Add MIAPPE metadata with an editor and legacy migration - #116
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jlegrand62 wants to merge 17 commits into
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Add MIAPPE metadata with an editor and legacy migration#116jlegrand62 wants to merge 17 commits into
jlegrand62 wants to merge 17 commits into
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…alidation Define the canonical MIAPPE-aligned biological metadata structure for Scan and validate it at the create and metadata-write boundaries (metadata.py, core.py). The block is optional; when present, known fields are type-checked.
…CLIs Add fsdb_migrate_metadata (one-time conversion of legacy Metadata.object to the MIAPPE tree, idempotent) and fsdb_clean_images_metadata (removes the now-redundant biological/hardware entries duplicated in images.json). Drop the legacy images.json fallback read in _load_scan_metadata.
get_scan_info now reads the canonical biologicalMaterial/study structure for species, plant and environment instead of the legacy Metadata.object block. Update scan API tests accordingly.
Add a Dash web UI to view, edit and bulk-fill MIAPPE-aligned biological metadata of local FSDB scans, with per-field specs, flatten/unflatten helpers and write-back with schema validation. Wire up the metadata_app CLI entry point.
Drop support for loose scan directories; a database root must now be a proper ROMI DB. Surface a clearer NotAnFSDBError message from FSDB.connect.
…r UI Auto-load the DB from --db-path, flag scans still on the legacy object schema, and add a one-click 'Migrate now' action in the editor. Add scan_needs_migration/migratable_scans/migrate_scans helpers in db_ops.
diskcache backs Dash background callbacks (used by the metadata editor for streaming migration progress). Ignore the .dashcache runtime directory.
Wrap list_scans in try/finally so the database connection is released even on error, matching other call sites.
Cache connected FSDB instances per database path (connect is expensive) with thread-safe access, close_db to switch databases, and atexit cleanup. Add migrate_scans_progress to report per-scan progress to a caller.
…gration modal Restructure the layout (FSDB location + About on top, scan selection beside a single field-edit form), merging the separate per-scan and bulk-edit flows into one form driven by the edit-accordion mode. Move migration behind a modal with a streaming progress bar via a DiskCache background callback, auto-closing on completion. Close cached DBs when switching databases.
Add Bootstrap icons to card headers, accordion and MIAPPE section titles, move field tooltips to a question-mark icon on each row, and add app.css to size the field labels consistently.
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Summary
Adds MIAPPE-aligned biological metadata support to PlantDB: a write-time schema/validator in the commons layer, CLI migration for legacy scans, and a web UI in the metadata editor to view, edit, and migrate scan metadata.
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