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
- Add fault tolerance for
- namespace:
-
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
- Update to use
- namespace:
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.
- namespace:
-
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
- Add new pipeline configuration parameter
- namespace:
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
- Update to use task script
- namespace:
DE-3880 Huxley Bertram HB100 - IDS
-
IDS
- namespace:
common
- slug:
compaction-simulator-huxley-bertram-hb100
- version:
v1.0.0
- changelog:
- First release
- namespace:
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
fromhttps://ids.tetrascience.com/common/microscope-leica-aperio/v0.1.0/schema.json
tohttps://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
fromv0.1.0
tov0.2.0
- Update
runs[*].tile_length
toruns[*].tile.length
- Update
runs[*].tile_width
toruns[*].tile.width
- Update
runs[*].tile_offsets
toruns[*].tile.offsets
- Update
runs[*].tile_bytes_count
toruns[*].tile.bytes_count
- Update
images[*].original_metdata.dsr_id
tomethods[*].digital_slide_repository_id
- Update
images[*].original_metdata.icc_profile
tomethods[*].international_color_consortium_profile
- Update
images[*].original_metadata.fileame
toresults[*].filename
- Update
images[*].pixel_information.size_c
toresults[*].pixel_information.size.c
- Update
images[*].pixel_information.size_t
toresults[*].pixel_information.size.t
- Update
images[*].pixel_information.size_x
toresults[*].pixel_information.size.x
- Update
images[*].pixel_information.size_y
toresults[*].pixel_information.size.y
- Update
images[*].pixel_information.size_z
toresults[*].pixel_information.size.z
- Update
images[*].pixel_information.phyisical_size_x.value
toresults[*].pixel_information.physical_size.x.value
- Update
images[*].pixel_information.phyisical_size_x.unit
toresults[*].pixel_information.physical_size.x.unit
- Update
images[*].pixel_information.phyisical_size_y.value
toresults[*].pixel_information.physical_size.y.value
- Update
images[*].pixel_information.phyisical_size_y.unit
toresults[*].pixel_information.physical_size.y.unit
- Update
images[*].original_metdata.objective_power
tomethods[*].magnification
- Update
images[*].original_metdata.q
toresults[*].original_metadata_q
- Update
images[*].channel
tomethods[*].channels[*]
- Update
samples[*].labels[*].source.name
type
fromstring
to['null', 'string']
- Update
systems[*].firmware[*]
add schema item"additionalProperties": false
- Remove property
images[*]
because the fields were moved toresults[*]
andmethods[*]
- Add property
- namespace:
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
fromhttps://ids.tetrascience.com/common/qpcr-thermofisher-viia7/v4.0.0/schema.json
tohttps://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
fromv4.0.0
tov5.0.0
- Update property
runs[*].bulb_usage
toruns[*].hardware_usage
- Update property
runs[*].bulb_usage.halogen_lamp_hours
toruns[*].hardware_usage.halogen_lamp_hours
- Update property
runs[*].bulb_usage.life_cycle_count
toruns[*].hardware_usage.block_life_cycle_count
- Update property
runs[*].bulb_usage.life_degrees_climbed
toruns[*].hardware_usage.block_life_degrees_climbed
- Update
datacubes[*].dimensions[*].scale[*]
type
fromnumber
to['null', 'number']
- Update
datacubes[*].measures[*].value[*][*]
type
from['null', 'number']
tonumber
- Update root
- namespace:
-
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
- Update task script to use
- namespace:
-
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
- Update to use task script
- namespace:
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
, andvalue_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
andparsed_number
that include both the numerically parsedvalue
field and araw_value
string field.
- Add data types for
- 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
, andmethods
)- Update
run
object field toruns
array - Update
sample
object field tosamples
array- Update mapping of
sample.position
tosamples[0].location.position
to follow the non-extendablesamples
GSF - Update mapping of
sample.weight
,sample.internal_standard_amount
, andsample.spike_group
to the respectivemethods[0].sample_preparation.<field>
to follow the non-extendablesamples
GSF
- Update mapping of
- Update
- Update definition of
software
insystems
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
orparsed_number
when appropriate to ensure compatibility with the Chromeleon Agent v2.0.0 - Update
methods[0].processing.peak_group_parameters[*]
andmethods[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
- Add type definitions for
- namespace:
Lunatic improvement
-
Task Script
- namespace:
common
- slug:
unchained-labs-lunatic-util
- version:
v6.0.2
- changelog:
- Update to run using Docker container tooling
- namespace:
Updated 10 months ago