✨ ⚡️Change PUT to PATCH in all resource APIs and minor updates

dataservice/__init__.py

@@ -23,7 +23,6 @@
 from config import config
 
 from sqlalchemy.exc import IntegrityError
-from werkzeug.exceptions import HTTPException
 
 
 def create_app(config_name):
@@ -119,10 +118,10 @@ def register_error_handlers(app):
     NB: Exceptions to be handled must be imported in the head of this module
     """
     from dataservice.api import errors
-    app.register_error_handler(HTTPException, errors.http_error)
     app.register_error_handler(IntegrityError, errors.integrity_error)
-    app.register_error_handler(404, errors.http_error)
-    app.register_error_handler(400, errors.http_error)
+    from werkzeug.exceptions import default_exceptions
+    for ex in default_exceptions:
+        app.register_error_handler(ex, errors.http_error)
 
 
 def register_blueprints(app):

dataservice/api/common/schemas.py

@@ -1,12 +1,12 @@
 from dataservice.extensions import ma
 from marshmallow import (
-        fields,
-        post_dump,
-        pre_dump,
-        validates_schema,
-        ValidationError
+    fields,
+    post_dump,
+    pre_dump,
+    validates_schema,
+    ValidationError
 )
-from flask import url_for, request
+from flask import url_for
 from dataservice.api.common.pagination import Pagination
 from flask_marshmallow import Schema
 
@@ -120,8 +120,8 @@ class StatusSchema(Schema):
     commit = fields.Str(description='API short commit hash', example='aef3b5a')
     branch = fields.Str(description='API branch name', example='master')
     tags = fields.List(
-            fields.String(description='Any tags associated with the version',
-                          example=['rc', 'beta']))
+        fields.String(description='Any tags associated with the version',
+                      example=['rc', 'beta']))
 
     @post_dump(pass_many=False)
     def wrap_envelope(self, data):

dataservice/api/common/views.py

@@ -1,7 +1,6 @@
 import yaml
 import jinja2
 from flask.views import MethodView
-from flask import render_template
 from dataservice.api.common.schemas import (
     response_generator,
     paginated_generator
@@ -42,9 +41,9 @@ def register_spec(cls, spec):
             for name, schema in c.schemas.items():
                 spec.definition(name, schema=schema)
                 ResponseSchema = response_generator(schema)
-                spec.definition(name+'Response', schema=ResponseSchema)
+                spec.definition(name + 'Response', schema=ResponseSchema)
                 PaginatedSchema = paginated_generator(schema)
-                spec.definition(name+'Paginated', schema=PaginatedSchema)
+                spec.definition(name + 'Paginated', schema=PaginatedSchema)
 
     @staticmethod
     def register_views(app):
@@ -80,7 +79,7 @@ def _format_docstring(func):
         # No yaml section
         if yaml_start == -1:
             return
-        yaml_spec = yaml.safe_load(func.__doc__[yaml_start+3:])
+        yaml_spec = yaml.safe_load(func.__doc__[yaml_start + 3:])
 
         # No template to insert
         if 'template' not in yaml_spec:
@@ -95,7 +94,7 @@ def _format_docstring(func):
         templated_spec.update(yaml_spec)
 
         # Dump the deserialized spec back to yaml in the docstring
-        func.__doc__ = func.__doc__[:yaml_start+4]
+        func.__doc__ = func.__doc__[:yaml_start + 4]
         func.__doc__ += yaml.dump(templated_spec, default_flow_style=False)
         # The docstring is now ready for further processing by apispec
 

dataservice/api/demographic/resources.py

@@ -1,5 +1,4 @@
 from flask import abort, request
-from sqlalchemy.orm.exc import NoResultFound
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
@@ -83,26 +82,16 @@ def get(self, kf_id):
             resource:
               Demographic
         """
+        dm = Demographic.query.get(kf_id)
+        if dm is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('demographic', kf_id))
 
