From c938e81f4317e1df288071988e645867e0b53a61 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 15 Sep 2026 10:40:37 +0100 Subject: [PATCH 1/4] script to capture terminfo fixtures for PR checks --- scripts/capture_term_info_fixtures.py | 156 + ...ass_FBbt_00000058_related_individuals.json | 55 + .../term_info/class_FBbt_00003686_kenyon.json | 1431 ++++++++ .../class_FBbt_00003748_medulla.json | 1572 +++++++++ ...ss_FBbt_00048514_taste_mechanosensory.json | 1603 +++++++++ .../term_info/class_FBbt_00048531.json | 143 + .../term_info/dataset_Cachero2010.json | 1080 ++++++ .../fixtures/term_info/dataset_Ito2013.json | 1077 ++++++ .../ep_class_VFBexp_FBtp0060056.json | 418 +++ .../term_info/ep_individual_VFB_00020530.json | 388 +++ .../term_info/gene_FBgn0010339_128up.json | 291 ++ .../fixtures/term_info/gene_FBgn0051882.json | 148 + .../individual_VFB_00010001_fru.json | 513 +++ .../individual_VFB_00101385_MEon.json | 257 ++ .../term_info/license_CC_BY_NC_3_0.json | 22 + .../neuron_class_FBbt_00047030_EPG.json | 1984 +++++++++++ .../term_info/neuron_class_FBbt_00048999.json | 1263 +++++++ .../neuron_class_FBbt_00100243_MBON.json | 3003 +++++++++++++++++ .../split_individual_VFB_00070031.json | 249 ++ .../template_VFB_00101567_JRC2018U.json | 2676 +++++++++++++++ .../term_info/template_VFB_00200000.json | 1291 +++++++ 21 files changed, 19620 insertions(+) create mode 100644 scripts/capture_term_info_fixtures.py create mode 100644 src/test/fixtures/term_info/class_FBbt_00000058_related_individuals.json create mode 100644 src/test/fixtures/term_info/class_FBbt_00003686_kenyon.json create mode 100644 src/test/fixtures/term_info/class_FBbt_00003748_medulla.json create mode 100644 src/test/fixtures/term_info/class_FBbt_00048514_taste_mechanosensory.json create mode 100644 src/test/fixtures/term_info/class_FBbt_00048531.json create mode 100644 src/test/fixtures/term_info/dataset_Cachero2010.json create mode 100644 src/test/fixtures/term_info/dataset_Ito2013.json create mode 100644 src/test/fixtures/term_info/ep_class_VFBexp_FBtp0060056.json create mode 100644 src/test/fixtures/term_info/ep_individual_VFB_00020530.json create mode 100644 src/test/fixtures/term_info/gene_FBgn0010339_128up.json create mode 100644 src/test/fixtures/term_info/gene_FBgn0051882.json create mode 100644 src/test/fixtures/term_info/individual_VFB_00010001_fru.json create mode 100644 src/test/fixtures/term_info/individual_VFB_00101385_MEon.json create mode 100644 src/test/fixtures/term_info/license_CC_BY_NC_3_0.json create mode 100644 src/test/fixtures/term_info/neuron_class_FBbt_00047030_EPG.json create mode 100644 src/test/fixtures/term_info/neuron_class_FBbt_00048999.json create mode 100644 src/test/fixtures/term_info/neuron_class_FBbt_00100243_MBON.json create mode 100644 src/test/fixtures/term_info/split_individual_VFB_00070031.json create mode 100644 src/test/fixtures/term_info/template_VFB_00101567_JRC2018U.json create mode 100644 src/test/fixtures/term_info/template_VFB_00200000.json diff --git a/scripts/capture_term_info_fixtures.py b/scripts/capture_term_info_fixtures.py new file mode 100644 index 0000000..31ec203 --- /dev/null +++ b/scripts/capture_term_info_fixtures.py @@ -0,0 +1,156 @@ +#!/usr/bin/env python3 +"""Capture / refresh committed term_info render-test fixtures from live SOLR. + +The term_info serialization, parity and expression-pattern render tests split +into a **fixture** variant (PR-blocking, deterministic) and a ``_live`` / +``data_health`` variant (scheduled, live). The fixture variants read a committed +complete ``vfb_json`` term_info document out of ``src/test/fixtures/term_info/``. +This script (re)captures those documents so they stay regenerable rather than +hand-authored. See ``TESTING.md`` -> "Fixture vs live (data_health)". + +A fixture is the raw term_info dict as ``vfb_queries._load_term_info_dict`` +returns it — the exact shape every ``_load_fixture`` / ``_fixture_raw`` / +``_fixture_term_info`` helper consumes. + +Usage:: + + python scripts/capture_term_info_fixtures.py # capture all in FIXTURES + python scripts/capture_term_info_fixtures.py ... # only these fixtures + python scripts/capture_term_info_fixtures.py --check # verify, don't write + +``--check`` fetches each id and reports whether the live document looks complete +(non-empty label/title etc.), without writing — a quick way to see, before a +scheduled run does, which production ``vfb_json`` documents are currently thin. + +IMPORTANT: this reads live SOLR, so run it only when the backend is healthy, and +eyeball the diff before committing — a fixture captured during an outage or an +incomplete indexer run would bake the wrong "correct" answer into a PR gate. +Some documents (title-less pubs, split classes missing their ``Expression_pattern`` +type) are known-incomplete in production; those fixtures are hand-completed from +the PDB and are marked ``hand_edited`` below so this script leaves them alone +unless explicitly named. +""" +import argparse +import json +import os +import sys + +FIXTURE_DIR = os.path.join(os.path.dirname(__file__), "..", "src", "test", + "fixtures", "term_info") + +#: fixture file name (without .json) -> the term whose term_info it holds. +#: Keep in sync with the fixtures the render tests load. ``hand_edited`` fixtures +#: are completed from the PDB because production SOLR serves them incomplete; +#: this script skips them unless named explicitly (so a bulk recapture during an +#: outage cannot silently hollow them out). +FIXTURES = { + # pub / split — known-incomplete in production, completed from the PDB. + "pub_FBrf0243986": {"id": "FBrf0243986", "hand_edited": True}, + "pub_FBrf0242477": {"id": "FBrf0242477", "hand_edited": True}, + "split_VFBexp_FBtp0124468FBtp0133404": {"id": "VFBexp_FBtp0124468FBtp0133404", "hand_edited": True}, + "split_VFBexp_FBtp0129935FBtp0129968": {"id": "VFBexp_FBtp0129935FBtp0129968", "hand_edited": True}, + + # term_info_queries_test.py — serialization render tests. + "class_FBbt_00048514_taste_mechanosensory": {"id": "FBbt_00048514"}, + "individual_VFB_00010001_fru": {"id": "VFB_00010001"}, + "class_FBbt_00048531": {"id": "FBbt_00048531"}, + "neuron_class_FBbt_00048999": {"id": "FBbt_00048999"}, + "neuron_class_FBbt_00047030_EPG": {"id": "FBbt_00047030"}, + "dataset_Ito2013": {"id": "Ito2013"}, + "license_CC_BY_NC_3_0": {"id": "VFBlicense_CC_BY_NC_3_0"}, + "template_VFB_00200000": {"id": "VFB_00200000"}, + + # test_term_info_parity.py — parity / coverage render tests. + "class_FBbt_00003748_medulla": {"id": "FBbt_00003748"}, + "class_FBbt_00003686_kenyon": {"id": "FBbt_00003686"}, + "individual_VFB_00101385_MEon": {"id": "VFB_00101385"}, + "gene_FBgn0010339_128up": {"id": "FBgn0010339"}, + "gene_FBgn0051882": {"id": "FBgn0051882"}, + "class_FBbt_00000058_related_individuals": {"id": "FBbt_00000058"}, + "dataset_Cachero2010": {"id": "Cachero2010"}, + "template_VFB_00101567_JRC2018U": {"id": "VFB_00101567"}, + "neuron_class_FBbt_00100243_MBON": {"id": "FBbt_00100243"}, + + # test_expression_pattern_individual_queries.py — menu / stock render tests. + "ep_class_VFBexp_FBtp0060056": {"id": "VFBexp_FBtp0060056"}, + "ep_individual_VFB_00020530": {"id": "VFB_00020530"}, + "split_individual_VFB_00070031": {"id": "VFB_00070031"}, +} + + +def _load(short_form): + from vfbquery.vfb_queries import _load_term_info_dict + return _load_term_info_dict(short_form) + + +def _looks_complete(doc): + """Cheap completeness heuristic for --check: a real label, and for pubs a + non-empty title. Not exhaustive — the tests are the real check.""" + if not doc: + return False, "no term_info document" + core = (doc.get("term") or {}).get("core") or {} + label, sf = core.get("label") or "", core.get("short_form") or "" + if not label or label == sf: + return False, "label is empty or just the id" + if "pub" in (core.get("types") or []): + if not ((doc.get("pub_specific_content") or {}).get("title") or "").strip(): + return False, "pub has no title" + return True, "ok" + + +def capture(names, check): + os.makedirs(FIXTURE_DIR, exist_ok=True) + rc = 0 + for name in names: + entry = FIXTURES[name] + sf = entry["id"] + doc = _load(sf) + ok, why = _looks_complete(doc) + path = os.path.join(FIXTURE_DIR, name + ".json") + if check: + print(f"[{'ok' if ok else 'INCOMPLETE'}] {name} ({sf}): {why}") + if not ok: + rc = 1 + continue + if not ok: + print(f"SKIP {name} ({sf}): live document {why} — not overwriting. " + f"Recapture when the backend is healthy, or hand-complete it.") + rc = 1 + continue + with open(path, "w", encoding="utf-8") as f: + json.dump(doc, f, indent=1, ensure_ascii=False) + print(f"wrote {os.path.relpath(path)} ({sf})") + return rc + + +def main(): + ap = argparse.ArgumentParser(description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + ap.add_argument("names", nargs="*", help="fixture names to capture (default: all " + "non-hand-edited)") + ap.add_argument("--check", action="store_true", + help="report completeness of the live documents; do not write") + ap.add_argument("--include-hand-edited", action="store_true", + help="also (re)capture fixtures marked hand_edited — use only " + "when you intend to rebuild them from live data") + args = ap.parse_args() + + if args.names: + unknown = [n for n in args.names if n not in FIXTURES] + if unknown: + ap.error("unknown fixture name(s): %s\nknown: %s" + % (", ".join(unknown), ", ".join(sorted(FIXTURES)))) + names = args.names + else: + names = [n for n, e in FIXTURES.items() + if args.include_hand_edited or not e.get("hand_edited")] + if not names and not args.include_hand_edited: + print("All registered fixtures are hand_edited; nothing to capture " + "automatically. Pass names explicitly or --include-hand-edited.") + return 0 + + return capture(names, args.check) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/src/test/fixtures/term_info/class_FBbt_00000058_related_individuals.json b/src/test/fixtures/term_info/class_FBbt_00000058_related_individuals.json new file mode 100644 index 0000000..7709ffd --- /dev/null +++ b/src/test/fixtures/term_info/class_FBbt_00000058_related_individuals.json @@ -0,0 +1,55 @@ +{ + "term": { + "core": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00000058", + "symbol": "", + "types": [ + "Entity", + "Class", + "Deprecated" + ], + "short_form": "FBbt_00000058", + "unique_facets": [ + "Deprecated" + ], + "label": "obsolete vitellophage" + }, + "description": [], + "comment": [ + "This term was obsoleted because it is the same as 'yolk nucleus' - mc141031." + ] + }, + "query": "Get JSON for Class", + "version": "0dcd736", + "parents": [], + "relationships": [], + "related_individuals": [ + { + "relation": { + "iri": "http://purl.obolibrary.org/obo/IAO_0100001", + "database_cross_reference": [], + "label": "term replaced by", + "type": "term_replaced_by", + "confidence_value": "" + }, + "object": { + "symbol": "", + "iri": "http://purl.obolibrary.org/obo/FBbt_00000057", + "types": [ + "Entity", + "Class", + "Anatomy" + ], + "short_form": "FBbt_00000057", + "unique_facets": [ + "Anatomy" + ], + "label": "yolk nucleus" + } + } + ], + "xrefs": [], + "anatomy_channel_image": [], + "pub_syn": [], + "def_pubs": [] +} \ No newline at end of file diff --git a/src/test/fixtures/term_info/class_FBbt_00003686_kenyon.json b/src/test/fixtures/term_info/class_FBbt_00003686_kenyon.json new file mode 100644 index 0000000..175a1f3 --- /dev/null +++ b/src/test/fixtures/term_info/class_FBbt_00003686_kenyon.json @@ -0,0 +1,1431 @@ +{ + "term": { + "core": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00003686", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Anatomy", + "Cell", + "Nervous_system", + "has_subClass", + "lineage_MBp", + "hasScRNAseq" + ], + "short_form": "FBbt_00003686", + "unique_facets": [ + "Neuron", + "lineage_MBp" + ], + "label": "Kenyon cell" + }, + "description": [ + "Intrinsic neuron of the mushroom body. They have tightly-packed cell bodies, situated in the rind above the calyx of the mushroom body (Ito et al., 1997). Four short fascicles, one per lineage, extend from the cell bodies of the Kenyon cells into the calyx (Ito et al., 1997). These 4 smaller fascicles converge in the calyx where they arborize and form pre- and post-synaptic terminals (Christiansen et al., 2011), with different Kenyon cells receiving input in different calyx regions/accessory calyces (Tanaka et al., 2008). They emerge from the calyx as a thick axon bundle referred to as the peduncle that bifurcates to innervate the dorsal and medial lobes of the mushroom body (Tanaka et al., 2008)." + ], + "comment": [ + "Pre-synaptic terminals were identified using two presynaptic markers (Brp and Dsyd-1) and post-synaptic terminals by labelling a subunit of the acetylcholine receptor (Dalpha7) in genetically labelled Kenyon cells (Christiansen et al., 2011)." + ] + }, + "query": "Get JSON for Neuron Class", + "version": "0dcd736", + "parents": [ + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00007484", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Anatomy", + "Cell", + "Nervous_system", + "has_subClass", + "hasScRNAseq" + ], + "short_form": "FBbt_00007484", + "unique_facets": [ + "Nervous_system", + "Neuron" + ], + "label": "mushroom body intrinsic neuron" + }, + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00025991", + "symbol": "", + "types": [ + "Entity", + "Class", + "Anatomy", + "has_subClass" + ], + "short_form": "FBbt_00025991", + "unique_facets": [ + "Anatomy" + ], + "label": "anterior ectoderm derivative" + } + ], + "relationships": [ + { + "relation": { + "iri": "http://purl.obolibrary.org/obo/RO_0002202", + "database_cross_reference": [], + "label": "develops from", + "type": "develops_from", + "confidence_value": "" + }, + "object": { + "symbol": "", + "iri": "http://purl.obolibrary.org/obo/FBbt_00007113", + "types": [ + "Entity", + "Class", + "Anatomy", + "Cell", + "Nervous_system", + "Neuroblast", + "has_subClass", + "lineage_MBp" + ], + "short_form": "FBbt_00007113", + "unique_facets": [ + "Nervous_system", + "Neuroblast" + ], + "label": "neuroblast MBp" + } + }, + { + "relation": { + "iri": "http://purl.obolibrary.org/obo/RO_0002131", + "database_cross_reference": [], + "label": "overlaps", + "type": "overlaps", + "confidence_value": "" + }, + "object": { + "symbol": "", + "iri": "http://purl.obolibrary.org/obo/FBbt_00003687", + "types": [ + "Entity", + "Class", + "Anatomy", + "Nervous_system", + "Synaptic_neuropil", + "Synaptic_neuropil_domain", + "has_subClass" + ], + "short_form": "FBbt_00003687", + "unique_facets": [ + "Nervous_system", + "Synaptic_neuropil_domain" + ], + "label": "mushroom body pedunculus" + } + }, + { + "relation": { + "iri": "http://purl.obolibrary.org/obo/RO_0013002", + "database_cross_reference": [], + "label": "receives synaptic input in region", + "type": "receives_synaptic_input_in_region", + "confidence_value": "" + }, + "object": { + "symbol": "", + "iri": "http://purl.obolibrary.org/obo/FBbt_00003685", + "types": [ + "Entity", + "Class", + "Anatomy", + "Nervous_system", + "Synaptic_neuropil", + "Synaptic_neuropil_domain", + "has_subClass" + ], + "short_form": "FBbt_00003685", + "unique_facets": [ + "Nervous_system", + "Synaptic_neuropil_domain" + ], + "label": "mushroom body calyx" + } + } + ], + "related_individuals": [], + "xrefs": [], + "anatomy_channel_image": [ + { + "anatomy": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFB_001000q6", + "types": [ + "Entity", + "Individual", + "VFB", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Cholinergic", + "Nervous_system", + "has_image", + "lineage_MBp", + "has_neuron_connectivity", + "FAFB" + ], + "short_form": "VFB_001000q6", + "unique_facets": [ + "Adult", + "Cholinergic", + "lineage_MBp" + ], + "label": "KC#774-a'b' (FAFB:8956373)" + }, + "channel_image": { + "image": { + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/volume.nrrd", + "image_swc": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/volume.swc", + "template_channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel", + "Template" + ], + "short_form": "VFBc_00101567", + "unique_facets": [ + "Channel" + ], + "label": "JRC2018Unisex_c" + }, + "index": [], + "template_anatomy": { + "symbol": "JRC2018U", + "iri": "http://virtualflybrain.org/reports/VFB_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Template", + "has_image" + ], + "short_form": "VFB_00101567", + "unique_facets": [ + "Adult", + "Nervous_system" + ], + "label": "JRC2018Unisex" + }, + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/volume_man.