:sparkless: Initial sample-relationships API

dataservice/api/sample_relationship/resources.py

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+from flask import abort, request
+from marshmallow import ValidationError
+from webargs.flaskparser import use_args
+
+from dataservice.extensions import db
+from dataservice.api.common.pagination import paginated, Pagination
+from dataservice.api.sample_relationship.models import SampleRelationship
+from dataservice.api.sample_relationship.schemas import (
+    SampleRelationshipSchema,
+    SampleRelationshipFilterSchema
+)
+from dataservice.api.common.views import CRUDView
+from dataservice.api.common.schemas import filter_schema_factory
+
+
+class SampleRelationshipListAPI(CRUDView):
+    """
+    SampleRelationship REST API
+    """
+    endpoint = 'sample_relationships_list'
+    rule = '/sample-relationships'
+    schemas = {'SampleRelationship': SampleRelationshipSchema}
+
+    @paginated
+    @use_args(filter_schema_factory(SampleRelationshipFilterSchema),
+              locations=('query',))
+    def get(self, filter_params, after, limit):
+        """
+        Get all sample_relationships
+        ---
+        description: Get all sample_relationships
+        template:
+          path:
+            get_list.yml
+          properties:
+            resource:
+              SampleRelationship
+        """
+        # Get and remove special filter parameters - those which are not
+        # part of model properties
+        # Study id
+        study_id = filter_params.pop('study_id', None)
+        # Sample id
+        sample_id = filter_params.pop('sample_id', None)
+
+        # Get sample relationships joined w samples
+        q = SampleRelationship.query_all_relationships(
+            sample_kf_id=sample_id,
+            model_filter_params=filter_params)
+
+        # Filter by study
+        if study_id:
+            from dataservice.api.participant.models import Participant
+            q = (q.join(Participant.samples)
+                 .filter(Participant.study_id == study_id))
+
+        return (SampleRelationshipSchema(many=True)
+                .jsonify(Pagination(q, after, limit)))
+
+    def post(self):
+        """
+        Create a new sample_relationship
+        ---
+        template:
+          path:
+            new_resource.yml
+          properties:
+            resource:
+              SampleRelationship
+        """
+
+        body = request.get_json(force=True)
+
+        # Deserialize
+        try:
+            sa = SampleRelationshipSchema(strict=True).load(body).data
+        # Request body not valid
+        except ValidationError as e:
+            abort(400, 'could not create sample_relationship: {}'
+                  .format(e.messages))
+
+        # Add to and save in database
+        db.session.add(sa)
+        db.session.commit()
+
+        return SampleRelationshipSchema(201, 'sample_relationship {} created'
+                                        .format(sa.kf_id)).jsonify(sa), 201
+
+
+class SampleRelationshipAPI(CRUDView):
+    """
+    SampleRelationship REST API
+    """
+    endpoint = 'sample_relationships'
+    rule = '/sample-relationships/<string:kf_id>'
+    schemas = {'SampleRelationship': SampleRelationshipSchema}
+
+    def get(self, kf_id):
+        """
+        Get a sample_relationship by id
+        ---
+        template:
+          path:
+            get_by_id.yml
+          properties:
+            resource:
+              SampleRelationship
+        """
+        # Get one
+        sa = SampleRelationship.query.get(kf_id)
+        if sa is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('sample_relationship', kf_id))
+        return SampleRelationshipSchema().jsonify(sa)
+
+    def patch(self, kf_id):
+        """
+        Update an existing sample_relationship.
+
+        Allows partial update of resource
+        ---
+        template:
+          path:
+            update_by_id.yml
+          properties:
+            resource:
+              SampleRelationship
+        """
+        sa = SampleRelationship.query.get(kf_id)
+        if sa is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('sample_relationship', kf_id))
+
+        # Partial update - validate but allow missing required fields
+        body = request.get_json(force=True) or {}
+        try:
+            sa = SampleRelationshipSchema(strict=True).load(body, instance=sa,
+                                                            partial=True).data
+        except ValidationError as err:
+            abort(400, 'could not update sample_relationship: {}'
+                  .format(err.messages))
+
+        db.session.add(sa)
+        db.session.commit()
+
+        return SampleRelationshipSchema(
+            200, 'sample_relationship {} updated'.format(sa.kf_id)
+        ).jsonify(sa), 200
+
+    def delete(self, kf_id):
+        """
+        Delete sample_relationship by id
+
+        Deletes a sample_relationship given a Kids First id
+        ---
+        template:
+          path:
+            delete_by_id.yml
+          properties:
+            resource:
+              SampleRelationship
+        """
+
+        # Check if sample_relationship exists
+        sa = SampleRelationship.query.get(kf_id)
+        if sa is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('sample_relationship', kf_id))
+
+        # Save in database
+        db.session.delete(sa)
+        db.session.commit()
+
+        return SampleRelationshipSchema(200, 'sample_relationship {} deleted'
+                                        .format(sa.kf_id)).jsonify(sa), 200