Merge branch...

Merge branch '186-datafile-annotation-return-as-json-in-graphql-output-instead-of-jsonstring' into 'dev'

Resolve "Datafile annotation return as json in graphql output instead of jsonstring"

Closes #186

See merge request !108

iric_data/settings.py

@@ -183,10 +183,10 @@ SESSION_COOKIE_AGE = config('SESSION_COOKIE_AGE', default=86400, cast=int)
 # django-auth-ldap ##############################
 AUTH_LDAP_SERVER_URI = config('AUTH_LDAP_SERVER_URI')
 AUTH_LDAP_USER_QUERY_FIELD = 'email'
-AUTH_LDAP_BIND_DN = config('AUTH_LDAP_BIND_DN')
-AUTH_LDAP_BIND_PASSWORD = config('AUTH_LDAP_BIND_PASSWORD')
+AUTH_LDAP_BIND_DN = config('AUTH_LDAP_BIND_DN', default=None)
+AUTH_LDAP_BIND_PASSWORD = config('AUTH_LDAP_BIND_PASSWORD', default=None)
 AUTH_LDAP_BIND_AS_AUTHENTICATING_USER = config('AUTH_LDAP_BIND_AS_AUTHENTICATING_USER', cast=bool)
-# AUTH_LDAP_USER_DN_TEMPLATE = "mail=%(user)s,ou=people,dc=sim,dc=umontreal,dc=ca"  # config('AUTH_LDAP_USER_DN_TEMPLATE')
+AUTH_LDAP_USER_DN_TEMPLATE = config('AUTH_LDAP_USER_DN_TEMPLATE')
 AUTH_LDAP_USER_SEARCH = LDAPSearch(config('AUTH_LDAP_SEARCH'), ldap.SCOPE_SUBTREE, "(|(samaccountname=%(user)s)(mail=%(user)s))")
 AUTH_LDAP_USER_ATTR_MAP = {
     "first_name": "givenName",

portal/forms.py

@@ -160,6 +160,14 @@ class InstitutionForm(forms.ModelForm):
         fields = ('__all__')
 
 
+class DataFileGraphQLForm(forms.ModelForm):
+    """Only enables modification of annotations, iric_data_id is used as a lookup key
+    """
+    class Meta:
+        model = DataFile
+        fields = ('iric_data_id', 'annotations')
+
+
 class DataFileForm(forms.ModelForm):
     class Meta:
         model = DataFile
@@ -229,7 +237,7 @@ class DataFileServletUploadForm(forms.ModelForm):
 class DataFileAnnotationForm(forms.Form):
     dropzone_files = forms.CharField(required=False, widget=forms.HiddenInput)
     annotations = HStoreField(required=False, label=_('Attach these annotations with the uploaded files:'), help_text=_('Pro Tip: You can also drop a tab separated value file onto this field'),
-                              widget=forms.Textarea(attrs={'placeholder':'{"key": "value"}'}))
+                              widget=forms.Textarea(attrs={'placeholder': '{"key": "value"}'}))
     lab = forms.ChoiceField(required=False, label=_('Attach uploaded files to this lab:'))
 
     def __init__(self, request, *args, **kwargs):
@@ -280,7 +288,7 @@ class DataSetForm(forms.ModelForm):
         is_valid = super().is_valid()
         if not is_valid:
             return is_valid
-        elif self.instance.id and self.request_profile: # Apply only to DS update
+        elif self.instance.id and self.request_profile:  # Apply only to DS update
             is_valid = self.instance in DataSet.objects.writable_by_profile(self.request_profile)
         return is_valid
 

portal/graphql_schema.py

@@ -7,12 +7,13 @@ from django.db import connection
 from django.utils import timezone
 from graphql.error import GraphQLError
 from graphene_django.types import DjangoObjectType
+from graphene.types.json import JSONString
 from graphene_django.views import GraphQLView
 from graphene_django.forms.mutation import DjangoModelFormMutation
 
 from portal.models import DataFile, DataSet, Lab, Profile, ProfileToken, ShareGroup
 from portal.views import TokenLoginMixin
-from portal.forms import DataSetForm
+from portal.forms import DataSetForm, DataFileGraphQLForm
 