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/thumbnail.png", + "image_folder": "http://www.virtualflybrain.org/data/VFB/i/0010/00q6/VFB_00101567/" + }, + "channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_001000q6", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel" + ], + "short_form": "VFBc_001000q6", + "unique_facets": [ + "Channel" + ], + "label": "KC#774-a\\'b\\'_c" + }, + "imaging_technique": { + "symbol": "TEM", + "iri": "http://purl.obolibrary.org/obo/FBbi_00000258", + "types": [ + "Entity", + "Class", + "has_subClass" + ], + "short_form": "FBbi_00000258", + "unique_facets": [ + "Class" + ], + "label": "transmission electron microscopy (TEM)" + } + } + }, + { + "anatomy": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFB_001000q2", + "types": [ + "Entity", + "Individual", + "VFB", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Cholinergic", + "Nervous_system", + "has_image", + "lineage_MBp", + "has_neuron_connectivity", + "FAFB" + ], + "short_form": "VFB_001000q2", + "unique_facets": [ + "Adult", + "Cholinergic", + "lineage_MBp" + ], + "label": "KC#770-a'b' (FAFB:8940379)" + }, + "channel_image": { + "image": { + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/volume.nrrd", + "image_swc": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/volume.swc", + "template_channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel", + "Template" + ], + "short_form": "VFBc_00101567", + "unique_facets": [ + "Channel" + ], + "label": "JRC2018Unisex_c" + }, + "index": [], + "template_anatomy": { + "symbol": "JRC2018U", + "iri": "http://virtualflybrain.org/reports/VFB_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Template", + "has_image" + ], + "short_form": "VFB_00101567", + "unique_facets": [ + "Adult", + "Nervous_system" + ], + "label": "JRC2018Unisex" + }, + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/volume_man.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/thumbnail.png", + "image_folder": "http://www.virtualflybrain.org/data/VFB/i/0010/00q2/VFB_00101567/" + }, + "channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_001000q2", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel" + ], + "short_form": "VFBc_001000q2", + "unique_facets": [ + "Channel" + ], + "label": "KC#770-a\\'b\\'_c" + }, + "imaging_technique": { + "symbol": "TEM", + "iri": "http://purl.obolibrary.org/obo/FBbi_00000258", + "types": [ + "Entity", + "Class", + "has_subClass" + ], + "short_form": "FBbi_00000258", + "unique_facets": [ + "Class" + ], + "label": "transmission electron microscopy (TEM)" + } + } + }, + { + "anatomy": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFB_001000ru", + "types": [ + "Entity", + "Individual", + "VFB", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Cholinergic", + "Nervous_system", + "has_image", + "lineage_MBp", + "has_neuron_connectivity", + "FAFB" + ], + "short_form": "VFB_001000ru", + "unique_facets": [ + "Adult", + 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Biol. 116: 247--271" + }, + "FlyBase": "FBrf0231227", + "PubMed": "26970623", + "DOI": "10.1016/bs.ctdb.2015.11.032" + } + ] +} \ No newline at end of file diff --git a/src/test/fixtures/term_info/class_FBbt_00048514_taste_mechanosensory.json b/src/test/fixtures/term_info/class_FBbt_00048514_taste_mechanosensory.json new file mode 100644 index 0000000..f6ef4ca --- /dev/null +++ b/src/test/fixtures/term_info/class_FBbt_00048514_taste_mechanosensory.json @@ -0,0 +1,1603 @@ +{ + "term": { + "core": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00048514", + "symbol": "BM-Taste", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Mechanosensory_system", + "Nervous_system", + "Sensory_neuron" + ], + "short_form": "FBbt_00048514", + "unique_facets": [ + "Adult", + "Mechanosensory_system", + "Nervous_system", + "Sensory_neuron" + ], + "label": "labellar taste bristle mechanosensory neuron" + }, + "description": [ + "Mechanosensory neuron that extends its sensory dendrite into a single labellar taste bristle and has its soma with the gustatory receptor neurons and support cells of the same bristle (Montell, 2021). It follows the labial nerve and joins the maxillary-labial nerve to enter the brain, terminating in the subesophageal zone (Eichler et al., 2024). There is one of these per labellar taste bristle (around 30-40 per side) (Eichler et al., 2024)." + ], + "comment": [ + "Distinct from the md-L neuron." + ] + }, + "query": "Get JSON for Neuron Class", + "version": "0dcd736", + "parents": [ + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00053588", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Mechanosensory_system", + "Nervous_system", + "Sensory_neuron", + "has_subClass" + ], + "short_form": "FBbt_00053588", + "unique_facets": [ + "Adult", + "Mechanosensory_system", + "Nervous_system", + "Sensory_neuron" + ], + "label": "mechanosensory neuron of labellum" + }, + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00052184", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Mechanosensory_system", + "Nervous_system", + "Sensory_neuron", + "has_subClass" + ], + "short_form": "FBbt_00052184", + "unique_facets": [ + "Adult", + 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/dev/null +++ b/src/test/fixtures/term_info/license_CC_BY_NC_3_0.json @@ -0,0 +1,22 @@ +{ + "term": { + "core": { + "symbol": "CC_BY_NC", + "iri": "http://virtualflybrain.org/reports/VFBlicense_CC_BY_NC_3_0", + "types": [ + "Entity", + "Individual", + "License" + ], + "short_form": "VFBlicense_CC_BY_NC_3_0", + "unique_facets": [], + "label": "CC-BY-NC_3.0" + }, + "link": "https://creativecommons.org/licenses/by-nc/3.0/legalcode", + "icon": "http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc.png", + "description": [], + "comment": [] + }, + "query": "Get JSON for License", + "version": "0dcd736" +} \ No newline at end of file diff --git a/src/test/fixtures/term_info/neuron_class_FBbt_00047030_EPG.json b/src/test/fixtures/term_info/neuron_class_FBbt_00047030_EPG.json new file mode 100644 index 0000000..b47e4c8 --- /dev/null +++ b/src/test/fixtures/term_info/neuron_class_FBbt_00047030_EPG.json @@ -0,0 +1,1984 @@ +{ + "term": { + "core": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00047030", + "symbol": "EPG", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Cholinergic", + "Nervous_system", + "has_subClass", + "secondary_neuron" + ], + "short_form": "FBbt_00047030", + "unique_facets": [ + "Adult", + "Cholinergic", + "Nervous_system", + "secondary_neuron" + ], + "label": "adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron" + }, + "description": [ + "Small field neuron of the central complex with dendritic and axonal arbors in the inner, outer and posterior layers of either a half or a full ellipsoid body (EB) slice (wedge), and axon terminals in the dorsal or ventral gall and a single protocerebral bridge glomerulus (excluding glomerulus 9) (Lin et al., 2013; Wolff et al., 2015). Neurons that target odd or even numbered protocerebral bridge glomeruli target the dorsal or ventral gall, respectively (Lin et al., 2013; Wolff et al., 2015). These neurons receive inhibitory input from delta 7 (PB 18 glomeruli) neurons and they are cholinergic (Turner-Evans et al., 2020). These cells output to P-EN1 neurons and P-EG neurons of the same glomerulus in the protocerebral bridge, and form less specific 'hyper-local' feedback loops with P-EN1 neurons in the EB (Turner-Evans et al., 2020). It also receives input from R4d ring neurons and P-EN2 neurons in the EB (Turner-Evans et al., 2020)." + ], + "comment": [ + "Based on images/diagrams in Lin et al. (2013), Wolff et al. (2015) and Turner-Evans et al. (2020), these appear to innervate the ipsilateral PB and contralateral gall, but could not find confirmation of this - https://orcid.org/0000-0002-1373-1705." + ] + }, + "query": "Get JSON for Neuron Class", + "version": "0dcd736", + "parents": [ + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00003637", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Nervous_system", + "has_subClass", + "secondary_neuron" + ], + "short_form": "FBbt_00003637", + "unique_facets": [ + "Adult", + "Nervous_system", + "secondary_neuron" + ], + "label": "adult ellipsoid body-protocerebral bridge-gall neuron" + }, + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00058205", + "symbol": "", + "types": [ + "Entity", + "Class", + "Neuron", + "Adult", + "Anatomy", + "Cell", + "Cholinergic", + "Nervous_system", + "has_subClass", + "hasScRNAseq" + ], + "short_form": "FBbt_00058205", + "unique_facets": [ + "Adult", + "Cholinergic", + "Nervous_system" + ], + 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It develops from a larval mushroom body input neuron of the CP3 (DL2) lineage (Truman et al., 2023). The cell body fiber runs anteriormedially and diverges above the ellipsoid body (Tanaka et al., 2008). Its dendrite forms four main arbors, in the superior intermediate protocerebrum, superior medial protocerebrum, dorsal crepine and ventral crepine (Otto et al., 2020). Another fiber turns ventromedially and projects to the opposite hemisphere (Tanaka et al., 2008; Li et al., 2020). A third fiber (axonal) turns ventrolaterally, runs in front of the anterior surface of the gamma lobe and then below the gamma lobe, and arborizes in the spur of the gamma lobe (slice 1) and inner core of the pedunculus (Tanaka et al., 2008; Li et al., 2020; Otto et al., 2020). The contralateral fiber innervates the same mushroom body regions (Li et al., 2020). There are 1-2 neurons of this type per hemisphere (Aso et al., 2014; Li et al., 2020; Otto et al., 2020; Truman et al., 2023). It is involved in food odor attraction (Sayin et al., 2019)." + ], + "comment": [ + "Names are assigned according to the area of the mushroom body they arborize, as detailed in Tanaka et al. (2008). The PPL1 cluster was identified by TH immunostaining and using a TH-GAL4 driver (FBtp0020119) (Liu et al., 2012). 1-2 per hemisphere in Aso et al. (2014), 1 in FAFB, 2 (each with different larval precursor cell) in Truman et al. 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"Nervous_system", + "Neuron_projection_bundle" + ], + "short_form": "FBbt_00047543", + "unique_facets": [ + "Adult", + "Nervous_system", + "Neuron_projection_bundle" + ], + "label": "ventral lateral tract of ventral cervical fasciculus" + }, + "center": [], + "anatomical_individual": { + "iri": "http://virtualflybrain.org/reports/VFB_00104637", + "symbol": "", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Neuron_projection_bundle", + "has_image" + ], + "short_form": "VFB_00104637", + "unique_facets": [ + "Adult", + "Nervous_system", + "Neuron_projection_bundle" + ], + "label": "ventral lateral tract on adult VNC, JRC2018VU" + }, + "index": [ + 5 + ], + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0010/4637/VFB_00200000/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0010/4637/VFB_00200000/volume_man.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0010/4637/VFB_00200000/thumbnail.png" + }, + { + "folder": "http://www.virtualflybrain.org/data/VFB/i/0010/4648/VFB_00200000/", + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0010/4648/VFB_00200000/volume.nrrd", + "image_swc": "", + "anatomical_type": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00110175", + "symbol": "", + "types": [ + "Entity", + "Class", + "Adult", + "Anatomy", + "Nervous_system", + "Neuromere" + ], + "short_form": "FBbt_00110175", + "unique_facets": [ + "Adult", + "Nervous_system", + "Neuromere" + ], + "label": "adult mesothoracic neuromere" + }, + "center": [], + "anatomical_individual": { + "iri": "http://virtualflybrain.org/reports/VFB_00104648", + "symbol": "", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Neuromere", + "has_image" + ], + "short_form": "VFB_00104648", + "unique_facets": [ + "Adult", + "Nervous_system", + "Neuromere" + ], + "label": "adult mesothoracic neuromere on adult VNC, JRC2018VU" + }, + "index": [ + 16 + ], + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0010/4648/VFB_00200000/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0010/4648/VFB_00200000/volume_man.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0010/4648/VFB_00200000/thumbnail.png" + }, + { + "folder": "http://www.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/", + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.nrrd", + "image_swc": "", + "anatomical_type": { + "iri": "http://purl.obolibrary.org/obo/FBbt_00004052", + "symbol": "", + "types": [ + "Entity", + "Class", + "Adult", + "Anatomy", + "Ganglion", + "Nervous_system" + ], + "short_form": "FBbt_00004052", + "unique_facets": [ + "Adult", + "Ganglion", + "Nervous_system" + ], + "label": "adult ventral nerve cord" + }, + "center": [ + "{\"X\":330,\"Y\":645,\"Z\":191}" + ], + "anatomical_individual": { + "iri": "http://virtualflybrain.org/reports/VFB_00200000", + "symbol": "JRCVNC2018U", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Ganglion", + "Nervous_system", + "Template", + "has_image" + ], + "short_form": "VFB_00200000", + "unique_facets": [ + "Adult", + "Ganglion", + "Nervous_system" + ], + "label": "JRC2018UnisexVNC" + }, + "index": [ + 0 + ], + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/volume_man.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0020/0000/VFB_00200000/thumbnail.png" + } + ], + "dataset_license": [ + { + "license": { + "core": { + "iri": "http://virtualflybrain.org/reports/VFBlicense_CC_BY_NC_SA_4_0", + "symbol": "CC-BY-NC-SA", + "types": [ + "Entity", + "Individual", + "License" + ], + "short_form": "VFBlicense_CC_BY_NC_SA_4_0", + "unique_facets": [ + "License" + ], + "label": "CC-BY-NC-SA_4.0" + }, + "icon": "http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc-sa.png", + "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode" + }, + "dataset": { + "core": { + "iri": "http://virtualflybrain.org/reports/JRC2018", + "symbol": "", + "types": [ + "Entity", + "Individual", + "DataSet", + "Adult", + "has_image" + ], + "short_form": "JRC2018", + "unique_facets": [ + "DataSet" + ], + "label": "JRC 2018 templates & ROIs" + }, + "link": "" + } + } + ], + "parents": [ + { + "iri": "http://purl.obolibrary.org/obo/FBbt_00004052", + "symbol": "", + "types": [ + "Entity", + "Class", + "Adult", + "Anatomy", + "Ganglion", + "Nervous_system" + ], + "short_form": "FBbt_00004052", + "unique_facets": [ + "Adult", + "Ganglion", + "Nervous_system" + ], + "label": "adult ventral nerve cord" + } + ], + "relationships": [], + "xrefs": [], + "related_individuals": [] +} \ No newline at end of file From e7ae7a04f12dc690499038a3e8afad9e6b4d2fe8 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 15 Sep 2026 10:40:51 +0100 Subject: [PATCH 2/4] clarify related_individuals --- src/test/test_term_info_parity.py | 11 +++++++++-- src/vfbquery/term_info_queries.py | 8 ++++++++ src/vfbquery/vfb_queries.py | 15 ++++++++++++--- 3 files changed, 29 insertions(+), 5 deletions(-) diff --git a/src/test/test_term_info_parity.py b/src/test/test_term_info_parity.py index 9d8293b..b3dd07c 100644 --- a/src/test/test_term_info_parity.py +++ b/src/test/test_term_info_parity.py @@ -128,11 +128,18 @@ def test_gene_xref_flybase(self): self.assertIn("flybase.org/reports/FBgn0051882", links, "gene FlyBase xref missing") # --- Coverage: related_individuals ------------------------------------- + # NB `related_individuals` is a MISNOMER: it is populated only from the + # `term_replaced_by` edge, so it is really the replacement pointer of a + # *deprecated* term (target is usually a Class, not an Individual). A + # deprecated term is therefore REQUIRED to exercise this path — hence the + # obsolete FBbt_00000058, which was replaced by FBbt_00000057. See the + # field/render notes in term_info_queries.py / vfb_queries.py. Do not "fix" + # this to a current term: it would render nothing and the test would break. def test_related_individuals_surface(self): - ti = self._parse("FBbt_00000058") # FBbt class carrying related_individuals + ti = self._parse("FBbt_00000058") # obsolete term; replaced_by -> FBbt_00000057 ri = ti.get("Meta", {}).get("RelatedIndividuals", "") self.assertTrue(ri, "related_individuals dropped") - self.assertIn("FBbt_00000057", ri, "related individual target id missing") + self.assertIn("FBbt_00000057", ri, "term_replaced_by target id missing") # --- Coverage: DataSet external link ----------------------------------- def test_dataset_link_present(self): diff --git a/src/vfbquery/term_info_queries.py b/src/vfbquery/term_info_queries.py index 32a31b8..a4e255e 100644 --- a/src/vfbquery/term_info_queries.py +++ b/src/vfbquery/term_info_queries.py @@ -525,6 +525,14 @@ class VfbTerminfo: license: Optional[List[License]] = None dataset_license: