vfbquery 0.3.3__tar.gz → 0.4.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (27) hide show
  1. {vfbquery-0.3.3 → vfbquery-0.4.0}/PKG-INFO +39 -40
  2. {vfbquery-0.3.3 → vfbquery-0.4.0}/README.md +39 -40
  3. {vfbquery-0.3.3 → vfbquery-0.4.0}/setup.py +1 -1
  4. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/test/term_info_queries_test.py +64 -9
  5. vfbquery-0.4.0/src/test/test_default_caching.py +173 -0
  6. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/test/test_examples_diff.py +6 -1
  7. vfbquery-0.4.0/src/vfbquery/__init__.py +65 -0
  8. vfbquery-0.4.0/src/vfbquery/cache_enhancements.py +465 -0
  9. vfbquery-0.4.0/src/vfbquery/cached_functions.py +227 -0
  10. vfbquery-0.4.0/src/vfbquery/solr_cache_integration.py +212 -0
  11. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery/solr_fetcher.py +47 -3
  12. vfbquery-0.4.0/src/vfbquery/solr_result_cache.py +613 -0
  13. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery/term_info_queries.py +18 -2
  14. vfbquery-0.4.0/src/vfbquery/test_utils.py +146 -0
  15. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery/vfb_queries.py +325 -54
  16. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery.egg-info/PKG-INFO +39 -40
  17. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery.egg-info/SOURCES.txt +5 -0
  18. vfbquery-0.3.3/src/vfbquery/__init__.py +0 -4
  19. vfbquery-0.3.3/src/vfbquery/test_utils.py +0 -39
  20. {vfbquery-0.3.3 → vfbquery-0.4.0}/LICENSE +0 -0
  21. {vfbquery-0.3.3 → vfbquery-0.4.0}/pyproject.toml +0 -0
  22. {vfbquery-0.3.3 → vfbquery-0.4.0}/setup.cfg +0 -0
  23. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/test/__init__.py +0 -0
  24. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/test/readme_parser.py +0 -0
  25. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery.egg-info/dependency_links.txt +0 -0
  26. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery.egg-info/requires.txt +0 -0
  27. {vfbquery-0.3.3 → vfbquery-0.4.0}/src/vfbquery.egg-info/top_level.txt +0 -0
{vfbquery-0.3.3 → vfbquery-0.4.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: vfbquery
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- Version: 0.3.3
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+ Version: 0.4.0
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  Summary: Wrapper for querying VirtualFlyBrain knowledge graph.
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  Home-page: https://github.com/VirtualFlyBrain/VFBquery
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  Author: VirtualFlyBrain
@@ -53,7 +53,7 @@ vfb.get_term_info('FBbt_00003748')
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  "Meta": {
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  "Name": "[medulla](FBbt_00003748)",
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  "Description": "The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).",
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- "Comment": "",
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+ "Comment": "Nern et al. (2025) - doi:10.1038/s41586-025-08746-0 say distal is M1-5 and M6-7 is central medulla.",
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  "Types": "[anterior ectoderm derivative](FBbt_00025991); [synaptic neuropil domain](FBbt_00040007)",
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  "Relationships": "[develops from](RO_0002202): [medulla anlage](FBbt_00001935); [is part of](BFO_0000050): [adult optic lobe](FBbt_00003701)"
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  },
@@ -117,25 +117,25 @@ vfb.get_term_info('FBbt_00003748')
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  "id": "VFB_00102107",
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  "label": "[ME on JRC2018Unisex adult brain](VFB_00102107)",
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  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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- "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018U')](VFB_00101567,VFB_00102107)"
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+ "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018Unisex](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018Unisex')](VFB_00101567,VFB_00102107)"
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  },
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  {
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  "id": "VFB_00101385",
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  "label": "[ME%28R%29 on JRC_FlyEM_Hemibrain](VFB_00101385)",
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  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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- "thumbnail": "[![ME%28R%29 on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum')](VFB_00101384,VFB_00101385)"
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+ "thumbnail": "[![ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain')](VFB_00101384,VFB_00101385)"
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  },
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  {
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  "id": "VFB_00030810",
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  "label": "[medulla on adult brain template Ito2014](VFB_00030810)",
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- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
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+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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  "thumbnail": "[![medulla on adult brain template Ito2014 aligned to adult brain template Ito2014](http://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png 'medulla on adult brain template Ito2014 aligned to adult brain template Ito2014')](VFB_00030786,VFB_00030810)"
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  },
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  {
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  "id": "VFB_00030624",
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  "label": "[medulla on adult brain template JFRC2](VFB_00030624)",
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- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
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- "thumbnail": "[![medulla on adult brain template JFRC2 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to JFRC2')](VFB_00017894,VFB_00030624)"
