Prepare chunk path format fix

exampleData/cactus.bed

@@ -1,4 +1,4 @@
 ref	10	100	this is a test region
 ref	1000	2000	another region with a very long description to see how it will be displayed
-ref	2000	3000	pre-fecthed region	test_prechunk
+ref	2000	3000	pre-fecthed region	chunk-ref-2000-3000
 ref	4000	4500	pre-fecthed region but the chunk is missing	test_prechunk_missing

exampleData/cactus_subgraph.bed

@@ -0,0 +1 @@
+ref	2000	3000	Region ref:2000-3000	chunk-ref-2000-3000

exampleData/chunk-ref-1-20/tracks.json

@@ -1,15 +1,26 @@
-{
-    "trackFile": "cactus.vg", 
-    "trackType": "graph", 
-    "trackColorSettings": {"mainPalette": "plainColors", "auxPalette": "greys"}
-},
-{
-    "trackFile": "cactus0_10.sorted.gam", 
-    "trackType": "read", 
-    "trackColorSettings": {"mainPalette": "blues", "auxPalette": "reds"}
-},
-{
-    "trackFile": "cactus10_20.sorted.gam", 
-    "trackType": "read", 
-    "trackColorSettings": {"mainPalette": "blues", "auxPalette": "reds"}
-}
+[
+  {
+    "trackFile": "exampleData/cactus.vg",
+    "trackType": "graph",
+    "trackColorSettings": {
+      "mainPalette": "plainColors",
+      "auxPalette": "greys"
+    }
+  },
+  {
+    "trackFile": "exampleData/cactus0_10.sorted.gam",
+    "trackType": "read",
+    "trackColorSettings": {
+      "mainPalette": "blues",
+      "auxPalette": "reds"
+    }
+  },
+  {
+    "trackFile": "exampleData/cactus10_20.sorted.gam",
+    "trackType": "read",
+    "trackColorSettings": {
+      "mainPalette": "blues",
+      "auxPalette": "reds"
+    }
+  }
+]

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

@@ -0,0 +1,5 @@
+chunk.vg
+chunk_0_ref_2000_3000.annotate.txt
+chunk_0_ref_2000_3000.gam
+regions.tsv
+tracks.json

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

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

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

@@ -1,7 +1,18 @@
-{
-  "graph_file": "cactus.vg",
-  "haplotype_file": "",
-  "gam_files": [
-    "cactus-NA12879.sorted.gam"
-  ]
-}
+[
+  {
+    "trackFile": "exampleData/cactus.vg",
+    "trackType": "graph",
+    "trackColorSettings": {
+      "mainPalette": "plainColors",
+      "auxPalette": "greys"
+    }
+  },
+  {
+    "trackFile": "exampleData/cactus-NA12879.sorted.gam",
+    "trackType": "read",
+    "trackColorSettings": {
+      "mainPalette": "blues",
+      "auxPalette": "reds"
+    }
+  }
+]

scripts/prepare_chunks.sh

@@ -67,26 +67,39 @@ mkdir -p $OUTDIR
 
 vg_chunk_params=(-x $GRAPH_FILE -g -c 20 -p $REGION -T -b $OUTDIR/chunk -E $OUTDIR/regions.tsv)
 
+
 # construct track JSON for graph file
+# get path relative to directory above the scripts directory
+GRAPH_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $GRAPH_FILE)
+echo ${GRAPH_FILE_PATH}
 GRAPH_PALETTE="$(cat src/config.json | jq '.defaultGraphColorPalette')"
-jq -n --arg trackFile "${GRAPH_FILE}" --arg trackType "graph" --argjson trackColorSettings "$GRAPH_PALETTE" '$ARGS.named' >> $OUTDIR/tracks.json
+jq -n --arg trackFile "${GRAPH_FILE_PATH}" --arg trackType "graph" --argjson trackColorSettings "$GRAPH_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
 
 # construct track JSON for haplotype file, if provided
 HAPLOTYPE_PALETTE="$(cat src/config.json | jq '.defaultHaplotypeColorPalette')"
 if [[ ! -z "${HAPLOTYPE_FILE}" ]] ; then
-    jq -n --arg trackFile "${HAPLOTYPE_FILE}" --arg trackType "haplotype" --argjson trackColorSettings "$HAPLOTYPE_PALETTE" '$ARGS.named' >> $OUTDIR/tracks.json
+    HAPLOTYPE_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $HAPLOTYPE_FILE)
+    echo ${HAPLOTYPE_FILE_PATH}
+    jq -n --arg trackFile "${HAPLOTYPE_FILE_PATH}" --arg trackType "haplotype" --argjson trackColorSettings "$HAPLOTYPE_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
 fi
 