Optional[List[DatasetLicense]] = None relationships: Optional[List[Rel]] = None + #: MISNOMER: despite the name, this does NOT hold related individuals. The + #: term_info queries (VFB_connect's VFB_TermInfo_queries.json, for Individual, + #: Class and Neuron Class alike) populate it from exactly one edge — + #: ``(o)<-[r:term_replaced_by]-(primary)`` — so it carries the + #: *term-replacement pointer of a deprecated term*, and ``o`` is whatever + #: replaced it (typically a Class, not an Individual). It is therefore + #: non-empty only for deprecated/obsolete terms. Kept under this name to match + #: the upstream field; see the render site in vfb_queries.py. related_individuals: Optional[List[Rel]] = None parents: Optional[List[MinimalEntityInfo]] = None channel_image: Optional[List[ChannelImage]] = None diff --git a/src/vfbquery/vfb_queries.py b/src/vfbquery/vfb_queries.py index 1482fc1..86f059c 100644 --- a/src/vfbquery/vfb_queries.py +++ b/src/vfbquery/vfb_queries.py @@ -1751,9 +1751,18 @@ def term_info_parse_object(results, short_form): if xrefs_out: termInfo["Xrefs"] = xrefs_out - # Related individuals — same Rel shape as relationships, rendered as its - # own panel section (VFBProcessTermInfoCachedJson.java:1529). Kept as a - # Meta string so it travels with the other Meta rows. + # "Related individuals" — same Rel shape as relationships, rendered as + # its own panel section (VFBProcessTermInfoCachedJson.java:1529). Kept as + # a Meta string so it travels with the other Meta rows. + # + # NAME IS A MISNOMER (do not be misled): the term_info queries populate + # `related_individuals` solely from the `term_replaced_by` edge, so it is + # the *replacement pointer of a deprecated term* — non-empty only for + # obsolete terms, and pointing at the replacement term (usually a Class, + # not an Individual). It is NOT a list of related instances. See the + # field definition in term_info_queries.py and the query + # `(o)<-[r:term_replaced_by]-(primary)` in VFB_connect's + # VFB_TermInfo_queries.json. if getattr(vfbTerm, 'related_individuals', None): grouped_ri = {} for rel in vfbTerm.related_individuals: From cdd600edea094e3b67a7f64bf41931a7e4acf24e Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 15 Sep 2026 11:44:23 +0100 Subject: [PATCH 3/4] split tests to PR (fixtures) vs scheduled (live) --- scripts/capture_term_info_fixtures.py | 1 + .../split_individual_VFB_00069525.json | 297 ++++++++++++++++++ src/test/term_info_queries_test.py | 122 +++++-- ...t_expression_pattern_individual_queries.py | 63 +++- src/test/test_term_info_parity.py | 168 +++++++++- 5 files changed, 602 insertions(+), 49 deletions(-) create mode 100644 src/test/fixtures/term_info/split_individual_VFB_00069525.json diff --git a/scripts/capture_term_info_fixtures.py b/scripts/capture_term_info_fixtures.py index 31ec203..24fffc6 100644 --- a/scripts/capture_term_info_fixtures.py +++ b/scripts/capture_term_info_fixtures.py @@ -75,6 +75,7 @@ "ep_class_VFBexp_FBtp0060056": {"id": "VFBexp_FBtp0060056"}, "ep_individual_VFB_00020530": {"id": "VFB_00020530"}, "split_individual_VFB_00070031": {"id": "VFB_00070031"}, + "split_individual_VFB_00069525": {"id": "VFB_00069525"}, } diff --git a/src/test/fixtures/term_info/split_individual_VFB_00069525.json b/src/test/fixtures/term_info/split_individual_VFB_00069525.json new file mode 100644 index 0000000..8acc7e4 --- /dev/null +++ b/src/test/fixtures/term_info/split_individual_VFB_00069525.json @@ -0,0 +1,297 @@ +{ + "term": { + "core": { + "iri": "http://virtualflybrain.org/reports/VFB_00069525", + "symbol": "SS00810", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Expression_pattern", + "Split", + "has_image", + "NBLASTexp" + ], + "short_form": "VFB_00069525", + "unique_facets": [ + "Split" + ], + "label": "JRC_SS00810 in the Adult Brain" + }, + "description": [], + "comment": [] + }, + "query": "Get JSON for Individual", + "version": "0dcd736", + "dataset_license": [ + { + "license": { + "core": { + "iri": "http://virtualflybrain.org/reports/VFBlicense_CC_BY_4_0", + "symbol": "CC_BY", + "types": [ + "Entity", + "Individual", + "License" + ], + "short_form": "VFBlicense_CC_BY_4_0", + "unique_facets": [ + "License" + ], + "label": "CC-BY_4.0" + }, + "icon": "http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by.png", + "link": "https://creativecommons.org/licenses/by/4.0/legalcode" + }, + "dataset": { + "core": { + "iri": "http://virtualflybrain.org/reports/Klapoetke2017", + "symbol": "", + "types": [ + "Entity", + "Individual", + "DataSet", + "Adult", + "Expression_pattern", + "Split", + "has_image", + "NBLASTexp" + ], + "short_form": "Klapoetke2017", + "unique_facets": [ + "DataSet", + "Split" + ], + "label": "Split-GAL4 lines from Klapoetke et al. 2017" + }, + "link": "" + } + } + ], + "parents": [ + { + "iri": "http://virtualflybrain.org/reports/VFBexp_FBtp0122003FBtp0118528", + "symbol": "SS00810", + "types": [ + "Entity", + "Class", + "Anatomy", + "Expression_pattern", + "Split" + ], + "short_form": "VFBexp_FBtp0122003FBtp0118528", + "unique_facets": [ + "Split" + ], + "label": "P{R55H05-GAL4.DBD} ∩ P{R28D05-p65.AD} expression pattern" + } + ], + "relationships": [], + "related_individuals": [], + "xrefs": [ + { + "link_base": "http://splitgal4.janelia.org/cgi-bin/view_splitgal4_imagery.cgi?line=", + "site": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/FlyLightSplit", + "types": [ + "Entity", + "Individual", + "Site" + ], + "short_form": "FlyLightSplit", + "unique_facets": [ + "Site" + ], + "label": "Driver Line on the FlyLight Split-GAL4 Site" + }, + "is_data_source": true, + "link_postfix": "", + "icon": "http://www.virtualflybrain.org/data/VFB/logos/fly_light_color.png", + "accession": "SS00810", + "link_text": "JRC_SS00810 in the Adult Brain on Driver Line on the FlyLight Split-GAL4 Site", + "homepage": "http://splitgal4.janelia.org/cgi-bin/splitgal4.cgi" + }, + { + "link_base": "https://neuronbridge.janelia.org/search?q=", + "site": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/neuronbridge", + "types": [ + "Entity", + "Individual", + "Site" + ], + "short_form": "neuronbridge", + "unique_facets": [ + "Site" + ], + "label": "neuronbridge" + }, + "is_data_source": false, + "link_postfix": "", + "icon": "http://www.virtualflybrain.org/data/VFB/logos/neuronbridge.png", + "accession": "SS00810", + "link_text": "JRC_SS00810 in the Adult Brain on neuronbridge", + "homepage": "https://neuronbridge.janelia.org/" + } + ], + "channel_image": [ + { + "image": { + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00017894/volume.nrrd", + "image_swc": "", + "template_channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00017894", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel", + "Template" + ], + "short_form": "VFBc_00017894", + "unique_facets": [ + "Channel" + ], + "label": "JFRC2_template_c" + }, + "index": [], + "template_anatomy": { + "symbol": "JFRC2", + "iri": "http://virtualflybrain.org/reports/VFB_00017894", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Template", + "has_image" + ], + "short_form": "VFB_00017894", + "unique_facets": [ + "Adult", + "Nervous_system" + ], + "label": "adult brain template JFRC2" + }, + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00017894/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00017894/volume.