@sjcrh/proteinpaint-server 2.188.1 → 2.190.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.188.1",
+  "version": "2.190.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -8,17 +8,16 @@
   "bin": "start.js",
   "imports": {
     "#types": "@sjcrh/proteinpaint-types",
-    "#types/checkers": "@sjcrh/proteinpaint-types/checkers",
     "#shared": "@sjcrh/proteinpaint-shared",
     "#shared/*": "@sjcrh/proteinpaint-shared/*",
     "#src/*": "./src/*",
-    "#routes/*": "./routes/*"
+    "#routes/*": "./src/routes/*"
   },
   "scripts": {
     "dev": "npm run start",
     "prestart": "tsx emitImports.js dev > server.js",
     "start": "tsx watch ./start.js",
-    "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx serverTests.js && rm -rf ./cache",
+    "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx --conditions=sjpp/dev serverTests.js && rm -rf ./cache",
     "test": "tsc && npm run test:unit",
     "precombined:coverage": "tsx emitImports.js unit > serverTests.js",
     "combined:coverage": "coverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
@@ -55,18 +54,16 @@
     "nodemon": "^3.1.10",
     "prettier": "^2.8.8",
     "tape": "^5.2.2",
-    "ts-node": "^10.9.1",
-    "ts-patch": "^3.0.2",
     "tsx": "^4.7.1",
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.181.1",
-    "@sjcrh/proteinpaint-python": "2.188.0",
-    "@sjcrh/proteinpaint-r": "2.188.0",
-    "@sjcrh/proteinpaint-rust": "2.188.0",
-    "@sjcrh/proteinpaint-shared": "2.188.1",
-    "@sjcrh/proteinpaint-types": "2.188.1",
+    "@sjcrh/augen": "2.190.0",
+    "@sjcrh/proteinpaint-python": "2.190.0",
+    "@sjcrh/proteinpaint-r": "2.190.0",
+    "@sjcrh/proteinpaint-rust": "2.190.0",
+    "@sjcrh/proteinpaint-shared": "2.190.0",
+    "@sjcrh/proteinpaint-types": "2.190.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/aiProjectAdmin.js

@@ -1,31 +1,5 @@
-import { aiProjectAdminPayload } from "#types/checkers";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
 import { runMultiStmtSQL, runSQL } from "#src/runSQLHelpers.ts";
-const api = {
-  endpoint: "aiProjectAdmin",
-  methods: {
-    get: {
-      //all requests
-      ...aiProjectAdminPayload,
-      init
-    },
-    post: {
-      //'admin' -> edit
-      ...aiProjectAdminPayload,
-      init
-    },
-    delete: {
-      //'admin' -> delete
-      ...aiProjectAdminPayload,
-      init
-    },
-    put: {
-      //'admin' -> add
-      ...aiProjectAdminPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -173,6 +147,6 @@ function addProject(connection, project) {
   runMultiStmtSQL(connection, [{ sql: classSql, params: classParams }], "add");
 }
 export {
-  api,
-  getImages
+  getImages,
+  init
 };

package/routes/aiProjectSelectedWSImages.js

@@ -1,19 +1,5 @@
-import { aiProjectSelectedWSImagesResponsePayload } from "#types/checkers";
-import { createSelectionID, SelectionPrefixes, FlagStatus } from "#shared";
+import { createSelectionID, SelectionPrefixes, FlagStatus } from "#types";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
-const api = {
-  endpoint: "aiProjectSelectedWSImages",
-  methods: {
-    get: {
-      ...aiProjectSelectedWSImagesResponsePayload,
-      init
-    },
-    post: {
-      ...aiProjectSelectedWSImagesResponsePayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -174,7 +160,6 @@ function validateWSIAnnotationsQuery(ds, connection) {
         return {
           zoomCoordinates: coords,
           class: r.label ?? "",
-          status: r.status,
           flag: r.flagged === void 0 ? FlagStatus.Normal : r.flagged,
           timestamp: r.timestamp,
           id: createSelectionID(SelectionPrefixes.Annotation, coords)
@@ -244,7 +229,7 @@ function validateWSIClassesQuery(ds, connection) {
   };
 }
 export {
-  api,
+  init,
   validateWSIAnnotationsQuery,
   validateWSIClassesQuery,
   validate_query_getWSIAnnotations,

