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

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

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

IDS

• namespace: common
• slug: compaction-simulator-huxley-bertram-hb100
• version: v1.0.0
• changelog:
  • First release

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[*]

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

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

Task Script

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