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00017894/thumbnail.png", + "image_folder": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00017894/" + }, + "channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00069525", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel" + ], + "short_form": "VFBc_00069525", + "unique_facets": [ + "Channel" + ], + "label": "JRC_SS00810 in the Adult Brain_c" + }, + "imaging_technique": { + "symbol": "Confocal", + "iri": "http://purl.obolibrary.org/obo/FBbi_00000251", + "types": [ + "Entity", + "Class", + "has_subClass" + ], + "short_form": "FBbi_00000251", + "unique_facets": [ + "Class" + ], + "label": "confocal microscopy" + } + }, + { + "image": { + "image_nrrd": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00101567/volume.nrrd", + "image_swc": "", + "template_channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel", + "Template" + ], + "short_form": "VFBc_00101567", + "unique_facets": [ + "Channel" + ], + "label": "JRC2018Unisex_c" + }, + "index": [], + "template_anatomy": { + "symbol": "JRC2018U", + "iri": "http://virtualflybrain.org/reports/VFB_00101567", + "types": [ + "Entity", + "Individual", + "VFB", + "Adult", + "Anatomy", + "Nervous_system", + "Template", + "has_image" + ], + "short_form": "VFB_00101567", + "unique_facets": [ + "Adult", + "Nervous_system" + ], + "label": "JRC2018Unisex" + }, + "image_wlz": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00101567/volume.wlz", + "image_obj": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00101567/volume.obj", + "image_thumbnail": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00101567/thumbnail.png", + "image_folder": "http://www.virtualflybrain.org/data/VFB/i/0006/9525/VFB_00101567/" + }, + "channel": { + "symbol": "", + "iri": "http://virtualflybrain.org/reports/VFBc_00069525", + "types": [ + "Entity", + "Individual", + "VFB", + "Channel" + ], + "short_form": "VFBc_00069525", + "unique_facets": [ + "Channel" + ], + "label": "JRC_SS00810 in the Adult Brain_c" + }, + "imaging_technique": { + "symbol": "Confocal", + "iri": "http://purl.obolibrary.org/obo/FBbi_00000251", + "types": [ + "Entity", + "Class", + "has_subClass" + ], + "short_form": "FBbi_00000251", + "unique_facets": [ + "Class" + ], + "label": "confocal microscopy" + } + } + ], + "pub_syn": [], + "def_pubs": [] +} \ No newline at end of file diff --git a/src/test/term_info_queries_test.py b/src/test/term_info_queries_test.py index 8ffc070..4cca5a3 100644 --- a/src/test/term_info_queries_test.py +++ b/src/test/term_info_queries_test.py @@ -95,12 +95,19 @@ def test_term_info_deserialization(self): self.assertEqual("", terminfo.pub_syn[0].pub.PubMed) def test_term_info_deserialization_from_dict(self): - import pkg_resources - print("vfb_connect version:", pkg_resources.get_distribution("vfb_connect").version) - vfbTerm = self.get_term_info_or_skip('FBbt_00048514') - start_time = time.time() + """Render code (PR-blocking): deserialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_deserialization_from_dict( + _load_fixture("class_FBbt_00048514_taste_mechanosensory")) + + @pytest.mark.data_health + def test_term_info_deserialization_from_dict_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_deserialization_from_dict( + self.get_term_info_or_skip('FBbt_00048514')) + + def _check_deserialization_from_dict(self, vfbTerm): terminfo = deserialize_term_info_from_dict(vfbTerm) - print("--- %s seconds ---" % (time.time() - start_time)) # print("vfbTerm:", vfbTerm) # print("terminfo:", terminfo) # Add debug for unique_facets @@ -141,11 +148,19 @@ def test_term_info_deserialization_from_dict(self): self.assertEqual("33657409", labellar_hmsn_entry.pub.PubMed) def test_term_info_serialization_individual_anatomy(self): - term_info_dict = self.get_term_info_or_skip('VFB_00010001') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_individual_anatomy( + _load_fixture("individual_VFB_00010001_fru")) + + @pytest.mark.data_health + def test_term_info_serialization_individual_anatomy_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_individual_anatomy( + self.get_term_info_or_skip('VFB_00010001')) + + def _check_serialization_individual_anatomy(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("fru-F-500075 [VFB_00010001]", serialized["label"]) self.assertFalse("title" in serialized) @@ -190,11 +205,17 @@ def test_term_info_serialization_individual_anatomy(self): 'reference': '[VFB_00017894,VFB_00010001]'} in serialized["thumbnail"]) def test_term_info_serialization_class(self): - term_info_dict = self.get_term_info_or_skip('FBbt_00048531') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_class(_load_fixture("class_FBbt_00048531")) + + @pytest.mark.data_health + def test_term_info_serialization_class_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_class(self.get_term_info_or_skip('FBbt_00048531')) + + def _check_serialization_class(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("female germline 2-cell cyst [FBbt_00048531]", serialized["label"]) self.assertFalse("title" in serialized) @@ -236,11 +257,19 @@ def test_term_info_serialization_class(self): self.assertFalse("downloads_label" in serialized) def test_term_info_serialization_neuron_class(self): - term_info_dict = self.get_term_info_or_skip('FBbt_00048999') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_neuron_class( + _load_fixture("neuron_class_FBbt_00048999")) + + @pytest.mark.data_health + def test_term_info_serialization_neuron_class_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_neuron_class( + self.get_term_info_or_skip('FBbt_00048999')) + + def _check_serialization_neuron_class(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("adult Drosulfakinin neuron [FBbt_00048999]", serialized["label"]) self.assertFalse("title" in serialized) @@ -294,11 +323,19 @@ def test_term_info_serialization_neuron_class(self): self.assertFalse("template" in serialized) def test_term_info_serialization_neuron_class2(self): - term_info_dict = self.get_term_info_or_skip('FBbt_00047030') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_neuron_class2( + _load_fixture("neuron_class_FBbt_00047030_EPG")) + + @pytest.mark.data_health + def test_term_info_serialization_neuron_class2_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_neuron_class2( + self.get_term_info_or_skip('FBbt_00047030')) + + def _check_serialization_neuron_class2(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("adult ellipsoid body-protocerebral bridge 1 glomerulus-dorsal/ventral gall neuron [FBbt_00047030]", serialized["label"]) self.assertFalse("title" in serialized) @@ -431,11 +468,17 @@ def test_term_info_serialization_split_class_live(self): self.assertFalse("template" in serialized) def test_term_info_serialization_dataset(self): - term_info_dict = self.get_term_info_or_skip('Ito2013') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_dataset(_load_fixture("dataset_Ito2013")) + + @pytest.mark.data_health + def test_term_info_serialization_dataset_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_dataset(self.get_term_info_or_skip('Ito2013')) + + def _check_serialization_dataset(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("Ito lab adult brain lineage clone image set [Ito2013]", serialized["label"]) self.assertFalse("title" in serialized) @@ -473,11 +516,18 @@ def test_term_info_serialization_dataset(self): self.assertTrue("clone of Ito 2013" in sample_example["name"]) def test_term_info_serialization_license(self): - term_info_dict = self.get_term_info_or_skip('VFBlicense_CC_BY_NC_3_0') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_license(_load_fixture("license_CC_BY_NC_3_0")) + + @pytest.mark.data_health + def test_term_info_serialization_license_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_license( + self.get_term_info_or_skip('VFBlicense_CC_BY_NC_3_0')) + + def _check_serialization_license(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("CC-BY-NC_3.0 [VFBlicense_CC_BY_NC_3_0]", serialized["label"]) self.assertFalse("title" in serialized) @@ -508,11 +558,17 @@ def test_term_info_serialization_license(self): self.assertFalse("template" in serialized) def test_term_info_serialization_template(self): - term_info_dict = self.get_term_info_or_skip('VFB_00200000') - print(term_info_dict) - start_time = time.time() + """Render code (PR-blocking): serialize a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_serialization_template(_load_fixture("template_VFB_00200000")) + + @pytest.mark.data_health + def test_term_info_serialization_template_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_serialization_template(self.get_term_info_or_skip('VFB_00200000')) + + def _check_serialization_template(self, term_info_dict): serialized = process(term_info_dict, self.variable) - print("--- %s seconds ---" % (time.time() - start_time)) self.assertEqual("JRC2018UnisexVNC [VFB_00200000]", serialized["label"]) self.assertFalse("title" in serialized) diff --git a/src/test/test_expression_pattern_individual_queries.py b/src/test/test_expression_pattern_individual_queries.py index c553721..def192e 100644 --- a/src/test/test_expression_pattern_individual_queries.py +++ b/src/test/test_expression_pattern_individual_queries.py @@ -81,10 +81,29 @@ def _anchors_or_skip(self, short_form): return _stock_anchors(ti) def