vfbquery 0.3.3__py3-none-any.whl → 0.4.0__py3-none-any.whl

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 (18) hide show
  1. test/term_info_queries_test.py +64 -9
  2. test/test_default_caching.py +173 -0
  3. test/test_examples_diff.py +6 -1
  4. vfbquery/__init__.py +62 -1
  5. vfbquery/cache_enhancements.py +465 -0
  6. vfbquery/cached_functions.py +227 -0
  7. vfbquery/solr_cache_integration.py +212 -0
  8. vfbquery/solr_fetcher.py +47 -3
  9. vfbquery/solr_result_cache.py +613 -0
  10. vfbquery/term_info_queries.py +18 -2
  11. vfbquery/test_utils.py +110 -3
  12. vfbquery/vfb_queries.py +325 -54
  13. {vfbquery-0.3.3.dist-info → vfbquery-0.4.0.dist-info}/METADATA +39 -40
  14. vfbquery-0.4.0.dist-info/RECORD +19 -0
  15. vfbquery-0.3.3.dist-info/RECORD +0 -14
  16. {vfbquery-0.3.3.dist-info → vfbquery-0.4.0.dist-info}/LICENSE +0 -0
  17. {vfbquery-0.3.3.dist-info → vfbquery-0.4.0.dist-info}/WHEEL +0 -0
  18. {vfbquery-0.3.3.dist-info → vfbquery-0.4.0.dist-info}/top_level.txt +0 -0
{vfbquery-0.3.3.dist-info → vfbquery-0.4.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: vfbquery
3
- Version: 0.3.3
3
+ Version: 0.4.0
4
4
  Summary: Wrapper for querying VirtualFlyBrain knowledge graph.
5
5
  Home-page: https://github.com/VirtualFlyBrain/VFBquery
6
6
  Author: VirtualFlyBrain
@@ -53,7 +53,7 @@ vfb.get_term_info('FBbt_00003748')
53
53
  "Meta": {
54
54
  "Name": "[medulla](FBbt_00003748)",
55
55
  "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).",
56
- "Comment": "",
56
+ "Comment": "Nern et al. (2025) - doi:10.1038/s41586-025-08746-0 say distal is M1-5 and M6-7 is central medulla.",
57
57
  "Types": "[anterior ectoderm derivative](FBbt_00025991); [synaptic neuropil domain](FBbt_00040007)",
58
58
  "Relationships": "[develops from](RO_0002202): [medulla anlage](FBbt_00001935); [is part of](BFO_0000050): [adult optic lobe](FBbt_00003701)"
59
59
  },
@@ -117,25 +117,25 @@ vfb.get_term_info('FBbt_00003748')
117
117
  "id": "VFB_00102107",
118
118
  "label": "[ME on JRC2018Unisex adult brain](VFB_00102107)",
119
119
  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
120
- "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)"
120
+ "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)"
121
121
  },
122
122
  {
123
123
  "id": "VFB_00101385",
124
124
  "label": "[ME%28R%29 on JRC_FlyEM_Hemibrain](VFB_00101385)",
125
125
  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
126
- "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)"
126
+ "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)"
127
127
  },
128
128
  {
129
129
  "id": "VFB_00030810",
130
130
  "label": "[medulla on adult brain template Ito2014](VFB_00030810)",
131
- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
131
+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
132
132
  "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)"
133
133
  },
134
134
  {
135
135
  "id": "VFB_00030624",
136
136
  "label": "[medulla on adult brain template JFRC2](VFB_00030624)",
137
- "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
138
- "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)"
137
+ "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
138
+ "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)"
139
139
  }
140
140
  ]
141
141
  },
@@ -143,20 +143,9 @@ vfb.get_term_info('FBbt_00003748')
143
143
  "count": 4
144
144
  }
145
145
  ],
146
- "IsIndividual": False,
147
- "IsClass": True,
146
+ "IsIndividual": false,
147
+ "IsClass": true,
148
148
