issue #1171 - get working for sample as well

analysis/tasks/analysis_grid_export_tasks.py

@@ -1,6 +1,7 @@
 import logging
 import os
 import uuid
+from typing import Optional
 
 import celery
 
@@ -16,6 +17,24 @@
 from snpdb.models import Cohort, Sample, CachedGeneratedFile
 
 
+def get_annotated_download_files_cgf(generator, pk) -> dict[str, Optional[CachedGeneratedFile]]:
+    annotated_download_files = {}
+    try:
+        AnalysisTemplate.get_template_from_setting("ANALYSIS_TEMPLATES_AUTO_COHORT_EXPORT")
+        params_hash_vcf = get_grid_downloadable_file_params_hash(pk, "vcf")
+        cgf_vcf = CachedGeneratedFile.objects.filter(generator=generator,
+                                                     params_hash=params_hash_vcf).first()
+        params_hash_csv = get_grid_downloadable_file_params_hash(pk, "csv")
+        cgf_csv = CachedGeneratedFile.objects.filter(generator=generator,
+                                                     params_hash=params_hash_csv).first()
+
+        annotated_download_files = {"vcf": cgf_vcf, "csv": cgf_csv}
+    except ValueError:
+        pass
+
+    return annotated_download_files
+
+
 def get_grid_downloadable_file_params_hash(pk, export_type):
     return sha256sum_str(f"{pk}-{export_type}")
 

analysis/templates/analysis/node_data/node_data_graph.html

@@ -2,7 +2,7 @@
 {% load static %}
 {% block top %}
 	<link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
-	<script src="{% static 'js/generated_graphs.js' %}"></script>
+	<script src="{% static 'js/cached_generated_files.js' %}"></script>
 {% endblock top %}
 
 {% block css %}

analysis/views/views_grid.py

@@ -133,7 +133,9 @@ def sample_grid_export(request, sample_id, export_type):
     params_hash = get_grid_downloadable_file_params_hash(sample_id, export_type)
     task = export_sample_to_downloadable_file.si(sample_id, export_type)
     cgf = CachedGeneratedFile.get_or_create_and_launch("export_sample_to_downloadable_file", params_hash, task)
-    return JsonResponse({"celery_task": cgf.task_id})
+    if cgf.exception:
+        raise ValueError(cgf.exception)
+    return redirect(cgf)
 
 
 def node_grid_export(request, analysis_id):

genes/templates/genes/view_gene_symbol.html

@@ -23,7 +23,7 @@
     <link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
     <script type="text/javascript" src="{% static 'js/lib/plotly-latest.min.js' %}"></script>
     <script type="text/javascript" src="{% static 'js/grid.js' %}"></script>
-    <script src="{% static 'js/generated_graphs.js' %}"></script>
+    <script src="{% static 'js/cached_generated_files.js' %}"></script>
     <style>
         #hotspot-graph, #hotspot-graph img {
             width: 100%;

pedigree/templates/pedigree/view_ped_file.html

@@ -6,7 +6,7 @@
 {% block head %}
     {{ block.super }}
 	<link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
-	<script src="{% static 'js/generated_graphs.js' %}"></script>
+	<script src="{% static 'js/cached_generated_files.js' %}"></script>
 {% endblock %}
 
 {% block css %}

seqauto/templates/seqauto/tabs/view_qc_exec_summary_tab.html

@@ -22,7 +22,7 @@
 }
 
 </style>
-<script src="{% static 'js/generated_graphs.js' %}"></script>
+<script src="{% static 'js/cached_generated_files.js' %}"></script>
 <script>
 {% if qc.data_state == 'C' and exec_summary.data_state == 'C' %}
     EXEC_SUMMARY_ID = {{ exec_summary.pk }};

seqauto/templates/seqauto/tabs/view_sequencing_run_stats_tab.html

@@ -3,7 +3,7 @@
 {% load seqauto_record_tags %}
 <link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
 <link rel="stylesheet" href="{% static 'css/seqauto.css' %}" />
-<script src="{% static 'js/generated_graphs.js' %}"></script>
+<script src="{% static 'js/cached_generated_files.js' %}"></script>
 <script>
 	var DELETE_URL = "{% url 'cached_generated_file_delete' %}";
 	var BASE_QC_POLL_URL = "{% url 'sequencing_run_qc_graph' sequencing_run.pk 'QC_COMPARE_TYPE' %}";

seqauto/templates/seqauto/view_sequencing_run.html

@@ -6,7 +6,7 @@
 {% block head %}
 	<link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
 	<link rel="stylesheet" href="{% static 'css/seqauto.css' %}" />
-	<script src="{% static 'js/generated_graphs.js' %}"></script>
+	<script src="{% static 'js/cached_generated_files.js' %}"></script>
 
 	<style>
 		input#id_path {

snpdb/models/models.py

@@ -7,6 +7,7 @@
 """
 import json
 import logging
+import os
 import re
 from dataclasses import dataclass
 from datetime import datetime
@@ -25,6 +26,8 @@
 from django.db import models
 from django.db.models import QuerySet, TextChoices
 from django.db.models.deletion import SET_NULL, CASCADE, PROTECT
+from django.db.models.signals import pre_delete
+from django.dispatch import receiver
 from django.urls import reverse
 from django.utils import timezone
 from django.utils.safestring import SafeString
@@ -121,6 +124,15 @@ def save(self, **kwargs):
             logging.debug("Not caching generated files - skipped save!")
 
