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feat: enhance safe_to_dict function to support sorting by ID and update term info parsing to sort images by ID
1 parent f003e25 commit 5c09171

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Lines changed: 41 additions & 121 deletions

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‎README.md‎

Lines changed: 19 additions & 119 deletions
Original file line numberDiff line numberDiff line change
@@ -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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},
@@ -81,106 +81,6 @@ vfb.get_term_info('FBbt_00003748')
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"0": "Asc"
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}
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},
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"tags": {
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"title": "Gross Types",
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"type": "tags",
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"order": 3
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},
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"thumbnail": {
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"title": "Thumbnail",
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"type": "markdown",
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"order": 9
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}
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},
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"rows": [
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{
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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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},
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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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},
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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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"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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}
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]
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},
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"output_format": "table",
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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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"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",
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"label": "ME(R) on JRC_FlyEM_Hemibrain",
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"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png",
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"thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnailT.png",
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"nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.nrrd",
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"wlz": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.wlz",
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"obj": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume_man.obj"
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}
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],
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"VFB_00101567": [
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{
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"id": "VFB_00102107",
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"label": "ME on JRC2018Unisex adult brain",
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"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png",
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"thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnailT.png",
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"nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/volume.nrrd",
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"wlz": "https://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/volume.wlz",
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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_00030786": [
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{
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"id": "VFB_00030810",
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"label": "medulla on adult brain template Ito2014",
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"thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png",
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"thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnailT.png",
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"nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume.nrrd",
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"wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume.wlz",
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"obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume_man.obj"
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}
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]
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},
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"IsTemplate": False,
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"Synonyms": [
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{
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"label": "ME",
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"scope": "has_exact_synonym",
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"type": "",
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"publication": "[Ito et al., 2014](FBrf0224194)"
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},
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{
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"label": "Med",
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"scope": "has_exact_synonym",
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"type": "",
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"publication": "[Chiang et al., 2011](FBrf0212704)"
@@ -303,14 +203,14 @@ 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)"
206+
"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",
@@ -327,32 +227,20 @@ 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",
@@ -364,6 +252,18 @@ 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,

‎src/vfbquery/test_utils.py‎

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ def default(self, obj):
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return obj.item()
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return super(NumpyEncoder, self).default(obj)
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def safe_to_dict(df):
21+
def safe_to_dict(df, sort_by_id=True):
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"""Convert DataFrame to dict with numpy types converted to native Python types"""
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if isinstance(df, pd.DataFrame):
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# Convert numpy dtypes to native Python types
@@ -28,6 +28,11 @@ def safe_to_dict(df):
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df_copy[col] = df_copy[col].astype('object')
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elif df_copy[col].dtype.name.startswith('float'):
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df_copy[col] = df_copy[col].astype('object')
31+
32+
# Sort by id column in descending order if it exists and sort_by_id is True
33+
if sort_by_id and 'id' in df_copy.columns:
34+
df_copy = df_copy.sort_values('id', ascending=False)
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return df_copy.to_dict("records")
3237
return df
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‎src/vfbquery/vfb_queries.py‎

Lines changed: 16 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@ def default(self, obj):
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return obj.item()
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return super(NumpyEncoder, self).default(obj)
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28-
def safe_to_dict(df):
28+
def safe_to_dict(df, sort_by_id=True):
2929
"""Convert DataFrame to dict with numpy types converted to native Python types"""
3030
if isinstance(df, pd.DataFrame):
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# Convert numpy dtypes to native Python types
@@ -35,6 +35,11 @@ def safe_to_dict(df):
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df_copy[col] = df_copy[col].astype('object')
3636
elif df_copy[col].dtype.name.startswith('float'):
3737
df_copy[col] = df_copy[col].astype('object')
38+
39+
# Sort by id column in descending order if it exists and sort_by_id is True
40+
if sort_by_id and 'id' in df_copy.columns:
41+
df_copy = df_copy.sort_values('id', ascending=False)
42+
3843
return df_copy.to_dict("records")
3944
return df
4045

@@ -518,6 +523,11 @@ def term_info_parse_object(results, short_form):
518523
if "image_" in key and not ("thumbnail" in key or "folder" in key) and len(vars(image.channel_image.image)[key]) > 1:
519524
record[key.replace("image_","")] = vars(image.channel_image.image)[key].replace("http://","https://")
520525
images[image.channel_image.image.template_anatomy.short_form].append(record)
526+
527+
# Sort each template's images by id in descending order (newest first)
528+
for template_key in images:
529+
images[template_key] = sorted(images[template_key], key=lambda x: x["id"], reverse=True)
530+
521531
termInfo["Examples"] = images
522532
# add a query to `queries` list for listing all available images
523533
q = ListAllAvailableImages_to_schema(termInfo["Name"], {"short_form":vfbTerm.term.core.short_form})
@@ -541,6 +551,11 @@ def term_info_parse_object(results, short_form):
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if "image_" in key and not ("thumbnail" in key or "folder" in key) and len(vars(image.image)[key]) > 1:
542552
record[key.replace("image_","")] = vars(image.image)[key].replace("http://","https://")
543553
images[image.image.template_anatomy.short_form].append(record)
554+
555+
# Sort each template's images by id in descending order (newest first)
556+
for template_key in images:
557+
images[template_key] = sorted(images[template_key], key=lambda x: x["id"], reverse=True)
558+
544559
# Add the thumbnails to the term info
545560
termInfo["Images"] = images
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