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+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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+ "thumbnail": "[![medulla on adult brain template JFRC2 aligned to adult brain template JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to adult brain template JFRC2')](VFB_00017894,VFB_00030624)"
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  }
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  ]
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  },
@@ -143,20 +143,9 @@ vfb.get_term_info('FBbt_00003748')
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  "count": 4
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  }
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  ],
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- "IsIndividual": False,
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- "IsClass": True,
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+ "IsIndividual": false,
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+ "IsClass": true,
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  "Examples": {
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- "VFB_00017894": [
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- {
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- "id": "VFB_00030624",
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- "label": "medulla on adult brain template JFRC2",
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- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
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- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
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- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
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- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
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- "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
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- }
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- ],
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  "VFB_00101384": [
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  {
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  "id": "VFB_00101385",
@@ -179,6 +168,17 @@ vfb.get_term_info('FBbt_00003748')
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  "obj": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/volume_man.obj"
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  }
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  ],
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+ "VFB_00017894": [
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+ {
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+ "id": "VFB_00030624",
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+ "label": "medulla on adult brain template JFRC2",
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+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
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+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
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+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
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+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
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+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
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+ }
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+ ],
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  "VFB_00030786": [
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  {
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  "id": "VFB_00030810",
@@ -191,7 +191,7 @@ vfb.get_term_info('FBbt_00003748')
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  }
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  ]
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  },
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- "IsTemplate": False,
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+ "IsTemplate": false,
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  "Synonyms": [
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  {
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  "label": "ME",
@@ -323,14 +323,14 @@ vfb.get_term_info('VFB_00000001')
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  "score": "0.61",
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  "name": "[fru-M-000204](VFB_00000333)",
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  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
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- "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00101567/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
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+ "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00017894/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
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  },
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  {
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  "id": "VFB_00000333",
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  "score": "0.61",
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  "name": "[fru-M-000204](VFB_00000333)",
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  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
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- "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00017894/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
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+ "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00101567/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
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  },
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  {
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  "id": "VFB_00002439",
@@ -347,32 +347,20 @@ vfb.get_term_info('VFB_00000001')
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  "thumbnail": "[![fru-M-900020 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00017894/thumbnail.png 'fru-M-900020 aligned to JFRC2')](VFB_00017894,VFB_00002439)"
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  },
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  {
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- "id": "VFB_00001880",
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+ "id": "VFB_00000845",