  "Examples": {
149
- "VFB_00017894": [
150
- {
151
- "id": "VFB_00030624",
152
- "label": "medulla on adult brain template JFRC2",
153
- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
154
- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
155
- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
156
- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
157
- "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
158
- }
159
- ],
160
149
  "VFB_00101384": [
161
150
  {
162
151
  "id": "VFB_00101385",
@@ -179,6 +168,17 @@ vfb.get_term_info('FBbt_00003748')
179
168
  "obj": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/volume_man.obj"
180
169
  }
181
170
  ],
171
+ "VFB_00017894": [
172
+ {
173
+ "id": "VFB_00030624",
174
+ "label": "medulla on adult brain template JFRC2",
175
+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png",
176
+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnailT.png",
177
+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.nrrd",
178
+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume.wlz",
179
+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
180
+ }
181
+ ],
182
182
  "VFB_00030786": [
183
183
  {
184
184
  "id": "VFB_00030810",
@@ -191,7 +191,7 @@ vfb.get_term_info('FBbt_00003748')
191
191
  }
192
192
  ]
193
193
  },
194
- "IsTemplate": False,
194
+ "IsTemplate": false,
195
195
  "Synonyms": [
196
196
  {
197
197
  "label": "ME",
@@ -323,14 +323,14 @@ vfb.get_term_info('VFB_00000001')
323
323
  "score": "0.61",
324
324
  "name": "[fru-M-000204](VFB_00000333)",
325
325
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
326
- "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)"
326
+ "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)"
327
327
  },
328
328
  {
329
329
  "id": "VFB_00000333",
330
330
  "score": "0.61",
331
331
  "name": "[fru-M-000204](VFB_00000333)",
332
332
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
333
- "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)"
333
+ "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)"
334
334
  },
335
335
  {
336
336
  "id": "VFB_00002439",
@@ -347,32 +347,20 @@ vfb.get_term_info('VFB_00000001')
347
347
  "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)"
348
348
  },
349
349
  {
350
- "id": "VFB_00001880",
350
+ "id": "VFB_00000845",
351
351
  "score": "0.59",
352
- "name": "[fru-M-100041](VFB_00001880)",
352
+ "name": "[fru-M-100191](VFB_00000845)",
353
353
  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
354
- "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)"
354
+ "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)"
355
355
  }
356
356
  ]
357
357
  },
358
358
  "output_format": "table",
359
- "count": 44
359
+ "count": 60
360
360
  }
361
361
  ],
362
362
  "IsIndividual": True,
363
363
  "Images": {
364
- "VFB_00101567": [
365
- {
366
- "id": "VFB_00000001",
367
- "label": "fru-M-200266",
368
- "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
369
- "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
370
- "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
371
- "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
372
- "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
373
- "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
374
- }
375
- ],
376
364
  "VFB_00017894": [
377
365
  {
378
366
  "id": "VFB_00000001",
@@ -384,6 +372,18 @@ vfb.get_term_info('VFB_00000001')
384
372
  "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.obj",
385
373