-        # Get all
-        if kf_id is None:
-            d = Demographic.query.all()
-            return DemographicSchema(many=True).jsonify(d)
-        # Get one
-        else:
-            try:
-                d = Demographic.query.filter_by(kf_id=kf_id).one()
-            # Not found in database
-            except NoResultFound:
-                abort(404, 'could not find {} `{}`'
-                      .format('demographic', kf_id))
-            return DemographicSchema().jsonify(d)
-
-    def put(self, kf_id):
-        """
-        Update existing demographic
+        return DemographicSchema().jsonify(dm)
 
-        Update an existing demographic given a Kids First id
+    def patch(self, kf_id):
+        """
+        Update an existing demographic. Allows partial update of resource
         ---
         template:
           path:
@@ -111,34 +100,25 @@ def put(self, kf_id):
             resource:
               Demographic
         """
-        body = request.json
-
-        # Check if demographic exists
-        try:
-            d1 = Demographic.query.filter_by(kf_id=kf_id).one()
-        # Not found in database
-        except NoResultFound:
-            abort(404, 'could not find {} `{}`'.format('demographic', kf_id))
+        dm = Demographic.query.get(kf_id)
+        if dm is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('demographic', kf_id))
 
-        # Validation only
+        # Partial update - validate but allow missing required fields
+        body = request.json or {}
         try:
-            d = DemographicSchema(strict=True).load(body).data
-        # Request body not valid
-        except ValidationError as e:
-            abort(400, 'could not update demographic: {}'.format(e.messages))
+            dm = DemographicSchema(strict=True).load(body, instance=dm,
+                                                     partial=True).data
+        except ValidationError as err:
+            abort(400, 'could not update demographic: {}'.format(err.messages))
 
-        # Deserialize
-        d1.external_id = body.get('external_id')
-        d1.race = body.get('race')
-        d1.gender = body.get('gender')
-        d1.ethnicity = body.get('ethnicity')
-        d1.participant_id = body.get('participant_id')
-
-        # Save to database
+        db.session.add(dm)
         db.session.commit()
 
-        return DemographicSchema(200, 'demographic {} updated'
-                                 .format(d1.kf_id)).jsonify(d1), 200
+        return DemographicSchema(
+            200, 'demographic {} updated'.format(dm.kf_id)
+        ).jsonify(dm), 200
 
     def delete(self, kf_id):
         """
@@ -154,15 +134,14 @@ def delete(self, kf_id):
               Demographic
         """
         # Check if demographic exists
-        try:
-            d = Demographic.query.filter_by(kf_id=kf_id).one()
-        # Not found in database
-        except NoResultFound:
-            abort(404, 'could not find {} `{}`'.format('demographic', kf_id))
+        dm = Demographic.query.get(kf_id)
+        if dm is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('demographic', kf_id))
 
         # Save in database
-        db.session.delete(d)
+        db.session.delete(dm)
         db.session.commit()
 
         return DemographicSchema(200, 'demographic {} deleted'
-                                 .format(d.kf_id)).jsonify(d), 200
+                                 .format(dm.kf_id)).jsonify(dm), 200

dataservice/api/demographic/schemas.py

@@ -5,11 +5,6 @@
 
 
 class DemographicSchema(BaseSchema):
-    # Should not have to do this, since participant_id is part of the
-    # Demographic model and should be dumped. However it looks like this is
-    # still a bug in marshmallow_sqlalchemy. The bug is that ma sets
-    # dump_only=True for foreign keys by default. See link below
-    # https://github.com/marshmallow-code/marshmallow-sqlalchemy/issues/20
     participant_id = field_for(Demographic, 'participant_id', required=True,
                                load_only=True)
 

dataservice/api/diagnosis/resources.py

@@ -1,5 +1,4 @@
 from flask import abort, request
-from sqlalchemy.orm.exc import NoResultFound
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
@@ -84,19 +83,15 @@ def get(self, kf_id):
               Diagnosis
         """
         # Get one
-        try:
-            d = Diagnosis.query.filter_by(kf_id=kf_id).one()
-        # Not found in database
-        except NoResultFound:
+        dg = Diagnosis.query.get(kf_id)
+        if dg is None:
             abort(404, 'could not find {} `{}`'
                   .format('diagnosis', kf_id))
-        return DiagnosisSchema().jsonify(d)
+        return DiagnosisSchema().jsonify(dg)
 
