Pandid v2

[BergsethCognite]

Bug fixes

• Outer except no longer raises a literal string "msg"; preserves message and chains original exception.
• push_result_to_annotations now always returns int (was sometimes a tuple); a malformed result item no longer aborts the whole batch.
• File-link entities now stored under the canonical search_property key, so file-to-file matches actually work.
• Cross-view entities normalised to the file view's search_property so the diagram-detect search_field finds them.
• Per-batch error_count / annotated_count arithmetic corrected (was over-counting whole pages).
• ANNOTATE_BATCH_SIZE no longer mutated as a module-level global; per-invocation local that can't leak across warm-container calls.
• Cursor preserved on transient 400 in get_new_files; persistent 400 fails loudly instead of silently restarting from scratch.
• read_state_store split into typed read_state_cursor / read_state_batch_num with safe coercion.

Hardening

• Narrowed except Exception to CogniteAPIError where .code / .message is read.
• Bounded exponential backoff added to run_diagram_detect, get_new_files, and the apply retry loop.
• Narrowed broad except in _detect_annotation_to_edge_applies to parse-shape errors only.
• daemon=True on the Mixpanel usage-tracker thread.

Cleanup / hygiene

• Dead sys.path.append and unused sys / Path imports removed.
• @DataClass on Enum removed.
• Optional hints fixed (str | None = None) for debug_file, filter_property, filter_values.
• Orphan pares_direct_relation typo'd classmethod deleted.
• cognite.client.utils._text.shorten (private API) replaced with a local _truncate helper.
• RawUploadQueue now lazy-imported (test-friendly; no behavior change).
• from future import annotations added.
• list[dict[str, any]] → list[dict[str, Any]] everywhere.
• Entities de-duplicated on (space, external_id) to prevent duplicate edges.
• Per-file delete_annotations_for_file replaced with a single batched delete_annotations_for_files per page.
• O(n²) get_file_source_id replaced with a one-shot (space, external_id) → sourceId index.
• create_table calls hoisted to a single setup step instead of running every batch.
• Per-file INFO log demoted to DEBUG.
• Missing ANNOTATE_BATCH_SIZE import added (latent NameError when debug=False).
• Various typos fixed ("For for view", "don't contains", "status an logged status", "tag PID" docstrings).

Tests (new)

• test_pipeline.py — 26 unit tests covering helpers, state coercion, get_all_entities, get_new_files retries, push_result_to_annotations.
• test_config.py — 21 unit tests covering Optional defaults, required fields, threshold validation, Literal enforcement.
• All 47 tests run locally with just pytest cognite-sdk pyyaml pydantic (no cognite-extractor-utils needed).

Rename / module alignment (related, outside the function dir)

• Function directory renamed to fn_dm_context_files_annotation; functions.Function.yaml externalId made static.
• Extraction pipeline externalId aligned to static ep_ctx_files_pandid_annotation (both ExtractionPipeline.yaml and config.yaml).
• Workflow task references updated to the new function/extraction-pipeline ids.
• handler.py::run_locally uses the new extraction-pipeline external id.
• README updated: stale ids replaced, dataset/RAW-DB confusion fixed, "Running functions locally" rewritten, new "Testing" section added.

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