2022.07_2 Artifact Release

RELEASE DATE: July 12, 2022

Bug Fixes

DE-4084 AKTA v3.1 parser failure
  • Task Script

    • namespace: common
    • slug: akta-raw-to-ids
    • version: v3.1.2
    • changelog:
      • Add fault tolerance for None or non-existent values where assumptions about the data were made
  • Protocol

    • namespace: common
    • slug: akta-raw-to-ids
    • version: v3.1.2
    • changelog:
      • Update to use common/akta-raw-to-ids:v3.1.2 task script
DE-3245 Update general FCS parser RAM limits
  • Task Script

    • namespace: common
    • slug: fcs-raw-to-ids
    • version: v3.0.1
    • changelog:
      • Fix logging calls to pass an object with the message and the level.
  • Protocol

    • namespace: common
    • slug: fcs-raw-to-ids
    • version: v1.3.0
    • changelog:
      • Add new pipeline configuration parameter parse-script-memory-allocation which defaults to 2048

Enhancements (New Features and Functionality)

Shimadzu Protocol Update
  • Protocol

    • namespace: common
    • slug: labsolutions-lcd-to-mzml
    • version: v1.0.1
    • changelog:
      • Update to use task script common/msconvert-windows:v1.0.2
      • Update to use task script common/shimadzu-windows:v1.0.6
      • Update to use task script common/lcd-to-mzml:v1.1.0
DE-3880 Huxley Bertram HB100 - IDS
  • IDS

    • namespace: common
    • slug: compaction-simulator-huxley-bertram-hb100
    • version: v1.0.0
    • changelog:
      • First release
DE-2887 Update the Leica Aperio IDS
  • IDS

    • namespace: common
    • slug: microscope-leica-aperio
    • version: v0.2.0
    • changelog:
      • Add property @idsConventionVersion
      • Add property methods[*]
      • Add property results[*]
      • Update root $id from https://ids.tetrascience.com/common/microscope-leica-aperio/v0.1.0/schema.json to https://ids.tetrascience.com/common/microscope-leica-aperio/v0.2.0/schema.json
      • Update root required from ['@idsNamespace', '@idsType', '@idsVersion'] to ['@idsConventionVersion', '@idsNamespace', '@idsType', '@idsVersion', 'methods', 'results', 'runs', 'samples', 'systems', 'users']
      • Update @idsVersion const from v0.1.0 to v0.2.0
      • Update runs[*].tile_length to runs[*].tile.length
      • Update runs[*].tile_width to runs[*].tile.width
      • Update runs[*].tile_offsets to runs[*].tile.offsets
      • Update runs[*].tile_bytes_count to runs[*].tile.bytes_count
      • Update images[*].original_metdata.dsr_id to methods[*].digital_slide_repository_id
      • Update images[*].original_metdata.icc_profile to methods[*].international_color_consortium_profile
      • Update images[*].original_metadata.fileame to results[*].filename
      • Update images[*].pixel_information.size_c to results[*].pixel_information.size.c
      • Update images[*].pixel_information.size_t to results[*].pixel_information.size.t
      • Update images[*].pixel_information.size_x to results[*].pixel_information.size.x
      • Update images[*].pixel_information.size_y to results[*].pixel_information.size.y
      • Update images[*].pixel_information.size_z to results[*].pixel_information.size.z
      • Update images[*].pixel_information.phyisical_size_x.value to results[*].pixel_information.physical_size.x.value
      • Update images[*].pixel_information.phyisical_size_x.unit to results[*].pixel_information.physical_size.x.unit
      • Update images[*].pixel_information.phyisical_size_y.value to results[*].pixel_information.physical_size.y.value
      • Update images[*].pixel_information.phyisical_size_y.unit to results[*].pixel_information.physical_size.y.unit
      • Update images[*].original_metdata.objective_power to methods[*].magnification
      • Update images[*].original_metdata.q to results[*].original_metadata_q
      • Update images[*].channel to methods[*].channels[*]
      • Update samples[*].labels[*].source.name type from string to ['null', 'string']
      • Update systems[*].firmware[*] add schema item "additionalProperties": false
      • Remove property images[*] because the fields were moved to results[*] and methods[*]
DE-4274 Update ViiA7 EDS Raw to IDS parser to use ViiA7 IDS v5.0.0
  • IDS

