@sjcrh/proteinpaint-server 2.84.0 → 2.85.0

package/routes/termdb.cohort.summary.js

@@ -1,16 +1,12 @@
+import { termdbCohortSummaryPayload } from "#types";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
 const api = {
   endpoint: "termdb/cohort/summary",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...termdbCohortSummaryPayload,
+      init
     }
   }
 };
@@ -23,7 +19,8 @@ function init({ genomes }) {
       if (!genome)
         throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      res.send({ count: ds.cohort.termdb.q.getCohortSampleCount(q.cohort) });
+      const count = ds.cohort.termdb.q.getCohortSampleCount(q.cohort);
+      res.send({ count });
     } catch (e) {
       res.send({ error: e.message || e });
       if (e.stack)

package/routes/termdb.cohorts.js

@@ -1,16 +1,12 @@
+import { termdbCohortsPayload } from "#types";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
 const api = {
   endpoint: "termdb/cohorts",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...termdbCohortsPayload,
+      init
     }
   }
 };

package/routes/{termdb.getdescrstats.js → termdb.descrstats.js}

@@ -1,53 +1,16 @@
+import { descrStatsPayload } from "#types";
 import Summarystats from "#shared/descriptive.stats.js";
 import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/descrstats",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "getdescrstatsRequest"
-      },
-      response: {
-        typeId: "getdescrstatsResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              tw: { term: { id: "hrtavg" }, q: { mode: "continuous" } },
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                lst: [
-                  {
-                    tag: "cohortFilter",
-                    type: "tvs",
-                    tvs: {
-                      term: {
-                        name: "Cohort",
-                        type: "categorical",
-                        values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
-                        id: "subcohort",
-                        isleaf: false,
-                        groupsetting: { disabled: true }
-                      },
-                      values: [{ key: "ABC", label: "ABC" }]
-                    }
-                  }
-                ]
-              }
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+    get: {
+      ...descrStatsPayload,
+      init
+    },
+    post: {
+      ...descrStatsPayload,
+      init
     }
   }
 };

package/routes/termdb.numericcategories.js

@@ -0,0 +1,51 @@
+import { numericCategoriesPayload } from "#types";
+import * as termdbsql from "#src/termdb.sql.js";
+const api = {
+  endpoint: "termdb/numericcategories",
+  methods: {
+    get: {
+      ...numericCategoriesPayload,
+      init
+    },
+    post: {
+      ...numericCategoriesPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    const q = req.query;
+    try {
+      const g = genomes[req.query.genome];
+      if (!g)
+        throw "invalid genome name";
+      const ds = g.datasets[req.query.dslabel];
+      if (!ds)
+        throw "invalid dataset name";
+      const tdb = ds.cohort.termdb;
+      if (!tdb)
+        throw "invalid termdb object";
+      const result = await trigger_getnumericcategories(q, tdb, ds);
+      res.send(result);
+    } catch (e) {
+      res.send({ error: e instanceof Error ? e.message : e });
+      if (e instanceof Error && e.stack)
+        console.log(e);
+    }
+  };
+}
+async function trigger_getnumericcategories(q, tdb, ds) {
+  if (!q.tid)
+    throw ".tid missing";
+  const arg = {
+    ds,
+    term_id: q.tid,
+    filter: q.filter
+  };
+  const lst = await termdbsql.get_summary_numericcategories(arg);
+  return { lst };
+}
+export {
+  api
+};

package/routes/{termdb.getpercentile.js → termdb.percentile.js}

@@ -1,57 +1,15 @@
+import { percentilePayload } from "#types";
 import * as termdbsql from "#src/termdb.sql.js";
 import computePercentile from "#shared/compute.percentile.js";
 const api = {
   endpoint: "termdb/getpercentile",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "getpercentileRequest"
-      },
-      response: {
-        typeId: "getpercentileResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              getpercentile: [50],
-              tid: "agedx",
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                lst: [
-                  {
-                    tag: "cohortFilter",
-                    type: "tvs",
-                    tvs: {
-                      term: {
-                        name: "Cohort",
-                        type: "categorical",
-                        values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
-                        id: "subcohort",
-                        isleaf: false,
-                        groupsetting: { disabled: true }
-                      },
-                      values: [{ key: "ABC", label: "ABC" }]
-                    }
-                  }
-                ]
-              }
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...percentilePayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...percentilePayload,
       init
     }
   }

package/routes/{termdb.getrootterm.js → termdb.rootterm.js}

@@ -1,34 +1,14 @@
+import { rootTermPayload } from "#types";
 import { get_ds_tdb } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/rootterm",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "getroottermRequest"
-      },
-      response: {
-        typeId: "getroottermResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              default_rootterm: 1,
-              cohortValues: "ABC"
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...rootTermPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...rootTermPayload,
       init
     }
   }