 
+@receiver(pre_delete, sender=CachedGeneratedFile)
+def cgf_pre_delete_handler(sender, instance, **kwargs):  # pylint: disable=unused-argument
+    if instance.filename:
+        if os.path.exists(instance.filename):
+            os.unlink(instance.filename)
+        dirname = os.path.dirname(instance.filename)
+        if os.path.isdir(dirname):
+            os.rmdir(dirname)
+
 class Company(models.Model):
     name = models.TextField(primary_key=True)
 

snpdb/templates/snpdb/data/sample_graphs_tab.html

@@ -1,5 +1,5 @@
 {% load static %}
-<script src="{% static 'js/generated_graphs.js' %}"></script>
+<script src="{% static 'js/cached_generated_files.js' %}"></script>
 <style>
     .generated-graph, .generated-graph img {
         width: 640px;

snpdb/templates/snpdb/data/view_genomic_intervals.html

@@ -6,7 +6,7 @@
 {% block title %}{{ gic.name }}{% endblock %}
 {% block head %}
 	<link rel="stylesheet" href="{% static 'css/graphs.css' %}" />
-	<script src="{% static 'js/generated_graphs.js' %}"></script>
+	<script src="{% static 'js/cached_generated_files.js' %}"></script>
 	<style>
 		#genomic-intervals-graph, #genomic-intervals-graph img {
 		    width: 640px;

snpdb/templates/snpdb/data/view_sample.html

@@ -30,6 +30,7 @@
         margin-left: 2px;
     }
 </style>
+<script type="text/javascript" src="{% static 'js/cached_generated_files.js' %}"></script>
 <script>
 function getBams() {
     const bams = {{ bam_list | jsonify }};
@@ -68,6 +69,24 @@
     const dialog = setupCreatePatientDialog();
     const sampleName = $("#id_name").val();
     addCreatePatientButton(dialog, patientSelect, sampleName, "p");
+
+    {% for file_type, cgf in annotated_download_files.items %}
+        var pollUrl = Urls.sample_grid_export({{ sample.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>
 <!-- jqGrid is used in variants tab -->
@@ -122,14 +141,13 @@ <h1>Sample: {{ sample.name }}</h1>
             <form method="post" id='sample-form'>
                 {% csrf_token %}
                 {% crispy form form_helper.horizontal %}
-                {% if can_download_vcf %}
+                {% if annotated_download_files %}
                     <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 can_download_annotated_vcf %}
-                                <div class="p-2"><a href="{% url 'sample_grid_export' sample.pk 'vcf' %}"><div class="icon24 left margin-r-5 vcf-icon"></div> Annotated Sample VCF</a></div>
-                                <div class="p-2"><a href="{% url 'sample_grid_export' sample.pk 'csv' %}"><div class="icon24 left margin-r-5 csv-icon"></div> Annotated Sample CSV</a></div>
-                            {% endif %}
+                            {% for file_type in annotated_download_files %}
+                                <div id="generate-{{ file_type }}-download" class="p-2"></div>
+                            {% endfor %}
                         </div>
                     </div>
                 {% endif %}

snpdb/templates/snpdb/data/view_vcf.html

@@ -10,7 +10,7 @@
 {% block title %}{{ vcf.name }}{% endblock %}
 {% block head %}
 <script type="text/javascript" src="{% static 'js/lib/plotly-latest.min.js' %}"></script>
-<script type="text/javascript" src="{% static 'js/generated_graphs.js' %}"></script>
+<script type="text/javascript" src="{% static 'js/cached_generated_files.js' %}"></script>
 <script type="text/javascript" src="{% static 'js/plotly_helper.js' %}"></script>
 
 <style>
@@ -283,51 +283,6 @@
         });
     });
 
