issue #1171 - generate download

SACGF · Sep 19, 2024 · 91f8e9a · 91f8e9a
1 parent 4f3d973
commit 91f8e9a
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Showing 7 changed files with 80 additions and 72 deletions.
diff --git a/analysis/grid_export.py b/analysis/grid_export.py
@@ -92,6 +92,14 @@ def _grid_export_vcf(genome_build, colmodels, items, sample_ids, sample_names_by
     pseudo_buffer = StashFile()
 
     vcf_writer = Writer(pseudo_buffer, vcf_reader)
+    # Need to pass escapechar
+    vcf_writer.writer = csv.writer(
+        pseudo_buffer,
+        delimiter="\t",
+        lineterminator="\n",
+        quoting=csv.QUOTE_NONE,
+        escapechar="\\",
+    )
 
     def iter_row_writer():
         for obj in items:

diff --git a/analysis/views/views_grid.py b/analysis/views/views_grid.py
@@ -119,6 +119,8 @@ def cohort_grid_export(request, cohort_id, export_type):
     params_hash = get_grid_downloadable_file_params_hash(cohort_id, export_type)
     task = export_cohort_to_downloadable_file.si(cohort_id, export_type)
     cgf = CachedGeneratedFile.get_or_create_and_launch("export_cohort_to_downloadable_file", params_hash, task)
+    if cgf.exception:
+        raise ValueError(cgf.exception)
     return redirect(cgf)
 
 

diff --git a/library/django_utils/jqgrid_view.py b/library/django_utils/jqgrid_view.py
@@ -136,7 +136,7 @@ def grid_export_csv(colmodels, items) -> Iterator[str]:
     pseudo_buffer = StashFile()
     header, labels = colmodel_header_labels(colmodels, label_overrides=label_overrides)
     # Don't use dictwriter as some sample names may be the same
-    writer = csv.writer(pseudo_buffer, dialect='excel')
+    writer = csv.writer(pseudo_buffer, dialect='excel', escapechar='\\', quoting=csv.QUOTE_NONE)
     writer.writerow(header)
 
     def iter_row_writer():

diff --git a/snpdb/models/models.py b/snpdb/models/models.py
@@ -57,7 +57,7 @@ class CachedGeneratedFile(models.Model):
     generator = models.TextField()
     params_hash = models.TextField()  # sha256 of params
     task_id = models.CharField(max_length=36, null=True)
-    task_status = models.TextField(null=True)  # TODO: what's the actual size?
+    task_status = models.TextField(null=True)
     generate_start = models.DateTimeField(null=True)
     generate_end = models.DateTimeField(null=True)
 

diff --git a/snpdb/templates/snpdb/data/view_vcf.html b/snpdb/templates/snpdb/data/view_vcf.html
@@ -283,42 +283,67 @@
         });
     });
 
-    function pollAndDownloadFile(selector, fileType) {
-        const spinnerId = 'spinner-' + fileType;
-        function downloadFile(data) {
-            /*
-            $("#" + spinnerId).replaceWith('<i class="fas fa-xmark"></i> Error retrieving download...');
-
-                                <a href="{{ annotated_vcf_url }}">
-                                    <div class="icon24 left margin-r-5 vcf-icon"></div> Annotated VCF
-                                </a>
+    class AnnotatedFileDownload {
+        constructor(selector, pollUrl, fileType) {
+            this.selector = $(selector);
+            this.pollUrl = pollUrl;
+            this.fileType = fileType;
+            this.ucFileType = this.fileType.toUpperCase()
+        }
 
+        setGenerateDownloadLink() {
+            // console.log("setGenerateDownloadLink");
+            const that = this;
+            const generateLink = $(`<a href="#" id="generate-${this.fileType}-download"><div class="icon24 left margin-r-5 ${this.fileType}-icon"></div> Annotated ${this.ucFileType}</a>`);
+            generateLink.click(function(event) {
+                event.preventDefault();
+                that.setPolling(true);
+            });
+            this.selector.empty();
+            this.selector.append(generateLink);
+            console.log("/setGenerateDownloadLink");
+        }
 
