Change ReportType and Status from hard coded choice fields to stand-a…

…lone models with API endpoints

code.json

@@ -3,7 +3,7 @@
     "name": "lide",
     "organization": "U.S. Geological Survey",
     "description": "Web services for LILI (LIDE (Laboratory for Infectious Disease and the Environment) Information Management System)",
-    "version": "v0.119.2",
+    "version": "v0.120.0",
     "status": "Release Candidate",
 
     "permissions": {
@@ -47,7 +47,7 @@
     },
 
     "date": {
-      "metadataLastUpdated": "2019-10-09"
+      "metadataLastUpdated": "2019-10-11"
     }
   }
 ]

lideservices/migrations/0011_historicalreporttype_historicalstatus_reporttype_status.py

@@ -0,0 +1,90 @@
+# Generated by Django 2.2 on 2019-10-11 11:26
+
+import datetime
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+import simple_history.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('lideservices', '0010_auto_20191008_2214'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Status',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created_date', models.DateField(blank=True, db_index=True, default=datetime.date.today, null=True)),
+                ('modified_date', models.DateField(auto_now=True, null=True)),
+                ('name', models.CharField(max_length=128, unique=True)),
+                ('created_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, related_name='status_creator', to=settings.AUTH_USER_MODEL)),
+                ('modified_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, related_name='status_modifier', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'db_table': 'lide_status',
+            },
+        ),
+        migrations.CreateModel(
+            name='ReportType',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created_date', models.DateField(blank=True, db_index=True, default=datetime.date.today, null=True)),
+                ('modified_date', models.DateField(auto_now=True, null=True)),
+                ('name', models.CharField(max_length=128, unique=True)),
+                ('created_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, related_name='reporttype_creator', to=settings.AUTH_USER_MODEL)),
+                ('modified_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, related_name='reporttype_modifier', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'db_table': 'lide_reporttype',
+            },
+        ),
+        migrations.CreateModel(
+            name='HistoricalStatus',
+            fields=[
+                ('id', models.IntegerField(auto_created=True, blank=True, db_index=True, verbose_name='ID')),
+                ('created_date', models.DateField(blank=True, db_index=True, default=datetime.date.today, null=True)),
+                ('modified_date', models.DateField(blank=True, editable=False, null=True)),
+                ('name', models.CharField(db_index=True, max_length=128)),
+                ('history_id', models.AutoField(primary_key=True, serialize=False)),
+                ('history_date', models.DateTimeField()),
+                ('history_change_reason', models.CharField(max_length=100, null=True)),
+                ('history_type', models.CharField(choices=[('+', 'Created'), ('~', 'Changed'), ('-', 'Deleted')], max_length=1)),
+                ('created_by', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('history_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('modified_by', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'verbose_name': 'historical status',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': 'history_date',
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.CreateModel(
+            name='HistoricalReportType',
+            fields=[
+                ('id', models.IntegerField(auto_created=True, blank=True, db_index=True, verbose_name='ID')),
+                ('created_date', models.DateField(blank=True, db_index=True, default=datetime.date.today, null=True)),
+                ('modified_date', models.DateField(blank=True, editable=False, null=True)),
+                ('name', models.CharField(db_index=True, max_length=128)),
+                ('history_id', models.AutoField(primary_key=True, serialize=False)),
+                ('history_date', models.DateTimeField()),
+                ('history_change_reason', models.CharField(max_length=100, null=True)),
+                ('history_type', models.CharField(choices=[('+', 'Created'), ('~', 'Changed'), ('-', 'Deleted')], max_length=1)),
+                ('created_by', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('history_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('modified_by', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'verbose_name': 'historical report type',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': 'history_date',
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+    ]

lideservices/migrations/0012_auto_20191011_1130.py

@@ -0,0 +1,34 @@
+# Generated by Django 2.2 on 2019-10-11 11:30
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('lideservices', '0011_historicalreporttype_historicalstatus_reporttype_status'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='historicalreportfile',
+            name='report_status',
+            field=models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='lideservices.Status'),
+        ),
+        migrations.AlterField(
+            model_name='historicalreportfile',
+            name='report_type',
+            field=models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='lideservices.ReportType'),
+        ),
+        migrations.AlterField(
+            model_name='reportfile',
+            name='report_status',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.PROTECT, related_name='reportfiles', to='lideservices.Status'),
+        ),
+        migrations.AlterField(
+            model_name='reportfile',
+            name='report_type',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.PROTECT, related_name='reportfiles', to='lideservices.ReportType'),
+        ),
+    ]

