Merge pull request #216 from elixir-luxembourg/fixes-to-importer

Fixes to importer

README.md

@@ -212,7 +212,7 @@ Single file mode:
 
 Batch mode:
 ```bash
-./manage.py import_projects -f path/to/dir/with/json/files/
+./manage.py import_projects -d path/to/dir/with/json/files/
 ```
 
 Available commands: `import_projects`, `import_datasets`, `import_partners`.

core/fixtures/contact-types.json

@@ -1,4 +1,7 @@
 [
+  {
+    "name": "Researcher"
+  },
   {
     "name": "Principal_Investigator"
   },

core/fixtures/elu-dataset.json

@@ -5,7 +5,7 @@
   "type": "object",
   "allOf": [
     {
-      "$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
+      "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/master/schemas/elu-core.json"
     }
   ],
   "properties": {
@@ -145,6 +145,7 @@
                   "US",
                   "PS",
                   "IS",
+                  "IP",
                   "Other"
                 ]
               },

core/fixtures/elu-project.json

@@ -11,7 +11,7 @@
       "type": "object",
       "allOf": [
         {
-          "$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-study.json"
+          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/master/schemas/elu-study.json"
         }
       ],
       "properties": {

core/fixtures/elu-study.json

@@ -13,7 +13,7 @@
       "type": "object",
       "allOf": [
         {
-          "$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
+          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/master/schemas/elu-core.json"
         }
       ],
       "properties": {

core/forms/data_declaration.py

@@ -1,11 +1,12 @@
 from django import forms
+from django.forms import  ValidationError
 from django.shortcuts import get_object_or_404
 from django.urls import reverse_lazy
 
+from core.forms.use_restriction import UseRestrictionForm
 from core.models import DataDeclaration, Partner, Contract, GDPRRole
 from core.models.contract import PartnerRole
-from django.forms import  ValidationError
-from core.forms.use_restriction import UseRestrictionForm
+
 
 class DataDeclarationEditForm(forms.ModelForm):
 

core/forms/dataset.py

@@ -46,7 +46,8 @@ def clean(self):
                 if contract.project:
                     if str(contract.project.id) != proj:
                         project_inconsistency = True
-                        self.add_error('project', "Dataset has existing link to Project {} via {}. Please remove link before updating this field.".format(contract.project.acronym, obj))
+                        error_msg = f"Dataset has existing link to Project {contract.project.acronym} via {obj}. Please remove link before updating this field."
+                        self.add_error('project', error_msg)
             if project_inconsistency:
                 errors.append("Unable to update project information.")
 

core/forms/use_restriction.py

@@ -2,6 +2,7 @@
 from django.forms import CharField, ModelForm, Select
 
 from core.models import UseRestriction, RestrictionClass
+from core.models.use_restriction import USE_RESTRICTION_CHOICES
 
 
 class UseRestrictionForm(ModelForm):
@@ -11,16 +12,19 @@ class UseRestrictionForm(ModelForm):
 
     class Meta:
         model = UseRestriction
-        fields = ('restriction_class', 'notes')
+        fields = ('use_restriction_rule', 'restriction_class', 'notes', 'use_class_note')
 
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         class_choices = [(None, "-----------------------")]
         class_choices.extend([(d.code, d.name) for d in RestrictionClass.objects.all()])
-        self.fields['restriction_class'] = CharField(label='Category', help_text= 'Select the category of restrictions. These are \'GA4GH Consent Codes\'', required=True, widget=Select(choices=class_choices, attrs={'class': 'dummy-select'}))
+        self.fields['restriction_class'] = CharField(label='Use category', help_text= 'Select the category of restrictions. These are \'GA4GH Consent Codes\'', required=True, widget=Select(choices=class_choices, attrs={'class': 'dummy-select'}))
         self.fields['notes'].widget.attrs['cols'] = '70'
-        self.fields['notes'].widget.attrs['rows'] = '1'
+        self.fields['notes'].widget.attrs['rows'] = '5'
+        self.fields['use_restriction_rule'] = CharField(label='Use Restriction Rule', help_text= 'Does the rule constraints or forbids?', required=False, widget=Select(choices=USE_RESTRICTION_CHOICES, attrs={'class': 'dummy-select'}))
+        self.fields['use_class_note'].widget.attrs['cols'] = '70'
+        self.fields['use_class_note'].widget.attrs['rows'] = '3'
 
 
     def clean(self):
@@ -36,4 +40,6 @@ def is_empty(self):
         cleaned_data = super().clean()
         restriction_class = cleaned_data.get('restriction_class')
         notes = cleaned_data.get('notes')
-        return not restriction_class and not notes
+        use_class_note = cleaned_data.get('use_class_note')
+        use_restriction_rule =  cleaned_data.get('use_restriction_rule')
+        return not restriction_class and not notes and not use_class_note and not use_restriction_rule

core/importer/JSONSchemaValidator.py

@@ -1,16 +1,19 @@
 import json
 import jsonschema
+import os
 import sys
 import urllib.request
 
+from django.conf import settings
+
 from core.exceptions import JSONSchemaValidationError
 from core.utils import DaisyLogger
 
 
 logger = DaisyLogger(__name__)
 
-JSONSCHEMA_BASE_LOCAL_PATH = './core/fixtures/'
-JSONSCHEMA_BASE_REMOTE_URL = "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/"
+JSONSCHEMA_BASE_LOCAL_PATH = os.path.join(settings.BASE_DIR, 'core', 'fixtures')
+JSONSCHEMA_BASE_REMOTE_URL = "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/master/schemas/"
 
 
 class BaseJSONSchemaValidator:
@@ -43,24 +46,26 @@ def _preload_schema(self):
             import os
             logger.warn("Error (1/2) loading schema from disk for JSON validation...: " + str(e))
             logger.warn("Working directory = " + os.getcwd()) 
-            logger.warn("File path = " + self.base_path + self.schema_name)
+            logger.warn("File path = " + os.path.join(self.base_path, self.schema_name))
             logger.warn("Will try to load the schema from URL...")
 
         try:
             self._cached_schema = self._load_schema_from_url()
             return
         except:
             logger.error("Error (2/2) loading schema from URI for JSON validation...: " + str(e))
-            logger.error("URL = " + self.base_url + self.schema_name) 
+            logger.error("URL = " + os.path.join(self.base_url, self.schema_name))
 
         raise Exception('Cannot load schema for JSON validation')
 
     def _load_schema_from_disk(self):
-        with open(self.base_path + self.schema_name, 'r') as opened_file:
+        file_path = os.path.join(self.base_path, self.schema_name)
+        with open(file_path, 'r') as opened_file:
             return json.load(opened_file)
 
     def _load_schema_from_url(self):
-        with urllib.request.urlopen(self.base_url + self.schema_name) as url:
+        file_path = os.path.join(self.base_url, self.schema_name)
+        with urllib.request.urlopen(file_path) as url:
             return json.loads(url.read().decode())
 
 class DatasetJSONSchemaValidator(BaseJSONSchemaValidator):