@sjcrh/proteinpaint-server 2.214.0 → 2.216.0

package/src/serverconfig.js

@@ -4,6 +4,7 @@
 */
 
 import fs from 'fs'
+import os from 'os'
 import path from 'path'
 import { fileURLToPath } from 'url'
 
@@ -202,6 +203,34 @@ if (serverconfig.debugmode && !serverconfig.binpath.includes('sjcrh/')) {
 	serverconfig.routeSetters = routeSetters
 }
 
+if (process.env.PP_CREDS_HANDOFF_FILE) {
+	// set by container/envHelpers.mjs, which passes {<NAME>_CREDS: value} as JSON in a private temp file instead
+	// of in this process env, so that the credentials are not in the initial env of this process
+	const file = process.env.PP_CREDS_HANDOFF_FILE
+	delete process.env.PP_CREDS_HANDOFF_FILE
+	const dir = path.dirname(file)
+	// only remove a dir as created by envHelpers.mjs
+	if (
+		path.basename(file) != 'creds.json' ||
+		// resolved, like the dir from path.join() in envHelpers.mjs, such as for TMPDIR=/tmp/.
+		path.dirname(dir) != path.resolve(os.tmpdir()) ||
+		!path.basename(dir).startsWith('pp-creds-')
+	)
+		throw `invalid process.env.PP_CREDS_HANDOFF_FILE`
+	let creds
+	try {
+		creds = JSON.parse(fs.readFileSync(file, 'utf8'))
+	} catch {
+		// do not include the parse error message, since it may quote part of the credentials
+		throw `unable to read credentials from process.env.PP_CREDS_HANDOFF_FILE`
+	} finally {
+		// before the server starts listening, so that a request cannot read this file
+		fs.rmSync(dir, { recursive: true, force: true })
+	}
+	// set at runtime instead of in the initial env; each <NAME>_CREDS is then read and deleted as before
+	for (const [name, value] of Object.entries(creds)) process.env[name] = value
+}
+
 if (process.env.PP_CREDS) {
 	// preferred over a dsCredentials file path, so that the server process does not need
 	// read access to a credentials file that a path traversal bug could expose;
@@ -413,7 +442,7 @@ export default serverconfig
 	  the top-level serverconfig{} already has a null prototype, as set above right after parsing
 
 	objects are locked in place instead of copied, so that a reference that a module captured at import time,
-	e.g. `const bamCache = serverconfig.features.bamCache` in bam.js, is locked too
+	e.g. `const opts = serverconfig.features.cacheMonitor`, is locked too
 
