Merge pull request #136 from c3g/tox-flake8

Add tox and flake8

.travis.yml

@@ -16,7 +16,7 @@ install:
   - pip install .
 script:
   - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5433
-  - python3 -m coverage run ./manage.py test
+  - python3 -m tox
   - codecov
   - rm -rf chord_metadata_service
   - python3 -m coverage run ./manage.py test chord_metadata_service

README.md

@@ -131,22 +131,28 @@ out and tagged from the tagged major/minor release in `master`.
 
 Tests are located in tests directory in an individual app folder.
 
-Run all tests for the whole project:
+Run all tests and linting checks for the whole project:
 
+```bash
+tox
 ```
+
+Run all tests for the whole project:
+
+```bash
 python manage.py test
 ```
 
 Run tests for an individual app, e.g.:
 
-```
+```bash
 python manage.py test chord_metadata_service.phenopackets.tests.test_api
 ```
 
-Create coverage html report:
+Test and create `coverage` HTML report:
 
-```
-coverage run manage.py test
+```bash
+tox
 coverage html
 ```
 

chord_metadata_service/experiments/models.py

@@ -4,7 +4,6 @@
 from chord_metadata_service.restapi.models import IndexableMixin
 from chord_metadata_service.restapi.description_utils import rec_help
 from chord_metadata_service.restapi.validators import ontology_list_validator, key_value_validator
-from chord_metadata_service.patients.models import Individual
 from chord_metadata_service.phenopackets.models import Biosample
 import chord_metadata_service.experiments.descriptions as d
 
@@ -53,8 +52,8 @@ class Experiment(models.Model, IndexableMixin):
     experiment_type = CharField(max_length=30, help_text=rec_help(d.EXPERIMENT, 'experiment_type'))
     experiment_ontology = JSONField(blank=True, default=list, validators=[ontology_list_validator],
                                     help_text=rec_help(d.EXPERIMENT, 'experiment_ontology'))
-    molecule_ontology   = JSONField(blank=True, default=list, validators=[ontology_list_validator],
-                                    help_text=rec_help(d.EXPERIMENT, 'molecule_ontology'))
+    molecule_ontology = JSONField(blank=True, default=list, validators=[ontology_list_validator],
+                                  help_text=rec_help(d.EXPERIMENT, 'molecule_ontology'))
     molecule = CharField(choices=MOLECULE, max_length=20, blank=True, null=True,
                          help_text=rec_help(d.EXPERIMENT, 'molecule'))
     library_strategy = CharField(choices=LIBRARY_STRATEGY, max_length=25,

chord_metadata_service/mcode/admin.py

@@ -1,52 +1,52 @@
 from django.contrib import admin
-from .models import *
+from . import models as m
 
 
-@admin.register(GeneticSpecimen)
+@admin.register(m.GeneticSpecimen)
 class GeneticSpecimenAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(CancerGeneticVariant)
+@admin.register(m.CancerGeneticVariant)
 class CancerGeneticVariantAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(GenomicRegionStudied)
+@admin.register(m.GenomicRegionStudied)
 class GenomicRegionStudiedAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(GenomicsReport)
+@admin.register(m.GenomicsReport)
 class GenomicsReportAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(LabsVital)
+@admin.register(m.LabsVital)
 class LabsVitalAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(CancerCondition)
+@admin.register(m.CancerCondition)
 class CancerConditionAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(TNMStaging)
+@admin.register(m.TNMStaging)
 class TNMStagingAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(CancerRelatedProcedure)
+@admin.register(m.CancerRelatedProcedure)
 class CancerRelatedProcedureAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(MedicationStatement)
+@admin.register(m.MedicationStatement)
 class MedicationStatementAdmin(admin.ModelAdmin):
     pass
 