test_class_stock_query_on_driver_feature(self): + """Render code (PR-blocking): FindStocks anchors on the EP class's own + `expresses` feature, from a complete fixture. See TESTING.md + 'Fixture vs live (data_health)'.""" + self.assertEqual( + _stock_anchors(_fixture_term_info("ep_class_VFBexp_FBtp0060056")), + ["FBtp0060056"]) + + @pytest.mark.data_health + def test_class_stock_query_on_driver_feature_live(self): + """Data-health (scheduled only): the same against live SOLR.""" self.assertEqual(self._anchors_or_skip(self.EP_CLASS), ["FBtp0060056"]) def test_instance_stock_query_matches_its_driver(self): # Regular EP image carries its own `expresses` edge — same feature as the class. + """Render code (PR-blocking): the EP image's own `expresses` edge yields + the same FindStocks feature as its class. See TESTING.md.""" + self.assertEqual( + _stock_anchors(_fixture_term_info("ep_individual_VFB_00020530")), + ["FBtp0060056"]) + + @pytest.mark.data_health + def test_instance_stock_query_matches_its_driver_live(self): + """Data-health (scheduled only): the same against live SOLR.""" self.assertEqual(self._anchors_or_skip(self.EP_INDIVIDUAL), ["FBtp0060056"]) def test_split_class_offers_a_stock_query_per_hemidriver(self): @@ -104,8 +123,13 @@ def test_split_class_offers_a_stock_query_per_hemidriver_live(self): self.assertEqual(self._anchors_or_skip(self.SPLIT_CLASS), ["FBtp0129935", "FBtp0129968"]) + @pytest.mark.data_health def test_split_instance_inherits_hemidriver_stock_queries(self): - # No own driver edge: features come from the pattern class it instantiates. + # No own driver edge: the features come from the pattern class it + # instantiates, which `_stock_features_via_parent_pattern` fetches with a + # LIVE `_load_term_info(parent)` call. A fixture for the individual alone + # cannot make this hermetic (the parent lookup still hits SOLR), so this + # stays a live (data_health) test rather than a PR-blocking fixture one. self.assertEqual(self._anchors_or_skip(self.SPLIT_INDIVIDUAL), ["FBtp0129935", "FBtp0129968"]) @@ -115,11 +139,17 @@ class TestExpressionPatternIndividualQueries(unittest.TestCase): EP_INDIVIDUAL = "VFB_00020530" # R40G10 in the adult brain (confocal) EP_CLASS = "VFBexp_FBtp0060056" # P{GMR40G10-GAL4} expression pattern + IND_FIXTURE = "ep_individual_VFB_00020530" + CLS_FIXTURE = "ep_class_VFBexp_FBtp0060056" @classmethod def setUpClass(cls): - cls.ind = get_term_info(cls.EP_INDIVIDUAL, preview=False) - cls.cls = get_term_info(cls.EP_CLASS, preview=False) + # Fixture-backed (PR-blocking, deterministic): every assertion below reads + # only the parsed term_info menu, so these run against committed fixtures + # rather than live SOLR. The live docs are re-checked on the schedule by + # test_menus_live (data_health). See TESTING.md 'Fixture vs live'. + cls.ind = _fixture_term_info(cls.IND_FIXTURE) + cls.cls = _fixture_term_info(cls.CLS_FIXTURE) def test_is_expression_pattern_individual(self): if not self.ind: @@ -174,16 +204,43 @@ def test_no_query_is_anchored_on_the_individual(self): self.assertNotEqual(anchor, self.EP_INDIVIDUAL, f"{qid} should not run on the individual") + @pytest.mark.data_health + def test_menus_live(self): + """Data-health (scheduled only): the live EP class/instance documents still + produce the inherited menu the fixtures encode — catches drift in the + built vfb_json. Deselected on PRs via ``-m 'not data_health'``.""" + ind = get_term_info(self.EP_INDIVIDUAL, preview=False) + cls = get_term_info(self.EP_CLASS, preview=False) + self.assertTrue(ind and cls, "live EP term_info unavailable") + class_menu, ind_menu = _menu(cls), _menu(ind) + self.assertFalse(set(class_menu) - set(ind_menu), + "instance is missing class queries (live)") + for qid in ("AnatomyExpressedIn", "epFrag", "ListAllAvailableImages"): + self.assertIn(qid, ind_menu, f"expected {qid} on the live EP instance") + class TestSplitIndividualQueries(unittest.TestCase): """A confocal split-GAL4 image was also missed by the technique gate.""" SPLIT_INDIVIDUAL = "VFB_00069525" # JRC_SS00810 in the Adult Brain + SPLIT_FIXTURE = "split_individual_VFB_00069525" + def test_split_individual_inherits_ep_queries(self): + """Render code (PR-blocking): the split image's inherited menu, from a + complete fixture. See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_split_individual_inherits_ep_queries( + _fixture_term_info(self.SPLIT_FIXTURE)) + + @pytest.mark.data_health + def test_split_individual_inherits_ep_queries_live(self): + """Data-health (scheduled only): the same against live SOLR.""" ind = get_term_info(self.SPLIT_INDIVIDUAL, preview=False) if not ind: self.skipTest("term_info unavailable (no live VFB backend)") + self._check_split_individual_inherits_ep_queries(ind) + + def _check_split_individual_inherits_ep_queries(self, ind): self.assertTrue(ind.get("IsIndividual")) self.assertIn("Split", ind.get("SuperTypes", [])) ind_menu = _menu(ind) diff --git a/src/test/test_term_info_parity.py b/src/test/test_term_info_parity.py index b3dd07c..02541b2 100644 --- a/src/test/test_term_info_parity.py +++ b/src/test/test_term_info_parity.py @@ -63,31 +63,81 @@ def _parse(self, short_form): self.assertIsNotNone(ti, f"parse returned None for {short_form}") return ti + def _parse_fixture(self, name): + """Parse a committed complete fixture through the render code — the + deterministic, PR-blocking counterpart of :meth:`_parse`. See TESTING.md + 'Fixture vs live (data_health)'.""" + results = _fixture_raw(name) + sf = json.loads(results.docs[0]["term_info"][0])["term"]["core"]["short_form"] + ti = q.term_info_parse_object(results, sf) + self.assertIsNotNone(ti, f"parse returned None for fixture {name}") + return ti + # --- Gap A: class definition references (def_pubs) -> inline in description # The legacy panel appends def_pubs as microref links to the definition # (VFBProcessTermInfoCachedJson.java:937), so parity is an inline render in # Meta.Description, not a separate Publications entry. def test_class_def_pubs_inline_in_description(self): - ti = self._parse("FBbt_00003748") # medulla + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_class_def_pubs_inline_in_description( + self._parse_fixture("class_FBbt_00003748_medulla")) + + @pytest.mark.data_health + def test_class_def_pubs_inline_in_description_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_class_def_pubs_inline_in_description(self._parse("FBbt_00003748")) + + def _check_class_def_pubs_inline_in_description(self, ti): desc = ti.get("Meta", {}).get("Description", "") self.assertIn("FBrf0231227", desc, "def_pub FBrf0231227 missing from description") self.assertIn("FBrf0224194", desc, "def_pub FBrf0224194 missing from description") def test_kenyon_def_pubs_all_inline(self): - ti = self._parse("FBbt_00003686") # Kenyon cell + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_kenyon_def_pubs_all_inline( + self._parse_fixture("class_FBbt_00003686_kenyon")) + + @pytest.mark.data_health + def test_kenyon_def_pubs_all_inline_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_kenyon_def_pubs_all_inline(self._parse("FBbt_00003686")) + + def _check_kenyon_def_pubs_all_inline(self, ti): desc = ti.get("Meta", {}).get("Description", "") for ref in ("FBrf0092568", "FBrf0214059", "FBrf0205263"): self.assertIn(ref, desc, f"def_pub {ref} missing from description") # --- Gap B: Individual synonyms (pub_syn) -> Synonyms ------------------- def test_individual_synonyms_present(self): - ti = self._parse("VFB_00101385") # individual image (MEon) + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_individual_synonyms_present( + self._parse_fixture("individual_VFB_00101385_MEon")) + + @pytest.mark.data_health + def test_individual_synonyms_present_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_individual_synonyms_present(self._parse("VFB_00101385")) + + def _check_individual_synonyms_present(self, ti): labels = {s.get("label") for s in ti.get("Synonyms", [])} self.assertIn("MEon JRC_FlyEM_Hemibrain", labels, "Individual pub_syn dropped from Synonyms") def test_class_synonyms_not_regressed(self): - ti = self._parse("FBgn0010339") # gene 128up: 7 synonyms + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_class_synonyms_not_regressed( + self._parse_fixture("gene_FBgn0010339_128up")) + + @pytest.mark.data_health + def