docs: Create simplified data model graphics from script

.gitignore

@@ -126,6 +126,7 @@ venv.bak/
 
 # mkdocs documentation
 /site
+_scripts/ER_DIAGRAM.md
 
 # mypy
 .mypy_cache/

docs/Makefile

@@ -12,7 +12,15 @@ BUILDDIR      = _build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help Makefile html
+
+dataorg:
+	@echo "Generating dataorg"
+	wget -O _scripts/ER_DIAGRAM.md https://raw.githubusercontent.com/chanzuckerberg/cryoet-data-portal-backend/refs/heads/main/schema/api/v2.0.0/codegen/ER_DIAGRAM.md
+	python _scripts/summarize_diagram.py
+
+html: dataorg
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/_scripts/ER_DIAGRAM-parsed.md

@@ -0,0 +1,52 @@
+```{eval-rst}
+.. md-mermaid::
+   erDiagram
+      Dataset ||--|o Deposition : "deposition"
+      Dataset ||--}o Run : "runs"
+      Run ||--}o Alignment : "alignments"
+      Run ||--}o Annotation : "annotations"
+      Run ||--|| Dataset : "dataset"
+      Run ||--}o Frame : "frames"
+      Run ||--}o Tiltseries : "tiltseries"
+      Run ||--}o TomogramVoxelSpacing : "tomogram_voxel_spacings"
+      Run ||--}o Tomogram : "tomograms"
+      Tomogram ||--|o Alignment : "alignment"
+      Tomogram ||--|o Deposition : "deposition"
+      Tomogram ||--|o Run : "run"
+      Tomogram ||--|o TomogramVoxelSpacing : "tomogram_voxel_spacing"
+      Tomogram ||--|o Any : "affine_transformation_matrix"
+      TomogramVoxelSpacing ||--}o AnnotationFile : "annotation_files"
+      TomogramVoxelSpacing ||--|o Run : "run"
+      TomogramVoxelSpacing ||--}o Tomogram : "tomograms"
+      AnnotationFile ||--|o Alignment : "alignment"
+      AnnotationFile ||--|o AnnotationShape : "annotation_shape"
+      AnnotationFile ||--|o TomogramVoxelSpacing : "tomogram_voxel_spacing"
+      AnnotationShape ||--|o Annotation : "annotation"
+      AnnotationShape ||--}o AnnotationFile : "annotation_files"
+      Annotation ||--|o Run : "run"
+      Annotation ||--}o AnnotationShape : "annotation_shapes"
+      Annotation ||--|o Deposition : "deposition"
+      Deposition ||--}o Alignment : "alignments"
+      Deposition ||--}o Annotation : "annotations"
+      Deposition ||--}o Dataset : "datasets"
+      Deposition ||--}o Frame : "frames"
+      Deposition ||--}o Tiltseries : "tiltseries"
+      Deposition ||--}o DepositionType : "deposition_types"
+      DepositionType ||--|o Deposition : "deposition"
+      Tiltseries ||--}o Alignment : "alignments"
+      Tiltseries ||--}o PerSectionParameters : "per_section_parameters"
+      Tiltseries ||--|| Run : "run"
+      Tiltseries ||--|o Deposition : "deposition"
+      PerSectionParameters ||--|| Frame : "frame"
+      PerSectionParameters ||--|| Tiltseries : "tiltseries"
+      Frame ||--|o Deposition : "deposition"
+      Frame ||--}o PerSectionParameters : "per_section_parameters"
+      Frame ||--|o Run : "run"
+      Alignment ||--}o AnnotationFile : "annotation_files"
+      Alignment ||--}o PerSectionAlignmentParameters : "per_section_alignments"
+      Alignment ||--|o Deposition : "deposition"
+      Alignment ||--|o Tiltseries : "tiltseries"
+      Alignment ||--}o Tomogram : "tomograms"
+      Alignment ||--|o Run : "run"
+      PerSectionAlignmentParameters ||--|| Alignment : "alignment"
+```