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  "score": "0.59",
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- "name": "[fru-M-100041](VFB_00001880)",
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+ "name": "[fru-M-100191](VFB_00000845)",
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  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
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- "thumbnail": "[![fru-M-100041 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/1880/VFB_00101567/thumbnail.png 'fru-M-100041 aligned to JRC2018U')](VFB_00101567,VFB_00001880)"
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+ "thumbnail": "[![fru-M-100191 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0845/VFB_00101567/thumbnail.png 'fru-M-100191 aligned to JRC2018U')](VFB_00101567,VFB_00000845)"
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  }
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  ]
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  },
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  "output_format": "table",
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- "count": 44
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+ "count": 60
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  }
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  ],
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  "IsIndividual": True,
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  "Images": {
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- "VFB_00101567": [
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- {
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- "id": "VFB_00000001",
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- "label": "fru-M-200266",
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- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
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- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
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- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
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- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
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- "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
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- "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
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- }
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- ],
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  "VFB_00017894": [
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  {
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  "id": "VFB_00000001",
@@ -384,6 +372,18 @@ vfb.get_term_info('VFB_00000001')
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  "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.obj",
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  "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.swc"
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  }
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+ ],
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+ "VFB_00101567": [
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+ {
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+ "id": "VFB_00000001",
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+ "label": "fru-M-200266",
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+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
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+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
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+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
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+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
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+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
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+ "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
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+ }
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  ]
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  },
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  "IsClass": False,
@@ -405,7 +405,6 @@ Template example:
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  ```python
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  vfb.get_term_info('VFB_00101567')
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  ```
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-
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  ```json
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  {
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  "Name": "JRC2018U",
{vfbquery-0.3.3 → vfbquery-0.4.0}/README.md RENAMED
@@ -33,7 +33,7 @@ vfb.get_term_info('FBbt_00003748')
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  "Meta": {
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  "Name": "[medulla](FBbt_00003748)",
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  "Description": "The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).",
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- "Comment": "",
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+ "Comment": "Nern et al. (2025) - doi:10.1038/s41586-025-08746-0 say distal is M1-5 and M6-7 is central medulla.",
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  "Types": "[anterior ectoderm derivative](FBbt_00025991); [synaptic neuropil domain](FBbt_00040007)",
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  "Relationships": "[develops from](RO_0002202): [medulla anlage](FBbt_00001935); [is part of](BFO_0000050): [adult optic lobe](FBbt_00003701)"
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  },
@@ -97,25 +97,25 @@ vfb.get_term_info('FBbt_00003748')
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  "id": "VFB_00102107",
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  "label": "[ME on JRC2018Unisex adult brain](VFB_00102107)",
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  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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- "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018U')](VFB_00101567,VFB_00102107)"
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+ "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018Unisex](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018Unisex')](VFB_00101567,VFB_00102107)"