lideservices/migrations/0013_auto_20191011_1139.py

@@ -0,0 +1,23 @@
+# Generated by Django 2.2 on 2019-10-11 11:39
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('lideservices', '0012_auto_20191011_1130'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='historicalreportfile',
+            old_name='report_status',
+            new_name='status',
+        ),
+        migrations.RenameField(
+            model_name='reportfile',
+            old_name='report_status',
+            new_name='status',
+        ),
+    ]

lideservices/models.py

@@ -1832,31 +1832,34 @@ def _get_filename(self):
 
     def reportfile_location(self, instance):
         """Returns a custom location for the report file, in a folder named for its report type"""
-        return 'reports/{0}/{1}'.format(self.get_report_type_display(), instance)
-
-    # TODO: confirm report names
-    REPORT_TYPES = (
-        (1, 'Inhibition',),
-        (2, 'ResultsSummary',),
-        (3, 'IndividualSample',),
-        (4, 'QualityControl',),
-        (5, 'ControlsResults',),
-    )
-
-    REPORT_STATUSES = (
-        (1, 'Pending',),
-        (2, 'Complete',),
-        (3, 'Failed',)
-    )
+        return 'reports/{0}/{1}'.format(self.report_type.name, instance)
 
     name = property(_get_filename)
     file = models.FileField(upload_to=reportfile_location, null=True)
-    report_type = models.IntegerField(choices=REPORT_TYPES)
-    report_status = models.IntegerField(choices=REPORT_STATUSES)
+    report_type = models.ForeignKey('ReportType', models.PROTECT, related_name='reportfiles')
+    status = models.ForeignKey('Status', models.PROTECT, related_name='reportfiles')
     fail_reason = models.TextField(blank=True)
 
     def __str__(self):
         return str(self.name)
 
     class Meta:
         db_table = "lide_reportfile"
+
+
+class ReportType(NameModel):
+
+    def __str__(self):
+        return str(self.name)
+
+    class Meta:
+        db_table = "lide_reporttype"
+
+
+class Status(NameModel):
+
+    def __str__(self):
+        return str(self.name)
+
+    class Meta:
+        db_table = "lide_status"

lideservices/serializers.py

@@ -1883,17 +1883,30 @@ class Meta:
 class ReportFileSerializer(serializers.ModelSerializer):
     created_by = serializers.StringRelatedField()
     modified_by = serializers.StringRelatedField()
-    report_type_string = serializers.SerializerMethodField()
-    report_status_string = serializers.SerializerMethodField()
+    report_type_string = serializers.StringRelatedField()
+    status_string = serializers.StringRelatedField()
 
-    def get_report_type_string(self, obj):
-        return obj.get_report_type_display()
-
-    def get_report_status_string(self, obj):
-        return obj.get_report_status_display()
 
     class Meta:
         model = ReportFile
-        fields = ('id', 'name', 'file', 'report_type', 'report_type_string', 'report_status', 'report_status_string',
-                  'fail_reason', 'created_date', 'created_by', 'modified_date', 'modified_by',)
+        fields = ('id', 'name', 'file', 'report_type', 'report_type_string', 'status', 'status_string', 'fail_reason',
+                  'created_date', 'created_by', 'modified_date', 'modified_by',)
         read_only_fields = ('name',)
+
+
+class ReportTypeSerializer(serializers.ModelSerializer):
+    created_by = serializers.StringRelatedField()
+    modified_by = serializers.StringRelatedField()
+
+    class Meta:
+        model = ReportType
+        fields = ('id', 'name', 'created_date', 'created_by', 'modified_date', 'modified_by',)
+
+
+class StatusSerializer(serializers.ModelSerializer):
+    created_by = serializers.StringRelatedField()
+    modified_by = serializers.StringRelatedField()
+
+    class Meta:
+        model = Status
+        fields = ('id', 'name', 'created_date', 'created_by', 'modified_date', 'modified_by',)

