamilton-star-log-raw-to-ids v1.0.0
  • Task Script

    • namespace: common
    • slug: hamilton-star-log-raw-to-ids
    • version: v1.0.0
    • changelog:
      • Update the logic to store multiple logs per IDS file
        • Specified by parameter log_number_per_ids, default 10,000
DE-2848 Fix Zeiss Bioformats segfault/DE-2849 Tweak Zeiss progress tracking logging statements
  • Protocol

    • namespace: common
    • slug: zeiss-microscope-raw-to-ids
    • version: v0.2.3
    • changelog:
      • Update to use task script zeiss-microscope-raw-to-ids v0.2.2
  • Task Script

    • namespace: common
    • slug: zeiss-microscope-raw-to-ids
    • version: v0.2.2
    • changelog:
      • Switched image extraction library to avoid segfault crash when reading/writing files
DE-2842 Attune NxT - Update IDS
  • IDS
    • namespace: common
    • slug: flow-cytometer
    • version: v3.0.0
    • changelog:
      • Add remaining FCS 3.1 optional fields to IDS
        • Add $PnF to methods[*].channels[*].filter
        • Add $PnL to methods[*].channels[*].excitation.wavelengths[*].value
        • Add field methods[*].channels[*].excitation.wavelengths[*].unit
        • Add $PnO to methods[*].channels[*].excitation.power.value
        • Add field methods[*].channels[*].excitation.power.unit
        • Add $PnP to methods[*].channels[*].light_collected.value
        • Add field methods[*].channels[*].light_collected.unit
        • Add $PnT to methods[*].channels[*].detector
        • Add $PnCALIBRATION value to methods[*].channels[*].calibration.value
        • Add $PnCALIBRATION unit to methods[*].channels[*].calibration.unit
        • Add $PnD scaling to methods[*].channels[*].visualization.scale
        • Add $PnD lower bound to methods[*].channels[*].visualization.lower_bound
        • Add $PnD upper bound to methods[*].channels[*].visualization.upper_bound
        • Add $CSMODE to methods[*].cell_subset_mode
        • Add $GATE to methods[*].number_of_gates
        • Add $GATING to methods[*].gating_setting
        • Add $COM to methods[*].comment
        • Add $ABRT to results[*].events_lost.coincidence
        • Add $LOST to results[*].events_lost.busy
        • Add $ORIGINALITY to results[*].originality
      • Update required fields to FCS 3.1 spec
        • Removed alternative_name from required fields for methods[*].channels[*]
        • Removed name from required fields for methods[*].lasers[*]
        • Removed number from required fields for methods[*].lasers[*]
        • Removed delay from required fields for methods[*].lasers[*]
        • Removed area_scaling_factor from required fields for methods[*].lasers[*]
        • Removed start from required fields for runs[*].time
        • Removed stop from required fields for runs[*].time
        • Removed acquired from required fields for results[*].time
        • Removed lookup from required fields for results[*].time
      • Update to IDS Convention Version v1.0.0
        • Add additionalProperties: false to most objects
DE-2737 Agilent Technology, Cary 60 (SoloVPE); UV-Vis - Create IDS
  • IDS
    • namespace: common
    • slug: uv-agilent-cary-c-technology-solovpe
    • version: v1.0.0
    • changelog:
      • First release
DE-2726 Waters Empwer IDS - Level
  • IDS

    • namespace: common
    • slug: lcuv-empower
    • version: v9.0.0
    • changelog:
      • Add injection.level to IDS from top level field Level
      • Add results[*].level to IDS from Results[*].Level
      • Add datacubes[*].level to ids from Channels[*].Level
  • Protocol

    • namespace: common
    • slug: empower-raw-to-ids
    • version: v3.9.0
    • changelog:
      • Update to use task script empower-raw-to-ids v8.0.0
  • Task Script

    • namespace: common
    • slug: empower-raw-to-ids
    • version: v8.0.0
    • changelog:
      • Update parser to follow common/lcuv-empower IDS v9.0.0
DE-2705 Create RAW to IDS pipeline for Ultrasound data
DE-2691 Create v0.1 Leica Aperio IDS
  • IDS
    • namespace: common
    • slug: microscope-leica-aperio
    • version: v0.1.0
    • changelog:
      • First release
DE-2682 Update Requirements for Octet Analysis Studio Raw to IDS Parser
  • Protocol