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  },
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  {
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  "id": "VFB_00101385",
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  "label": "[ME%28R%29 on JRC_FlyEM_Hemibrain](VFB_00101385)",
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  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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- "thumbnail": "[![ME%28R%29 on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum')](VFB_00101384,VFB_00101385)"
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+ "thumbnail": "[![ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain')](VFB_00101384,VFB_00101385)"
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  },
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  {
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  "id": "VFB_00030810",
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  "label": "[medulla on adult brain template Ito2014](VFB_00030810)",
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- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
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+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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  "thumbnail": "[![medulla on adult brain template Ito2014 aligned to adult brain template Ito2014](http://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png 'medulla on adult brain template Ito2014 aligned to adult brain template Ito2014')](VFB_00030786,VFB_00030810)"
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  },
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  {
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  "id": "VFB_00030624",
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  "label": "[medulla on adult brain template JFRC2](VFB_00030624)",
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- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
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- "thumbnail": "[![medulla on adult brain template JFRC2 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to JFRC2')](VFB_00017894,VFB_00030624)"
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+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
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+ "thumbnail": "[![medulla on adult brain template JFRC2 aligned to adult brain template JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to adult brain template JFRC2')](VFB_00017894,VFB_00030624)"
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  }
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  ]
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  },
@@ -123,20 +123,9 @@ vfb.get_term_info('FBbt_00003748')
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  "count": 4
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  }
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  ],
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- "IsIndividual": False,
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- "IsClass": True,
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+ "IsIndividual": false,
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+ "IsClass": true,
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  "Examples": {
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- "VFB_00017894": [
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- {
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- "id": "VFB_00030624",
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- "label": "medulla on adult brain template JFRC2",
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- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
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- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
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- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
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- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
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- "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
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- }
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- ],
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  "VFB_00101384": [
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  {
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  "id": "VFB_00101385",
@@ -159,6 +148,17 @@ vfb.get_term_info('FBbt_00003748')
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  "obj": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/volume_man.obj"
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  }
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  ],
151
+ "VFB_00017894": [
152
+ {
153
+ "id": "VFB_00030624",
154
+ "label": "medulla on adult brain template JFRC2",
155
+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
156
+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
157
+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
158
+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
159
+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
160
+ }
161
+ ],
162
162
  "VFB_00030786": [
163
163
  {
164
164
  "id": "VFB_00030810",
@@ -171,7 +171,7 @@ vfb.get_term_info('FBbt_00003748')
171
171
  }
172
172
  ]
173
173
  },
174
- "IsTemplate": False,
174
+ "IsTemplate": false,
175
175
  "Synonyms": [
176
176
  {
177
177
  "label": "ME",
@@ -303,14 +303,14 @@ vfb.get_term_info('VFB_00000001')
303
303
  "score": "0.61",
304
304
  "name": "[fru-M-000204](VFB_00000333)",
305
305
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
306
- "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00101567/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
306
+ "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00017894/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
307
307
  },
308
308
  {
309
309
  "id": "VFB_00000333",
310
310
  "score": "0.61",
311
311
  "name": "[fru-M-000204](VFB_00000333)",
312
312
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
313
- "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00017894/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
313
+ "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00101567/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
314
314
  },
315
315
  {
316
316
  "id": "VFB_00002439",
@@ -327,32 +327,20 @@ vfb.get_term_info('VFB_00000001')
