Merge branch 'dev' of https://github.com/ProteinsWebTeam/interpro7-api …

…into dev

webfront/exceptions.py

@@ -10,18 +10,22 @@ class EmptyQuerysetError(Exception):
     def __init__(self, message):
         self.message = message
 
+
 class ExpectedUniqueError(Exception):
     def __init__(self, message):
         self.message = message
 
+
 class HmmerWebError(Exception):
     def __init__(self, message):
         self.message = message
 
+
 class BadURLParameterError(Exception):
     def __init__(self, message):
         self.message = message
 
+
 class InvalidOperationRequest(Exception):
     def __init__(self, message):
-        self.message = message    
+        self.message = message

webfront/migrations/0010_wiki_field_type_change.py

@@ -6,14 +6,12 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0009_entry_annotation_changes'),
-    ]
+    dependencies = [("webfront", "0009_entry_annotation_changes")]
 
     operations = [
         migrations.AlterField(
-            model_name='entry',
-            name='wikipedia',
+            model_name="entry",
+            name="wikipedia",
             field=jsonfield.fields.JSONField(null=True),
-        ),
+        )
     ]

webfront/migrations/0016_structural_model_algorithm.py

@@ -5,20 +5,16 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0015_structural_model_lddt'),
-    ]
+    dependencies = [("webfront", "0015_structural_model_lddt")]
 
     operations = [
         migrations.AddField(
-            model_name='structuralmodel',
-            name='algorithm',
-            field=models.CharField(default='trRosetta', max_length=20),
+            model_name="structuralmodel",
+            name="algorithm",
+            field=models.CharField(default="trRosetta", max_length=20),
             preserve_default=False,
         ),
         migrations.AlterField(
-            model_name='structuralmodel',
-            name='lddt',
-            field=models.BinaryField(),
+            model_name="structuralmodel", name="lddt", field=models.BinaryField()
         ),
     ]

webfront/migrations/0017_structural_model_plddt.py

@@ -5,14 +5,10 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0016_structural_model_algorithm'),
-    ]
+    dependencies = [("webfront", "0016_structural_model_algorithm")]
 
     operations = [
         migrations.RenameField(
-            model_name='structuralmodel',
-            old_name='lddt',
-            new_name='plddt',
-        ),
+            model_name="structuralmodel", old_name="lddt", new_name="plddt"
+        )
     ]

webfront/migrations/0018_taxa_modifier.py

@@ -6,14 +6,10 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0017_structural_model_plddt'),
-    ]
+    dependencies = [("webfront", "0017_structural_model_plddt")]
 
     operations = [
         migrations.AddField(
-            model_name='entry',
-            name='taxa',
-            field=jsonfield.fields.JSONField(null=True),
-        ),
+            model_name="entry", name="taxa", field=jsonfield.fields.JSONField(null=True)
+        )
     ]

webfront/migrations/0019_entrytaxa_table.py

@@ -7,23 +7,25 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0018_taxa_modifier'),
-    ]
+    dependencies = [("webfront", "0018_taxa_modifier")]
 
     operations = [
         migrations.CreateModel(
-            name='EntryTaxa',
+            name="EntryTaxa",
             fields=[
-                ('accession', models.OneToOneField(db_column='accession', on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='webfront.entry')),
-                ('tree', jsonfield.fields.JSONField(null=True)),
+                (
+                    "accession",
+                    models.OneToOneField(
+                        db_column="accession",
+                        on_delete=django.db.models.deletion.CASCADE,
+                        primary_key=True,
+                        serialize=False,
+                        to="webfront.entry",
+                    ),
+                ),
+                ("tree", jsonfield.fields.JSONField(null=True)),
             ],
-            options={
-                'db_table': 'webfront_entrytaxa',
-            },
-        ),
-        migrations.RemoveField(
-            model_name='entry',
-            name='taxa',
+            options={"db_table": "webfront_entrytaxa"},
         ),
+        migrations.RemoveField(model_name="entry", name="taxa"),
     ]

webfront/migrations/0020_alter_entryannotation_num_sequences.py

@@ -5,14 +5,12 @@
 
 class Migration(migrations.Migration):
 
