Merge pull request #375 from vgteam/reproduce-pan-problem

Add example needed to reproduce pannign issue (without crashing)

exampleData/cactus.bed

@@ -1,5 +1,6 @@
 ref	10	100	this is a test region
+ref	500	600	region without read tracks	chunk-cactus-no-reads
 ref	1000	2000	another region with a very long description to see how it will be displayed
 ref	2000	3000	pre-fetched region	chunk-ref-2000-3000
 ref	4000	4500	pre-fetched region but the chunk is missing	test_prechunk_missing
-ref	482	2450	region without read tracks	chunk-cactus-no-reads
+

exampleData/chunk-ref-2000-3000/chunk_contents.txt

@@ -1,5 +1,5 @@
 chunk.vg
-chunk_0_ref_2000_3000.annotate.txt
-chunk_0_ref_2000_3000.gam
+chunk_0_ref_1955_5023.annotate.txt
+chunk_0_ref_1955_5023.gam
 regions.tsv
 tracks.json

exampleData/chunk-ref-2000-3000/regions.tsv

@@ -1 +1 @@
-ref	2000	3000	chunk_0_ref_2000_3000.gam	chunk_0_ref_2000_3000.annotate.txt
+ref	1955	5024	exampleData/chunk-ref-2000-3000/chunk_0_ref_1955_5023.gam	exampleData/chunk-ref-2000-3000/chunk_0_ref_1955_5023.annotate.txt

exampleData/chunk-ref-2000-3000/tracks.json

@@ -1,18 +1,20 @@
 [
   {
-    "trackFile": "exampleData/cactus.vg",
+    "trackFile": "exampleData/cactus.vg.xg",
     "trackType": "graph",
     "trackColorSettings": {
-      "mainPalette": "plainColors",
-      "auxPalette": "greys"
+      "mainPalette": "#000000",
+      "auxPalette": "greys",
+      "colorReadsByMappingQuality": false
     }
   },
   {
     "trackFile": "exampleData/cactus-NA12879.sorted.gam",
     "trackType": "read",
     "trackColorSettings": {
       "mainPalette": "blues",
-      "auxPalette": "reds"
+      "auxPalette": "reds",
+      "colorReadsByMappingQuality": false
     }
   }
 ]