  "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.swc"
386
374
  }
375
+ ],
376
+ "VFB_00101567": [
377
+ {
378
+ "id": "VFB_00000001",
379
+ "label": "fru-M-200266",
380
+ "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
381
+ "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
382
+ "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
383
+ "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
384
+ "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
385
+ "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
386
+ }
387
387
  ]
388
388
  },
389
389
  "IsClass": False,
@@ -405,7 +405,6 @@ Template example:
405
405
  ```python
406
406
  vfb.get_term_info('VFB_00101567')
407
407
  ```
408
-
409
408
  ```json
410
409
  {
411
410
  "Name": "JRC2018U",
vfbquery-0.4.0.dist-info/RECORD ADDED
@@ -0,0 +1,19 @@
1
+ test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
+ test/readme_parser.py,sha256=puvcq4_oEltjx_faw1kQJ8mmIWiQU-40oLJjtJBQCsQ,4170
3
+ test/term_info_queries_test.py,sha256=Od3i2DfaOlYFQGNQh2G7EiTC5ZqzgySyH3Wk6GntkWE,36902
4
+ test/test_default_caching.py,sha256=-KW2Mkz9x0tjlhXMreqJvjgo3pWOg49G0r22Woa9U5U,6616
5
+ test/test_examples_diff.py,sha256=TPo7gHPcus-24T7kxBXMQiCl0EHcXaEXeVuOG7C3rUo,15853
6
+ vfbquery/__init__.py,sha256=oKdgjIoseGwhdNwejXndg0CSpZdPgZes-PlHtYZT0zk,2262
7
+ vfbquery/cache_enhancements.py,sha256=-PCM0YZHPjwUJwJODZLgmz91sDyFGuYz_QRph_kTbB8,17341
8
+ vfbquery/cached_functions.py,sha256=5-aIiRP9mfEhVT3mXkLvIPDmdFq6iIExiLZAyir12IQ,10255
9
+ vfbquery/solr_cache_integration.py,sha256=Q87z_pXPdS9zn0r9kp2YBLGpCKOXVvcmzNmkRN7D8MU,7984
10
+ vfbquery/solr_fetcher.py,sha256=1FAyqaLrvZLaAmCW96en9y8lKTcs-ZFjt_UlnohP0jo,5683
11
+ vfbquery/solr_result_cache.py,sha256=oIUPCNmxG_nmyhfvx1gSiy5uvtvVrkLMJFgA6MNEqpY,27864
12
+ vfbquery/term_info_queries.py,sha256=oE-Ogm7jCPPlKtD3W3EtttYZcHnInwDOpOj-phAEOaI,42009
13
+ vfbquery/test_utils.py,sha256=7wUA3xgaGu3eLnjC98msNYt1wL538nOimVJjkC0ZLjU,5791
14
+ vfbquery/vfb_queries.py,sha256=50phVwDP28YaZdOmLom_Opem0Bdf2cEPo18jLjGig1I,76626
15
+ vfbquery-0.4.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
16
+ vfbquery-0.4.0.dist-info/METADATA,sha256=skaC5fQa-atagVzYyDmL7bAvgGcSF7KIAkxT2HueGa8,63157
17
+ vfbquery-0.4.0.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
18
+ vfbquery-0.4.0.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
19
+ vfbquery-0.4.0.dist-info/RECORD,,
vfbquery-0.3.3.dist-info/RECORD DELETED
@@ -1,14 +0,0 @@
1
- test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
- test/readme_parser.py,sha256=puvcq4_oEltjx_faw1kQJ8mmIWiQU-40oLJjtJBQCsQ,4170
3
- test/term_info_queries_test.py,sha256=9FxV3ZmRdi9TRjAS-1N0YRpCKAu4EthdQYOe_NluUuc,34527
4
- test/test_examples_diff.py,sha256=ep_BzA-7az2OUPxUIsS3ReFV8LwuzGv8yIL0HirOGsc,15699
5
- vfbquery/__init__.py,sha256=fvjBDvRlhtKkMa69WAVHY0bteLh4qlLH4FAhiZBOLRE,76
6
- vfbquery/solr_fetcher.py,sha256=U8mHaBJrwjncl1eU_gnNj5CGhEb-s9dCpcUTXTifQOY,3984
7
- vfbquery/term_info_queries.py,sha256=79Bm2RJzAZyVPQE5HWhsvybeBYrz2AbFgbM0ympIxao,41399
8
- vfbquery/test_utils.py,sha256=HKFsQ2wqZYxR_wS9V6RIM3SguIi9kX5kyYDAXgpfp1A,1623
9
- vfbquery/vfb_queries.py,sha256=04CulLonZ_O7vgoiMvN3zBP5y2Ww9AXRdmO-ljD_r6Y,63914
10
- vfbquery-0.3.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
11
- vfbquery-0.3.3.dist-info/METADATA,sha256=mmUICAjBFXeF8poNW_I3wkbyssbeNE5RzmXXRaKhk7Q,62999
12
- vfbquery-0.3.3.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
13
- vfbquery-0.3.3.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
14
- vfbquery-0.3.3.dist-info/RECORD,,