-             */
-            window.location.href = data.url;
+        setDownloadLink(url) {
+            // console.log("setDownloadLink");
+            this.selector.html(`<a href="${url}"><div class="icon24 left margin-r-5 ${this.fileType}-icon"></div> Annotated ${this.ucFileType}</a>`);
         }
 
-        let failureFunc = function(data) {
-            console.log("Fail!");
-            $("#" + spinnerId).replaceWith('<i class="fas fa-xmark"></i> Error retrieving download...');
+        setError() {
+            // console.log("setError");
+            this.selector.html('<i class="fas fa-xmark"></i> Error retrieving download...');
         }
 
-        $(selector).replaceWith(`<span id="${spinnerId}"><i class="fas fa-spinner fa-spin"></i> Preparing download...</span>`);
-        let pollUrl = Urls.cohort_grid_export({{ vcf.cohort.pk  }}, fileType);
-        poll_cached_generated_file(pollUrl, downloadFile, failureFunc);
+        setPolling(download) {
+            // console.log("setPolling");
+            let that = this;
+            function downloadFile(data) {
+                that.setDownloadLink(data.url);
+                if (download) {
+                    window.location.href = data.url;
+                }
+            }
+            $(this.selector).html(`<span><i class="fas fa-spinner fa-spin"></i> Preparing download...</span>`);
+            poll_cached_generated_file(this.pollUrl, downloadFile, this.setError)
+        }
     }
 
-    $("#generate-vcf-download").click(function(event) {
-        event.preventDefault();
-        pollAndDownloadFile(this, "vcf");
-    });
-
-
-    $("#generate-csv-download").click(function(event) {
-        event.preventDefault();
-        pollAndDownloadFile(this, "csv");
-    });
-
+    {% for file_type, cgf in annotated_download_files.items %}
+        var pollUrl = Urls.cohort_grid_export({{ vcf.cohort.pk  }}, "{{ file_type }}");
+        var afdSelector = $("div#generate-{{ file_type }}-download");
+        var afd = new AnnotatedFileDownload(afdSelector, pollUrl, "{{ file_type }}");
+        {% if cgf %}
+            {% if cgf.exception %}
+                afd.setError()
+            {% elif cgf.status == "SUCCESS" %}
+                afd.setDownloadLink("{{ cgf.get_media_url  }}");
+            {% else %}
+                afd.setPolling(false);
+            {% endif %}
+        {% else %}
+            afd.setGenerateDownloadLink();
+        {% endif %}
+    {% endfor %}
 });
 </script>
 <script type="text/javascript" src="{% static 'js/grid.js' %}"></script>
@@ -351,38 +376,16 @@ <h1>VCF: {{ vcf.name }}</h1>
         {% csrf_token %}
         {% crispy vcf_form form_helper.horizontal %}
 
-        {% if can_download_vcf %}
+        {% if annotated_download_files or vcf.uploadedvcf.uploaded_file.exists %}
             <div class="form-group-row row">
                 <label class="col-form-label col-12 col-md-3 text-md-right">Download</label>
                 <div class="d-flex flex-row">
                     {% if vcf.uploadedvcf.uploaded_file.exists %}
                         <div class="p-2"><a href="{% url 'download_uploaded_file' vcf.uploadedvcf.uploaded_file.pk %}"><div class="icon24 left margin-r-5 vcf-icon"></div> Original VCF</a> ({{ vcf.uploadedvcf.uploaded_file.size|filesizeformat }})</div>
                     {% endif %}
-                    {% if can_download_annotated_vcf %}
-                        <div class="p-2">
-                            {% if annotated_vcf_url %}
-                                <a href="{{ annotated_vcf_url }}">
-                                    <div class="icon24 left margin-r-5 vcf-icon"></div> Annotated VCF
-                                </a>
-                            {% else %}
-                                <a href="#" id="generate-vcf-download">
-                                    <div class="icon24 left margin-r-5 vcf-icon"></div> Annotated VCF
-                                </a>
-                            {% endif %}
-                        </div>
-                        <div class="p-2">
-                            {% if annotated_csv_url %}
-                                <a href="{{ annotated_csv_url }}">
-                                    <div class="icon24 left margin-r-5 csv-icon"></div> Annotated CSV
-                                </a>
-                            {% else %}
-                                <a href="#" id="generate-csv-download">
-                                    <div class="icon24 left margin-r-5 csv-icon"></div> Annotated CSV
-                                </a>
-                            {% endif %}
-
-                        </div>
-                    {% endif %}
+                    {% for file_type in annotated_download_files %}
+                        <div id="generate-{{ file_type }}-download" class="p-2"></div>
+                    {% endfor %}
                 </div>
             </div>
         {% endif %}

