Adds support for Health-RI v2 by agjharms · Pull Request #65 · Health-RI/img2catalog

agjharms · 2025-05-09T08:42:36Z

In this pull request:

Support for the required fields of the Health-RI v2 model is implemented. This is done by modifying the input xnat and adding a mapping from XNAT variables to the Health-RI v2 Sempyro classes.
Refactor the CLI so the input, mapping and output components get more modular.
Update the documentation in the form of the Readme.

Due to the change of the CLI and the upgrade to Health-RI v2, this version will be a 2.0.0 release.

This pull request uses the Health-RI v2 Sempyro classes as defined in this version of Sempyro: Health-RI/SeMPyRO#56. This is the reason the tests aren't passing.
These additions to Sempyro will most likely also be released as a 2.0.0 release.

… example config

sourcery-ai · 2025-05-09T08:42:40Z

Reviewer's Guide

This pull request implements support for the Health-RI v2 model. This was achieved by refactoring the Command Line Interface (CLI) into a modular input-mapping-output structure using chained click commands, updating the XNAT-to-Health-RI mapping logic to use Health-RI v2 Sempyro Pydantic classes, and modifying the configuration system and tests accordingly. The documentation (README) was also comprehensively updated to reflect these changes.

File-Level Changes

Change	Details	Files
Refactored CLI into a modular input-mapping-output structure.	Decomposed the main CLI command into chained subcommands for input (e.g., `xnat`, `xnat-project`), mapping (`map-xnat-hriv2`), and output (e.g., `rdf`, `fdp`). Utilized `click.Context` (`ctx.obj`) to pass data like configuration, XNAT connection, and metadata objects between these chained commands.	`src/img2catalog/cli_app.py`
Updated metadata mapping to support Health-RI v2 model using new Sempyro classes.	Replaced `map_xnat_to_healthriv1` with `map_xnat_to_healthriv2` function. Integrated Health-RI v2 Sempyro Pydantic classes (HRICatalog, HRIDataset, HRIVCard, HRIAgent). Updated mapping logic to populate new/revised fields for Health-RI v2 (e.g., `access_rights`, `applicable_legislation`, structured `contact_point`, `publisher`, `creator` with `mbox`/`homepage`). Upgraded `sempyro` dependency to version `2.0.0` or higher and bumped package version to `2.0.0`.	`src/img2catalog/mappings/xnat.py` `pyproject.toml` `src/img2catalog/__about__.py`
Enhanced configuration to support Health-RI v2 fields and control private project processing.	Revised default and example configurations to include Health-RI v2 specific fields (e.g., `applicable_legislation`, `access_rights`, `formatted_name`, `mbox`, `homepage`). Improved `ConfigInput.update_metadata` method for deep updates of nested dictionary structures from the configuration. Added an `include_private` configuration option and corresponding logic in `XNATInput` to control the processing of private XNAT projects.	`src/img2catalog/configmanager.py` `src/img2catalog/inputs/config.py` `src/img2catalog/inputs/xnat.py` `src/img2catalog/const.py` `tests/example-config.toml` `tests/xnat_integration_test_config.toml`
Overhauled test suite for new CLI, Health-RI v2 models, and added mapping-specific tests.	Adapted existing unit and integration tests to the new modular CLI structure and Health-RI v2 data models. Introduced a new test file (`test_mappings_xnat_hri_v2.py`) for the Health-RI v2 mapping logic. Added test cases for new functionalities, such as the `include_private` project handling. Updated test fixtures and reference data files to align with Health-RI v2.	`tests/test_inputs_xnat.py` `tests/test_cliapp.py` `tests/test_xnat_integration_tests.py` `tests/test_mappings_xnat_hri_v2.py` `tests/conftest.py` `tests/references/valid_project.ttl` `tests/references/xnat_integration_test-single_dataset.ttl` `tests/references/xnat_integration_test.ttl`
Updated README to reflect new CLI structure and Health-RI v2 support.	Rewrote the README to accurately describe the new modular CLI usage (input, mapping, output commands). Detailed the support for the Health-RI v2 model. Updated information on configuration options, authentication, and FDP integration.	`README.md`

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PatrickDekkerHealthRI

Why was this overwrite mechanism for private projects added ? I would expect the project should decide and not the person who runs the img2catalog tool, would optin keyword not be a better solution ?