 	throws, to fail the launch, when a value cannot be fully locked
 */

package/routes/brainImaging.js

@@ -1,154 +0,0 @@
-import fs from "fs";
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
-import { getData } from "../src/termdb.matrix.js";
-import { filterSampleNamesByAccess } from "#src/termdb.sql.js";
-import { isNumericTerm } from "#shared";
-import { getColors } from "#shared";
-import { run_python } from "@sjcrh/proteinpaint-python";
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const query = req.query;
-      const g = genomes[query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[query.dslabel];
-      if (!ds) throw "invalid dataset name";
-      let plane, index;
-      if (query.l != void 0) {
-        plane = "L";
-        index = query.l;
-      } else if (query.f != void 0) {
-        plane = "F";
-        index = query.f;
-      } else {
-        plane = "T";
-        index = query.t;
-      }
-      const [brainImage, legend] = await getBrainImage(query, genomes, plane, index);
-      res.send({ brainImage, plane, legend });
-    } catch (e) {
-      console.log(e);
-      res.status(404).send(typeof e == "string" ? e : "Sample brain image not found");
-    }
-  };
-}
-async function getBrainImage(query, genomes, plane, index) {
-  const ds = genomes[query.genome].datasets[query.dslabel];
-  const q = ds.queries.NIdata;
-  if (q.checkDataAccess) {
-    if (!q.checkDataAccess(query)) throw "no access";
-  }
-  const ref = q.references[query.refKey];
-  if (!ref) throw "invalid refKey";
-  if (ref.referenceFile && ref.samples) {
-    const refFile = path.join(serverconfig.tpmasterdir, ref.referenceFile);
-    const dirPath = path.join(serverconfig.tpmasterdir, ref.samples);
-    const terms = [];
-    const divideByTW = query.divideByTW;
-    const overlayTW = query.overlayTW;
-    if (divideByTW) terms.push(divideByTW);
-    if (overlayTW) terms.push(overlayTW);
-    let selectedSampleNames = query.selectedSampleFileNames.map((s) => s.split(".nii")[0]);
-    const existingFiles = new Set(await fs.promises.readdir(dirPath));
-    selectedSampleNames = selectedSampleNames.filter((s) => existingFiles.has(s + ".nii"));
-    if (!selectedSampleNames.length) throw "no brain imaging data for the requested sample(s)";
-    selectedSampleNames = await filterSampleNamesByAccess(query, ds, selectedSampleNames);
-    if (!selectedSampleNames.length) throw "no selected samples pass the current filter";
-    const data = await getData({ terms, __protected__: query.__protected__ }, ds);
-    if (data.error) throw data.error;
-    const divideByCat = {};
-    const uniqueOverlayTwCats = /* @__PURE__ */ new Set();
-    const getCategories = (tw, value) => {
-      const keys = value.values ? value.values.map((v) => v.key) : [value.key];
-      return keys.map((k) => tw.term.values?.[k]?.label || k);
-    };
-    for (const sampleName of selectedSampleNames) {
-      const sampleId = ds.sampleName2Id.get(sampleName);
-      const sampleData = data.samples[sampleId];
-      const samplePath = path.join(dirPath, sampleName) + ".nii";
-      let divideCategories = ["default"];
-      let overlayCategory = "default";
-      if (divideByTW && sampleData) {
-        const value = sampleData[divideByTW.$id];
-        if (value) divideCategories = getCategories(divideByTW, value);
-      }
-      if (overlayTW && sampleData) {
-        const value = sampleData[overlayTW.$id];
-        if (value) {
-          overlayCategory = getCategories(overlayTW, value).join(", ");
-          uniqueOverlayTwCats.add(overlayCategory);
-        }
-      }
-      for (const divideCategory of divideCategories) {
-        if (!divideByCat[divideCategory]) divideByCat[divideCategory] = {};
-        if (!query.legendFilter?.includes(overlayCategory)) {
-          if (!divideByCat[divideCategory][overlayCategory]) {
-            let color = overlayTW?.term?.values?.[overlayCategory]?.color;
-            if (overlayTW && isNumericTerm(overlayTW.term)) {
-              const bins = data.refs.byTermId[overlayTW.$id].bins;
-              color = bins.find((b) => b.label == overlayCategory).color;
-            }
-            divideByCat[divideCategory][overlayCategory] = {
-              samples: [],
-              color
-            };
-          }
-          divideByCat[divideCategory][overlayCategory].samples.push(samplePath);
-        }
-      }
-    }
-    const k2c = getColors(uniqueOverlayTwCats.size);
-    const lengths = [];
-    for (const dcategory in divideByCat) {
-      for (const category in divideByCat[dcategory]) {
-        const overlayCat = divideByCat[dcategory][category];
-        const samples = overlayCat.samples;
-        lengths.push(samples.length);
-        if (!overlayCat.color) overlayCat.color = category == "default" ? "red" : k2c(category);
-      }
-    }
-    const maxLength = Math.max(...lengths);
-    const brainImageDict = {};
-    const legend = {};
-    for (const dcategory in divideByCat) {
-      let catNum = 0;
-      const filesByCat = divideByCat[dcategory];
-      for (const category in filesByCat) {
-        if (filesByCat[category].samples.length < 1) continue;
-        catNum += filesByCat[category].samples.length;
-        if (!legend[category]) legend[category] = { color: filesByCat[category].color, maxLength };
-      }
-      const arg = {
-        refFile,
-        plane,
-        index,
-        maxLength,
-        filesByCat: JSON.stringify(filesByCat)
-      };
-      let url;
-      try {
-        url = await run_python("plotBrainImaging.py", JSON.stringify(arg));
-      } catch (error) {
-        const errmsg = "Error running Python script:" + error;
-        throw new Error(errmsg);
-      }
-      brainImageDict[dcategory] = { url, catNum };
-    }
-    if (query.legendFilter) {
-      for (const cat of query.legendFilter) {
-        legend[cat] = {
-          color: "white",
-          maxLength,
-          crossedOut: true
-        };
-      }
-    }
-    return [brainImageDict, legend];
-  } else {
-    throw "no reference or sample files";
-  }
-}
-export {
-  init
-};