package/routes/brainImaging.js

@@ -1,23 +1,9 @@
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-import { brainImagingPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { isNumericTerm } from "#shared";
 import { getColors } from "#shared";
 import { run_python } from "@sjcrh/proteinpaint-python";
-const api = {
-  endpoint: "brainImaging",
-  methods: {
-    get: {
-      ...brainImagingPayload,
-      init
-    },
-    post: {
-      ...brainImagingPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -146,5 +132,5 @@ async function getBrainImage(query, genomes, plane, index) {
   }
 }
 export {
-  api
+  init
 };

package/routes/brainImagingSamples.js

@@ -2,20 +2,6 @@ import fs from "fs";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { getData } from "#src/termdb.matrix.js";
-const api = {
-  endpoint: "brainImagingSamples",
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "BrainImagingSamplesRequest"
-      },
-      response: {
-        typeId: "BrainImagingSamplesResponse"
-      }
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -71,5 +57,5 @@ async function getBrainImageSamples(query, genomes) {
   }
 }
 export {
-  api
+  init
 };

package/routes/burden.js

@@ -1,20 +1,6 @@
-import { burdenPayload } from "#types/checkers";
 import { run_R } from "@sjcrh/proteinpaint-r";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "burden",
-  methods: {
-    get: {
-      init,
-      ...burdenPayload
-    },
-    post: {
-      init,
-      ...burdenPayload
-    }
-  }
-};
 function init({ genomes }) {
   return async function handler(req, res) {
     try {
@@ -155,5 +141,5 @@ const defaultInputValues = Object.freeze({
   abd: 2.4
 });
 export {
-  api
+  init
 };

package/routes/correlationVolcano.js

@@ -1,22 +1,8 @@
-import { CorrelationVolcanoPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { run_R } from "@sjcrh/proteinpaint-r";
 import { mayLog } from "#src/helpers.ts";
 import { getStdDev } from "./termdb.descrstats.ts";
 const minArrayLength = 3;
-const api = {
-  endpoint: "termdb/correlationVolcano",
-  methods: {
-    get: {
-      ...CorrelationVolcanoPayload,
-      init
-    },
-    post: {
-      ...CorrelationVolcanoPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
@@ -121,6 +107,6 @@ function validate_correlationVolcano(ds) {
   }
 }
 export {
-  api,
+  init,
   validate_correlationVolcano
 };

package/routes/dataset.js

@@ -1,20 +1,5 @@
 import * as mds3_init from "#src/mds3.init.js";
 import * as common from "#shared/common.js";
-import { datasetPayload } from "#types/checkers";
-const api = {
-  endpoint: "getDataset",
-  // should rename to simply 'dataset', method is based on HTTP method
-  methods: {
-    get: {
-      init,
-      ...datasetPayload
-    },
-    post: {
-      init,
-      ...datasetPayload
-    }
-  }
-};
 function init({ genomes }) {
   return function(req, res) {
     try {
@@ -244,5 +229,5 @@ function copy_legacyDataset(ds) {
   return ds2;
 }
 export {
-  api
+  init
 };

package/routes/deleteWSITileSelection.js

@@ -1,15 +1,5 @@
-import { deleteWSITileSelectionPayload } from "#types/checkers";
-import { checkSelectionType, SelectionPrefixes, FlagStatus } from "#shared";
+import { checkSelectionType, SelectionPrefixes, FlagStatus } from "#types";
 import { getDbConnection } from "#src/aiHistoDBConnection.ts";
-const api = {
-  endpoint: `deleteWSITileSelection`,
-  methods: {
-    delete: {
-      ...deleteWSITileSelectionPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -139,6 +129,6 @@ function validateQuery(ds, connection) {
   };
 }
 export {
-  api,
+  init,
   validate_query_deleteWSIAnnotation
 };