 # construct track JSON for each gam file
 echo >&2 "Gam Files:"
 READ_PALETTE="$(cat src/config.json | jq '.defaultReadColorPalette')"
 echo >&2 "Read Palette: $READ_PALETTE"
 for GAM_FILE in "${GAM_FILES[@]}"; do
-    echo >&2 " - $GAM_FILE"
-    jq -n --arg trackFile "${GAM_FILE}" --arg trackType "read" --argjson trackColorSettings "$READ_PALETTE" '$ARGS.named' >> $OUTDIR/tracks.json
+    GAM_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $GAM_FILE)
+    echo >&2 " - $GAM_FILE_PATH"
+    jq -n --arg trackFile "${GAM_FILE_PATH}" --arg trackType "read" --argjson trackColorSettings "$READ_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
     vg_chunk_params+=(-a $GAM_FILE)
 done
 
+# put all tracks objects into an array
+(jq -s '.' < $OUTDIR/temp.json) > $OUTDIR/tracks.json
+
+rm $OUTDIR/temp.json
+
+
 # construct node file
 if [[ ! -z "${NODE_COLORS}" ]] ; then
     for NODENAME in "${NODE_COLORS[@]}"; do

scripts/prepare_local_chunk.sh

@@ -67,9 +67,12 @@ REGION_END="$(echo ${REGION} | rev | cut -f1 -d'-' | rev)"
 REGION_START="$(echo ${REGION} | rev | cut -f2 -d'-' | cut -f1 -d':' | rev)"
 REGION_CONTIG="$(echo ${REGION} | rev| cut -f2- -d':' | rev)"
 
+# get path relative to directory above the scripts directory
+GRAPH_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $GRAPH_FILE)
+
 # construct track JSON for graph file
 GRAPH_PALETTE="$(cat src/config.json | jq '.defaultGraphColorPalette')"
-jq -n --arg trackFile "${GRAPH_FILE}" --arg trackType "graph" --argjson trackColorSettings "$GRAPH_PALETTE" '$ARGS.named' >> $OUTDIR/tracks.json
+jq -n --arg trackFile "${GRAPH_FILE_PATH}" --arg trackType "graph" --argjson trackColorSettings "$GRAPH_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
 
 # Put the graphy file in place
 vg convert -p "${GRAPH_FILE}" > $OUTDIR/chunk.vg
@@ -82,8 +85,10 @@ GAM_NUM=0
 READ_PALETTE="$(cat src/config.json | jq '.defaultReadColorPalette')"
 for GAM_FILE in "${GAM_FILES[@]}"; do
     echo >&2 " - $GAM_FILE"
+
+    GAM_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $GAM_FILE)
     # construct track JSON for each gam file
-    jq -n --arg trackFile "${GAM_FILE}" --arg trackType "read" --argjson trackColorSettings "$READ_PALETTE" '$ARGS.named' >> $OUTDIR/tracks.json
+    jq -n --arg trackFile "${GAM_FILE_PATH}" --arg trackType "read" --argjson trackColorSettings "$READ_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
     # Work out a chunk-internal GAM name with the same leading numbering vg chunk uses
     if [[ "${GAM_NUM}" == "0" ]] ; then
         GAM_LEADER="chunk"
@@ -98,6 +103,11 @@ for GAM_FILE in "${GAM_FILES[@]}"; do
     GAM_NUM=$((GAM_NUM + 1))
 done
 
+# put all tracks objects into an array
+(jq -s '.' < $OUTDIR/temp.json) > $OUTDIR/tracks.json
+
+rm $OUTDIR/temp.json
+
 # construct node file
 if [[ ! -z "${NODE_COLORS}" ]] ; then
     for NODENAME in "${NODE_COLORS[@]}"; do

src/components/CopyLink.js

@@ -30,6 +30,7 @@ export function CopyLink(props) {
     // Don't stringify objects for readability
     // https://github.com/ljharb/qs#stringifying
     const params = qs.stringify(viewTarget, { encodeValuesOnly: true });
+    console.log("params ", params);
     // complete url
     const full = window.location.origin + "?" + params;
     console.log(full);

src/server.mjs

@@ -1432,21 +1432,9 @@ async function getBedRegions(bed) {
       if (fs.existsSync(track_json)) {
         // Create string of tracks data
         const string_data = fs.readFileSync(track_json);
-        const parser = new JSONParser({separator: ''});
-        parser.onValue = ({value, key, parent, stack}) => {
-          if (stack.length > 0) {
-            // ignore inner values
-            return;
-          }
-          if (!Object.hasOwn(value, 'trackFile')) {
-            throw new BadRequestError('Non-track object in tracks.json: ' + JSON.stringify(value))
-          }
-          // put tracks in array
-          tracks_array.push(value);
-        };
-        parser.write(string_data);
+
         // Convert to object container like the client component prop types expect
-        tracks = {...tracks_array}; 
+        tracks = JSON.parse(string_data);
       }
     }