package/routes/{termdb.getSampleImages.js → termdb.sampleImages.js}

@@ -1,17 +1,17 @@
+import { termdbSampleImagesPayload } from "#types";
 import path from "path";
 import fs from "fs";
 import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "termdb/getSampleImages",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbGetSampleImagesRequest"
-      },
-      response: {
-        typeId: "TermdbGetSampleImagesResponse"
-      }
+    get: {
+      ...termdbSampleImagesPayload,
+      init
+    },
+    post: {
+      ...termdbSampleImagesPayload,
+      init
     }
   }
 };
@@ -33,7 +33,7 @@ function init({ genomes }) {
     }
   };
 }
-function validate_query_getSampleImages(ds, genome) {
+function validate_query_getSampleImages(ds) {
   const q = ds.queries.images;
   if (!q)
     return;

package/routes/termdb.singleSampleMutation.js

@@ -2,18 +2,14 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
+import { termdbSingleSampleMutationPayload } from "#types";
 import { gdcValidate_query_singleSampleMutation } from "#src/mds3.gdc.js";
 const api = {
   endpoint: "termdb/singleSampleMutation",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "TermdbSingleSampleMutationRequest"
-      },
-      response: {
-        typeId: "TermdbSingleSampleMutationResponse"
-      }
+      ...termdbSingleSampleMutationPayload,
+      init
     }
   }
 };

package/routes/termdb.singlecellDEgenes.js

@@ -1,15 +1,15 @@
+import { termdbSingleCellDEgenesPayload } from "#types";
 import { gdc_validate_query_singleCell_DEgenes } from "#src/mds3.gdc.js";
 const api = {
   endpoint: "termdb/singlecellDEgenes",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbSinglecellDEgenesRequest"
-      },
-      response: {
-        typeId: "TermdbSinglecellDEgenesResponse"
-      }
+    get: {
+      ...termdbSingleCellDEgenesPayload,
+      init
+    },
+    post: {
+      ...termdbSingleCellDEgenesPayload,
+      init
     }
   }
 };

package/routes/termdb.singlecellData.js

@@ -1,17 +1,13 @@
+import { termdbSingleCellDataPayload } from "#types";
 const api = {
   endpoint: "termdb/singlecellData",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "TermdbSinglecellDataRequest"
-      },
-      response: {
-        typeId: "TermdbSinglecellDataResponse"
-      }
+      ...termdbSingleCellDataPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...termdbSingleCellDataPayload,
       init
     }
   }

package/routes/termdb.singlecellSamples.js

@@ -4,20 +4,20 @@ import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
+import { termdbSingleCellSamplesPayload } from "#types";
 import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
 import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 import ky from "ky";
 const api = {
   endpoint: "termdb/singlecellSamples",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbSinglecellsamplesRequest"
-      },
-      response: {
-        typeId: "TermdbSinglecellsamplesResponse"
-      }
+    get: {
+      ...termdbSingleCellSamplesPayload,
+      init
+    },
+    post: {
+      ...termdbSingleCellSamplesPayload,
+      init
     }
   }
 };

package/routes/{termdb.gettermchildren.js → termdb.termchildren.js}

@@ -1,35 +1,14 @@
+import { termChildrenPayload } from "#types";
 import { copy_term, get_ds_tdb } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/termchildren",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "gettermchildrenRequest"
-      },
-      response: {
-        typeId: "gettermchildrenResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              get_children: 1,
-              cohortValues: "ABC",
-              tid: "GO:0000001"
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+      ...termChildrenPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...termChildrenPayload,
       init
     }
   }
@@ -46,7 +25,8 @@ function init({ genomes }) {
         throw "invalid dataset name";
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_children(q, res, tdb);
+      const result = await trigger_children(q, tdb);
+      res.send(result);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
       if (e instanceof Error && e.stack)
@@ -54,13 +34,13 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_children(q, res, tdb) {
+async function trigger_children(q, tdb) {
   if (!q.tid)
     throw "no parent term id";
   const cohortValues = q.cohortValues ? q.cohortValues : "";
   const treeFilter = q.treeFilter ? q.treeFilter : "";
   const terms = await tdb.q.getTermChildren(q.tid, cohortValues, treeFilter);
-  res.send({ lst: terms.map(copy_term) });
+  return { lst: terms.map(copy_term) };
 }
 export {
   api