-    def put(self, kf_id):
+    def patch(self, kf_id):
         """
-        Update existing diagnosis
-
-        Update an existing diagnosis given a Kids First id
+        Update an existing diagnosis. Allows partial update of resource
         ---
         template:
           path:
@@ -105,34 +100,25 @@ def put(self, kf_id):
             resource:
               Diagnosis
         """
-        body = request.json
-        try:
-            # Check if diagnosis exists
-            d1 = Diagnosis.query.filter_by(kf_id=kf_id).one()
-        # Not found in database
-        except NoResultFound:
-            abort(404, 'could not find {} `{}`'.format('diagnosis', kf_id))
+        dg = Diagnosis.query.get(kf_id)
+        if dg is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('diagnosis', kf_id))
 
-        # Validation only
+        # Partial update - validate but allow missing required fields
+        body = request.json or {}
         try:
-            d = DiagnosisSchema(strict=True).load(body).data
-        # Request body not valid
-        except ValidationError as e:
-            abort(400, 'could not update diagnosis: {}'.format(e.messages))
+            dg = DiagnosisSchema(strict=True).load(body, instance=dg,
+                                                   partial=True).data
+        except ValidationError as err:
+            abort(400, 'could not update diagnosis: {}'.format(err.messages))
 
-        # Deserialize
-        d1.external_id = body.get('external_id')
-        d1.diagnosis = body.get('diagnosis')
-        d1.diagnosis_category = body.get('diagnosis_category')
-        d1.tumor_location = body.get('tumor_location')
-        d1.age_at_event_days = body.get('age_at_event_days')
-        d1.participant_id = body.get('participant_id')
-
-        # Save to database
+        db.session.add(dg)
         db.session.commit()
 
-        return DiagnosisSchema(200, 'diagnosis {} updated'
-                               .format(d1.kf_id)).jsonify(d1), 200
+        return DiagnosisSchema(
+            200, 'diagnosis {} updated'.format(dg.kf_id)
+        ).jsonify(dg), 200
 
     def delete(self, kf_id):
         """
@@ -149,15 +135,14 @@ def delete(self, kf_id):
         """
 
         # Check if diagnosis exists
-        try:
-            d = Diagnosis.query.filter_by(kf_id=kf_id).one()
-        # Not found in database
-        except NoResultFound:
-            abort(404, 'could not find {} `{}`'.format('diagnosis', kf_id))
+        dg = Diagnosis.query.get(kf_id)
+        if dg is None:
+            abort(404, 'could not find {} `{}`'
+                  .format('diagnosis', kf_id))
 
         # Save in database
-        db.session.delete(d)
+        db.session.delete(dg)
         db.session.commit()
 
         return DiagnosisSchema(200, 'diagnosis {} deleted'
-                               .format(d.kf_id)).jsonify(d), 200
+                               .format(dg.kf_id)).jsonify(dg), 200

dataservice/api/diagnosis/schemas.py

@@ -1,5 +1,4 @@
 from marshmallow_sqlalchemy import field_for
-from marshmallow import validates, ValidationError
 
 from dataservice.api.diagnosis.models import Diagnosis
 from dataservice.api.common.schemas import BaseSchema
@@ -8,11 +7,6 @@
 
 
 class DiagnosisSchema(BaseSchema):
-    # Should not have to do this, since participant_id is part of the
-    # Diagnosis model and should be dumped. However it looks like this is
-    # still a bug in marshmallow_sqlalchemy. The bug is that ma sets
-    # dump_only=True for foreign keys by default. See link below
-    # https://github.com/marshmallow-code/marshmallow-sqlalchemy/issues/20
     participant_id = field_for(Diagnosis, 'participant_id', required=True,
                                load_only=True, example='DZB048J5')
     age_at_event_days = field_for(Diagnosis, 'age_at_event_days',

dataservice/api/docs/resources.py

@@ -1,6 +1,4 @@
-import os
 import glob
-import subprocess
 from flask.views import View
 from flask import jsonify, current_app, render_template