Creator / identifier I often see [ ] so it look like a list, but in the datamodel these two have cardinality 1..1

I like your comment, it helped me to understand the code.

PatrickDekkerHealthRI · 2025-05-09T11:27:30Z

 name = ["Example publishing institution",]
-identifier = "http://www.example.com/institution#example"
+identifier = ["http://www.example.com/institution#example"]
+mbox = "publisher@example.com"


All example emails have been prefixed with 'mailto:'

PatrickDekkerHealthRI · 2025-05-09T11:44:32Z

 # Default License for datasets is "available upon reasonable request"
 # I can't find that, so putting a placeholder here
-license = "http://example.com/license#nolicense"
+# license = "http://example.com/license#nolicense"


I have removed all unused, commented out statements from the test configuration

agjharms · 2025-05-09T12:55:33Z

The reason to include a feature to index metadata from private projects is allow for broader use of the tool on our XNAT server. To get metadata from a private project, you will still need to have access to that project. It will not be possible to set 'include_private = true' and get the metadata from these projects without the knowledge of the data holder.

It is also still possible to set an opt-in or opt-out keyword to filter projects. This functionality still holds also for private projects.

codecov · 2025-06-12T05:56:30Z

Codecov Report

Attention: Patch coverage is 85.71429% with 10 lines in your changes missing coverage. Please review.

Project coverage is 93.88%. Comparing base (2624490) to head (3a60734).
Report is 23 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/img2catalog/mappings/xnat.py	64.28%	2 Missing and 3 partials ⚠️
src/img2catalog/cli_app.py	92.10%	1 Missing and 2 partials ⚠️
src/img2catalog/inputs/config.py	86.66%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #65      +/-   ##
===========================================
- Coverage    94.65%   93.88%   -0.78%     
===========================================
  Files           10       10              
  Lines          393      425      +32     
  Branches        48       58      +10     
===========================================
+ Hits           372      399      +27     
  Misses          12       12              
- Partials         9       14       +5

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sonarqubecloud · 2025-07-09T09:36:58Z

Quality Gate failed

Failed conditions
57 Security Hotspots
63.9% Coverage on New Code (required ≥ 80%)
38.0% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud

PatrickDekkerHealthRI

Looks good to me.

agjharms added 9 commits May 2, 2025 16:44

feat: update to health-ri v2

f3454bf

test: add mapping test without keywords

cc33ad2

fix(tests): fixes test now that publisher identifier is a list in the…

4ed09d0

… example config

feat: makes cli modular

7fc43d3

feat: make cli more modular add include_private flag

3f54202

docs: update readme

a974f8c

fix: update version and required sempyro version

de67b45

fix: flow of unmapped and mapped objects in CLI

ee1c0a7

fix(tests): integration tests for private projects

598cbf4

agjharms added 2 commits May 9, 2025 11:31

fix(tests): integration tests for private projects

712202d

fix(tests): adds reference for integration test with private projects

bdb4fa6

PatrickDekkerHealthRI reviewed May 9, 2025

View reviewed changes

agjharms added 4 commits May 9, 2025 15:14

fix: add mailto: prefix to example emails

9f5e3e9

fix: remove unused commented out code

684c20f

fix: upgrades SeMPyRO to v2.0.1

55312a0

fix: removes old test for health-ri v1

8a80979

agjharms added 3 commits July 9, 2025 11:15

fix: removes harvesting from private projects

346880c

fix: removes integration test for private projects

7d5425b

tests: removed unused statements from test configuration

3a60734

agjharms requested a review from PatrickDekkerHealthRI July 9, 2025 09:40

PatrickDekkerHealthRI approved these changes Jul 9, 2025

View reviewed changes

agjharms merged commit 32a4f24 into develop Jul 9, 2025
17 of 20 checks passed

agjharms deleted the feature/health-ri-v2-rc1-required branch July 9, 2025 10:37

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agjharms commented May 9, 2025

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Quality Gate failed

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