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zooma: batching, retry logic, and ontology filter support - #797

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hechth with Copilot wants to merge 2 commits into
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copilot/zooma-make-tool-more-robust
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zooma: batching, retry logic, and ontology filter support#797
hechth with Copilot wants to merge 2 commits into
masterfrom
copilot/zooma-make-tool-more-robust

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Copilot AI commented Aug 26, 2026

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The zooma tool was processing one row per API call with no fault tolerance, making it brittle for large inputs. This adds batched processing, retry/skip logic, and ontology scoping controls matching the ZOOMA web GUI.

Changes

zooma.py

  • Batching: Collects all query values upfront, then sends them in configurable batches (--batch-size, default 10)
  • Retry logic:
    • Failed batch → logged to stdout, retried once
    • Second failure → values skipped, logged to stdout
    • Two consecutive batch failures → job fails (server considered unavailable)
  • Ontology filter: --ontology-filter (all | efo_obo | obo | custom) + --ontologies for custom comma-separated list; filter is passed as params on annotate requests and as ontologies body field on map requests
  • query_zooma_map now accepts a list of values, building the full properties batch array in one call; results matched back to query values by propertyValue field

zooma.xml

  • batch_size integer param (default 10, range 1–100)
  • ontology_filter conditional with 4 options: All, EFO+OBO, OBO only, Custom; Custom exposes a multi-select (dummy for now — ontology list to be driven by data table in a future release)

macros.xml

  • Help text updated to document batching behaviour, retry/skip semantics, and ontology filter options

Copilot AI linked an issue Aug 26, 2026 that may be closed by this pull request
Co-authored-by: hechth <12066490+hechth@users.noreply.github.com>
Copilot AI changed the title [WIP] Add batching approach and retry logic for annotating inputs zooma: batching, retry logic, and ontology filter support Aug 26, 2026
Copilot AI requested a review from hechth August 26, 2026 08:01
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zooma: make tool more robust and flexible

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