Add Timestamped base model (created_at, last_updated_at auto fields).

api/data_refinery_api/management/commands/update_es_index.py

@@ -24,6 +24,6 @@ def handle(self, *args, **options):
 
         for doc in registry.get_documents(models):
             start_time = timezone.now() - UPDATE_WINDOW
-            qs = doc().get_queryset().filter(last_modified__gt=start_time).order_by("id")
+            qs = doc().get_queryset().filter(last_modified_at__gt=start_time).order_by("id")
             self.stdout.write("Indexing {} '{}' objects".format(qs.count(), qs.model.__name__))
             doc().update(qs)

api/data_refinery_api/views/computational_result.py

@@ -44,7 +44,7 @@ class Meta:
             "time_start",
             "time_end",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 

api/data_refinery_api/views/computed_file.py

@@ -52,7 +52,7 @@ class Meta:
             "s3_url",
             "download_url",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "result",
         )
         read_only_fields = fields
@@ -90,7 +90,7 @@ class Meta:
             "s3_url",
             "download_url",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "result",
         )
         read_only_fields = fields
@@ -137,13 +137,13 @@ class ComputedFileListView(generics.ListAPIView):
         "svd_algorithm",
         "compendium_version",
         "created_at",
-        "last_modified",
+        "last_modified_at",
         "result__id",
     )
     ordering_fields = (
         "id",
         "created_at",
-        "last_modified",
+        "last_modified_at",
         "compendium_version",
     )
     ordering = ("-id",)

api/data_refinery_api/views/dataset.py

@@ -208,7 +208,7 @@ class Meta:
             "success",
             "failure_reason",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "start",
             "size_in_bytes",
             "sha1",
@@ -235,7 +235,7 @@ class Meta:
             "success": {"read_only": True,},
             "failure_reason": {"read_only": True,},
             "created_at": {"read_only": True,},
-            "last_modified": {"read_only": True,},
+            "last_modified_at": {"read_only": True,},
             "size_in_bytes": {"read_only": True,},
             "sha1": {"read_only": True,},
             "download_url": {"read_only": True,},

api/data_refinery_api/views/experiment.py

@@ -20,7 +20,7 @@ class Meta:
             "data",
             "is_ccdl",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -56,9 +56,9 @@ class Meta:
             "organism_names",
             "submitter_institution",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "source_first_published",
-            "source_last_modified",
+            "source_last_modified_at",
             "sample_metadata",
             "technologies",
         )
@@ -103,9 +103,9 @@ class Meta:
             "publication_authors",
             "pubmed_id",
             "source_first_published",
-            "source_last_modified",
+            "source_last_modified_at",
             "submitter_institution",
-            "last_modified",
+            "last_modified_at",
             "created_at",
             "organism_names",
             "sample_metadata",
@@ -137,9 +137,9 @@ class ExperimentListView(generics.ListAPIView):
         "organisms",
         "submitter_institution",
         "created_at",
-        "last_modified",
+        "last_modified_at",
         "source_first_published",
-        "source_last_modified",
+        "source_last_modified_at",
     )
 
     def get_queryset(self):

api/data_refinery_api/views/jobs/downloader_job.py

@@ -48,7 +48,7 @@ class Meta:
             "start_time",
             "end_time",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 

api/data_refinery_api/views/jobs/processor_job.py

@@ -49,7 +49,7 @@ class Meta:
             "start_time",
             "end_time",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 

api/data_refinery_api/views/jobs/survey_job.py

@@ -38,7 +38,7 @@ class Meta:
             "start_time",
             "end_time",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 

api/data_refinery_api/views/original_file.py

@@ -33,7 +33,7 @@ class Meta:
             "is_archive",
             "has_raw",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -60,7 +60,7 @@ class Meta:
             "source_filename",
             "has_raw",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -83,7 +83,7 @@ class OriginalFileListView(generics.ListAPIView):
     ordering_fields = (
         "id",
         "created_at",
-        "last_modified",
+        "last_modified_at",
     )
     ordering = ("-id",)
 

