Merge pull request #23 from chanzuckerberg/uermel/linkml

Add LinkML schema for metadata files and the ability to generate docs and pydantic classes from the schema.

schema/v1.1.0/Makefile

@@ -0,0 +1,14 @@
+.DEFAULT_GOAL := build
+
+.PHONY: clean
+clean:
+	rm -rf metadata-docs
+	rm -rf metadata_materialized.yaml
+	rm -rf metadata_models.py
+
+.PHONY: build
+build:
+	python schema.py materialize metadata.yaml common.yaml metadata_materialized.yaml
+	gen-doc -d metadata-docs --no-mergeimports  --hierarchical-class-view --stacktrace metadata_materialized.yaml
+	gen-pydantic --pydantic-version 2 metadata_materialized.yaml > metadata_models.py
+	black -l 88 metadata_models.py

schema/v1.1.0/README.md

@@ -0,0 +1,50 @@
+# cryoET data portal metadata schema
+
+This directory contains the metadata schema for the cryoET data portal. Browse contained classes [here](metadata-docs/index.md).
+
+Metadata file and directory layout specs:
+
+<pre>
+[dataset_identifier]/
+|-- <a href="metadata-docs/Dataset.md">dataset_metadata.json</a>
+|-- [run_name]/
+|   |-- run_metadata.json
+|   |-- Frames/
+|   |   |-- [tiff|eer|mrc]
+|   |   |-- Gain_reference.mrc|dm4
+|   |   |-- frame_acquisition_order.json
+|   |-- TiltSeries/
+|   |   |-- <a href="metadata-docs/TiltSeries.md">tiltseries_metadata.json</a>
+|   |   |-- [run_name].mrc
+|   |   |-- [run_name].zarr/
+|   |   |   |-- [subdirectories according to <a href="https://ngff.openmicroscopy.org/latest/">OME-NGFF spec</a> at 100%, 50% and 25% scale]
+|   |   |-- [run_name].mdoc [optional, sometimes]
+|   |   |-- [run_name].rawtlt [optional, sometimes]
+|   |   |-- [run_name].tlt [optional, sometimes]
+|   |-- Tomograms/
+|   |   |-- VoxelSpacing[xx.yyy]
+|   |   |   |-- CanonicalTomogram
+|   |   |   |   |-- <a href="metadata-docs/Tomogram.md">tomogram_metadata.json</a>
+|   |   |   |   |-- neuroglancer_config.json
+|   |   |   |   |-- [run_name].mrc
+|   |   |   |   |-- [run_name].xf [optional, sometimes]
+|   |   |   |   |-- [run_name].zarr/
+|   |   |   |   |   |-- [subdirectories according to <a href="https://ngff.openmicroscopy.org/latest/">OME-NGFF spec</a> at 100%, 50% and 25% scale]
+|   |   |   |-- Annotations/
+|   |   |   |   |-- XXX_[object_name]_[version]_point.ndjson
+|   |   |   |   |-- <a href="metadata-docs/Annotation.md">XXX_[object_name]_[version].json</a>
+|   |   |   |   |-- YYY_[object_name]_[version]_segmentationmask.mrc
+|   |   |   |   |-- YYY_[object_name]_[version]_segmentationmask.zarr
+|   |   |   |   |   |-- [subdirectories according to <a href="https://ngff.openmicroscopy.org/latest/">OME-NGFF spec</a> at 100%, 50% and 25% scale]
+|   |   |   |   |-- <a href="metadata-docs/Annotation.md">YYY_[object_name]_[version].json</a>
+
+</pre>
+
+## Building the schema and docs
+
+To build the schema, markdown docs and pydantic classes:
+
+```bash
+cd schema/v1.1.0
+make build
+```