fair-metadata-integration 0.1.0__py3-none-any.whl

fair_metadata_integration/__init__.py

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+from .metadata_integration import create_ro_crate
+
+__all__ = ["create_ro_crate"]

fair_metadata_integration/metadata_integration.py

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+import os.path
+from rocrate.rocrate import ROCrate
+from rocrate.model import ComputerLanguage, ContextEntity
+
+
+def create_ro_crate(dest_path, workflow_schema_filename, input_path, output_paths=[]):
+    crate = ROCrate()
+
+    crate.metadata.extra_terms = {
+        "organism_classification": "https://schema.org/taxonomicRange",
+        "BioChemEntity": "https://schema.org/BioChemEntity",
+        "channel": "https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Channel",
+        "obo": "http://purl.obolibrary.org/obo/",
+        "FBcv": "http://ontobee.org/ontology/FBcv/",
+        "acquisiton_method": {
+            "@reverse": "https://schema.org/result",
+            "@type": "@id",
+        },
+        "biological_entity": "https://schema.org/about",
+        "biosample": "http://purl.obolibrary.org/obo/OBI_0002648",
+        "preparation_method": "https://www.wikidata.org/wiki/Property:P1537",
+        "specimen": "http://purl.obolibrary.org/obo/HSO_0000308",
+    }
+
+    output_entities = []
+    for image_path in output_paths:
+        rel_path = os.path.basename(image_path.rstrip('\\/'))
+        output_entities.append(crate.add_dataset(
+            source=image_path, dest_path=rel_path,
+            properties=get_additional_filetype_property(image_path)))
+
+    input_entity = crate.add_dataset(source=input_path,
+                                     dest_path=os.path.basename(input_path.rstrip('\\/')),
+                                     properties=get_additional_filetype_property(input_path))
+
+    # main=True sets the root dataset's mainEntity and declares the Workflow RO-Crate
+    # profile in conformsTo (on the metadata descriptor for rocrate < 0.16, on the
+    # root dataset for rocrate >= 0.16).
+    workflow = crate.add_workflow(source=workflow_schema_filename,
+                                  dest_path=os.path.basename(workflow_schema_filename),
+                                  main=True, lang=get_bilayers_language(crate))
+
+    # The Workflow RO-Crate profile ranges input/output over FormalParameter rather
+    # than over the data entities themselves; each data entity is linked back to its
+    # parameter with exampleOfWork.
+    workflow['input'] = [add_formal_parameter(crate, input_entity, 'input')]
+    if output_entities:
+        workflow['output'] = [
+            add_formal_parameter(crate, entity, 'output' if i == 0 else f'output_{i + 1}')
+            for i, entity in enumerate(output_entities)
+        ]
+
+    crate.write(dest_path)
+    return crate
+
+
+def get_additional_filetype_property(path):
+    ext = os.path.splitext(path)[1]
+    ref = None
+    if '.zar' in ext:
+        ref = 'http://edamontology.org/format_3915'
+    elif '.tif' in ext:
+        ref = 'http://edamontology.org/format_3591'
+    if ref:
+        return {'additionalType': ref}
+    return None
+
+
+def get_bilayers_language(crate):
+    """Return the ComputerLanguage entity for a bilayers workflow specification.
+
+    Identified by the Zenodo concept DOI, which is version-independent and
+    resolves to the latest release of the specification.
+    """
+    return crate.add(ComputerLanguage(
+        crate,
+        identifier='https://doi.org/10.5281/zenodo.17652333',
+        properties={
+            'name': 'Bilayers',
+            'alternateName': 'Bilayers workflow specification',
+            'identifier': {'@id': 'https://doi.org/10.5281/zenodo.17652333'},
+            'url': {'@id': 'https://github.com/bilayer-containers/bilayers'},
+        },
+    ))
+
+
+def add_formal_parameter(crate, data_entity, name):
+    """Add a FormalParameter describing *data_entity* and link the two together."""
+    properties = {'@type': 'FormalParameter', 'name': name}
+    format_ref = data_entity.get('additionalType')
+    if format_ref:
+        properties['format'] = {'@id': format_ref}
+    parameter = crate.add(ContextEntity(crate, f'#{name}', properties))
+    data_entity['exampleOfWork'] = parameter
+    return parameter