    • namespace: common
    • slug: qpcr-thermofisher-viia7
    • version: v5.0.0
    • changelog:
      • Update root $id from https://ids.tetrascience.com/common/qpcr-thermofisher-viia7/v4.0.0/schema.json to https://ids.tetrascience.com/common/qpcr-thermofisher-viia7/v5.0.0/schema.json
      • Update root required from ['@idsNamespace', '@idsType', '@idsVersion', 'datacubes', 'methods', 'results', 'runs', 'samples', 'systems', 'users'] to ['@idsConventionVersion', '@idsNamespace', '@idsType', '@idsVersion', 'datacubes', 'methods', 'results', 'runs', 'samples', 'systems', 'users']
      • Update @idsVersion const from v4.0.0 to v5.0.0
      • Update property runs[*].bulb_usage to runs[*].hardware_usage
      • Update property runs[*].bulb_usage.halogen_lamp_hours to runs[*].hardware_usage.halogen_lamp_hours
      • Update property runs[*].bulb_usage.life_cycle_count to runs[*].hardware_usage.block_life_cycle_count
      • Update property runs[*].bulb_usage.life_degrees_climbed to runs[*].hardware_usage.block_life_degrees_climbed
      • Update datacubes[*].dimensions[*].scale[*] type from number to ['null', 'number']
      • Update datacubes[*].measures[*].value[*][*] type from ['null', 'number'] to number
  • Task Script

    • namespace: common
    • slug: thermofisher-viia7-eds-raw-to-ids
    • version: v2.0.0
    • changelog:
      • Update task script to use common/qpcr-thermofisher-viia7:v5.0.0 IDS
  • Protocol

    • namespace: common
    • slug: thermofisher-viia7-eds-raw-to-ids
    • version: v2.0.0
    • changelog:
      • Update to use task script common/thermofisher-viia7-eds-raw-to-ids:v2.0.0
Chromeleon IDS v1
  • IDS

    • namespace: common
    • slug: thermofisher-chromeleon
    • version: v1.0.0
    • changelog:
      • Add type definitions for nullable_string, nullable_integer, nullable_number, nullable_boolean, and value_unit_object, and change type definitions in the IDS appropriately
      • Add support for inclusion of string values of numeric types and their parsed equivalents to preserve the number of significant digits
        • Add data types for raw_value_unit_object and parsed_number that include both the numerically parsed value field and a raw_value string field.
      • Update IDS Mapping table for fields that will change under Chromeleon Agent v2.0.0
      • Update common fields to comply with GSF requirements (systems, runs, samples, and methods)
        • Update run object field to runs array
        • Update sample object field to samples array
          • Update mapping of sample.position to samples[0].location.position to follow the non-extendable samples GSF
          • Update mapping of sample.weight, sample.internal_standard_amount, and sample.spike_group to the respective methods[0].sample_preparation.<field> to follow the non-extendable samples GSF
      • Update definition of software in systems to comply with IDS Convention v1.0.0
      • Update methods[*] to capture more information on injections and detections
        • Add fields for detector settings for flame ionization, charged aerosol, UV-Vis, mass spec, and conductivity detectors
        • Add injection parameters
        • Add fields to capture mobile phase information, and encompasses information for solvents in LC and IC, carrier gas in GC, and temperature gradients in all instruments
          • Mobile phase is now an array to accommodate 2D HPLC, which has different solvent gradients for the two columns
      • Update results[*] to better capture detector/peak information
        • Add descriptions in schema for peak parameters
        • Updated groupings for parameters and statistics for each peak into a logical format
      • Update ability to capture column and module information for different chromatography instrumentation configurations using parsed information from systems[0].component
      • Update fields to raw_value_unit_object or parsed_number when appropriate to ensure compatibility with the Chromeleon Agent v2.0.0
      • Update methods[0].processing.peak_group_parameters[*] and methods[0].processing.components[*] to have similar structures for more intuitive mapping and field access
      • Remove data_vault_name fields from some creation/update metadata fields as this information is included in the audit trail and is redundant.
      • Add support for 3D UV-VIS detector
Lunatic improvement
  • Task Script

    • namespace: common
    • slug: unchained-labs-lunatic-util
    • version: v6.0.2
    • changelog:
      • Update to run using Docker container tooling

Did this page help you?