exampleData/chunk-without-source/chunk.vg

@@ -0,0 +1,162 @@
+VG�%
+g
+cAGACGGAGTCTTGCTCTTGTTGCTCAGCCTGGAATGCAATGGCACGATCTCAGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTC
+g
+cAGCCTCCCAAGTAGCAGGGATTACAGGTGCCTGCCACCATGCCAGGCTAATTGTTTTTTCTTTTTTTTCAGATGGAGTCTCACTCTGTCACTCAGGCTG
+g
+cGATTGTGATGGTGTGATCTCAGCTCACTGCAACCTCAACATCCTGGGTTCAAGCGATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACTACAAGTGCG
+g
+cTGCCACCATGCCTGGCTAATTTTTTTTAGTATTTTTAGTAGAGATGGGGTTTCGCCATATTGGCCAGGCTGGTCTCAAACTCCTGATGTCAGGTGATCC
+g
+cGCCCTGAGGCTGAGGCAGGAGAATCATTTAAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGACTGGGCCACTGCACTCCAGCCTGCTAAGTGACAGAG
+g
+cTGAGACTCCACCTCAAAAAAAAAAAAAAAAGGCAATGCTTCAGGACATAAGGCCTTGCTCTGAAGAGGCCCTAGGAGTGACTCCTGGTGACAGTGAAAG
+g
+cCCCACAGCCTCTGGCAACTGTATTAACATGAACTTCAATCTGTTAAAGGAAAGCCACCAGGAAAACAGCACTGTAATTTAACGATGTGGAAAAATGTAT 
+g
+cGTAATATCTTAAGGAAAAAAGCAAAACAGTGTAATTATGATCACATTTTATAAAATACACGTGTATATATACGCACATATGCCTGGTGGAGTTTTATGG!
+g
+cTGATCATCTCCAAGTGGTGGAATTACTGGGATTATTTTATTGTTTTTGTGTAAATTTATACTTTCTTTTTTCTTTTTGAGACACGGTCTCGCTCTGTCG"
+g
+cCCCAGGCTGGAGTACAGTGGTGTGATCGTGGCTCACTGAAGCATCAACCTCCTGAGCTCAAGTGATCCTCCCACCTCAGCTTCCCAAGTAGCTGCGACT#
+g
+cACAGGCATCTGCCACCACACCCAGCTACTTTTTAAATTTGTTGTACAGATGAAGTCTCCTTATGTTGCCCAGGCTGGTCTCGAACTTCTAGGCTCCCAC$
+g
+cCTTGACCTCCATCTTGACCTCCCAAAGTGCTGGAATTATAGGCATGAGCCACCATGCCCGGCCTTGATTTATGTTTTTGTGATGAACATTCATATCTTA%
+g
+cCTCCCACCCCATGGAAACAGTTCATGTATTACTTTTACAATATAAAACAAATAACAATAAAAACATCAAAAAGACATTTTAGCCATTCATTCAACAAAT&
+g
+cATTTAAAATGTGCCAAGAACTGTGCTACTCAAGCACCAGGTAATGAGTGATAAACCAAACCCATGCAAAAGGACCCCATATAGCACAGGTACATGCAGG'
+g
+cCACCTTACCATGGAAGCCATTGTCCTCTGTCCAGGCATCTGGCTGCACAACCACAATTGGGTGGACACCCTGGATCCCCAGGAAGGAAAGAGCATTCAA(
+g
+cAGTGTCAAAGTAGGACTACTGGAACTGTCACTTCATCATTTTTTTTGTTTGTTTTTGAGACAGGGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGT)
+g
+cGTGATCTCAGCTCACTGCCACCTCTGCCTCCTGGGCTCAAGCAATCCTTCCATCTCAGCCTCCTAAGTAGCTGGAACTACAGACACGTACCACCACCCC*
+g
+cTGGCTAATTTTTTTGTATTTTTGGTAGAGACAGGGTTTTGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAACTTCACCCCCGGGATTATAGG+
+g
+cCATGAGCCACCGCACCCAGCCTTGGCTAATTTTTAATAATTTTTTTGTAGACATGAGGTCCTACTGTATTGCCCAGGCTGGTCTTCAGCTCCCAGGCTC,
+g
+cAAGCGATTCTCCCACCTTGGCCTCCCAGTGTTGTGATTACAGGGGTGGGGCACTGGCCCAGCCCATCATTTCTCTCTCTCTCTTTTTTTTTGAGACGGA-
+g
+cGTCTCGCTCTGTCGCCCGGGCTGGAGTGCAGTGGCGCGATCTTGGCTCACTGCAACCTCCGCCTCCGGGGTTCAAGCGATTCTCCTGCCCCAGCCCCTC.
+g
+cAAGTAGCTGGGACTACAGGCGTGCGCCCCTACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTTGGCCAGGATGGTCTC/
+g
+cGATCTCTTGACCTCGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTAGCTTTTCTCTCTCTCTCTTTTTTT0
+g
+cTTTTTTTTAGACAAAGTCTCACTCTGTCACCCAGTCTGGAGTGCAGTGGTGCAATCTTGGCTCACTGCAACCTCTGCCTCCCACGTTCAAGCGATGCTC1
+g
+cACACCTCAACTTCCCAAATAGCTGGCATTACAGGCATGCTCCACCAGGCCTGGCTACTTTTTGTTTTTTTTTTTTTAGTACAGATGGGGTTTCACCATG2
+g
+cTTGGCCAGGCTGGTCTCAAACTCCTGACAAGTGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGACATGAGCCACCATGCCCAGCCTCCAG3
+g
+cCCCATCATTTCTTGATGATTTGTTGAAACACAGTATGCTGGGGCAGTCACAGAGAGGAGGGGGAGGGACATATGGGAAAAAGAGTTAGAGGGAAAAAGT4
+g
+cCTTCCCTCAGTATATTTAATATGTGCAGTTCTCAAATCCTTACCCATCCCTTACAGATGGAGTCTTTTGGCACAGGTATGTGGGCAGAGAAGACTTCTG5
+g
+cAGGCTACAGTAGGGGCATCCATAGGGACTGACAGGTGCCAGTCTTGCTCACAGGAGAGAATATTGTGTCCTCCCTCTCTGACAGGGCACCCAATACTTA6
+g
+cCTGTGCCAAGGGTGAATGATGAAAGCTCCTTCACCACAGAAGCACCACACAGCTGTACCATCCATTCCAGTTGATCTAAAATGGACATTTAGATGTAAA7
+g
+cATCACTGCAGTAATCTGCATACTTAACCCAGGCCCTCTACCCTACACTCTCCGGATGAAGGCTTATAGCAAGACCTCTCAATGGGAGAGTCTGTCTCTC8  !!""##$$%%&&''(())**++,,--..//00112233445566778�
+GI262359905[76167]
+8 
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+GI528476558[1937]
+cc(

