2021.09_1 Artifact Release

RELEASE DATE: 17 SEPTEMBER 2021

Bug Fixes

DE-2550 AT70 bug fix
  • IDS
    • Slug: common/dissolution-tester-sotax-at70
    • Version: v3.0.0
    • Changes: No change
  • Task Script
    • Slug: common/sotax-at70-raw-to-ids
    • Version: v2.0.1
    • Changes:
      • Updated to support both of software version 2.60.3 and 2.84
      • Bug fix on converting Sampling Information, Run Protocol Information sections
  • Protocol
    • Slug: common/sotax-at70-raw-to-ids
    • Version: v2.0.1
    • Changes:
      • Updated to use v2.0.1 task script
MassLynx v4.0.0

DE-2555 Waters MassLynx - Address MassLynx parsing error
DE-2493 Waters MassLynx - Use raw value for vendor model
DE-2396 Waters MassLynx - Parser shouldn't be case-sensitive to raw filename
DE-2484 Waters Masslynx - Improve sample position parsing

  • IDS
    • Slug: common/ms-masslynx
    • Version: v4.0.0
    • Changes:
      • Update to IDS convention v1.0.0
      • Add an additional index field to samples[*].location.position as an alternative to row and column for one-dimensional indexing
  • Task Script
    • Slug: common/masslynx-util
    • Version: v4.0.0
    • Changes:
      • Fix and improve parsing of _header.txt:Bottle Number using _header.txt:Plate Desc to populate samples[*].location according to the MassLynx 4.1 Interfacing Guide
        • Use the newly added field samples[*].location.index for sequentially indexed samples
        • Populate row and column only if Plate Desc contains enough information to do so accurately
        • Use the tray name to populate holder.name except for the format V:{vial_number} where V indicates a vial holder type
      • Use case insensitive filename matching for _header.txt, _inlet.inf and extern.inf
      • Improve detection of "Xevo G2-XS QTof" when filling MS systems
      • Make systems[1] for Waters MS systems default to a vendor of Waters Corporation, a type of Mass Spectrometer and the model name in _header.txt:Instrument in cases where a display name isn't defined for that model
      • Update to use IDS ms-masslynx v4.0.0
  • Protocol
    • Slug: common/waters-masslynx-raw-to-ids
    • Version: v2.2.0
    • Changes:
      • Updated to use the latest task script
Xcalibur v5.0.0

DE-2485 Thermo Xcalibur - Incorrect sample position parsing
DE-2520 Thermo Xcalibur - Add SampleInformation.InstrumentMethodFile to the raw data the Windows task script produces
DE-2492 Thermo Xcalibur - vendor model value shouldn't be null
DE-2397 Thermo Xcalibur - Support method file location and processing method
DE-2291 Thermo Xcalibur - Update MS start times, add in description field
DE-1807 Thermo Xcalibur - figure out how to interpret a vial position

  • IDS
    • Slug: common/ms-xcalibur
    • Version: v5.0.0
    • Changes:
      • Add index field as a nullable_number to the samples.items.location object.
  • Task Script
    • Slug: common/thermofisher-xcalibur-raw-json-to-ids
    • Version: v5.0.0
    • Changes:
      • Update run.["name" == "ms"] start and stop times to be the lc start time plus the values from ScanSettings.scan start time and the seconds half of ScanSettings.Retention time range, respectively
      • Add FileProperties.Description to samples.labels
      • Change how headers are chosen in _func_create_samples_labels to a blacklist so when new fields are added, they're automatically included in the final output ids json file.
      • Add logic to instrument_library.py to parse model, vendor, and type more flexibly. If the name of the system is not found within the instrument library JSON object, values from InstrumentMethodProperties and InstrumentProperties within the raw JSON are used
      • Add slicing to jmespath_util.py help fetch full position numbers for index and row values.
      • Add new location parsing and parsing types
  • Protocol
    • Slug: common/thermofisher-xcalibur-raw-to-ids
    • Version: v3.3.0
    • Changes:
      • Updated to use the latest task script

Enhancements (New Features and Functionality)

BioTek Gen5

DE-2526 BioTek Cytation 5 - Create IDS
DE-2525 Biotek Synergy H1 plate reader - Create IDS
DE-2554 BioTek Gen5 - Create Raw to IDS Parser

  • IDS
    • Slug: common/plate-reader-biotek-gen5
    • Version: v1.0.0
    • Changes:
      • First release
  • Task Script
    • Slug: common/biotek-gen5-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
  • Protocol
    • Slug: common/biotek-gen5-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
DE-2537 Sartorius Octet RED96 - Create IDS
  • IDS
    • Slug: common/plate-reader-sartorius-octet-analysis-studio
    • Version: v1.0.0
    • Changes:
      • First release
  • 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-2521 Empower Project User Access Data - Raw JSON to IDS v1
  • IDS
    • Slug: common/empower-project-user
    • Version: v1.0.0
    • Changes:
      • First release
  • Task Script
    • Slug: common/empower-project-user-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release. Support files produced by Empower Agent v4.1
  • Protocol
    • Slug: common/empower-project-user-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
DE-2439 Empower Audit Trail and Message Center Data - RAW to IDS v1
  • IDS

    • Slug: common/empower-audit-trail
    • Version: v1.0.0
    • Changes:
      • First release
  • Task Script

    • Slug: common/empower-audit-trail-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release. Support files produced by Empower Agent v4.1
  • Protocol

    • Slug: common/empower-audit-trail-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
  • IDS

    • Slug: common/empower-message-center
    • Version: v1.0.0
    • Changes:
      • First release
  • Task Script

    • Slug: common/empower-message-center-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release. Support files produced by Empower Agent v4.1
  • Protocol

    • Slug: common/empower-message-center-raw-to-ids
    • Version: v1.0.0
    • Changes:
      • First release
DE-2421 Update Benchling Util using DataWeave
  • IDS
    • Slug: N/A
    • Version: N/A
    • Changes: N/A
  • Task Script
    • Slug: common/benchling-util
    • Version: v2.0.0
    • Changes:
      • Add benchling_supplemental_data in input to pass in data fields required by Benchling run schema and results schema but don't exist in input file
      • Use DataWeave dataweave_script to transform data to generalized JSON structure, and create run and/or result on Benchling
      • Add run_schema_id and results_schema_id in input parameters
      • Be able to handle two data creation scenarios:
        • Create both run and result on Benchling
        • Only create result on Benchling
  • Protocol
    • Slug: common/push-to-benchling
    • Version: v1.0.0
    • Changes:
      • Updated to use v2.0.0 task script
DE-2355 Retroactive parser permissive update - iQue3
  • IDS
    • Slug: common/flow-cytometer-intellicyt-ique3
    • Version: v3.0.0
    • Changes:
      • Add @idsConventionVersion
      • Update most of the fields in IDS to allow null
      • Update samples and users schema to follow IDS convention v1
      • Make some fields not required
  • Task Script
    • Slug: common/intellicyt-ique3-util
    • Version: v3.0.0
    • Changes:
      • Updated to use v3.0.0 IDS
  • Protocol
    • Slug: common/intellicyt-ique3-util
    • Version: v2.2.0
    • Changes:
      • Updated to use v3.0.0 task script
DE-2293 MSD Sector S 600 - IDS creation
  • IDS
    • Slug: common/plate-reader-msd-sector-s-600
    • Version: v1.0.0
    • Changes:
      • First release
  • 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

Did this page help you?