package/routes/termdb.termsbyids.js

@@ -1,18 +1,14 @@
+import { termsByIdsPayload } from "#types";
 import { copy_term } from "#src/termdb.js";
 const api = {
   endpoint: "termdb/termsbyids",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "gettermsbyidsRequest"
-      },
-      response: {
-        typeId: "gettermsbyidsResponse"
-      }
+      ...termsByIdsPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...termsByIdsPayload,
       init
     }
   }
@@ -30,7 +26,8 @@ function init({ genomes }) {
       const tdb = ds.cohort.termdb;
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_gettermsbyid(q, res, tdb);
+      const results = await trigger_gettermsbyid(q, tdb);
+      res.send(results);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
       if (e instanceof Error && e.stack)
@@ -38,10 +35,8 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_gettermsbyid(q, res, tdb) {
-  const terms = {
-    terms: {}
-  };
+async function trigger_gettermsbyid(q, tdb) {
+  const terms = {};
   for (const id of q.ids) {
     const term = tdb.q.termjsonByOneid(id);
     if (term) {
@@ -52,9 +47,7 @@ async function trigger_gettermsbyid(q, res, tdb) {
     }
     terms[id] = term ? copy_term(term) : void 0;
   }
-  res.send({
-    terms
-  });
+  return { terms };
 }
 export {
   api

package/routes/{termdb.getTopTermsByType.js → termdb.topTermsByType.js}

@@ -1,17 +1,17 @@
+import { termdbTopTermsByTypePayload } from "#types";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { get_samples } from "#src/termdb.sql.js";
 import { TermTypes } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/getTopTermsByType",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbTopTermsByTypeRequest"
-      },
-      response: {
-        typeId: "TermdbTopTermsByTypeResponse"
-      }
+    get: {
+      ...termdbTopTermsByTypePayload,
+      init
+    },
+    post: {
+      ...termdbTopTermsByTypePayload,
+      init
     }
   }
 };
@@ -28,7 +28,6 @@ function init({ genomes }) {
         throw "invalid dslabel";
       if (!ds.queries[type])
         throw "not supported on dataset";
-      const t = Date.now();
       const terms = await ds.queries[type].getTopTerms(q);
       res.send({ terms });
     } catch (e) {
@@ -96,7 +95,7 @@ async function computeTopTerms(file, samples, type) {
   return varMetabolite;
 }
 function gdcValidateQuery(ds, genome, type) {
-  ds.queries[type].getTopTerms = async (q) => {
+  ds.queries[type].getTopTerms = async () => {
     return [];
   };
 }

package/routes/termdb.topVariablyExpressedGenes.js

@@ -1,3 +1,4 @@
+import { termdbTopVariablyExpressedGenesPayload } from "#types";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { get_samples } from "#src/termdb.sql.js";
@@ -7,14 +8,13 @@ import { joinUrl } from "#src/helpers.ts";
 const api = {
   endpoint: "termdb/topVariablyExpressedGenes",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbTopVariablyExpressedGenesRequest"
-      },
-      response: {
-        typeId: "TermdbTopVariablyExpressedGenesResponse"
-      }
+    get: {
+      ...termdbTopVariablyExpressedGenesPayload,
+      init
+    },
+    post: {
+      ...termdbTopVariablyExpressedGenesPayload,
+      init
     }
   }
 };

package/routes/termdb.violin.js

@@ -1,53 +1,15 @@
+import { violinPayload } from "#types";
 import { trigger_getViolinPlotData } from "#src/termdb.violin.js";
 const api = {
   endpoint: "termdb/violin",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "getViolinRequest"
-      },
-      response: {
-        typeId: "getViolinResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              devicePixelRatio: 2.200000047683716,
-              maxThickness: 150,
-              screenThickness: 1218,
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                lst: [
-                  {
-                    tag: "cohortFilter",
-                    type: "tvs",
-                    tvs: { term: { id: "subcohort", type: "categorical" }, values: [{ key: "ABC", label: "ABC" }] }
-                  }
-                ]
-              },
-              svgw: 227.27272234672367,
-              orientation: "horizontal",
-              datasymbol: "bean",
-              radius: 5,
-              strokeWidth: 0.2,
-              axisHeight: 60,
-              rightMargin: 50,
-              unit: "abs",
-              termid: "agedx"
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
+    get: {
+      ...violinPayload,
+      init
+    },
+    post: {
+      ...violinPayload,
+      init
     }
   }
 };

package/routes/tileserver.js

@@ -1,20 +1,15 @@
+import { tilePayload } from "#types";
 import ky from "ky";
 import serverconfig from "#src/serverconfig.js";
-const routePath = "tileserver";
 const api = {
-  endpoint: `${routePath}/layer/slide/:sampleId/zoomify/:TileGroup/:z-:x-:y@1x.jpg`,
+  endpoint: `tileserver/layer/slide/:sampleId/zoomify/:TileGroup/:z-:x-:y@1x.jpg`,
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...tilePayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...tilePayload,
       init
     }
   }