Merge branch '159-create-a-dataset-programmatically' into 'master'

implements GRAPHQL Dataset and Datafile mutations

Closes #156 and #159

See merge request !85

iric_data/settings.py

@@ -95,6 +95,10 @@ CRISPY_TEMPLATE_PACK = 'bootstrap4'
 
 WSGI_APPLICATION = 'iric_data.wsgi.application'
 
+# Graphene / GraphQL
+GRAPHENE = {
+    "ATOMIC_MUTATIONS": True,
+}
 
 # Database
 # https://docs.djangoproject.com/en/2.1/ref/settings/#databases

portal/forms.py

@@ -94,7 +94,6 @@ class AlertForm(forms.ModelForm):
         )
 
 
-
 class UserForm(forms.ModelForm):
     class Meta:
         model = User

portal/graphql_schema.py

+import os
 import graphene
+import hashlib
+
 from django.contrib.auth import get_user_model
+from django.db import connection
+from django.utils import timezone
+from graphql.error import GraphQLError
 from graphene_django.types import DjangoObjectType
 from graphene_django.views import GraphQLView
+from graphene_django.forms.mutation import DjangoModelFormMutation
 
-from portal.models import DataFile, DataSet, Profile
+from portal.models import DataFile, DataSet, Lab, Profile
 from portal.views import TokenLoginMixin
+from portal.forms import DataSetForm
 
 
 # Protect graphql API page
@@ -25,7 +33,7 @@ class DataSetType(DjangoObjectType):
         fields = "__all__"
 
 
-class ProfileSetType(DjangoObjectType):
+class ProfileType(DjangoObjectType):
     class Meta:
         model = Profile
 
@@ -35,20 +43,27 @@ class UserType(DjangoObjectType):
         model = get_user_model()
 
 
+class LabType(DjangoObjectType):
+    class Meta:
+        model = Lab
+
+
 # Create a Query type
 class Query(graphene.ObjectType):
-    datafile = graphene.Field(DataFileType, id=graphene.String(), dbid=graphene.Int())
-    dataset = graphene.Field(DataSetType, id=graphene.String(), dbid=graphene.Int())
+    datafile = graphene.Field(DataFileType, id=graphene.String(), dbid=graphene.ID())
+    dataset = graphene.Field(DataSetType, id=graphene.String(), dbid=graphene.ID())
     datafiles = graphene.List(
-            DataFileType,
-            key=graphene.String(),
-            value=graphene.String(),
-            key_values=graphene.JSONString(),
-            keys=graphene.JSONString(),
-            values=graphene.JSONString(),
-            dataset=graphene.String()
-            )
+        DataFileType,
+        key=graphene.String(),
+        value=graphene.String(),
+        key_values=graphene.JSONString(),
+        keys=graphene.JSONString(),
+        values=graphene.JSONString(),
+        dataset=graphene.String(),
+        file_hash=graphene.String()
+    )
     datasets = graphene.List(DataSetType)
+    lab = graphene.Field(LabType, name=graphene.String(), dbid=graphene.ID())
 
     def resolve_datafile(self, info, **kwargs):
         id = kwargs.get('id')
@@ -80,6 +95,7 @@ class Query(graphene.ObjectType):
         keys = kwargs.get('keys', None)
         values = kwargs.get('values', None)
         dataset = kwargs.get('dataset', None)
+        file_hash = kwargs.get('file_hash', None)
 
         if type(key_values) is not dict:
             key_values = {}
@@ -109,14 +125,92 @@ class Query(graphene.ObjectType):
         if dataset:
             qs = qs.filter(datasets__iric_data_id=dataset)
 
+        if file_hash:
+            iric_data_file_hash = os.path.join(file_hash[:3], file_hash)
+            qs = qs.filter(file=iric_data_file_hash)
+
         return qs.distinct()
 
     def resolve_datasets(self, info, **kwargs):
         return DataSet.objects.all()
 
+    def resolve_lab(self, info, **kwargs):
+        name = kwargs.get('name')
+        dbid = kwargs.get('dbid')
+
+        if name is not None:
+            return Lab.objects.get(name=name)
+        elif dbid is not None:
+            return Lab.objects.get(pk=dbid)
+
+
+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"""
+
+    class Meta:
+        form_class = DataSetForm
+        return_field_name = 'dataset'
+
+    @classmethod
+    def perform_mutate(cls, form, info):
+        object = form.save(commit=False)
+        if not object.pk:
+            object.read_only = True
+            object.created_by = info.context.user.profile
+
+        object.last_update_by = info.context.user.profile
+        object.save()
+        return super().perform_mutate(form, info)
+
+
+class DataFileAttachMutation(graphene.Mutation):
+    attached_datafile = graphene.Field(DataFileType)
+
+    class Arguments:
+        # The input arguments for this mutation
+        file_hash = graphene.String(required=True)
+        filename = graphene.String(required=True)
+        target_user_email = graphene.String(required=True)
+        annotations = graphene.String()
+
+    @classmethod
+    def mutate(cls, root, info, file_hash, filename, target_user_email, annotations=None):
+        # check that calling user is staff:
+        if not info.context.user.is_staff:
+            raise GraphQLError("You are not allowed to use this API function")
+
+        # transform file_hash
+        iric_data_file_hash = os.path.join(file_hash[:3], file_hash)
+
+        target_profile = Profile.objects.get(user__email=target_user_email)
+
+        if not DataFile.objects.filter(file=iric_data_file_hash).exists():
+            raise GraphQLError("No datafile associated with the provided hash")
+
+        with connection.cursor() as cursor:
+            cursor.execute(
+                "INSERT INTO portal_datafile(file, filename, uploaded_by_id, upload_timestamp, annotations) VALUES (%s, %s, %s, %s, %s)",
+                [
+                    iric_data_file_hash,
+                    filename,
+                    target_profile.id,
+                    timezone.now(),
+                    annotations
+                ]
+            )
+
+            df = DataFile.objects.latest('id')
+
+        df.iric_data_id = "DF{}".format(hashlib.md5(str(df.id).encode()).hexdigest()[:8]).upper()
+        df.save()
+
+        return DataFileAttachMutation(attached_datafile=df)
+
 
 class Mutation(graphene.ObjectType):
-    pass
+    dataset = DataSetMutation.Field()
+    attach_datafile_by_hash = DataFileAttachMutation.Field()
 
 
-schema = graphene.Schema(query=Query, auto_camelcase=False)
+schema = graphene.Schema(query=Query, mutation=Mutation, auto_camelcase=False)

portal/migrations/0028_auto_20230105_1026.py

+# Generated by Django 2.2.17 on 2023-01-05 15:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('portal', '0028_profile_update_timestamp'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='lab',
+            name='ldap',
+            field=models.CharField(blank=True, max_length=32, null=True, unique=True, verbose_name='LDAP'),
+        ),
+        migrations.AlterField(
+            model_name='lab',
+            name='name',
+            field=models.CharField(max_length=64, unique=True, verbose_name='Name'),
+        ),
+    ]

portal/models.py

@@ -97,8 +97,8 @@ class Lab(models.Model):
     class Meta:
         ordering = ['name']
 
-    name = models.CharField(max_length=64, verbose_name=_('Name'))
-    ldap = models.CharField(max_length=32, null=True, blank=True, verbose_name='LDAP')
+    name = models.CharField(max_length=64, verbose_name=_('Name'), unique=True)
+    ldap = models.CharField(max_length=32, null=True, blank=True, verbose_name='LDAP', unique=True)
 
     pi = models.OneToOneField(
         Profile,