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+"cc(	
+#cc(
+
+$cc(
+%cc(
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exampleData/chunk-without-source/chunk_contents.txt

@@ -0,0 +1,5 @@
+chunk.vg
+chunk_0_ref_1955_5023.annotate.txt
+chunk_0_ref_1955_5023.gam
+regions.tsv
+tracks.json

exampleData/chunk-without-source/regions.tsv

@@ -0,0 +1 @@
+ref	2000	3000	chunk_0_ref_2000_3000.gam	chunk_0_ref_2000_3000.annotate.txt

exampleData/chunk-without-source/tracks.json

@@ -0,0 +1,18 @@
+[
+  {
+    "trackFile": "exampleData/nonexistent.vg",
+    "trackType": "graph",
+    "trackColorSettings": {
+      "mainPalette": "plainColors",
+      "auxPalette": "greys"
+    }
+  },
+  {
+    "trackFile": "exampleData/stillnotareal.sorted.gam",
+    "trackType": "read",
+    "trackColorSettings": {
+      "mainPalette": "blues",
+      "auxPalette": "reds"
+    }
+  }
+]

exampleData/no_source.bed

@@ -0,0 +1 @@
+ref	2000	3000	region with no source graph available	chunk-without-source

scripts/prepare_chunks.sh

@@ -115,6 +115,10 @@ do
     printf "$file\n" >> $OUTDIR/chunk_contents.txt
 done
 
-# Print BED line
-cat $OUTDIR/regions.tsv | cut -f1-3 | tr -d "\n"
+# Print BED line, using the region we were passed as the coordinates
+echo "${REGION%:*}" | tr -d "\n"
+printf "\t"
+echo "${REGION}" | rev | cut -f1 -d'-' | rev | tr -d "\n"
+printf "\t"
+echo "${REGION}" | rev | cut -f2 -d'-' | cut -f1 -d':' | rev | tr -d "\n"
 printf "\t${DESC}\t${OUTDIR}\n"

src/server.mjs

@@ -206,19 +206,23 @@ async function lockDirectories(directoryPaths, lockType, func) {
   // attempt to acquire a lock for the next directory, and call lockDirectories on the remaining directories
   const currDirectory = directoryPaths.pop();
   return lockDirectory(currDirectory, lockType, async function() {
-    lockDirectories(directoryPaths, lockType, func);
+    return lockDirectories(directoryPaths, lockType, func);
   })
 }
 
