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Clearing the UBKG cache (prod) via `/admin` results in the organ dropdown not displaying correctly #926

Closed maxsibilla closed 1 year ago

maxsibilla commented 1 year ago
image
maxsibilla commented 1 year ago

Request is made to https://data.sennetconsortium.org/api/ontology/C000008 Response:

[{
    "code": "C030024",
    "sab": "SENNET",
    "term": "Adipose Tissue"
}, {
    "code": "C030025",
    "sab": "SENNET",
    "term": "Blood "
}, {
    "code": "C030027",
    "sab": "SENNET",
    "term": "Breast"
}, {
    "code": "C030031",
    "sab": "SENNET",
    "term": "Large Intestine"
}, {
    "code": "C030032",
    "sab": "SENNET",
    "term": "Liver "
}, {
    "code": "C030052",
    "sab": "SENNET",
    "term": "Lymph Node"
}, {
    "code": "C030054",
    "sab": "SENNET",
    "term": "Pancreas"
}, {
    "code": "C030055",
    "sab": "SENNET",
    "term": "Placenta "
}, {
    "code": "C030035",
    "sab": "SENNET",
    "term": "Lung (Right)"
}, {
    "code": "C030034",
    "sab": "SENNET",
    "term": "Lung (Left)"
}, {
    "code": "C030030",
    "sab": "SENNET",
    "term": "Kidney (Right)"
}, {
    "code": "C030029",
    "sab": "SENNET",
    "term": "Kidney (Left)"
}, {
    "code": "C030041",
    "sab": "SENNET",
    "term": "Ovary (Right)"
}, {
    "code": "C030038",
    "sab": "SENNET",
    "term": "Ovary (Left)"
}, {
    "code": "C020105",
    "sab": "SENNET",
    "term": "biopsy "
}, {
    "code": "C030040",
    "sab": "SENNET",
    "term": "Skin "
}, {
    "code": "C030026",
    "sab": "SENNET",
    "term": "Brain"
}, {
    "code": "C030036",
    "sab": "SENNET",
    "term": "Muscle"
}, {
    "code": "C030039",
    "sab": "SENNET",
    "term": "Other "
}]
maxsibilla commented 1 year ago

Both .ontology_C000008_bk and .ontology_C000008 look correct

maxsibilla commented 1 year ago

Contents of .ontology_C000008_bk

[{
    "code": "C030024",
    "sab": "SENNET",
    "term": "Adipose Tissue"
}, {
    "code": "C030025",
    "sab": "SENNET",
    "term": "Blood "
}, {
    "code": "C030027",
    "sab": "SENNET",
    "term": "Breast"
}, {
    "code": "C030031",
    "sab": "SENNET",
    "term": "Large Intestine"
}, {
    "code": "C030032",
    "sab": "SENNET",
    "term": "Liver "
}, {
    "code": "C030052",
    "sab": "SENNET",
    "term": "Lymph Node"
}, {
    "code": "C030054",
    "sab": "SENNET",
    "term": "Pancreas"
}, {
    "code": "C030055",
    "sab": "SENNET",
    "term": "Placenta "
}, {
    "code": "C030035",
    "sab": "SENNET",
    "term": "Lung (Right)"
}, {
    "code": "C030034",
    "sab": "SENNET",
    "term": "Lung (Left)"
}, {
    "code": "C030030",
    "sab": "SENNET",
    "term": "Kidney (Right)"
}, {
    "code": "C030029",
    "sab": "SENNET",
    "term": "Kidney (Left)"
}, {
    "code": "C030041",
    "sab": "SENNET",
    "term": "Ovary (Right)"
}, {
    "code": "C030038",
    "sab": "SENNET",
    "term": "Ovary (Left)"
}, {
    "code": "C020105",
    "sab": "SENNET",
    "term": "biopsy "
}, {
    "code": "C030040",
    "sab": "SENNET",
    "term": "Skin "
}, {
    "code": "C030026",
    "sab": "SENNET",
    "term": "Brain"
}, {
    "code": "C030036",
    "sab": "SENNET",
    "term": "Muscle"
}, {
    "code": "C030039",
    "sab": "SENNET",
    "term": "Other "
}]
maxsibilla commented 1 year ago

