Delete sample (#19)

* Update OpenAPI generator

* Delete sample endpoint

* Fixed requirement to avoid currently open issue: python-openapi/openapi-spec-validator#126

* Change return status

* Update specs

.openapi-generator/FILES

@@ -0,0 +1,21 @@
+openapi_server/__init__.py
+openapi_server/controllers/__init__.py
+openapi_server/controllers/event_controller.py
+openapi_server/controllers/file_controller.py
+openapi_server/controllers/qc_result_controller.py
+openapi_server/controllers/sample_controller.py
+openapi_server/controllers/sample_status_controller.py
+openapi_server/controllers/security_controller_.py
+openapi_server/encoder.py
+openapi_server/models/__init__.py
+openapi_server/models/base_model_.py
+openapi_server/models/error.py
+openapi_server/models/event.py
+openapi_server/models/file.py
+openapi_server/models/qc_result.py
+openapi_server/models/sample.py
+openapi_server/models/status.py
+openapi_server/openapi/openapi.yaml
+openapi_server/typing_utils.py
+openapi_server/util.py
+setup.py

.openapi-generator/VERSION

@@ -1 +1 @@
-4.3.1
+5.2.1

openapi_server/controllers/sample_controller.py

@@ -121,4 +121,25 @@ def samples_id_patch(id, new_sample=None):  # noqa: E501
     except IntegrityError:
         return Error(409, 'Already existed'), 409
     else:
-        return old_sample.to_model(), 200
+        return old_sample.to_model(), 200
+
+
+def samples_id_delete(id):  # noqa: E501
+    """samples_id_delete
+
+    Delete a sample. # noqa: E501
+
+    :param id:
+    :type id:
+
+    :rtype: Sample
+    """
+
+    inst = orm.Sample.query.get(id)
+    if not inst:
+        return Error(404, 'Not found'), 404
+
+    db.session.delete(inst)
+    db.session.commit()
+
+    return '', 204

openapi_server/models/__init__.py

@@ -5,7 +5,7 @@
 # import models into model package
 from openapi_server.models.error import Error
 from openapi_server.models.event import Event
+from openapi_server.models.file import File
 from openapi_server.models.qc_result import QcResult
 from openapi_server.models.sample import Sample
 from openapi_server.models.status import Status
-from openapi_server.models.file import File

openapi_server/models/file.py

@@ -10,9 +10,9 @@
 
 
 class File(Model):
-    """NOTE: This class is COPIED FROM A GENERATED MODEL because OpenAPI Generator (https://openapi-generator.tech) couldn't generate the model (unknown reason).
+    """NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
 
-    Do not edit the class manually ANY FURTHER.
+    Do not edit the class manually.
     """
 
     def __init__(self, md5sum=None, filename=None, file_type=None):  # noqa: E501
@@ -22,7 +22,7 @@ def __init__(self, md5sum=None, filename=None, file_type=None):  # noqa: E501
         :type md5sum: str
         :param filename: The filename of this File.  # noqa: E501
         :type filename: str
-        :param file_type: The file_type of this Event.  # noqa: E501
+        :param file_type: The file_type of this File.  # noqa: E501
         :type file_type: str
         """
         self.openapi_types = {
@@ -47,7 +47,7 @@ def from_dict(cls, dikt) -> 'File':
 
         :param dikt: A dict.
         :type: dict
-        :return: The File of this Event.  # noqa: E501
+        :return: The File of this File.  # noqa: E501
         :rtype: File
         """
         return util.deserialize_model(dikt, cls)
@@ -70,6 +70,8 @@ def md5sum(self, md5sum):
         :param md5sum: The md5sum of this File.
         :type md5sum: str
         """
+        if md5sum is None:
+            raise ValueError("Invalid value for `md5sum`, must not be `None`")  # noqa: E501
 
         self._md5sum = md5sum
 
@@ -91,6 +93,9 @@ def filename(self, filename):
         :param filename: The filename of this File.
         :type filename: str
         """
+        if filename is None:
+            raise ValueError("Invalid value for `filename`, must not be `None`")  # noqa: E501
+
         self._filename = filename
 