 
-@admin.register(MCodePacket)
+@admin.register(m.MCodePacket)
 class MCodePacketAdmin(admin.ModelAdmin):
     pass

chord_metadata_service/mcode/api_views.py

@@ -3,10 +3,8 @@
 from rest_framework.decorators import api_view, permission_classes
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
-from .serializers import *
 from .schemas import MCODE_SCHEMA
-from .models import *
-from .serializers import *
+from . import models as m, serializers as s
 from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 
@@ -17,53 +15,53 @@ class McodeModelViewSet(viewsets.ModelViewSet):
 
 
 class GeneticSpecimenViewSet(McodeModelViewSet):
-    queryset = GeneticSpecimen.objects.all()
-    serializer_class = GeneticSpecimenSerializer
+    queryset = m.GeneticSpecimen.objects.all()
+    serializer_class = s.GeneticSpecimenSerializer
 
 
 class CancerGeneticVariantViewSet(McodeModelViewSet):
-    queryset = CancerGeneticVariant.objects.all()
-    serializer_class = CancerGeneticVariantSerializer
+    queryset = m.CancerGeneticVariant.objects.all()
+    serializer_class = s.CancerGeneticVariantSerializer
 
 
 class GenomicRegionStudiedViewSet(McodeModelViewSet):
-    queryset = GenomicRegionStudied.objects.all()
-    serializer_class = GenomicRegionStudiedSerializer
+    queryset = m.GenomicRegionStudied.objects.all()
+    serializer_class = s.GenomicRegionStudiedSerializer
 
 
 class GenomicsReportViewSet(McodeModelViewSet):
-    queryset = GenomicsReport.objects.all()
-    serializer_class = GenomicsReportSerializer
+    queryset = m.GenomicsReport.objects.all()
+    serializer_class = s.GenomicsReportSerializer
 
 
 class LabsVitalViewSet(McodeModelViewSet):
-    queryset = LabsVital.objects.all()
-    serializer_class = LabsVitalSerializer
+    queryset = m.LabsVital.objects.all()
+    serializer_class = s.LabsVitalSerializer
 
 
 class CancerConditionViewSet(McodeModelViewSet):
-    queryset = CancerCondition.objects.all()
-    serializer_class = CancerConditionSerializer
+    queryset = m.CancerCondition.objects.all()
+    serializer_class = s.CancerConditionSerializer
 
 
 class TNMStagingViewSet(McodeModelViewSet):
-    queryset = TNMStaging.objects.all()
-    serializer_class = TNMStagingSerializer
+    queryset = m.TNMStaging.objects.all()
+    serializer_class = s.TNMStagingSerializer
 
 
 class CancerRelatedProcedureViewSet(McodeModelViewSet):
-    queryset = CancerRelatedProcedure.objects.all()
-    serializer_class = CancerRelatedProcedureSerializer
+    queryset = m.CancerRelatedProcedure.objects.all()
+    serializer_class = s.CancerRelatedProcedureSerializer
 
 
 class MedicationStatementViewSet(McodeModelViewSet):
-    queryset = MedicationStatement.objects.all()
-    serializer_class = MedicationStatementSerializer
+    queryset = m.MedicationStatement.objects.all()
+    serializer_class = s.MedicationStatementSerializer
 
 
 class MCodePacketViewSet(McodeModelViewSet):
-    queryset = MCodePacket.objects.all()
-    serializer_class = MCodePacketSerializer
+    queryset = m.MCodePacket.objects.all()
+    serializer_class = s.MCodePacketSerializer
 
 
 @api_view(["GET"])

chord_metadata_service/mcode/mappings/mappings.py

@@ -1,77 +1,77 @@
-from .mcode_profiles import *
+from . import mcode_profiles as mp
 