    • namespace: common
    • slug: sartorius-octet-analysis-studio-raw-to-ids
    • version: v1.1.0
    • changelog:
      • Update to use task script sartorius-octet-analysis-studio-raw-to-ids v1.1.0
  • Task Script

    • namespace: common
    • slug: sartorius-octet-analysis-studio-raw-to-ids
    • version: v1.1.0
    • changelog:
      • Removed hard requirements for specific tabs to exist in input .xlsx file
DE-2592 BMG Labtech parser - investigate if we can combine parsers into one
  • IDS

    • namespace: common
    • slug: plate-reader-bmg-labtech-absorbance
    • version: v1.0.0
    • changelog:
      • Create new IDS plate-reader-bmg-labtech-absorbance as a combination of all fields from plate-reader-bmg-labtech-clariostar and plate-reader-bmg-labtech-spectrostar.
        This IDS is for all BMG Labtech plate reader absorbance and absorbance spectra measurement data.
        All fields from both previous schemas are in the new IDS except for the changes listed below.
      • Change field name runs[*].extended_IR_PMT to runs[*].extended_ir_pmt, lower case to match normalization of fields in the Tetra Data Platform
      • Add fields systems[*].firmware[*].name and systems[*].software[*].name to follow globally shared field definitions from the IDS Conventions
      • Change mapping of systems[*].model to come from the Reader type in the input file instead of being a constant value
      • Replace datacubes[*].interval from plate-reader-bmg-labtech-clariostar with datacubes[*].interval_or_cycle
      • Change the datacubes structure to use a single dimension for sample position named "sample index" instead of separate row and column dimensions.
      • Add the field samples[*].location.index to contain an integer index for referencing samples.
        This is not in IDS Convention v1.0.0 but will be part of future versions of the IDS Convention.
  • IDS

    • namespace: common
    • slug: plate-reader-bmg-labtech-nephelometry-fluorescence
    • version: v1.0.0
    • changelog:
      • Create new IDS plate-reader-bmg-labtech-nephelometry-fluorescence as a replacement for plate-reader-bmg-labtech-nephelostar-fluostar to reflect that other BMG Labtech plate reader models may also produce nephelometry and fluorescence data.
        All fields are the same except for the changes below.
      • Change systems[*] vendor, model and type to nullable strings
      • Add globally shared fields name and last_updated_timestamp to systems[*].firmware
      • Add globally shared fields name and last_updated_timestamp to systems[*].software
      • Change the datacubes structure to use a single dimension for the sample position named "sample index" instead of separate row and column dimensions.
      • Add the field samples[*].location.index to contain an integer index for referencing samples.
        This is not in IDS Convention v1.0.0 but will be part of future versions of the IDS Convention.
  • Protocol

    • namespace: common
    • slug: bmg-labtech-plate-reader-raw-to-ids
    • version: v1.0.0
    • changelog:
      • Create a new BMG Labtech Protocol as an alternative to Protocols bmg-labtech-clariostar-raw-to-ids, bmg-labtech-fluostar-raw-to-ids, bmg-labtech-nephelostar-raw-to-ids and bmg-labtech-spectrostar-raw-to-ids.
        This Protocol is a single entry point to produce an IDS from any of the supported BMG Labtech plate readers based on their measurement mode instead of the instrument model.
  • Task Script

    • namespace: common
    • slug: bmg-labtech-util
    • version: v6.0.0
    • changelog:
      • Combine parsers into one entry point function bmg_labtech_raw_to_ids which will read the Configuration within the file to decide how to parse the file.
      • Update to output these IDS versions (see IDS README changelogs for more detail)
        • plate-reader-bmg-labtech-absorbance v1.0.0 which combines the previous SPECTROstar and CLARIOstar IDS content.
        • plate-reader-bmg-labtech-nephelometry-fluorescence v1.0.0 which is similar to the previous NEPHELOstar/FLUOstar IDS.
DE-2524 MSD Sector S 600 - Create Raw to IDS Parser
  • Protocol

    • namespace: common
    • slug: msd-sector-s-600-raw-to-ids
    • version: v1.0.0
    • changelog:
      • First release
  • Task Script

    • namespace: common
    • slug: msd-sector-s-600-raw-to-ids
    • version: v1.0.0
    • changelog:
      • First release

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