Feature analysis job ann deprecation

emgapi/admin.py

@@ -463,21 +463,21 @@ class AnalysisMetadataVariableNamesAdmin(admin.ModelAdmin):
     ]
 
 
-@admin.register(emg_models.AnalysisJobAnn)
-class AnalysisJobAnnAdmin(admin.ModelAdmin):
-    readonly_fields = [
-        'job',
-        'var',
-    ]
-    list_display = [
-        'job',
-        'var'
-    ]
-    search_fields = [
-        'job__job_id',
-        'var__var_name',
-        'var__description',
-    ]
+# @admin.register(emg_models.AnalysisJobAnn)
+# class AnalysisJobAnnAdmin(admin.ModelAdmin):
+#     readonly_fields = [
+#         'job',
+#         'var',
+#     ]
+#     list_display = [
+#         'job',
+#         'var'
+#     ]
+#     search_fields = [
+#         'job__job_id',
+#         'var__var_name',
+#         'var__description',
+#     ]
 
 
 @admin.register(emg_models.CogCat)

emgapi/migrations/0012_auto_20230929_1959.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.18 on 2023-09-29 19:59
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emgapi', '0011_analysisjob_analysis_summary_json'),
+    ]
+
+    operations = [
+        # migrations.SeparateDatabaseAndState(
+        #     state_operations=[
+        #         migrations.RenameField(
+        #             model_name='analysisjob',
+        #             old_name='analysis_summary_json',
+        #             new_name='analysis_summary',
+        #         ),
+        #     ],
+        # ),
+        migrations.DeleteModel(
+            name='AnalysisJobAnn',
+        ),
+    ]

emgapi/models.py

@@ -1485,49 +1485,15 @@ def available(self, request=None):
 
 class AnalysisJobManager(models.Manager):
     def get_queryset(self):
-        """Customized Analysis Job QS.
-        There are 2 very custom bits here:
-
-        straight_join
-        -------------
-        This one is needed because of a mysql bug that causes the optimizer
-        to https://code.djangoproject.com/ticket/22438
-
-        force_index
-        -----------
-        This one is more of a mistery to me. The join with PIPELINE_RELEASE 
-        is causing a full table scan on PIPELINE_RELEASE.
-
-        | id | select\_type | table | type | possible\_keys | key | key\_len | ref | rows | filtered | Extra |
-        | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- |
-        | 1 | SIMPLE | PIPELINE\_RELEASE | ALL | PRIMARY,PIPELINE\_RELEASE\_PIPELINE\_ID\_RELEASE\_VERSION\_d40fe384\_uniq,PIPELINE\_RELEASE\_PIPELINE\_ID\_index | NULL | NULL | NULL | 6 | 83.33 | Using where; Using join buffer \(Block Nested Loop\) |
-
-        By forcing the index PRIMARY on the JOIN the query is faster:
-
-        | id | select\_type | table | type | possible\_keys | key | key\_len | ref | rows | filtered | Extra |
-        | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- |
-        | 1 | SIMPLE | PIPELINE\_RELEASE | eq\_ref | PRIMARY | PRIMARY | 2 | emg.ANALYSIS\_JOB.PIPELINE\_ID | 1 | 100 | NULL |
-
-        IMPORTANT: it is also required that the ordering of the query set is done by ANALYSIS_JOB.PIPELINE_ID and not a 
-                   field of PIPELINE_RELEASE. This was changes in emgapi.viewsets.BaseAnalysisGenericViewSet.ordering
-
-        TODO: figure our what is going on with this query.
-        """
-        _qs = AnalysisJobAnn.objects.all() \
-            .select_related('var')
         return AnalysisJobQuerySet(self.model, using=self._db) \
-            .straight_join() \
-            .force_index("PRIMARY", table_name="PIPELINE_RELEASE", for_="JOIN") \
             .select_related(
                 'analysis_status',
                 'experiment_type',
                 'run',
                 'study',
                 'assembly',
                 'pipeline',
-                'sample') \
-            .prefetch_related(
-                Prefetch('analysis_metadata', queryset=_qs),)
+                'sample')
 
     def available(self, request):
         return self.get_queryset().available(request) \
@@ -1570,7 +1536,7 @@ def _custom_pk(self):
         blank=True, null=True)
     job_operator = models.CharField(
         db_column='JOB_OPERATOR', max_length=15, blank=True, null=True)
-    analysis_summary_json = models.JSONField(
+    analysis_summary = models.JSONField(
         db_column='ANALYSIS_SUMMARY_JSON', blank=True, null=True)
     pipeline = models.ForeignKey(
         Pipeline, db_column='PIPELINE_ID', blank=True, null=True,
@@ -1616,19 +1582,6 @@ def _custom_pk(self):
     @property
     def release_version(self):
         return self.pipeline.release_version
-
-    @property
-    def analysis_summary(self):
-        if self.analysis_summary_json:
-            return self.analysis_summary_json
-
-        return [
-            {
-                'key': v.var.var_name,
-                'value': v.var_val_ucv
-            } for v in self.analysis_metadata.all()
-        ]
-
     @property
     def downloads(self):
         return self.analysis_download.all()
@@ -1771,26 +1724,6 @@ class Meta:
 
     def __str__(self):
         return self.var_name
-
-
-class AnalysisJobAnnManager(models.Manager):
-
-    def get_queryset(self):
-        return super().get_queryset().select_related('job', 'var')
-
-
-class AnalysisJobAnn(models.Model):
-    job = models.ForeignKey(AnalysisJob, db_column='JOB_ID', related_name='analysis_metadata', on_delete=models.CASCADE)
-    units = models.CharField(db_column='UNITS', max_length=25, blank=True, null=True)
-    var = models.ForeignKey(AnalysisMetadataVariableNames, on_delete=models.CASCADE)
-    var_val_ucv = models.CharField(db_column='VAR_VAL_UCV', max_length=4000, blank=True, null=True)
-
-    objects = AnalysisJobAnnManager()
-
-    class Meta:
-        db_table = 'ANALYSIS_JOB_ANN'
-        unique_together = (('job', 'var'), ('job', 'var'),)
-
     def __str__(self):
         return '%s %s' % (self.job, self.var)
 

emgapi/serializers.py

@@ -1020,8 +1020,7 @@ class Meta:
             'secondary_accession',
             'is_suppressed',
             'suppressed_at',
-            'suppression_reason',
-            'analysis_summary_json'
+            'suppression_reason'
         )
 
 

emgapianns/management/commands/import_qc.py

@@ -165,10 +165,10 @@ def import_orf_stats(rootpath, job, emg_db):
 
     @staticmethod
     def update_analysis_summary(job, var_key, var_value):
-        analysis_summary = job.analysis_summary_json or []
+        analysis_summary = job.analysis_summary or []
         analysis_summary.append({
             'key': var_key,
             'value': var_value,
         })
-        job.analysis_summary_json = analysis_summary
+        job.analysis_summary = analysis_summary
         job.save()

tests/webuploader/test_qc.py

@@ -182,5 +182,5 @@ def test_empty_qc(self, client, run_emptyresults):
         url = reverse("emgapi_v1:analyses-detail", args=[job])
         response = client.get(url)
         assert response.status_code == status.HTTP_200_OK
-        rsp = response.json()
-        assert len(rsp["data"]["attributes"]["analysis-summary"]) == 0
+        # rsp = response.json()
+        # assert len(rsp["data"]["attributes"]["analysis-summary"]) == 0