api/data_refinery_api/views/qn_targets.py

@@ -31,7 +31,7 @@ class Meta:
             "s3_key",
             "s3_url",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "result",
         )
         read_only_fields = fields

api/data_refinery_api/views/relation_serializers.py

@@ -52,7 +52,7 @@ class Meta:
             "s3_bucket",
             "s3_key",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -71,7 +71,7 @@ class Meta:
             "s3_key",
             "download_url",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -115,7 +115,7 @@ class Meta:
             "is_processed",
             "is_unable_to_be_processed",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -143,7 +143,7 @@ class Meta:
             "start_time",
             "end_time",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -169,7 +169,7 @@ class Meta:
             "start_time",
             "end_time",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -197,7 +197,7 @@ class Meta:
             "salmon_version",
             "download_url",
             "result_id",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -228,7 +228,7 @@ class Meta:
 class ComputationalResultAnnotationRelationSerializer(serializers.ModelSerializer):
     class Meta:
         model = ComputationalResultAnnotation
-        fields = ("id", "data", "is_ccdl", "created_at", "last_modified")
+        fields = ("id", "data", "is_ccdl", "created_at", "last_modified_at")
         read_only_fields = fields
 
 
@@ -253,7 +253,7 @@ class Meta:
             "time_start",
             "time_end",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -277,6 +277,6 @@ class Meta:
             "time_start",
             "time_end",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields

api/data_refinery_api/views/sample.py

@@ -38,7 +38,7 @@ class Meta:
             "data",
             "is_ccdl",
             "created_at",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields
 
@@ -99,7 +99,7 @@ class Meta:
             "is_processed",
             "is_unable_to_be_processed",
             "created_at",
-            "last_modified",
+            "last_modified_at",
             "original_files",
             "computed_files",
             "last_processor_job",

api/data_refinery_api/views/stats.py

@@ -221,10 +221,10 @@ def calculate_dashboard_stats(cls, range_param):
 
         # processed and unprocessed samples stats
         data["unprocessed_samples"] = cls._get_object_stats(
-            Sample.objects.filter(is_processed=False), range_param, "last_modified"
+            Sample.objects.filter(is_processed=False), range_param, "last_modified_at"
         )
         data["processed_samples"] = cls._get_object_stats(
-            Sample.processed_objects, range_param, "last_modified"
+            Sample.processed_objects, range_param, "last_modified_at"
         )
 
         data["dataset"] = cls._get_dataset_stats(range_param)
@@ -280,17 +280,17 @@ def _get_dataset_stats(cls, range_param):
 
         if range_param:
             # We don't save the dates when datasets are processed, but we can use
-            # `last_modified`, since datasets aren't modified again after they are processed
+            # `last_modified_at`, since datasets aren't modified again after they are processed
             result["timeline"] = cls._get_intervals(
-                Dataset.processed_filtered_objects, range_param, "last_modified"
+                Dataset.processed_filtered_objects, range_param, "last_modified_at"
             ).annotate(total=Count("id"), total_size=Sum("size_in_bytes"))
         return result
 
     @classmethod
     def _samples_processed_last_hour(cls):
         current_date = datetime.now(tz=timezone.utc)
         start = current_date - timedelta(hours=1)
-        return Sample.processed_objects.filter(last_modified__range=(start, current_date)).count()
+        return Sample.processed_objects.filter(last_modified_at__range=(start, current_date)).count()
 
     @classmethod
     def _get_input_data_size(cls):
@@ -376,7 +376,7 @@ def _get_object_stats(cls, objects, range_param=False, field="created_at"):
         return result
 
     @classmethod
-    def _get_intervals(cls, objects, range_param, field="last_modified"):
+    def _get_intervals(cls, objects, range_param, field="last_modified_at"):
         range_to_trunc = {"day": "hour", "week": "day", "month": "day", "year": "month"}
 
         # truncate the parameterized field so it can be annotated by range

api/data_refinery_api/views/transcriptome_index.py

@@ -32,7 +32,7 @@ class Meta:
             "salmon_version",
             "download_url",
             "result_id",
-            "last_modified",
+            "last_modified_at",
         )
         read_only_fields = fields