327
327
  "thumbnail": "[![fru-M-900020 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00017894/thumbnail.png 'fru-M-900020 aligned to JFRC2')](VFB_00017894,VFB_00002439)"
328
328
  },
329
329
  {
330
- "id": "VFB_00001880",
330
+ "id": "VFB_00000845",
331
331
  "score": "0.59",
332
- "name": "[fru-M-100041](VFB_00001880)",
332
+ "name": "[fru-M-100191](VFB_00000845)",
333
333
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
334
- "thumbnail": "[![fru-M-100041 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/1880/VFB_00101567/thumbnail.png 'fru-M-100041 aligned to JRC2018U')](VFB_00101567,VFB_00001880)"
334
+ "thumbnail": "[![fru-M-100191 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0845/VFB_00101567/thumbnail.png 'fru-M-100191 aligned to JRC2018U')](VFB_00101567,VFB_00000845)"
335
335
  }
336
336
  ]
337
337
  },
338
338
  "output_format": "table",
339
- "count": 44
339
+ "count": 60
340
340
  }
341
341
  ],
342
342
  "IsIndividual": True,
343
343
  "Images": {
344
- "VFB_00101567": [
345
- {
346
- "id": "VFB_00000001",
347
- "label": "fru-M-200266",
348
- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
349
- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
350
- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
351
- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
352
- "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
353
- "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
354
- }
355
- ],
356
344
  "VFB_00017894": [
357
345
  {
358
346
  "id": "VFB_00000001",
@@ -364,6 +352,18 @@ vfb.get_term_info('VFB_00000001')
364
352
  "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.obj",
365
353
  "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.swc"
366
354
  }
355
+ ],
356
+ "VFB_00101567": [
357
+ {
358
+ "id": "VFB_00000001",
359
+ "label": "fru-M-200266",
360
+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
361
+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
362
+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
363
+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
364
+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
365
+ "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
366
+ }
367
367
  ]
368
368
  },
369
369
  "IsClass": False,
@@ -385,7 +385,6 @@ Template example:
385
385
  ```python
386
386
  vfb.get_term_info('VFB_00101567')
387
387
  ```
388
-
389
388
  ```json
390
389
  {
391
390
  "Name": "JRC2018U",
@@ -1293,4 +1292,4 @@ vfb.get_templates(return_dataframe=False)
1293
1292
  ],
1294
1293
  "count": 10
1295
1294
  }
1296
- ```
1295
+ ```
{vfbquery-0.3.3 → vfbquery-0.4.0}/setup.py RENAMED
@@ -3,7 +3,7 @@ from os import path
3
3
 
4
4
  here = path.abspath(path.dirname(__file__))
5
5
 
6
- __version__ = "0.3.3"
6
+ __version__ = "0.4.0"
7
7
 
8
8
  # Get the long description from the README file
9
9
  with open(path.join(here, 'README.md')) as f:
{vfbquery-0.3.3 → vfbquery-0.4.0}/src/test/term_info_queries_test.py RENAMED
@@ -64,7 +64,7 @@ class TermInfoQueriesTest(unittest.TestCase):
64
64
 
65
65
  self.assertEqual(0, len(terminfo.xrefs))
66
66
 
67
- self.assertEqual(6, len(terminfo.pub_syn))
67
+ self.assertEqual(7, len(terminfo.pub_syn))
68
68
 
69
69
  # Check that we have the expected synonym labels (order-independent)
70
70
  synonym_labels = [entry.synonym.label for entry in terminfo.pub_syn]
@@ -145,7 +145,7 @@ class TermInfoQueriesTest(unittest.TestCase):
145
145
  self.assertFalse("link" in serialized)
146
146
  self.assertEqual(4, len(serialized["types"]))
147
147
  self.assertTrue("Anatomy" in serialized["types"])
148
- self.assertEqual("Cyst composed of two cyst cells following the division of a newly-formed cystoblast in the germarium. The two cells are connected by a cytoplasmic bridge.\n([Spradling, 1993](FBrf0064777), [King, 1970](FBrf0021038))", serialized["description"])
148
+ self.assertEqual("Cyst composed of two cyst cells following the division of a newly-formed cystoblast in the germarium. The two cells are connected by a cytoplasmic bridge.\n([King, 1970](FBrf0021038))", serialized["description"])
149
149
  self.assertTrue("synonyms" in serialized)
150
150
  self.assertEqual(1, len(serialized["synonyms"]))
151
151
  self.assertEqual("has_exact_synonym: germarial 2-cell cluster ([King, 1970](FBrf0021038))", serialized["synonyms"][0])
@@ -166,13 +166,10 @@ class TermInfoQueriesTest(unittest.TestCase):
166
166
  self.assertFalse("examples" in serialized)
167
167
  self.assertFalse("thumbnail" in serialized)
168
168
  self.assertTrue("references" in serialized)
169
- self.assertEqual(2, len(serialized["references"]))
170
- self.assertEqual({'link': '[Spradling, 1993, Bate, Martinez Arias, 1993: 1--70](FBrf0064777)',
171
- 'refs': ['http://flybase.org/reports/FBrf0064777'],
172
- 'types': ' pub'}, serialized["references"][0])
169
+ self.assertEqual(1, len(serialized["references"]))
173
170
  self.assertEqual({'link': '[King, 1970, Ovarian Development in Drosophila melanogaster. ](FBrf0021038)',
174
171
  'refs': ['http://flybase.org/reports/FBrf0021038'],
175
- 'types': ' pub'}, serialized["references"][1])
172
+ 'types': ' pub'}, serialized["references"][0])
176
173
  self.assertFalse("targetingSplits" in serialized)
177
174
  self.assertFalse("targetingNeurons" in serialized)
178
175
 
@@ -261,7 +258,7 @@ class TermInfoQueriesTest(unittest.TestCase):
261
258
  self.assertTrue("Turner-Evans et al., 2020" in description)
262
259
 
263
260
  self.assertTrue("synonyms" in serialized)
264
- self.assertEqual(9, len(serialized["synonyms"]))
261
+ self.assertEqual(10, len(serialized["synonyms"]))
265
262
  print(serialized["synonyms"][0])
266
263
  self.assertTrue("has_exact_synonym: EB-PB 1 glomerulus-D/Vgall neuron" in serialized["synonyms"])
267
264
  self.assertFalse("source" in serialized)
@@ -293,7 +290,7 @@ class TermInfoQueriesTest(unittest.TestCase):
293
290
  self.assertFalse("thumbnail" in serialized)
294
291
 
295
292
  self.assertTrue("references" in serialized)
296
- self.assertEqual(6, len(serialized["references"]))
293
+ self.assertEqual(7, len(serialized["references"]))
297
294
 
298
295
  self.assertTrue("targetingSplits" in serialized)
299
296
  self.assertEqual(6, len(serialized["targetingSplits"]))
@@ -527,6 +524,64 @@ class TermInfoQueriesTest(unittest.TestCase):
527
524
  self.assertFalse("filemeta" in serialized)
528
525
  self.assertFalse("template" in serialized)
529
526
 
527
+ def test_term_info_performance(self):
528
+ """
529
+ Performance test for specific term info queries.