lideservices/tasks.py

@@ -38,13 +38,13 @@ def generate_inhibition_report(sample, report_file_id, username):
         new_file_content = ContentFile(json.dumps(data, cls=DecimalEncoder))
 
         report_file.file.save(new_file_name, new_file_content)
-        report_file.report_status = 2
+        report_file.status = Status.objects.filter(id=2).first()
         report_file.save()
         return "generate_inhibition_report completed and created file {0}".format(new_file_name)
 
     except Exception as exc:
         message = "generate_inhibition_report failed and no file was created, error message: {0}".format(exc)
-        report_file.report_status = 3
+        report_file.status = Status.objects.filter(id=3).first()
         report_file.fail_reason = message
         report_file.save()
         return message
@@ -179,13 +179,13 @@ def generate_results_summary_report(sample, target, statistic, report_file_id, u
         new_file_content = ContentFile(json.dumps(data, cls=DecimalEncoder))
 
         report_file.file.save(new_file_name, new_file_content)
-        report_file.report_status = 2
+        report_file.status = Status.objects.filter(id=2).first()
         report_file.save()
         return "results_summary_report completed and created file {0}".format(new_file_name)
 
     except Exception as exc:
         message = "results_summary_report failed and no file was created, error message: {0}".format(exc)
-        report_file.report_status = 3
+        report_file.status = Status.objects.filter(id=3).first()
         report_file.fail_reason = message
         report_file.save()
         return message
@@ -216,13 +216,13 @@ def generate_individual_sample_report(sample, target, report_file_id, username):
         new_file_content = ContentFile(json.dumps(data, cls=DecimalEncoder))
 
         report_file.file.save(new_file_name, new_file_content)
-        report_file.report_status = 2
+        report_file.status = Status.objects.filter(id=2).first()
         report_file.save()
         return "individual_sample_report_task completed and created file {0}".format(new_file_name)
 
     except Exception as exc:
         message = "individual_sample_report_task failed and no file was created, error message: {0}".format(exc)
-        report_file.report_status = 3
+        report_file.status = Status.objects.filter(id=3).first()
         report_file.fail_reason = message
         report_file.save()
         return message
@@ -390,13 +390,13 @@ def generate_quality_control_report(samples, report_file_id, username):
         new_file_content = ContentFile(json.dumps(data, cls=DecimalEncoder))
 
         report_file.file.save(new_file_name, new_file_content)
-        report_file.report_status = 2
+        report_file.status = Status.objects.filter(id=2).first()
         report_file.save()
         return "quality_control_report_task completed and created file {0}".format(new_file_name)
 
     except Exception as exc:
         message = "quality_control_report_task failed and no file was created, error message: {0}".format(exc)
-        report_file.report_status = 3
+        report_file.status = Status.objects.filter(id=3).first()
         report_file.fail_reason = message
         report_file.save()
         return message
@@ -684,13 +684,13 @@ def generate_control_results_report(sample_ids, target_ids, report_file_id, user
         new_file_content = ContentFile(json.dumps(data, cls=DecimalEncoder, default=str))
 
         report_file.file.save(new_file_name, new_file_content)
-        report_file.report_status = 2
+        report_file.status = Status.objects.filter(id=2).first()
         report_file.save()
         return "control_results_report_task completed and created file {0}".format(new_file_name)
 
     except Exception as exc:
         message = "control_results_report_task failed and no file was created, error message: {0}".format(exc)
-        report_file.report_status = 3
+        report_file.status = Status.objects.filter(id=3).first()
         report_file.fail_reason = message
         report_file.save()
         return message

lideservices/urls.py

@@ -41,6 +41,8 @@
 router.register(r'otheranalyses', views.OtherAnalysisViewSet, 'otheranalyses')
 router.register(r'users', views.UserViewSet, 'users')
 router.register(r'reportfiles', views.ReportFileViewSet, 'reportfiles')
+router.register(r'reporttypes', views.ReportTypeViewSet, 'reporttypes')
+router.register(r'statuses', views.StatusViewSet, 'statuses')
 
 urlpatterns = [
     url(r'^', include(router.urls)),