Contents of .ontology_C000008_bk

[{
    "code": "C030024",
    "organ_cui": "C0001527",
    "organ_uberon": "UBERON:0001013",
    "rui_code": "AD",
    "sab": "SENNET",
    "term": "Adipose Tissue"
}, {
    "code": "C030025",
    "organ_cui": "C0005767",
    "organ_uberon": "UBERON:0000178",
    "rui_code": "BD",
    "sab": "SENNET",
    "term": "Blood "
}, {
    "code": "C030026",
    "organ_cui": "C1269537",
    "organ_uberon": "UBERON:0000955",
    "rui_code": "BR",
    "sab": "SENNET",
    "term": "Brain"
}, {
    "code": "C030027",
    "organ_cui": "C0006141",
    "organ_uberon": "UBERON:0000310",
    "rui_code": "BS",
    "sab": "SENNET",
    "term": "Breast"
}, {
    "code": "C030029",
    "organ_cui": "C0227614",
    "organ_uberon": "UBERON:0004538",
    "rui_code": "LK",
    "sab": "SENNET",
    "term": "Kidney (Left)"
}, {
    "code": "C030030",
    "organ_cui": "C0227613",
    "organ_uberon": "UBERON:0004539",
    "rui_code": "RK",
    "sab": "SENNET",
    "term": "Kidney (Right)"
}, {
    "code": "C030031",
    "organ_cui": "C0021851",
    "organ_uberon": "UBERON:0000059",
    "rui_code": "LI",
    "sab": "SENNET",
    "term": "Large Intestine"
}, {
    "code": "C030032",
    "organ_cui": "C0023884",
    "organ_uberon": "UBERON:0002107",
    "rui_code": "LV",
    "sab": "SENNET",
    "term": "Liver "
}, {
    "code": "C030034",
    "organ_cui": "C0225730",
    "organ_uberon": "UBERON:0002168",
    "rui_code": "LL",
    "sab": "SENNET",
    "term": "Lung (Left)"
}, {
    "code": "C030035",
    "organ_cui": "C0225706",
    "organ_uberon": "UBERON:0002167",
    "rui_code": "RL",
    "sab": "SENNET",
    "term": "Lung (Right)"
}, {
    "code": "C030052",
    "organ_cui": "C0024204",
    "organ_uberon": "UBERON:0000029",
    "rui_code": "LN",
    "sab": "SENNET",
    "term": "Lymph Node"
}, {
    "code": "C030036",
    "organ_cui": "C4083049",
    "organ_uberon": "UBERON 0005090",
    "rui_code": "MU",
    "sab": "SENNET",
    "term": "Muscle"
}, {
    "code": "C030038",
    "organ_cui": "C0227874",
    "organ_uberon": "UBERON:0002119",
    "rui_code": "LO",
    "sab": "SENNET",
    "term": "Ovary (Left)"
}, {
    "code": "C030041",
    "organ_cui": "C0227873",
    "organ_uberon": "UBERON:0002118",
    "rui_code": "RO",
    "sab": "SENNET",
    "term": "Ovary (Right)"
}, {
    "code": "C030054",
    "organ_cui": "C0030274",
    "organ_uberon": "UBERON:0001264",
    "rui_code": "PA",
    "sab": "SENNET",
    "term": "Pancreas"
}, {
    "code": "C030055",
    "organ_cui": "C0032043",
    "organ_uberon": "UBERON:0001987",
    "rui_code": "PL",
    "sab": "SENNET",
    "term": "Placenta "
}, {
    "code": "C030040",
    "organ_cui": "C1123023",
    "organ_uberon": "UBERON 0002097",
    "rui_code": "SK",
    "sab": "SENNET",
    "term": "Skin "
}]
libpitt commented 1 year ago

Contents of .ontology_C000008_bk

[{
  "code": "C030024",
  "sab": "SENNET",
  "term": "Adipose Tissue"
}, {
  "code": "C030025",
  "sab": "SENNET",
  "term": "Blood "
}, {
  "code": "C030027",
  "sab": "SENNET",
  "term": "Breast"
}, {
  "code": "C030031",
  "sab": "SENNET",
  "term": "Large Intestine"
}, {
  "code": "C030032",
  "sab": "SENNET",
  "term": "Liver "
}, {
  "code": "C030052",
  "sab": "SENNET",
  "term": "Lymph Node"
}, {
  "code": "C030054",
  "sab": "SENNET",
  "term": "Pancreas"
}, {
  "code": "C030055",
  "sab": "SENNET",
  "term": "Placenta "
}, {
  "code": "C030035",
  "sab": "SENNET",
  "term": "Lung (Right)"
}, {
  "code": "C030034",
  "sab": "SENNET",
  "term": "Lung (Left)"
}, {
  "code": "C030030",
  "sab": "SENNET",
  "term": "Kidney (Right)"
}, {
  "code": "C030029",
  "sab": "SENNET",
  "term": "Kidney (Left)"
}, {
  "code": "C030041",
  "sab": "SENNET",
  "term": "Ovary (Right)"
}, {
  "code": "C030038",
  "sab": "SENNET",
  "term": "Ovary (Left)"
}, {
  "code": "C020105",
  "sab": "SENNET",
  "term": "biopsy "
}, {
  "code": "C030040",
  "sab": "SENNET",
  "term": "Skin "
}, {
  "code": "C030026",
  "sab": "SENNET",
  "term": "Brain"
}, {
  "code": "C030036",
  "sab": "SENNET",
  "term": "Muscle"
}, {
  "code": "C030039",
  "sab": "SENNET",
  "term": "Other "
}]

This should not be the content.

libpitt commented 1 year ago

Fix note: "organ_types":"C000008" in NEXT_PUBLIC_UBKG_CODES must have a corresponding endpoint to retrieve ubkg result with the rui_code prop and others. Please add "C000008": "organs?application_context=SENNET" to NEXT_PUBLIC_UBKG_CODES_PATHS