530
+ Tests the execution time for FBbt_00003748 and VFB_00101567.
531
+ """
532
+ import vfbquery as vfb
533
+
534
+ # Test performance for FBbt_00003748 (mushroom body)
535
+ start_time = time.time()
536
+ result_1 = vfb.get_term_info('FBbt_00003748')
537
+ duration_1 = time.time() - start_time
538
+
539
+ # Test performance for VFB_00101567 (individual anatomy)
540
+ start_time = time.time()
541
+ result_2 = vfb.get_term_info('VFB_00101567')
542
+ duration_2 = time.time() - start_time
543
+
544
+ # Print performance metrics for GitHub Actions logs
545
+ print(f"\n" + "="*50)
546
+ print(f"Performance Test Results:")
547
+ print(f"="*50)
548
+ print(f"FBbt_00003748 query took: {duration_1:.4f} seconds")
549
+ print(f"VFB_00101567 query took: {duration_2:.4f} seconds")
550
+ print(f"Total time for both queries: {duration_1 + duration_2:.4f} seconds")
551
+
552
+ # Performance categories
553
+ total_time = duration_1 + duration_2
554
+ if total_time < 1.0:
555
+ performance_level = "🟢 Excellent (< 1 second)"
556
+ elif total_time < 2.0:
557
+ performance_level = "🟡 Good (1-2 seconds)"
558
+ elif total_time < 4.0:
559
+ performance_level = "🟠 Acceptable (2-4 seconds)"
560
+ else:
561
+ performance_level = "🔴 Slow (> 4 seconds)"
562
+
563
+ print(f"Performance Level: {performance_level}")
564
+ print(f"="*50)
565
+
566
+ # Basic assertions to ensure the queries succeeded
567
+ self.assertIsNotNone(result_1, "FBbt_00003748 query returned None")
568
+ self.assertIsNotNone(result_2, "VFB_00101567 query returned None")
569
+
570
+ # Performance assertions - fail if queries take too long
571
+ # These thresholds are based on observed performance characteristics
572
+ max_single_query_time = 2.0 # seconds
573
+ max_total_time = 4.0 # seconds (2 queries * 2 seconds each)
574
+
575
+ self.assertLess(duration_1, max_single_query_time,
576
+ f"FBbt_00003748 query took {duration_1:.4f}s, exceeding {max_single_query_time}s threshold")
577
+ self.assertLess(duration_2, max_single_query_time,
578
+ f"VFB_00101567 query took {duration_2:.4f}s, exceeding {max_single_query_time}s threshold")
579
+ self.assertLess(duration_1 + duration_2, max_total_time,
580
+ f"Total query time {duration_1 + duration_2:.4f}s exceeds {max_total_time}s threshold")
581
+
582
+ # Log success
583
+ print("Performance test completed successfully!")
584
+
530
585
 
531
586
  class TestVariable:
532
587