diff --git a/snpdb/views/views.py b/snpdb/views/views.py
@@ -282,21 +282,18 @@ def view_vcf(request, vcf_id):
     except UploadedVCF.DoesNotExist:
         can_view_upload_pipeline = False
 
-    can_download_annotated_vcf = False
-    annotated_vcf_url = None
-    annotated_csv_url = None
+    annotated_download_files = {}
     if vcf.import_status == ImportStatus.SUCCESS and cohort_id:
         try:
             AnalysisTemplate.get_template_from_setting("ANALYSIS_TEMPLATES_AUTO_COHORT_EXPORT")
-            can_download_annotated_vcf = True
             params_hash_vcf = get_grid_downloadable_file_params_hash(cohort_id, "vcf")
-            if cgf_vcf := CachedGeneratedFile.objects.filter(generator="export_cohort_to_downloadable_file",
-                                                             params_hash=params_hash_vcf).first():
-                annotated_vcf_url = cgf_vcf.get_media_url()
+            cgf_vcf = CachedGeneratedFile.objects.filter(generator="export_cohort_to_downloadable_file",
+                                                         params_hash=params_hash_vcf).first()
             params_hash_csv = get_grid_downloadable_file_params_hash(cohort_id, "csv")
-            if cgf_csv := CachedGeneratedFile.objects.filter(generator="export_cohort_to_downloadable_file",
-                                                             params_hash=params_hash_csv).first():
-                annotated_csv_url = cgf_csv.get_media_url()
+            cgf_csv = CachedGeneratedFile.objects.filter(generator="export_cohort_to_downloadable_file",
+                                                         params_hash=params_hash_csv).first()
+
+            annotated_download_files = {"vcf": cgf_vcf, "csv": cgf_csv}
         except ValueError:
             pass
 
@@ -311,10 +308,8 @@ def view_vcf(request, vcf_id):
         'patient_form': PatientForm(user=request.user),  # blank
         'has_write_permission': has_write_permission,
         'can_download_vcf': (not settings.VCF_DOWNLOAD_ADMIN_ONLY) or request.user.is_superuser,
-        'can_download_annotated_vcf': can_download_annotated_vcf,
         'can_view_upload_pipeline': can_view_upload_pipeline,
-        'annotated_vcf_url': annotated_vcf_url,
-        'annotated_csv_url': annotated_csv_url,
+        'annotated_download_files': annotated_download_files,
         "variant_zygosity_count_collections": variant_zygosity_count_collections,
     }
     return render(request, 'snpdb/data/view_vcf.html', context)

diff --git a/variantgrid/static_files/default_static/js/generated_graphs.js b/variantgrid/static_files/default_static/js/generated_graphs.js
@@ -48,7 +48,7 @@ function poll_graph_status(graph_selector, poll_url, delete_url) {
 
 
 function poll_cached_generated_file(poll_url, success_func, failure_func) {
-	$.getJSON(poll_url, function(data) {
+	$.getJSON(poll_url, function (data) {
 		if (data.status == "SUCCESS") {
 			success_func(data);
 		} else if (data.status == 'FAILURE') {
@@ -59,5 +59,5 @@ function poll_cached_generated_file(poll_url, success_func, failure_func) {
 			};
 			window.setTimeout(retry_func, freq);
 		}
-	});
-}
+	}).fail(failure_func);
+}