2021.08_2 Artifact Release

Suggest Edits

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

Updated about 1 year ago