     @property

openapi_server/openapi/openapi.yaml

@@ -119,6 +119,35 @@ paths:
       - sample
       x-openapi-router-controller: openapi_server.controllers.sample_controller
   /samples/{id}:
+    delete:
+      description: Delete a sample.
+      operationId: samples_id_delete
+      parameters:
+      - explode: false
+        in: path
+        name: id
+        required: true
+        schema:
+          $ref: '#/components/schemas/SampleID'
+        style: simple
+      responses:
+        "204":
+          description: Deleted
+        "404":
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Error'
+          description: Not found
+        default:
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Error'
+          description: Unexpected error
+      tags:
+      - sample
+      x-openapi-router-controller: openapi_server.controllers.sample_controller
     get:
       description: Return a sample by its ID.
       operationId: samples_id_get
@@ -818,6 +847,7 @@ components:
     SampleID:
       format: uuid
       pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
+      title: id
       type: string
     Sample:
       example:
@@ -826,13 +856,17 @@ components:
         experiment-id: experiment-id
       properties:
         experiment-id:
+          title: experiment-id
           type: string
         isolate-id:
+          title: isolate-id
           type: string
         id:
           format: uuid
           pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
+          title: id
           type: string
+      title: Sample
       type: object
     File:
       example:
@@ -841,18 +875,22 @@ components:
         md5sum: md5sum
       properties:
         md5sum:
+          title: md5sum
           type: string
         filename:
+          title: filename
           type: string
         file-type:
           enum:
           - fastq
           - vcf
+          title: file-type
           type: string
       required:
       - file-type
       - filename
       - md5sum
+      title: File
       type: object
     Event:
       example:
@@ -865,6 +903,7 @@ components:
         command: command
       properties:
         id:
+          title: id
           type: integer
         name:
           enum:
@@ -874,17 +913,23 @@ components:
           - prediction
           - bigsi-building
           - distance-calculation
+          title: name
           type: string
         software:
+          title: software
           type: string
         software-version:
+          title: software-version
           type: string
         start-time:
+          title: start-time
           type: number
         duration:
           format: int32
+          title: duration
           type: integer
         command:
+          title: command
           type: string
       required:
       - command
@@ -893,6 +938,7 @@ components:
       - software
       - software-version
       - start-time
+      title: Event
       type: object
     QcResult:
       example:
@@ -902,19 +948,23 @@ components:
       properties:
         coverage:
           format: float
+          title: coverage
           type: number
         number_of_het_snps:
           format: int32
+          title: number_of_het_snps
           type: integer
         decision:
           enum:
           - passed
           - failed
+          title: decision
           type: string
       required:
       - coverage
       - decision
       - number_of_het_snps
+      title: QcResult
       type: object
     Status:
       example:
@@ -932,48 +982,55 @@ components:
           - started
           - complete
           - failed
+          title: de-contamination
           type: string
         qc:
           enum:
           - pending
           - started
           - complete
           - failed
+          title: qc
           type: string
         variant-calling:
           enum:
           - pending
           - started
           - complete
           - failed
+          title: variant-calling
           type: string
         prediction:
           enum:
           - pending
           - started
           - complete
           - failed
+          title: prediction
           type: string
         bigsi-building:
           enum:
           - pending
           - started
           - complete
           - failed
+          title: bigsi-building
           type: string
         distance-calculation:
           enum:
           - pending
           - started
           - complete
           - failed
+          title: distance-calculation
           type: string
         stage:
           enum:
           - accepted
           - qc-failed
           - live
           - deprecated
+          title: stage
           type: string
       required:
       - bigsi-building
@@ -982,15 +1039,19 @@ components:
       - prediction
       - qc
       - variant-calling
+      title: Status
       type: object
     Error:
       properties:
         code:
           format: int32
+          title: code
           type: integer
         message:
+          title: message
           type: string
       required:
       - code
       - message
+      title: Error
       type: object

openapi_server/test/conftest.py

@@ -1,6 +1,6 @@
 import logging
 
-from hypothesis import settings
+from hypothesis import settings, HealthCheck
 from pytest import fixture
 
 from openapi_server.migrate import migrate
@@ -202,11 +202,9 @@ def _(sample_id):
 
 
 @fixture
-def delete_sample():
-    def _(sample_id):
-        inst = Sample.query.get(sample_id)
-        db.session.delete(inst)
-        db.session.commit()
+def delete_sample(make_request):
+    def _(sample_id, *args, **kwargs):
+        return make_request(f'/api/v1/samples/{sample_id}', 'DELETE', *args, **kwargs)
     return _
 
 
@@ -219,5 +217,5 @@ def _(model):
     return _
 
 
-settings.register_profile('e2e', deadline=None)
+settings.register_profile('e2e', deadline=None, suppress_health_check=(HealthCheck.function_scoped_fixture,))
 settings.load_profile('e2e')

openapi_server/test/test_invalid_sample_id.py

@@ -56,7 +56,7 @@ def _(sample_id, *args, **kwargs):
     return _
 
 
-@settings(suppress_health_check=(HealthCheck.filter_too_much,))
+@settings(suppress_health_check=(HealthCheck.filter_too_much, HealthCheck.function_scoped_fixture))
 @given(sample_id=safe_strings(min_size=1))
 def test_invalid_sample_id(sample_id, call_endpoint):
     def is_uuid(s):