 MCODE_PROFILES_MAPPING = {
     "patient": {
-        "profile": MCODE_PATIENT,
+        "profile": mp.MCODE_PATIENT,
         "properties_profile": {
-            "comorbid_condition": MCODE_COMORBID_CONDITION,
-            "ecog_performance_status": MCODE_ECOG_PERFORMANCE_STATUS,
-            "karnofsky": MCODE_KARNOFSKY
+            "comorbid_condition": mp.MCODE_COMORBID_CONDITION,
+            "ecog_performance_status": mp.MCODE_ECOG_PERFORMANCE_STATUS,
+            "karnofsky": mp.MCODE_KARNOFSKY
         }
     },
     "genetic_specimen": {
-        "profile": MCODE_GENETIC_SPECIMEN,
+        "profile": mp.MCODE_GENETIC_SPECIMEN,
         "properties_profile": {
-            "laterality": MCODE_LATERALITY
+            "laterality": mp.MCODE_LATERALITY
         }
     },
     "cancer_genetic_variant": {
-        "profile": MCODE_CANCER_GENETIC_VARIANT
+        "profile": mp.MCODE_CANCER_GENETIC_VARIANT
     },
     "genomic_region_studied": {
-        "profile": MCODE_GENOMIC_REGION_STUDIED
+        "profile": mp.MCODE_GENOMIC_REGION_STUDIED
     },
     "genomics_report": {
-        "profile": MCODE_GENOMICS_REPORT
+        "profile": mp.MCODE_GENOMICS_REPORT
     },
     "labs_vital": {
-        "profile": MCODE_TUMOR_MARKER
+        "profile": mp.MCODE_TUMOR_MARKER
     },
     "cancer_condition": {
         "profile": {
-            "primary": MCODE_PRIMARY_CANCER_CONDITION,
-            "secondary": MCODE_SECONDARY_CANCER_CONDITION
+            "primary": mp.MCODE_PRIMARY_CANCER_CONDITION,
+            "secondary": mp.MCODE_SECONDARY_CANCER_CONDITION
         },
         "properties_profile": {
-            "histology_morphology_behavior": MCODE_HISTOLOGY_MORPHOLOGY_BEHAVIOR
+            "histology_morphology_behavior": mp.MCODE_HISTOLOGY_MORPHOLOGY_BEHAVIOR
         }
     },
     "tnm_staging": {
         "properties_profile": {
             "stage_group": {
-                "clinical": MCODE_TNM_CLINICAL_STAGE_GROUP,
-                "pathologic": MCODE_TNM_PATHOLOGIC_STAGE_GROUP
+                "clinical": mp.MCODE_TNM_CLINICAL_STAGE_GROUP,
+                "pathologic": mp.MCODE_TNM_PATHOLOGIC_STAGE_GROUP
             },
             "primary_tumor_category": {
-                "clinical": MCODE_TNM_CLINICAL_PRIMARY_TUMOR_CATEGORY,
-                "pathologic": MCODE_TNM_PATHOLOGIC_PRIMARY_TUMOR_CATEGORY
+                "clinical": mp.MCODE_TNM_CLINICAL_PRIMARY_TUMOR_CATEGORY,
+                "pathologic": mp.MCODE_TNM_PATHOLOGIC_PRIMARY_TUMOR_CATEGORY
             },
             "regional_nodes_category": {
-                "clinical": MCODE_TNM_CLINICAL_REGIONAL_NODES_CATEGORY,
-                "pathologic": MCODE_TNM_PATHOLOGIC_REGIONAL_NODES_CATEGORY
+                "clinical": mp.MCODE_TNM_CLINICAL_REGIONAL_NODES_CATEGORY,
+                "pathologic": mp.MCODE_TNM_PATHOLOGIC_REGIONAL_NODES_CATEGORY
             },
             "distant_metastases_category": {
-                "clinical": MCODE_TNM_CLINICAL_DISTANT_METASTASES_CATEGORY,
-                "pathologic": MCODE_TNM_PATHOLOGIC_DISTANT_METASTASES_CATEGORY
+                "clinical": mp.MCODE_TNM_CLINICAL_DISTANT_METASTASES_CATEGORY,
+                "pathologic": mp.MCODE_TNM_PATHOLOGIC_DISTANT_METASTASES_CATEGORY
             }
         }
     },
     "cancer_related_procedure": {
         "profile": {
-            "radiation": MCODE_CANCER_RELATED_RADIATION_PROCEDURE,
-            "surgical": MCODE_CANCER_RELATED_SURGICAL_PROCEDURE
+            "radiation": mp.MCODE_CANCER_RELATED_RADIATION_PROCEDURE,
+            "surgical": mp.MCODE_CANCER_RELATED_SURGICAL_PROCEDURE
         }
     },
     "medication_statement": {
-        "profile": MCODE_MEDICATION_STATEMENT,
+        "profile": mp.MCODE_MEDICATION_STATEMENT,
         "properties_profile": {
-            "termination_reason": MCODE_TERMINATION_REASON,
-            "treatment_intent": MCODE_TREATMENT_INTENT
+            "termination_reason": mp.MCODE_TERMINATION_REASON,
+            "treatment_intent": mp.MCODE_TREATMENT_INTENT
         }
     },
     "mcodepacket": {
         "properties_profile": {
-            "cancer_disease_status": MCODE_CANCER_DISEASE_STATUS
+            "cancer_disease_status": mp.MCODE_CANCER_DISEASE_STATUS
         }
     }
 }