Ensure upload directories exist for sequencing results

rosalindfranklininstitute · Oct 4, 2023 · d29075f · d29075f
1 parent ef73fec
commit d29075f
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Showing 2 changed files with 42 additions and 27 deletions.
diff --git a/backend/antigenapi/views.py b/backend/antigenapi/views.py
@@ -1,4 +1,5 @@
 import collections.abc
+import io
 import os
 import urllib.error
 import urllib.parse
@@ -597,22 +598,38 @@ def upload_sequencing_run_results(self, request, pk, submission_idx):
         # TODO: Validate submission_idx
 
         # Run bioinformatics using .zip file
-        print("Extracting zip file...")
+        # print("Extracting zip file...")
         seq_data = load_sequences(results_file.temporary_file_path())
 
         # Convert to FASTA in-memory (vquest api handles chunking to
         # max 50 seqs per file)
         fasta_file = as_fasta_files(seq_data, max_file_size=None)[0]
 
         # Submit to vquest
-        print("Running vquest...")
+        # print("Running vquest...")
         vquest_results = run_vquest(fasta_file)
 
         parameters_file_data = vquest_results["Parameters.txt"]
         vquest_airr_data = vquest_results["vquest_airr.tsv"]
 
         base_filename = f"SequencingResults_{pk}_{submission_idx}"
 
+        # Make sure directory exists
+        base_dirs = set(
+            [
+                os.path.join(
+                    settings.MEDIA_ROOT,
+                    SequencingRunResults.parameters_file.field.upload_to,
+                ),
+                os.path.join(
+                    settings.MEDIA_ROOT, SequencingRunResults.airr_file.field.upload_to
+                ),
+            ]
+        )
+
+        for base_dir in base_dirs:
+            os.makedirs(base_dir, exist_ok=True)
+
         # Create SequencingRunResults object
         with open(
             os.path.join(
@@ -655,7 +672,7 @@ def upload_sequencing_run_results(self, request, pk, submission_idx):
         name="Get sequencing results.",
         url_path="results",
     )
-    def upload_sequencing_run_results(self, request, pk):
+    def get_sequencing_run_results(self, request, pk):
         """Get sequencing results."""
         IMPORTANT_COLUMNS = (
             "sequence_id",
@@ -673,7 +690,8 @@ def upload_sequencing_run_results(self, request, pk):
             sequencing_run_id=int(pk)
         ).order_by("seq")
 
-        import io
+        if not results:
+            return JsonResponse({"records": []})
 
         csvs = []
         for r in results:

diff --git a/frontend/src/crudtemplates/utils.js b/frontend/src/crudtemplates/utils.js
@@ -145,7 +145,6 @@ export const uploadSequencingResults = (event, props) => {
   ).then((res) => {
     props.setLoading(false);
     res.json().then((json) => {
-      console.log(json);
       props.setRecord(json);
     });
   });
@@ -208,28 +207,26 @@ export const displayFieldSingle = (field, record, context, props) => {
           </button>
         </a>,
       );
-      if (record.sequencingrunresults_set.find((x) => x.seq === p)) {
-        // Sequencing results found
-      } else {
-        // Sequencing results not uploaded yet
-        retVal.push(
-          <label
-            key={"resultsFileUpload" + p}
-            type="button"
-            className="w-full cursor-pointer sm:w-auto mb-2 mt-2 sm:mb-0 relative inline-flex items-center justify-center rounded-md border border-transparent bg-teal-600 px-4 py-2 text-sm font-medium text-white shadow-sm hover:bg-teal-700 focus:outline-none focus:ring-2 focus:ring-teal-500 focus:ring-offset-2"
-          >
-            <input
-              type="file"
-              data-residx={p}
-              data-seqidx={record.id}
-              onChange={(event) => uploadSequencingResults(event, props)}
-              className="hidden"
-              name={"resultsFile" + p}
-            />
-            Upload sequencing results file
-          </label>,
-        );
-      }
+      retVal.push(
+        <label
+          key={"resultsFileUpload" + p}
+          type="button"
+          className="w-full cursor-pointer sm:w-auto mb-2 mt-2 sm:mb-0 relative inline-flex items-center justify-center rounded-md border border-transparent bg-teal-600 px-4 py-2 text-sm font-medium text-white shadow-sm hover:bg-teal-700 focus:outline-none focus:ring-2 focus:ring-teal-500 focus:ring-offset-2"
+        >
+          <input
+            type="file"
+            data-residx={p}
+            data-seqidx={record.id}
+            onChange={(event) => uploadSequencingResults(event, props)}
+            className="hidden"
+            name={"resultsFile" + p}
+          />
+          {(record.sequencingrunresults_set.find((x) => x.seq === p) &&
+            "Replace") ||
+            "Upload"}{" "}
+          sequencing results file
+        </label>,
+      );
     }
     return retVal;
   } else if (field.type === "platethreshold" && record[field.field]) {