 // runs every hour
 // deletes any files in the download directory past the set fileExpirationTime set in config
-cron.schedule('0 * * * *', () => {
+cron.schedule('0 * * * *', async () => {
   console.log("cron scheduled check");
   // attempt to acquire a write lock for each on the directory before attemping to delete files
   for (const dir of [DOWNLOAD_DATA_PATH, UPLOAD_DATA_PATH]) {
-    lockDirectory(dir, lockTypes.WRITE_LOCK, async function() {
-      deleteExpiredFiles(dir);
-    });
+    try {
+      await lockDirectory(dir, lockTypes.WRITE_LOCK, async function() {
+        deleteExpiredFiles(dir);
+      });
+    } catch (e) {
+      console.error("Error checking for expired files in " + dir + ":", e);
+    }
   }
 });
 
@@ -349,20 +353,28 @@ function getGams(tracks) {
   return getFilesOfType(tracks, fileTypes.READ);
 }
 
+// To bridge Express next(err) error handling and async function error
+// handling, we have this adapter. It takes Express's next and an async
+// function and calls next with any error raised when the async function is
+// initially called *or* when its promise is awaited.
+async function captureErrors(next, callback) {
+  try {
+    await callback();
+  } catch (e) {
+    next(e);
+  }
+}
+
 api.post("/getChunkedData", (req, res, next) => {
   // We would like this to be an async function, but then Express error
   // handling doesn't work, because it doesn't detect returned promise
   // rejections until Express 5. We have to pass an error to next() or else
   // throw synchronously.
-  //
-  // So we set up a promise here and we make sure to handle failures
-  // ourselves with next().
-
-  // put readlock on necessary directories while processing chunked data
-  lockDirectories([DOWNLOAD_DATA_PATH, UPLOAD_DATA_PATH], lockTypes.READ_LOCK, async function() {
-    let promise = getChunkedData(req, res, next);
-    promise.catch(next);
-    await promise;
+  captureErrors(next, async () => {
+    // put readlock on necessary directories while processing chunked data
+    return lockDirectories([DOWNLOAD_DATA_PATH, UPLOAD_DATA_PATH], lockTypes.READ_LOCK, async function() {
+      return getChunkedData(req, res, next);
+    });
   });
 });
 
@@ -1529,28 +1541,23 @@ async function getChunkTracks (bedFile, chunk) {
 // Expects a request with a bed file and a chunk name
 // Returns tracks retrieved from getChunkTracks
 api.post("/getChunkTracks", (req, res, next) => {
-  console.log("received request for chunk tracks");
-  if (!req.body.bedFile || !req.body.chunk) {
-    throw new BadRequestError("Invalid request format", req.body.bedFile, req.body.chunk);
-  }
-  let promise = (async () => {
+  captureErrors(next, async () => {
+    console.log("received request for chunk tracks");
+    if (!req.body.bedFile || !req.body.chunk) {
+      throw new BadRequestError("Invalid request format", req.body.bedFile, req.body.chunk);
+    }
+
     // tracks are falsy if fetch is unsuccessful
 
     // TODO: This operation needs to hold a reader lock on the upload/download directories.
     // waiting for lock changes to be merged
     const tracks = await getChunkTracks(req.body.bedFile, req.body.chunk);
     res.json({ tracks: tracks });
-  })();
-
-  // schedules next to be called if promise is rejected
-  promise.catch(next);
-
+  });
 });
 
 api.post("/getBedRegions", (req, res, next) => {
-  // Bridge async functions to Express error handling with next(err). Don't
-  // return a promise. 
-  let promise = (async () => {
+  captureErrors(next, async () => {
     console.log("received request for bedRegions");
     const result = {
       bedRegions: [],
@@ -1564,8 +1571,7 @@ api.post("/getBedRegions", (req, res, next) => {
     } else {
       throw new BadRequestError("No BED file specified");
     }
-  })();
-  promise.catch(next);
+  });
 });
 
 // Load up the given BED file by URL or path, and