Add aug 21 release

[shuchenliu]

1. add more benchmarks on /publications searching strategies
2. clean up ES configs

[Copilot]

Pull request overview

This PR expands the /publications lookup/benchmarking surface by adding a new combined-search strategy (single ES query that can match both PMIDs and alternate identifiers) and by improving benchmark integrity reporting, while also simplifying Elasticsearch connection presets/configuration.

Changes:

• Add combined-search as a supported /publications lookup strategy, plus _meta.lookup_fallback to indicate when a speculative ES path was rejected and the request fell back.
• Generalize the publications benchmark harness to support explicitly ordered strategy pairs (--compare-strategies), enforce lookup_fallback == false for paired integrity, and improve changed-path/order accounting.
• Clean up Elasticsearch connection presets (drop legacy aliases, standardize on in_cluster, ci_forward, test_forward) and update docs/tests accordingly.

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_pubmed.py	Updates default integration ES connection preset name.
tests/test_publications_load.py	Extends CLI/paired-benchmark tests for explicit strategy pairs and fallback attribution.
tests/test_elasticsearch.py	Adds coverage for search_ids_or_terms and updates expected connection preset set.
tests/test_document_metadata.py	Adds extensive coverage for combined-search behavior and lookup-fallback metadata in /publications.
tests/test_backend_parity.py	Updates parity tests to use in_cluster connection preset.
README.md	Documents new strategy options, fallback attribution semantics, and updated ES preset names.
biothings_annotator/application/views/document_metadata.py	Adds combined-search service instance and exposes _meta.lookup_fallback in responses.
biothings_annotator/annotator/settings.py	Simplifies ES preset config and introduces DEFAULT_ELASTICSEARCH_CONNECTION.
biothings_annotator/annotator/elasticsearch.py	Introduces search_ids_or_terms query helper with named-clause attribution passthrough.
biothings_annotator/annotator/document_metadata.py	Implements combined-search fetch + reverse-mapping and returns per-request fallback metadata.
biothings_annotator/annotator/annotator.py	Uses DEFAULT_ELASTICSEARCH_CONNECTION for env defaulting.
benchmarks/publications/workload.py	Adds strategy defaults and default comparison pair constants.
benchmarks/publications/runner.py	Generalizes paired comparison to arbitrary strategy pairs; tracks fallback attribution; changed-path stratification.
benchmarks/publications/report.py	Renders dynamic “experiment minus control” deltas and includes fallback integrity counters.
benchmarks/publications/metrics.py	Tracks lookup_fallback counts in stage/arm summaries.
benchmarks/publications/main.py	Adds --compare-strategies, fixes lookup-strategy defaulting, and threads strategies into comparison runs.
benchmarks/publications/init.py	Exports new defaults for external callers.

Suppressed comments (4)

tests/test_document_metadata.py:1653

• This test uses elasticsearch_connection="ci", but the preset was removed from ELASTICSEARCH_CONNECTIONS in this PR. Prefer a valid preset name (e.g. in_cluster) to keep the test aligned with supported configuration values.

    results, not_found, lookup_fallback = await DocumentMetadataService(
        elasticsearch_connection="ci",
        lookup_strategy=lookup_strategy,
    ).get_publications_with_metadata(publication_ids)

tests/test_document_metadata.py:1685

• This test uses elasticsearch_connection="ci", but the preset was removed from ELASTICSEARCH_CONNECTIONS in this PR. Using a supported preset here avoids confusing future readers about which connection names are valid.

    _, not_found, lookup_fallback = await DocumentMetadataService(
        elasticsearch_connection="ci",
        lookup_strategy=lookup_strategy,
    ).get_publications_with_metadata(publication_ids)

tests/test_document_metadata.py:1711

• This test uses elasticsearch_connection="ci", but the preset was removed from ELASTICSEARCH_CONNECTIONS in this PR. Prefer a supported preset name so the test input reflects real configuration.

    results, not_found, lookup_fallback = await DocumentMetadataService(
        elasticsearch_connection="ci",
        lookup_strategy=lookup_strategy,
    ).get_publications_with_metadata([PMID, DOI])

tests/test_document_metadata.py:1744

• This test uses elasticsearch_connection="ci", but the preset was removed from ELASTICSEARCH_CONNECTIONS in this PR. Switching to a supported preset keeps the test consistent with the cleaned-up connection config.

    service = DocumentMetadataService(
        elasticsearch_connection="ci",
        lookup_strategy=BULK_SEARCH_LOOKUP_STRATEGY,
    )

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