fair_metadata_integration-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: fair-metadata-integration
+Version: 0.1.0
+Summary: Integrate and package all metadata into RO-Crate, linking to other metadata files
+Author-email: Joost de Folter <folterj@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/NL-BioImaging/fair-metadata-integration
+Project-URL: Repository, https://github.com/NL-BioImaging/fair-metadata-integration
+Keywords: RO-Crate,FAIR,metadata,bioimaging,OME-Zarr
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: rocrate>=0.15.1
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Dynamic: license-file
+
+# fair-metadata-integration
+
+Integrate and package all metadata into RO-Crate, linking to other metadata files.
+
+Given a [Bilayers](https://github.com/bilayer-containers/bilayers) workflow
+specification and the image data an analysis consumed and produced, this package
+writes a [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/1.0):
+an `ro-crate-metadata.json` describing the run, alongside copies of the files it
+describes.
+
+## Installation
+
+```bash
+pip install fair-metadata-integration
+```
+
+Requires Python 3.12 or newer. [`rocrate`](https://pypi.org/project/rocrate/) is
+installed automatically.
+
+## Usage
+
+```python
+from fair_metadata_integration import create_ro_crate
+
+create_ro_crate(
+    dest_path="crate",
+    workflow_schema_filename="config.yaml",
+    input_path="input.ome.zarr",
+    output_paths=["output.ome.zarr"],
+)
+```
+
+- `dest_path` — directory the crate is written to, created if it does not exist.
+- `workflow_schema_filename` — the Bilayers `config.yaml` describing the workflow.
+- `input_path` — the input image (an OME-Zarr directory or a TIFF file).
+- `output_paths` — the images the workflow produced. Each gets its own parameter.
+
+The source files are copied into the crate, so `dest_path` ends up
+self-contained:
+
+```
+crate/
+├── config.yaml
+├── input.ome.zarr/
+├── output.ome.zarr/
+└── ro-crate-metadata.json
+```
+
+### What the crate contains
+
+The workflow specification is the crate's `mainEntity`, typed as a
+`ComputationalWorkflow`, and the metadata descriptor declares the Workflow
+RO-Crate profile:
+
+```json
+{
+  "@id": "ro-crate-metadata.json",
+  "@type": "CreativeWork",
+  "about": { "@id": "./" },
+  "conformsTo": [
+    { "@id": "https://w3id.org/ro/crate/1.2" },
+    { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" }
+  ]
+}
+```
+
+The workflow's `programmingLanguage` is a `ComputerLanguage` entity for the
+Bilayers specification, identified by its Zenodo concept DOI
+[`10.5281/zenodo.17652333`](https://doi.org/10.5281/zenodo.17652333), which
+resolves to the latest release of the spec.
+
+Inputs and outputs are modelled as `FormalParameter` entities carrying an
+[EDAM](https://edamontology.org/) format IRI — `format_3915` for Zarr,
+`format_3591` for TIFF. Each image dataset points back at the parameter it
+realises via `exampleOfWork`:
+
+```json
+{
+  "@id": "input.ome.zarr/",
+  "@type": "Dataset",
+  "additionalType": "http://edamontology.org/format_3915",
+  "exampleOfWork": { "@id": "#input" }
+}
+```
+
+The crate's JSON-LD context is extended with terms for describing biological
+imaging metadata — `biosample`, `specimen`, `organism_classification`,
+`preparation_method`, `channel` and others — so those properties can be added to
+the crate's entities.
+
+## Development
+
+```bash
+git clone https://github.com/NL-BioImaging/fair-metadata-integration.git
+cd fair-metadata-integration
+pip install -e ".[test]"
+pytest
+```
+
+## License
+
+MIT

fair_metadata_integration-0.1.0.dist-info/RECORD

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+fair_metadata_integration/__init__.py,sha256=SnFC0fNZ4TLsdr8KaOZNgONT0xJVWk1I2x6h7xYAWwo,81
+fair_metadata_integration/metadata_integration.py,sha256=HicirGwXaKwR-MUg18Jd6PVZkf3IeT8g7q8fwdj52Q8,3966
+fair_metadata_integration-0.1.0.dist-info/licenses/LICENSE,sha256=lM752AVCWLqhoLjgYBwOn6aZPSyJF4F37p5HTp9rmLw,1070
+fair_metadata_integration-0.1.0.dist-info/METADATA,sha256=Wz5PzsqjzLX-tgBPbLQcQMbTXxyK3ssDXICGbvSyGI4,3853
+fair_metadata_integration-0.1.0.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+fair_metadata_integration-0.1.0.dist-info/top_level.txt,sha256=MCH6Wq-pmgeqiPsZvydDNhn6hI6Ox96rJSvbYgGafAQ,26
+fair_metadata_integration-0.1.0.dist-info/RECORD,,

fair_metadata_integration-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

fair_metadata_integration-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 NL-BioImaging
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fair_metadata_integration-0.1.0.dist-info/top_level.txt

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+fair_metadata_integration