test_class_synonyms_not_regressed_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_class_synonyms_not_regressed(self._parse("FBgn0010339")) + + def _check_class_synonyms_not_regressed(self, ti): self.assertGreaterEqual(len(ti.get("Synonyms", [])), 7, "class synonyms regressed") @@ -115,7 +165,17 @@ def _check_pub_external_content(self, ti): # --- Coverage: external xref links (genes, anatomy) -------------------- def test_xrefs_surface_as_links(self): - ti = self._parse("FBbt_00003748") # medulla -> Insect Brain DB + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_xrefs_surface_as_links( + self._parse_fixture("class_FBbt_00003748_medulla")) + + @pytest.mark.data_health + def test_xrefs_surface_as_links_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_xrefs_surface_as_links(self._parse("FBbt_00003748")) + + def _check_xrefs_surface_as_links(self, ti): xr = ti.get("Xrefs") or [] self.assertTrue(xr, "Xrefs dropped for medulla") ibdb = [x for x in xr if x.get("label") == "Insect Brain DB"] @@ -123,7 +183,16 @@ def test_xrefs_surface_as_links(self): self.assertIn("insectbraindb.org/app/structures/38", ibdb[0].get("link", "")) def test_gene_xref_flybase(self): - ti = self._parse("FBgn0051882") # a gene with a FlyBase xref + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_gene_xref_flybase(self._parse_fixture("gene_FBgn0051882")) + + @pytest.mark.data_health + def test_gene_xref_flybase_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_gene_xref_flybase(self._parse("FBgn0051882")) + + def _check_gene_xref_flybase(self, ti): links = " ".join(x.get("link", "") for x in (ti.get("Xrefs") or [])) self.assertIn("flybase.org/reports/FBgn0051882", links, "gene FlyBase xref missing") @@ -136,25 +205,65 @@ def test_gene_xref_flybase(self): # field/render notes in term_info_queries.py / vfb_queries.py. Do not "fix" # this to a current term: it would render nothing and the test would break. def test_related_individuals_surface(self): - ti = self._parse("FBbt_00000058") # obsolete term; replaced_by -> FBbt_00000057 + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_related_individuals_surface( + self._parse_fixture("class_FBbt_00000058_related_individuals")) + + @pytest.mark.data_health + def test_related_individuals_surface_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_related_individuals_surface(self._parse("FBbt_00000058")) + + def _check_related_individuals_surface(self, ti): ri = ti.get("Meta", {}).get("RelatedIndividuals", "") self.assertTrue(ri, "related_individuals dropped") self.assertIn("FBbt_00000057", ri, "term_replaced_by target id missing") # --- Coverage: DataSet external link ----------------------------------- def test_dataset_link_present(self): - ti = self._parse("Ito2013") + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_dataset_link_present(self._parse_fixture("dataset_Ito2013")) + + @pytest.mark.data_health + def test_dataset_link_present_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_dataset_link_present(self._parse("Ito2013")) + + def _check_dataset_link_present(self, ti): link = ti.get("Meta", {}).get("Link", "") self.assertIn("flybase.org/reports/FBrf0221438", link, "DataSet link dropped") # --- Targeting queries (splits<->neurons) as live query types ---------- def test_neuron_class_offers_splits_targeting(self): - ti = self._parse("FBbt_00100243") # MBON neuron class with split drivers + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_neuron_class_offers_splits_targeting( + self._parse_fixture("neuron_class_FBbt_00100243_MBON")) + + @pytest.mark.data_health + def test_neuron_class_offers_splits_targeting_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_neuron_class_offers_splits_targeting(self._parse("FBbt_00100243")) + + def _check_neuron_class_offers_splits_targeting(self, ti): self.assertTrue(any(x.get("query") == "SplitsTargeting" for x in ti.get("Queries", [])), "SplitsTargeting not offered on neuron class") def test_split_class_offers_target_neurons(self): - ti = self._parse("VFBexp_FBtp0129935FBtp0129968") # a split class + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_split_class_offers_target_neurons( + self._parse_fixture("split_VFBexp_FBtp0129935FBtp0129968")) + + @pytest.mark.data_health + def test_split_class_offers_target_neurons_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_split_class_offers_target_neurons( + self._parse("VFBexp_FBtp0129935FBtp0129968")) + + def _check_split_class_offers_target_neurons(self, ti): self.assertTrue(any(x.get("query") == "TargetNeurons" for x in ti.get("Queries", [])), "TargetNeurons not offered on split class") @@ -193,7 +302,17 @@ def test_license_term_info_does_not_5xx(self): # serialiser only read `dataset_license`, so every dataset page rendered # without a License row even though the edge was in the KB. def test_dataset_own_license_reaches_licenses(self): - ti = self._parse("Cachero2010") + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_dataset_own_license_reaches_licenses( + self._parse_fixture("dataset_Cachero2010")) + + @pytest.mark.data_health + def test_dataset_own_license_reaches_licenses_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_dataset_own_license_reaches_licenses(self._parse("Cachero2010")) + + def _check_dataset_own_license_reaches_licenses(self, ti): licenses = ti.get("Licenses", {}) self.assertTrue(licenses, "DataSet own licence dropped from Licenses{}") lic = licenses[0] @@ -203,16 +322,39 @@ def test_dataset_own_license_reaches_licenses(self): self.assertTrue(lic.get("iri"), "licence iri missing") def test_dataset_own_license_has_no_self_source(self): + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_dataset_own_license_has_no_self_source( + self._parse_fixture("dataset_Cachero2010")) + + @pytest.mark.data_health + def test_dataset_own_license_has_no_self_source_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_dataset_own_license_has_no_self_source(self._parse("Cachero2010")) + + def _check_dataset_own_license_has_no_self_source(self, ti): # The dataset is its own source, so leave source empty rather than # rendering a Source row that links back to the same page. - lic = self._parse("Cachero2010").get("Licenses", {})[0] + lic = ti.get("Licenses", {})[0] self.assertEqual("", lic.get("source", "")) self.assertEqual("", lic.get("source_iri", "")) def test_dataset_license_still_attributes_source_on_images(self): + """Render code (PR-blocking): assert against a complete fixture, deterministically. + See TESTING.md 'Fixture vs live (data_health)'.""" + self._check_dataset_license_still_attributes_source_on_images( + self._parse_fixture("template_VFB_00101567_JRC2018U")) + + @pytest.mark.data_health + def test_dataset_license_still_attributes_source_on_images_live(self): + """Data-health (scheduled only): the same assertions against live SOLR.""" + self._check_dataset_license_still_attributes_source_on_images( + self._parse("VFB_00101567")) + + def _check_dataset_license_still_attributes_source_on_images(self, ti): # The dataset_license path is unchanged: an image/template still gets # its licence via the dataset it came from, with that dataset as source. - licenses = self._parse("VFB_00101567").get("Licenses", {}) + licenses = ti.get("Licenses", {}) self.assertTrue(licenses, "template lost its inherited licence") self.assertTrue(licenses[0].get("source"), "inherited licence lost its source") From 8574ebd5571d180be3b1e143e15b13161a412043 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 15 Sep 2026 12:25:37 +0100 Subject: [PATCH 4/4] rename testing workflows --- .github/workflows/python-test.yml | 4 ++-- .github/workflows/test-lint.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 44a461d..42fa76e 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -1,4 +1,4 @@ -name: Python Package using Conda +name: Tests on: push: @@ -27,7 +27,7 @@ permissions: checks: write # a neutral (grey) "Backend coverage" check when skipped jobs: - notebooks: + tests: name: "Run Tests" runs-on: ubuntu-latest steps: diff --git a/.github/workflows/test-lint.yml b/.github/workflows/test-lint.yml index 0bf2146..fc741b2 100644 --- a/.github/workflows/test-lint.yml +++ b/.github/workflows/test-lint.yml @@ -1,4 +1,4 @@ -name: Test Lint +name: Lint tests # Fast, static check that a PR doesn't introduce the silently-passing test # anti-patterns documented in TESTING.md (empty-suppressing guards, stale keys,