v3.1.1: Minor fixes and improvements

What's Changed

• DIG-1819: Warn instead of error when reference date missing & add validation to required fields by @mshadbolt and @yavyx in #86
• DIG-1860: Move missing cases to validation file by @yavyx in #89
• Allows to be run as a stand alone. by @DavidBrownlee in #87
• GitHub workflow test fix by @DavidBrownlee in #88
• Update documentation & remove dist files by @yavyx in #90

Full Changelog: v3.1.0...v3.1.1

v3.1.0: MoH Clinical Data Model v3.1 compatibility

• Changes needed for updated clinical data model
• Handling not available and -99 values
• Counting not available values as missing

What's Changed

• Add RedCap export splitting script by @mshadbolt in #78
• Update validation and test data for model 3.1 by @mshadbolt in #80
• update schema urls by @daisieh in #82
• DIG-1772 & DIG-1782: Handle -99 and 'Not available' as missing by @mshadbolt in #83

Full Changelog: v3.0.0...v3.1.0

v3.0.0: MoH data model v3 and date format

This release of Clinical ETL includes updates to enable a user to transform their tabular data into a json file compatible with the latest MoH clinical data model (v3.0).

It also adds a new required field to the manifest file that allows a user to specify a date format to ensure date values are being properly parsed.

What's Changed

• DIG-1671: Adding date format to manifest by @yavyx in #66
• add sample redcap files by @kcranston in #67
• DIG-1684: Update clinical_etl to v3 clinical data model by @yavyx in #68
• Fix up some of the validations by @mshadbolt in #69
• Update to version 3 by @mshadbolt in #70

Full Changelog: v2.2.1...v3.0.0

v2.2.1: Documentation, validation improvements

Highlights

• Documentation improvements
• Improved output
• Validation and completeness can be saved to files

What's Changed

• Improve output, save validation results to file, add more date validations by @mshadbolt in #61
• Merge changes from stable to develop by @mshadbolt in #63
• Improved documentation, validation and completeness summarization by @yavyx in #64

Full Changelog: v2.2.0...v2.2.1

v2.2.0

What's Changed

• Merge release v2.1.0 into stable branch by @yavyx in #60
• Improve output, save validation results to file, add more date validations by @mshadbolt in #61

Full Changelog: v2.1.0...v2.2.0

v2.1.0: Native DateInterval support, improved CLI options

What's Changed

• Module path changes to allow running standalone (not as an included m… by @DavidBrownlee in #50
• DIG-1473: Accept date intervals (rather than absolute dates). by @DavidBrownlee in #51
• change float() to floating() in mapping functions by @lilyyangyi301 in #54
• DIG-1150: Template update and documentation for DateIntervals by @mshadbolt in #53
• Add index and minify command line arguments by @mshadbolt in #55
• Update docs for the recent addition of args by @mshadbolt in #56
• add main and have CSVConvert as CLI script by @mshadbolt in #57
• fix int method, more details in warning by @mshadbolt in #58

New Contributors

• @DavidBrownlee made their first contribution in #50
• @lilyyangyi301 made their first contribution in #54

Full Changelog: v2.0.0...v2.1.0

v2.0.0: genomic schema ingest, date intervals

What's Changed

• Generalize schema class used for conversion/validation by @daisieh in #48
• DIG-1245: dates as date intervals by @daisieh in #49

Full Changelog: v1.2.1...v2.0.0

v1.2.1: Update python to 3.12

What's Changed

• DIG-1144: Update to Python 3.12 by @daisieh in #47

Full Changelog: v1.2.0...v1.2.1

Clinical_etl as a package

What's Changed

• Update for katsu uuids by @daisieh in #44
• Small fixes by @daisieh in #45
• DIG-1219: clinical_ETL_code as a package by @daisieh in #46

Full Changelog: v1.1.0...v1.2.0

Stable release for CanDIGv2 v2.1.1

MoH data model support

This version supports the MoH data model v2, including mapping and validation.

What's Changed

• Coverage tool by @daisieh in #4
• Complex references to sheets and fields by @daisieh in #5
• Remove nulls from mapping by @daisieh in #6
• Separate template code by @kcranston in #7
• DIG-1045: First pass at MoH model by @daisieh in #13
• Bug fixes for the MoH model by @daisieh in #14
• DIG-1194: don't map .id properties into template by @daisieh in #15
• DIG-1152: Validate output file against schema using jsonschema by @daisieh in #16
• DIG-1195: indexed_on is now a function; refactoring as well by @daisieh in #17
• change license to lgpl-3 by @kcranston in #18
• DIG-1079, DIG-1226: validate ETL beyond jsonschema by @daisieh in #20
• DIG-1267, DIG-1268 by @daisieh in #21
• Validate coverage separate function by @justin-ys in #23
• HOTFIX: Missing format string by @justin-ys in #25
• DIG-1261: Fix indexing by @daisieh in #24
• DIG-1247: Check that submitter_specimen_id refers to a valid specimen by @daisieh in #26
• Mappings over multiple sheets by @daisieh in #27
• DIG-1140: ETL outputs missing clinical data summary by @daisieh in #28
• Tiny fixes that were missed before by @daisieh in #29
• Increase python version by @mshadbolt in #30
• DIG-1285: check for diffs in moh_template by @daisieh in #31
• DIG-1285 redux: forgot latest bits in moh_template by @daisieh in #32
• Hotfix for treatment_type missing by @daisieh in #33
• added single_map helper function by @yavyx in #34
• DIG-1325: Don't add required_but_missing fields to failure list by @daisieh in #35
• DIG-1344: make sure no dup IDs in schemas by @daisieh in #36
• DIG-1346: distinguish between errors and warnings by @daisieh in #37
• Add REPO_DIR to paths by @daisieh in #39
• fix mapping functions for surgeries in mapping template by @mshadbolt in #38
• DIG-1361: comment out radiation/surgery counts by @daisieh in #40
• Pass on statistics by @daisieh in #41
• DIG-1359: Documentation, error handling and code improvements for usability by @mshadbolt in #42
• Split out jsonschema conversion by @daisieh in #43

New Contributors

• @kcranston made their first contribution in #7
• @justin-ys made their first contribution in #23
• @mshadbolt made their first contribution in #30
• @yavyx made their first contribution in #34

Full Changelog: v1.0.1...v1.1.0