-    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 ${this.ucFileType}</a>`);
-            generateLink.click(function(event) {
-                event.preventDefault();
-                that.setPolling(true);
-            });
-            this.selector.empty();
-            this.selector.append(generateLink);
-            console.log("/setGenerateDownloadLink");
-        }
-
-        setDownloadLink(url) {
-            // console.log("setDownloadLink");
-            this.selector.html(`<a href="${url}"><div class="icon24 left margin-r-5 ${this.fileType}-icon"></div> Annotated ${this.ucFileType}</a>`);
-        }
-
-        setError() {
-            // console.log("setError");
-            this.selector.html('<i class="fas fa-xmark"></i> Error retrieving download...');
-        }
-
-        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)
-        }
-    }
-
     {% 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");

snpdb/views/views.py

@@ -28,7 +28,8 @@
 from analysis.analysis_templates import get_sample_analysis
 from analysis.forms import AnalysisOutputNodeChoiceForm
 from analysis.models import AnalysisTemplate
-from analysis.tasks.analysis_grid_export_tasks import get_grid_downloadable_file_params_hash
+from analysis.tasks.analysis_grid_export_tasks import get_grid_downloadable_file_params_hash, \
+    get_annotated_download_files_cgf
 from annotation.forms import GeneCountTypeChoiceForm
 from annotation.manual_variant_entry import create_manual_variants, can_create_variants
 from annotation.models import AnnotationVersion, SampleVariantAnnotationStats, SampleGeneAnnotationStats, \
@@ -283,19 +284,9 @@ def view_vcf(request, vcf_id):
         can_view_upload_pipeline = False
 
     annotated_download_files = {}
-    if vcf.import_status == ImportStatus.SUCCESS and cohort_id:
-        try:
-            AnalysisTemplate.get_template_from_setting("ANALYSIS_TEMPLATES_AUTO_COHORT_EXPORT")
-            params_hash_vcf = get_grid_downloadable_file_params_hash(cohort_id, "vcf")
-            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")
-            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
+    if not settings.VCF_DOWNLOAD_ADMIN_ONLY or request.user.is_superuser:
+        if vcf.import_status == ImportStatus.SUCCESS and cohort_id:
+            annotated_download_files = get_annotated_download_files_cgf("export_cohort_to_downloadable_file", cohort_id)
 
     context = {
         'vcf': vcf,
@@ -307,7 +298,6 @@ def view_vcf(request, vcf_id):
         'samples_form': samples_form,
         '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_view_upload_pipeline': can_view_upload_pipeline,
         'annotated_download_files': annotated_download_files,
         "variant_zygosity_count_collections": variant_zygosity_count_collections,
@@ -406,22 +396,18 @@ def view_sample(request, sample_id):
         related_samples = SomalierRelatePairs.get_for_sample(sample).order_by("relate")
 
     sample_stats_variant_class_df, sample_stats_zygosity_df = _sample_stats(sample)
-    can_download_annotated_vcf = False
-    if sample.import_status == ImportStatus.SUCCESS:
-        try:
-            AnalysisTemplate.get_template_from_setting("ANALYSIS_TEMPLATES_AUTO_SAMPLE")
-            can_download_annotated_vcf = True
-        except ValueError:
-            pass
+    annotated_download_files = {}
+    if not settings.VCF_DOWNLOAD_ADMIN_ONLY or request.user.is_superuser:
+        if sample.import_status == ImportStatus.SUCCESS:
+            annotated_download_files = get_annotated_download_files_cgf("export_sample_to_downloadable_file", sample.pk)
 
     context = {
+        'annotated_download_files': annotated_download_files,
         'sample': sample,
         'samples': [sample],
         'sample_locus_count': sample_locus_count,
         'form': form,
         'patient_form': patient_form,
-        'can_download_vcf': (not settings.VCF_DOWNLOAD_ADMIN_ONLY) or request.user.is_superuser,
-        'can_download_annotated_vcf': can_download_annotated_vcf,
         'cohorts': cohorts,
         'has_write_permission': has_write_permission,
         'igv_data': igv_data,

variantgrid/static_files/default_static/js/generated_graphs.js → variantgrid/static_files/default_static/js/cached_generated_files.js

@@ -61,3 +61,49 @@ function poll_cached_generated_file(poll_url, success_func, failure_func) {
 		}
 	}).fail(failure_func);
 }
+
+
+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 ${this.ucFileType}</a>`);
+		generateLink.click(function(event) {
+			event.preventDefault();
+			that.setPolling(true);
+		});
+		this.selector.empty();
+		this.selector.append(generateLink);
+		// console.log("/setGenerateDownloadLink");
+	}
+
+	setDownloadLink(url) {
+		// console.log("setDownloadLink");
+		this.selector.html(`<a href="${url}"><div class="icon24 left margin-r-5 ${this.fileType}-icon"></div> Annotated ${this.ucFileType}</a>`);
+	}
+
+	setError() {
+		// console.log("setError");
+		this.selector.html('<i class="fas fa-xmark"></i> Error retrieving download...');
+	}
+
+	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)
+	}
+}