Feature: extra assembly annotations (sanntis) (#294)

* fixes typo in ENASyncableModel logging

* [WIP] adding "Extra Assembly Annotations" model and importer

* adds SanntiS annotations as "extra" (non-pipeline) annotations

* adds assembly extra annotation to expected api surface

* adds api test for assembly-extra-annotations (and fix assemblies fixture)

* farewell python3.6 (`requests` has deprecated it)

* fixes py3.8.6 no longer available on GHA ubuntu-latest

* adds support for (optional) virify GFF in genome importer

* use in-mem cache of download description/format/subdir/group instances when uploading assembly extra annotation files

* cleanup old (now squashed) migrations

* [DEBUG] debugging failing test on GHA

* adds virify genome download label to test fixtures

* adds virify txt file to optional genome downloads

.github/workflows/test.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.8.6]
+        python-version: [3.8, 3.9]
         # TODO: Temporarily removed 3.7.1, waiting for https://github.com/celery/celery/issues/7783
 
     steps:

emgapi/admin.py

@@ -229,6 +229,19 @@ class PublicationAdmin(admin.ModelAdmin):
     ]
 
 
+class AssemblyExtraAnnotationDownloads(admin.TabularInline):
+    model = emg_models.AssemblyExtraAnnotation
+    raw_id_fields = [
+        'assembly',
+        'parent_id',
+        'group_type',
+        'subdir',
+        'description',
+        'file_format'
+    ]
+    extra = 0
+
+
 @admin.register(emg_models.Assembly)
 class AssemblyAdmin(admin.ModelAdmin):
     change_list_template = "admin/change_list_filter_sidebar.html"
@@ -244,6 +257,9 @@ class AssemblyAdmin(admin.ModelAdmin):
         'legacy_accession',
         'experiment_type__experiment_type'
     ]
+    inlines = [
+        AssemblyExtraAnnotationDownloads
+    ]
 
 
 @admin.register(emg_models.AssemblyRun)

emgapi/fields.py

@@ -25,6 +25,7 @@ class DownloadHyperlinkedIdentityField(serializers.HyperlinkedIdentityField):
     def get_url(self, obj, view_name, request, format):
         if obj.pk is None:
             return None
+        kwargs = {}
         # if study
         if hasattr(obj, 'study') and hasattr(obj, 'pipeline'):
             kwargs = {
@@ -44,6 +45,10 @@ def get_url(self, obj, view_name, request, format):
             kwargs = {
                 'catalogue_id': obj.genome_catalogue.catalogue_id,
             }
+        elif hasattr(obj, 'assembly'):
+            kwargs = {
+                'accession': obj.assembly.accession
+            }
         kwargs['alias'] = obj.alias
 
         return reverse(