Setup from scratch - show sites name to make deployment mistakes easi…

…er to catch
SACGF · Aug 5, 2024 · 5c0caf6 · 5c0caf6
1 parent 2eff210
commit 5c0caf6
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Showing 3 changed files with 12 additions and 2 deletions.
diff --git a/annotation/templates/annotation/annotation_build_detail.html b/annotation/templates/annotation/annotation_build_detail.html
@@ -183,7 +183,11 @@ <h5>RefSeq GRCh38</h5>
                        Not installed
                     {% endif %}
                     {% install-instructions "Somalier" installed=details.somalier %}
-                        Upload the Somalier sites VCF for {{ build_name }}.
+                        Upload the Somalier sites VCF for {{ build_name }}
+                        {% if expected_somalier_sites_name %}
+                            : '{{ expected_somalier_sites_name }}'
+                        {% endif %}
+                        .
                     {% endinstall-instructions %}
                 {% endlabelled %}
             {% endif %}

diff --git a/annotation/views.py b/annotation/views.py
@@ -148,9 +148,11 @@ def annotation_build_detail(request, genome_build_name):
         if settings.ANNOTATION_GENE_ANNOTATION_VERSION_ENABLED:
             annotation_sub_components.append(gene_annotation_counts)
 
+        expected_somalier_sites_name = None
         if settings.SOMALIER.get("enabled"):
             somalier_cfg = SomalierConfig()
             try:
+                expected_somalier_sites_name = somalier_cfg.get_sites_vcf_name(genome_build)
                 vcf = somalier_cfg.get_sites_vcf(genome_build)
                 annotation_details["somalier"] = f"Sites VCF: {vcf.name}"
                 somalier = True
@@ -164,6 +166,7 @@ def annotation_build_detail(request, genome_build_name):
         "build_name": genome_build.name,
         "details": annotation_details,
         "cdot_version": cdot.__version__,
+        "expected_somalier_sites_name": expected_somalier_sites_name,
     }
     return render(request, "annotation/annotation_build_detail.html", context)
 

diff --git a/snpdb/models/models_somalier.py b/snpdb/models/models_somalier.py
@@ -272,8 +272,11 @@ def get_sites(self, genome_build: 'GenomeBuild'):
         sites = self.settings["annotation"]["sites"][genome_build.name]
         return self._annotation_dir(sites)
 
+    def get_sites_vcf_name(self, genome_build: 'GenomeBuild') -> str:
+        return os.path.basename(self.get_sites(genome_build))
+
     def get_sites_vcf(self, genome_build: 'GenomeBuild'):
-        sites_name = os.path.basename(self.get_sites(genome_build))
+        sites_name = self.get_sites_vcf_name(genome_build)
         sites_vcf_kwargs = {"name": sites_name, "genome_build": genome_build}
         try:
             return VCF.objects.get(**sites_vcf_kwargs)