@sjcrh/proteinpaint-server 2.83.0 → 2.85.0

package/routes/sampledzimages.js

@@ -1,40 +1,40 @@
 import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
+import { dzImagesPayload } from "#types";
 const api = {
   endpoint: "sampledzimages",
   methods: {
     get: {
       init,
-      request: {
-        typeId: "GetSampleDZImagesRequest"
-      },
-      response: {
-        typeId: "GetSampleDZImagesResponse"
-      }
+      ...dzImagesPayload
     },
     post: {
-      alternativeFor: "get",
-      init
+      init,
+      ...dzImagesPayload
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
+    const q = req.query;
     try {
-      const g = genomes[req.query.genome];
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
+      const ds = g.datasets[q.dslabel];
       if (!ds)
         throw "invalid dataset name";
-      const sampleId = req.query.sample_id;
+      const sampleId = q.sample_id || "";
       const sampleDZImagesPath = path.join(
         `${serverconfig.tpmasterdir}/${ds.queries.DZImages.imageBySampleFolder}`,
         sampleId
       );
       const sampleDZImages = getDZImages(sampleDZImagesPath);
-      res.send({ sampleDZImages });
+      res.send(
+        { sampleDZImages }
+        /*satisfies DZImagesResponse*/
+      );
     } catch (e) {
       console.log(e);
       res.status(404).send("Sample images not found");

package/routes/samplewsimages.js

@@ -1,17 +1,13 @@
+import { sampleWSImagesPayload } from "#types";
 const api = {
   endpoint: "samplewsimages",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "GetSampleWSImagesRequest"
-      },
-      response: {
-        typeId: "GetSampleWSImagesResponse"
-      }
+      ...sampleWSImagesPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...sampleWSImagesPayload,
       init
     }
   }
@@ -35,8 +31,8 @@ function init({ genomes }) {
     }
   };
 }
-function validate_query_getSampleWSImages(ds, genome) {
-  const q = ds.queries.WSImages;
+function validate_query_getSampleWSImages(ds) {
+  const q = ds.queries?.WSImages;
   if (!q)
     return;
   nativeValidateQuery(ds);

package/routes/snp.js

@@ -1,3 +1,4 @@
+import { snpPayload } from "#types";
 import * as utils from "#src/utils.js";
 const api = {
   // route endpoint
@@ -7,16 +8,11 @@ const api = {
   endpoint: "snp",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
+      ...snpPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...snpPayload,
       init
     }
   }
@@ -24,10 +20,12 @@ const api = {
 function init({ genomes }) {
   return async function handle_snp(req, res) {
     try {
-      const n = req.query.genome;
+      const q = req.query;
+      const n = q.genome;
       if (!n)
         throw "no genome";
-      res.send({ results: await searchSNP(req.query, genomes[n]) });
+      const results = await searchSNP(q, genomes[n]);
+      res.send({ results });
     } catch (e) {
       if (e.stack)
         console.log(e.stack);

package/routes/termdb.DE.js

@@ -1,4 +1,5 @@
 import path from "path";
+import { diffExpPayload } from "#types";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { get_ds_tdb } from "../src/termdb.js";
 import run_R from "../src/run_R.js";
@@ -6,16 +7,13 @@ import serverconfig from "../src/serverconfig.js";
 const api = {
   endpoint: "DEanalysis",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "DERequest"
-      },
-      response: {
-        typeId: "DEResponse"
-        // will combine this with type checker
-        //valid: (t) => {}
-      }
+    get: {
+      ...diffExpPayload,
+      init
+    },
+    post: {
+      ...diffExpPayload,
+      init
     }
   }
 };