package/routes/brainImagingSamples.js

@@ -1,71 +0,0 @@
-import fs from "fs";
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
-import { getData } from "#src/termdb.matrix.js";
-import { filterSampleNamesByAccess } from "#src/termdb.sql.js";
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const query = req.query;
-      const g = genomes[query.genome];
-      if (!g) throw "invalid genome name";
-      const ds = g.datasets[query.dslabel];
-      if (!ds) throw "invalid dataset name";
-      const samples = await getBrainImageSamples(query, genomes);
-      res.send({ samples });
-    } catch (e) {
-      console.log(e);
-      res.status(404).send(typeof e == "string" ? e : "Cannot get brain imaging samples");
-    }
-  };
-}
-async function getBrainImageSamples(query, genomes) {
-  const ds = genomes[query.genome].datasets[query.dslabel];
-  const q = ds.queries.NIdata;
-  if (q.checkDataAccess) {
-    if (!q.checkDataAccess(query)) throw "no access";
-  }
-  const ref = q.references[query.refKey];
-  if (!ref) throw "invalid refKey";
-  if (ref.referenceFile && ref.samples) {
-    const dirPath = path.join(serverconfig.tpmasterdir, ref.samples);
-    const files = (await fs.promises.readdir(dirPath, { withFileTypes: true })).filter((f) => f.isFile() && f.name.endsWith(".nii")).map((f) => f.name);
-    let sampleNames = files.map((name) => name.split(".nii")[0]);
-    sampleNames = await filterSampleNamesByAccess(query, ds, sampleNames);
-    if (query.samplesOnly) return sampleNames.map((name) => ({ sample: name }));
-    if (ref.sampleColumns) {
-      const terms = ref.sampleColumns.map((term) => {
-        const termjson = ds.cohort.termdb.q.termjsonByOneid(term.termid);
-        return {
-          $id: term.termid,
-          term: termjson,
-          q: termjson?.type == "float" || termjson?.type == "integer" ? { mode: "continuous" } : {}
-        };
-      });
-      const data = await getData({ terms, __protected__: query.__protected__ }, ds);
-      if (data.error) throw data.error;
-      const samples = {};
-      for (const s of sampleNames) {
-        const annoForOneS = { sample: s };
-        const sid = ds.cohort.termdb.q.sampleName2id(s);
-        const sampleData = data.samples?.[sid];
-        if (sampleData) {
-          for (const term of ref.sampleColumns) {
-            const v = sampleData[term.termid];
-            if (!v) continue;
-            if (v.values) annoForOneS[term.termid] = v.values.map((x) => x.key).join(", ");
-            else if (v.value !== void 0) annoForOneS[term.termid] = v.value;
-          }
-        }
-        samples[s] = annoForOneS;
-      }
-      return Object.values(samples);
-    }
-    return sampleNames.map((name) => ({ sample: name }));
-  } else {
-    throw "no reference or sample files";
-  }
-}
-export {
-  init
-};