-    dependencies = [
-        ('webfront', '0019_entrytaxa_table'),
-    ]
+    dependencies = [("webfront", "0019_entrytaxa_table")]
 
     operations = [
         migrations.AlterField(
-            model_name='entryannotation',
-            name='num_sequences',
+            model_name="entryannotation",
+            name="num_sequences",
             field=models.IntegerField(null=True),
-        ),
+        )
     ]

webfront/pagination.py

@@ -31,29 +31,51 @@ class CustomPagination(CursorPagination):
     current_size = None
     after_key = None
     before_key = None
+    elastic_result = None
 
     def get_paginated_response(self, data):
         base = [
             ("count", self.current_size),
             ("next", self.get_next_link()),
             ("previous", self.get_previous_link()),
-            ("results", data["data"]),
+            ("results", self._sortBasedOnElastic(data["data"])),
         ]
         if "extensions" in data and len(data["extensions"]) > 0:
             for ext in data["extensions"]:
                 base.append((ext, data["extensions"][ext]))
         return Response(OrderedDict(base))
 
+    # If there is data in elastic_result, implies that the wueryset was created by querying elastic first.
+    # This method uses the list of accession retrieved via elastic to order the results.
+    def _sortBasedOnElastic(self, data):
+        if self.elastic_result is None:
+            return data
+        ordered_data = []
+        for acc in self.elastic_result:
+            obj = next(
+                filter(
+                    lambda item: item.get("metadata", {}).get("accession", "").lower()
+                    == acc.lower(),
+                    data,
+                ),
+                None,
+            )
+            if obj is not None:
+                ordered_data.append(obj)
+        return ordered_data
+
     def _get_position_from_instance(self, instance, ordering):
         if type(instance) == tuple:
             return instance[0]
         return super(CustomPagination, self)._get_position_from_instance(
             instance, ordering
         )
 
+    # Extract some values passed as kwargs before invoking the implementation in the super class
     def paginate_queryset(self, queryset, request, **kwargs):
         self.current_size = None
         self.after_key = None
+        self.elastic_result = None
         if (
             hasattr(queryset, "model")
             and queryset.model._meta.ordering != []
@@ -69,6 +91,8 @@ def paginate_queryset(self, queryset, request, **kwargs):
             self.after_key = kwargs["after_key"]
         if "before_key" in kwargs and kwargs["before_key"] is not None:
             self.before_key = kwargs["before_key"]
+        if "elastic_result" in kwargs and kwargs["elastic_result"] is not None:
+            self.elastic_result = kwargs["elastic_result"]
         return super(CustomPagination, self).paginate_queryset(
             queryset, request, kwargs["view"]
         )
@@ -105,61 +129,3 @@ def get_previous_link(self):
         return replace_query_param(
             self.base_url, "cursor", "-{}".format(self.before_key)
         )
-
-
-class CustomPaginationOld(PageNumberPagination):
-    page_size = settings.INTERPRO_CONFIG.get("default_page_size", 20)
-    page_size_query_param = "page_size"
-    max_page_size = 200
-    ordering = "-accession"
-    django_paginator_class = CustomPaginator
-    current_size = None
-
-    def get_paginated_response(self, data):
-        self.current_size = (
-            self.page.paginator.count
-            if self.current_size is None
-            else self.current_size
-        )
-        return Response(
-            OrderedDict(
-                [
-                    ("count", self.current_size),
-                    ("next", self.get_next_link()),
-                    ("previous", self.get_previous_link()),
-                    ("results", data),
-                ]
-            )
-        )
-
-    def paginate_queryset(self, queryset, request, **kwargs):
-        self.current_size = None
-        if "search_size" in kwargs and kwargs["search_size"] is not None:
-            if not queryset.ordered:
-                queryset = queryset.order_by("accession")
-            self.current_size = kwargs["search_size"]
-
-        return super(CustomPagination, self).paginate_queryset(
-            queryset, request, kwargs["view"]
-        )
-
-    def get_next_link(self):
-        if not self.has_next():
-            return None
-        url = replace_url_host(self.request.build_absolute_uri())
-        page_number = self.page.number + 1
-        return replace_query_param(url, self.page_query_param, page_number)
-
-    def has_next(self):
-        if self.current_size is None:
-            return False
-        return self.page.number * self.page.paginator.per_page < self.current_size
-
-    def get_previous_link(self):
-        if not self.page.has_previous():
-            return None
-        url = replace_url_host(self.request.build_absolute_uri())
-        page_number = self.page.previous_page_number()
-        if page_number == 1:
-            return remove_query_param(url, self.page_query_param)
-        return replace_query_param(url, self.page_query_param, page_number)