 
 # Protect graphql API page
@@ -20,6 +21,15 @@ class PrivateGraphQLView(TokenLoginMixin, GraphQLView):
     pass
 
 
+class IRICDataJSONString(JSONString):
+    """
+    Overrides JSONString to avoid the stringification of the JSON object on serialize().
+    """
+    @staticmethod
+    def serialize(dt):
+        return dt
+
+
 # Create a GraphQL type for the various models
 class DataFileType(DjangoObjectType):
     class Meta:
@@ -27,6 +37,7 @@ class DataFileType(DjangoObjectType):
         fields = "__all__"
 
     created_by_user = graphene.Boolean()
+    annotations = IRICDataJSONString()
 
     def resolve_created_by_user(self, info):
         return self.uploaded_by == info.context.user.profile
@@ -175,7 +186,7 @@ class Query(graphene.ObjectType):
         qs = DataSet.objects.accessible_to_profile(info.context.user.profile)
 
         if id_list is not None:
-            qs =  qs.filter(iric_data_id__in=id_list)
+            qs = qs.filter(iric_data_id__in=id_list)
 
         return qs.distinct()
 
@@ -229,6 +240,26 @@ class Query(graphene.ObjectType):
         return qs.distinct()
 
 
+class DataFileAnnotationMutation(DjangoModelFormMutation):
+    """Enable the modification of a DataFile
+    Makes use of the DataFileForm, so all exposed fields from that form are available"""
+
+    class Meta:
+        form_class = DataFileGraphQLForm
+        model_operations = ['update']
+        return_field_name = 'datafile'
+
+    @classmethod
+    def get_form_kwargs(cls, root, info, **input) -> dict:
+        kwargs = super().get_form_kwargs(root, info, **input)
+        if 'instance' not in kwargs.keys():
+            iric_data_id = input.pop("iric_data_id", None)
+            instance = cls._meta.model._default_manager.get(iric_data_id=iric_data_id)
+            kwargs["instance"] = instance
+
+        return kwargs
+
+
 class DataSetMutation(DjangoModelFormMutation):
     """Enable the creation or modification of a DataSet
     Makes use of the DataSetForm, so all exposed fields from that form are available"""
@@ -264,7 +295,7 @@ class DataFileAttachMutation(graphene.Mutation):
         file_hash = graphene.String(required=True)
         filename = graphene.String(required=True)
         target_user_email = graphene.String(required=True)
-        annotations = graphene.JSONString()
+        annotations = IRICDataJSONString()
 
     @classmethod
     def mutate(cls, root, info, file_hash, filename, target_user_email, annotations=None):
@@ -301,6 +332,7 @@ class DataFileAttachMutation(graphene.Mutation):
 
 
 class Mutation(graphene.ObjectType):
+    datafile = DataFileAnnotationMutation.Field()
     dataset = DataSetMutation.Field()
     attach_datafile_by_hash = DataFileAttachMutation.Field()
 

portal/migrations/0033_auto_20230711_1634.py

+# Generated by Django 2.2.17 on 2023-07-11 20:34
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('portal', '0032_auto_20230620_1628'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='datafile',
+            name='iric_data_id',
+            field=models.CharField(max_length=10, null=True, unique=True, verbose_name='ID'),
+        ),
+        migrations.AlterField(
+            model_name='dataset',
+            name='iric_data_id',
+            field=models.CharField(max_length=10, null=True, unique=True, verbose_name='ID'),
+        ),
+    ]

portal/models.py

@@ -183,7 +183,7 @@ class DataFile(models.Model):
 
     filename = models.CharField(max_length=256, verbose_name=_('Filename'))
 
-    iric_data_id = models.CharField(max_length=10, verbose_name=_('ID'), null=True)
+    iric_data_id = models.CharField(max_length=10, verbose_name=_('ID'), null=True, unique=True)
 
     uploaded_by = models.ForeignKey(Profile, on_delete=models.PROTECT, verbose_name=_('Uploaded by'), related_name='uploaded_files')
     lab = models.ForeignKey(Lab, null=True, blank=True, on_delete=models.PROTECT, related_name='files', verbose_name=_('Belongs to this lab'), default=None)
@@ -348,7 +348,7 @@ class DataSet(models.Model):
     files = models.ManyToManyField(DataFile, related_name='datasets', verbose_name=_('Files'), blank=True)
     read_only = models.BooleanField(default=True, verbose_name=_('Read only'), help_text=_('Prevent edits from users with which you share this DataSet'))
 
-    iric_data_id = models.CharField(max_length=10, verbose_name=_('ID'), null=True)
+    iric_data_id = models.CharField(max_length=10, verbose_name=_('ID'), null=True, unique=True)
 
     objects = DataSetManager()