package/routes/termdb.boxplot.js

@@ -1,18 +1,17 @@
+import { boxplotPayload } from "#types";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortKey2values } from "../src/termdb.violin.js";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "BoxplotRequest"
-      },
-      response: {
-        typeId: "BoxplotResponse"
-      },
-      examples: []
+    get: {
+      ...boxplotPayload,
+      init
+    },
+    post: {
+      ...boxplotPayload,
+      init
     }
   }
 };
@@ -43,14 +42,18 @@ function init({ genomes }) {
       const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;
       const key2values = /* @__PURE__ */ new Map();
       const overlayTerm = q.divideTw;
-      for (const [key, val] of Object.entries(data.samples)) {
+      for (const val of Object.values(data.samples)) {
         const value = val[q.tw.$id];
         if (!Number.isFinite(value?.value))
           continue;
+        if (q.tw.term.values?.[value.value]?.uncomputable)
+          continue;
         if (overlayTerm) {
           if (!val[overlayTerm?.$id])
             continue;
           const value2 = val[overlayTerm.$id];
+          if (overlayTerm.term?.values?.[value2.key]?.uncomputable)
+            continue;
           if (!key2values.has(value2.key))
             key2values.set(value2.key, []);
           key2values.get(value2.key).push(value.value);
@@ -64,57 +67,52 @@ function init({ genomes }) {
       let absMin, absMax, maxLabelLgth;
       for (const [key, values] of sortKey2values(data, key2values, overlayTerm)) {
         const sortedValues = values.sort((a, b) => a - b);
-        if (!absMin || sortedValues[0] < absMin)
+        if (absMin === null || absMin === void 0 || sortedValues[0] < absMin)
           absMin = sortedValues[0];
-        if (!absMax || sortedValues[sortedValues.length - 1] > absMax)
+        if (absMax === null || absMax === void 0 || sortedValues[sortedValues.length - 1] > absMax)
           absMax = sortedValues[sortedValues.length - 1];
         const vs = sortedValues.map((v) => {
           const value = { value: v };
           return value;
         });
+        const _plot = {
+          // label,
+          // values,
+          // plotValueCount: values.length
+          boxplot: boxplot_getvalue(vs),
+          min: sortedValues[0],
+          max: sortedValues[sortedValues.length - 1]
+        };
         if (overlayTerm) {
           let label = overlayTerm?.term?.values?.[key]?.label || key;
           label = `${label}, n=${values.length}`;
-          if (!maxLabelLgth || label.length > maxLabelLgth.length)
+          if (!maxLabelLgth || label.length > maxLabelLgth)
             maxLabelLgth = label.length;
-          const plot = {
-            // label,
-            // values,
+          const plot = Object.assign(_plot, {
             seriesId: key,
-            color: overlayTerm?.term?.values?.[key]?.color || null,
-            boxplot: boxplot_getvalue(vs),
-            //Need sd and mean?
-            // plotValueCount: values.length,
-            min: sortedValues[0],
-            max: sortedValues[sortedValues.length - 1]
-          };
+            color: overlayTerm?.term?.values?.[key]?.color || null
+          });
           plot.boxplot.label = label;
           plots.push(plot);
         } else {
           const label = `${sampleType}, n=${values.length}`;
           if (!maxLabelLgth || label.length > maxLabelLgth.length)
             maxLabelLgth = label.length;
-          const plot = {
-            // label,
-            // values,
-            // plotValueCount: values.length,
-            boxplot: boxplot_getvalue(vs),
-            min: sortedValues[0],
-            max: sortedValues[sortedValues.length - 1]
-          };
-          plot.boxplot.label = label;
-          plots.push(plot);
+          _plot.boxplot.label = label;
+          plots.push(_plot);
         }
       }
-      data.plots = plots;
-      data.absMin = absMin;
-      data.absMax = absMax;
-      data.maxLabelLgth = maxLabelLgth;
-      res.send(data);
+      const returnData = {
+        absMin,
+        absMax,
+        maxLabelLgth,
+        plots
+      };
+      res.send(returnData);
     } catch (e) {
       res.send({ error: e?.message || e });
       if (e instanceof Error && e.stack)
-        console.log(e);
+        console.error(e);
     }
   };
 }

package/routes/termdb.categories.js

@@ -1,56 +1,15 @@
+import { termdbCategoriesPayload } from "#types";
 import { getOrderedLabels } from "#src/termdb.barchart.js";
 import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/categories",
   methods: {
     get: {
-      init,
-      request: {
-        typeId: "getcategoriesRequest"
-      },
-      response: {
-        typeId: "getcategoriesResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              term: { id: "diaggrp" },
-              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 }
-          }
-        }
-      ]
+      ...termdbCategoriesPayload,
+      init
     },
     post: {
-      alternativeFor: "get",
+      ...termdbCategoriesPayload,
       init
     }
   }

package/routes/termdb.cluster.js

@@ -1,5 +1,6 @@
 import path from "path";
 import run_R from "#src/run_R.js";
+import { termdbClusterPayload } from "#types";
 import * as utils from "#src/utils.js";
 import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
@@ -11,14 +12,13 @@ import { getData } from "#src/termdb.matrix.js";
 const api = {
   endpoint: "termdb/cluster",
   methods: {
-    all: {
-      init,
-      request: {
-        typeId: "TermdbClusterRequest"
-      },
-      response: {
-        typeId: "TermdbClusterResponse"
-      }
+    get: {
+      ...termdbClusterPayload,
+      init
+    },
+    post: {
+      ...termdbClusterPayload,
+      init
     }
   }
 };
@@ -135,7 +135,7 @@ async function doClustering(data, q, numCases = 1e3) {
     for (const s of inputData.col_names) {
       row.push(o[s] || 0);
     }
-    inputData.matrix.push(getZscore(row));
+    inputData.matrix.push(q.zScoreTransformation ? getZscore(row) : row);
   }
   if (inputData.matrix.length == 0)
     throw "Clustering matrix is empty";

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;