Add capability to support Collection and Default experiment during parsing #223
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#222) * Initial plan * Add collection_type parameter to parser infrastructure - Add collection_type parameter to run_parser() with default value "COLLECTION" - Add --collection-type CLI option with choices between COLLECTION and DEFAULT_EXPERIMENT - Update tests to cover both collection types and default behavior - Update documentation to explain the new parameter --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: JosePizarro3 <[email protected]>
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Pull Request Overview
This PR adds support for configurable collection types in the run_parser function, allowing users to choose between "COLLECTION" and "DEFAULT_EXPERIMENT" when creating collections in openBIS. Previously, the function was hardcoded to use "DEFAULT_EXPERIMENT".
Key Changes:
- Added a new
collection_typeparameter to therun_parserfunction with a default value of"COLLECTION" - Added validation to ensure only valid collection types are accepted
- Updated the CLI to include a
--collection-typeoption with case-insensitive choices - Updated existing tests to explicitly specify collection types and added new tests for the feature
Reviewed Changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| bam_masterdata/cli/run_parser.py | Added collection_type parameter with default "COLLECTION", added validation logic, and replaced hardcoded "DEFAULT_EXPERIMENT" with the parameter |
| bam_masterdata/cli/cli.py | Added --collection-type CLI option with case-insensitive choice validation and uppercase conversion |
| tests/cli/test_run_parser.py | Updated existing tests to specify collection type explicitly, added tests for DEFAULT_EXPERIMENT type and default behavior |
| docs/tutorials/parsing.md | Added documentation for the new collection_type parameter with examples and best practices |
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JosePizarro3
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Pull Request Test Coverage Report for Build 18934679482Details
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This pull request adds support for specifying the type of collection to create in openBIS, either
"COLLECTION"or"DEFAULT_EXPERIMENT", through the CLI and programmatic interfaces. It updates the documentation and tests to reflect this new capability and ensures that invalid collection types are handled gracefully.Feature: Collection type selection
--collection-typeCLI option and a correspondingcollection_typeparameter to theparserandrun_parserfunctions, allowing users to choose between"COLLECTION"and"DEFAULT_EXPERIMENT"when creating collections in openBIS. [1] [2]run_parserto validatecollection_typeand use it when creating new collections, including error handling for invalid types. [1] [2]Documentation updates
docs/tutorials/parsing.mdto describe thecollection_typeparameter, its options, usage examples, and recommendations for future compatibility. [1] [2]Testing improvements
run_parsersupports both collection types, defaults to"COLLECTION"when not specified, and correctly creates objects in openBIS for each scenario.collection_typeparameter for completeness. [1] [2]