Merge pull request #275 from elixir-luxembourg/develop

develop to master (1.6.0)

.github/workflows/main.yml

@@ -0,0 +1,35 @@
+name: Execute the tests
+
+on:
+  push:
+    branches:
+    - use-github-actions
+    - master
+    - develop
+    - dependabot/**
+  pull_request:
+    branches:
+    - develop
+    - master
+
+jobs:
+  tests:
+    timeout-minutes: 15
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout the repository
+      uses: actions/checkout@v2
+
+    - name: Prepare DAISY settings for CI
+      run: cp elixir_daisy/settings_compose_ci.py elixir_daisy/settings_compose.py
+
+    - name: Build and start containers
+      run: docker-compose up -d --build
+
+    - name: Execute the tests
+      run: docker-compose exec -T web python setup.py pytest
+
+    - name: Stop containers
+      if: always()
+      run: docker-compose down

.travis.yml

@@ -2,7 +2,6 @@ language: python
 
 python:
   - "3.6"
-  - "3.5"
 
 services:
   - docker
@@ -18,4 +17,9 @@ install:
   - sleep 60
 
 script:
-  - docker-compose exec web python setup.py pytest 
+  - docker-compose exec web python setup.py pytest 
+
+branches:
+  only:
+  - master
+  - develop

conftest.py

@@ -123,6 +123,14 @@ def user_data_steward(django_user_model):
     return u
 
 
+@pytest.fixture
+def user_admin(django_user_model):
+    u = django_user_model.objects.create_superuser(username="test.admin",
+                                      email="test.admin@mail.com",
+                                      password="password")
+    return u
+
+
 @pytest.fixture
 def users(django_user_model, user_normal, user_vip, user_data_steward):
     """

core/apps.py

@@ -1,8 +1,25 @@
 from django.apps import AppConfig
+from django.conf import settings
+import os
+import json
+from django.core.exceptions import ImproperlyConfigured
 
 
 class CoreConfig(AppConfig):
     name = 'core'
 
     def ready(self):
-        import core.models.signals
+        import core.models.signals
+
+        # Prevent use of conflicting versions of import JSON schemas
+        json_schema_uri = getattr(settings,'IMPORT_JSON_SCHEMAS_URI')
+        json_schema_dir = getattr(settings,'IMPORT_JSON_SCHEMAS_DIR')
+        for file in os.listdir(json_schema_dir):
+            with open(os.path.join(json_schema_dir, file), 'r', encoding='utf-8') as schema_file:
+                schema = json.loads(schema_file.read())
+                local_schema_uri_basename = os.path.dirname(schema['$id'])
+                settings_schema_uri_basename = os.path.dirname(json_schema_uri)
+            if local_schema_uri_basename != settings_schema_uri_basename:
+                raise ImproperlyConfigured('Version of import JSON schema is not matching version set in settings.py.\n'
+                                           f'{file} property $id: {local_schema_uri_basename}\n'
+                                           f'settings.py schema URI: {settings_schema_uri_basename}')

core/exceptions.py

@@ -16,6 +16,14 @@ def __repr__(self):
         return "{}({!r})".format(self.__class__.__name__, msg)
 
 
+class PartnerImportError(DaisyError):
+    """Error when importing partner into daisy."""
+
+    default_message = "Error when importing partner:' {data}'"
+
+    def __init__(self, data, msg=None):
+        self.data = data
+        super().__init__(msg=msg)
 
 
 class DatasetImportError(DaisyError):
@@ -28,6 +36,15 @@ def __init__(self, data, msg=None):
         super().__init__(msg=msg)
 
 
+class ProjectImportError(DaisyError):
+    """Error when importing project into daisy."""
+
+    default_message = "Error when importing project:' {data}'"
+
+    def __init__(self, data, msg=None):
+        self.data = data
+        super().__init__(msg=msg)
+
 
 class FixtureImportError(DaisyError):
     """Error when importing initial definition data into daisy."""

core/fixtures/document-types.json

@@ -1,27 +1,32 @@
-[
-  {
-    "name": "Other"
-  },
-
-  {
-    "name": "Contract/Agreement"
-  },
-  {
-    "name": "Consent Form Template"
-  },
-  {
-    "name":  "CNER Approval"
-  },
-  {
-    "name": "CNPD Authorisation"
-  },
-  {
-    "name": "CNPD Notification"
-  },
-  {
-    "name": "ERP Approval"
-  },
-  {
-    "name": "Subject Information Sheet Template"
-  }
-]
+[{
+        "name": "Other"
+    },
+
+    {
+        "name": "Data Protection Impact Assessment"
+    },
+
+    {
+        "name": "Contract/Agreement"
+    },
+    {
+        "name": "Consent Form Template"
+    },
+    {
+        "name": "CNER Approval"
+    },
+    {
+        "name": "CNPD Authorisation"
+    },
+    {
+        "name": "CNPD Notification"
+    },
+
+
+    {
+        "name": "ERP Approval"
+    },
+    {
+        "name": "Subject Information Sheet Template"
+    }
+]

core/fixtures/elu-cohorts.json

@@ -1,6 +1,6 @@
 [
   {
-    "elu_accession": "ELU_C_1",
+    "external_id": "ELU_C_1",
     "title": "LuxPARK",
     "owners": [
       "Rejko Kr\u00fcger"
@@ -14,7 +14,7 @@
     ]
   },
   {
-    "elu_accession": "ELU_C_2",
+    "external_id": "ELU_C_2",
     "title": "MUST (Diabetes MUltiplex family STudy)",
     "owners": [
       "Carine de Beaufort"
@@ -27,7 +27,7 @@
     ]
   },
   {
-    "elu_accession": "ELU_C_3",
+    "external_id": "ELU_C_3",
     "title": "COSMIC (Colonisation, Succession and Evolution of Human Gastrointestinal Microbiome from Birth to Infancy)",
     "owners": [
       "Carine de Beaufort"
@@ -40,7 +40,7 @@
     ]
   },
   {
-    "elu_accession": "ELU_C_4",
+    "external_id": "ELU_C_4",
     "title": "DeNoPa (De Novo Parkinson Longitudinal Study)",
     "owners": [
       "Brit Mollenhauer"
@@ -51,7 +51,7 @@
     ]
   },
   {
-    "elu_accession": "ELU_C_5",
+    "external_id": "ELU_C_5",
     "title": "TREND (T\u00fbbinger evaluation of Risk factors for Early detection of NeuroDegeneration.)",
     "owners": [
       "Daniela Berg"
@@ -62,23 +62,23 @@
     ]
   },
   {
-    "elu_accession": "ELU_C_6",
+    "external_id": "ELU_C_6",
     "title": "ADNI (Alzheimer's Disease Neuroimaging Initiative.)",
     "comments": "...TBD...",
     "institutes": [
       "ELU_I_84"
     ]
   },
   {
-    "elu_accession": "ELU_C_7",
+    "external_id": "ELU_C_7",
     "title": "PPMI (Partkinsons Progressive Markers Inititative Study Cohort.)",
     "comments": "...TBD...",
     "institutes": [
       "ELU_I_85"
     ]
   },
   {
-    "elu_accession": "ELU_C_8",
+    "external_id": "ELU_C_8",
     "title": "Supercentenarians (Betterhumans Inc. Supercentenarians Research Study)",
     "comments": "...TBD...",
     "institutes": [