package/routes/dsdata.js

@@ -2,24 +2,6 @@ import path from "path";
 import { spawn } from "child_process";
 import serverconfig from "#src/serverconfig.js";
 import * as common from "#shared/common.js";
-import { dsDataPayload } from "#types/checkers";
-const api = {
-  // route endpoint
-  // - no need for trailing slash
-  // - should be a noun (method is based on HTTP GET, POST, etc)
-  // - don't add 'Data' as response is assumed to be data
-  endpoint: "dsdata",
-  methods: {
-    get: {
-      ...dsDataPayload,
-      init
-    },
-    post: {
-      ...dsDataPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async function handle_dsdata(req, res) {
     try {
@@ -113,5 +95,5 @@ function handle_dsdata_vcf(query, req) {
   });
 }
 export {
-  api
+  init
 };

package/routes/gdc.grin2.list.js

@@ -1,4 +1,3 @@
-import { gdcGRIN2listPayload } from "#types/checkers";
 import ky from "ky";
 import { joinUrl } from "#shared/joinUrl.js";
 import serverconfig from "#src/serverconfig.js";
@@ -7,19 +6,6 @@ const mafMaxFileNumber = 1e3, cnvMaxFileNumber = 1e3;
 const allowedWorkflowType = "Aliquot Ensemble Somatic Variant Merging and Masking";
 const maxFileSizeAllowed = 1e6;
 const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 4e8;
-const api = {
-  endpoint: "gdc/GRIN2list",
-  methods: {
-    get: {
-      ...gdcGRIN2listPayload,
-      init
-    },
-    post: {
-      ...gdcGRIN2listPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -247,6 +233,6 @@ async function listCnvFiles(q, result, ds) {
   }
 }
 export {
-  api,
+  init,
   maxTotalSizeCompressed
 };

package/routes/gdc.grin2.run.js

@@ -1,23 +1,9 @@
-import { runGRIN2Payload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import path from "path";
 import { run_python } from "@sjcrh/proteinpaint-python";
 import { mayLog } from "#src/helpers.ts";
 const MAX_RECORD = 1e5;
-const api = {
-  endpoint: "gdc/runGRIN2",
-  methods: {
-    get: {
-      ...runGRIN2Payload,
-      init
-    },
-    post: {
-      ...runGRIN2Payload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -137,5 +123,5 @@ function parseRustOutput(rustOutput) {
   }
 }
 export {
-  api
+  init
 };

package/routes/gdc.maf.js

@@ -1,4 +1,3 @@
-import { gdcMafPayload } from "#types/checkers";
 import ky from "ky";
 import { joinUrl } from "#shared/joinUrl.js";
 import serverconfig from "#src/serverconfig.js";
@@ -6,19 +5,6 @@ import { getGdcSampletypes } from "#src/mds3.gdc.js";
 const maxFileNumber = 1e3;
 const allowedWorkflowType = "Aliquot Ensemble Somatic Variant Merging and Masking";
 const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 4e8;
-const api = {
-  endpoint: "gdc/maf",
-  methods: {
-    get: {
-      ...gdcMafPayload,
-      init
-    },
-    post: {
-      ...gdcMafPayload,
-      init
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -94,6 +80,6 @@ async function listMafFiles(q, ds) {
   return result;
 }
 export {
-  api,
+  init,
   maxTotalSizeCompressed
 };

package/routes/gdc.mafBuild.js

@@ -1,22 +1,8 @@
 import ky from "ky";
 import { joinUrl } from "#shared/joinUrl.js";
 import { stream_rust } from "@sjcrh/proteinpaint-rust";
-import { gdcMafPayload } from "#types/checkers";
 import { maxTotalSizeCompressed } from "./gdc.maf.ts";
 import { mayLog } from "#src/helpers.ts";
-const api = {
-  endpoint: "gdc/mafBuild",
-  methods: {
-    get: {
-      init,
-      ...gdcMafPayload
-    },
-    post: {
-      init,
-      ...gdcMafPayload
-    }
-  }
-};
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -125,5 +111,5 @@ async function getFileLstUnderSizeLimit(lst, host, headers) {
   return out;
 }
 export {
-  api
+  init
 };