Adding REST API versioning (#333)

Closes #333
varfish-org · Feb 7, 2022 · a106e7f · a106e7f
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -91,6 +91,7 @@ Full Change List
 - Fixing CADD annotation (#319)
 - Adding mitochondrial inheritance to case phenotype annotation (#325)
 - Fix issue with variant annotation export (#328)
+- Adding REST API versioning to (#333)
 
 -------
 v0.23.9

diff --git a/beaconsite/tests/test_views_api.py b/beaconsite/tests/test_views_api.py
@@ -1,11 +1,5 @@
-import urllib
-import datetime
-
 import cattr
-from Crypto.PublicKey import RSA
 from django.shortcuts import reverse
-from django.utils import timezone
-from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
 from projectroles.tests.test_views_api import TestAPIViewsBase
 
 from variants.tests.factories import SmallVariantFactory

diff --git a/docs_manual/api_overview.rst b/docs_manual/api_overview.rst
@@ -0,0 +1,63 @@
+.. _api_overview:
+
+=================
+REST API Overview
+=================
+
+Varfish provides a growing set of REST APIs.
+You can find an Python library for accessing the API and a command line interface in `varfish-cli <https://github.com/bihealth/varfish-cli>`_.
+
+.. note::
+    This documentation section is under development.
+
+-------------
+Using the API
+-------------
+
+Usage of the REST API is detailed in this section.
+Basic knowledge of HTTP APIs is assumed.
+
+Authentication
+==============
+
+The API supports authentication through Knox authentication tokens as well as logging in using your SODAR username and password.
+Tokens are the recommended method for security purposes.
+
+For token access, first retrieve your token using the **API Tokens** site app on the VarFish web UI.
+Note that you can you only see the token once when creating it.
+
+Add the token in the ``Authorization`` header of your HTTP request as follows:
+
+.. code-block:: console
+
+    Authorization: token 90c2483172515bc8f6d52fd608e5031db3fcdc06d5a83b24bec1688f39b72bcd
+
+Versioning
+==========
+
+The SODAR REST API uses accept header versioning.
+While specifying the desired API version in your HTTP requests is optional, it is **strongly recommended**.
+This ensures you will get the appropriate return data and avoid running into unexpected incompatibility issues.
+
+To enable versioning, add the ``Accept`` header to your request with the following media type and version syntax.
+Replace the version number with your expected version.
+
+Specific sections of the SODAR API may require their own accept header.
+See the exact header requirement in the respective documentation on each section of the API.
+
+Model Access and Permissions
+============================
+
+Objects in SODAR API views are accessed through their ``sodar_uuid`` field.
+
+In the REST API documentation, *"UUID"* refers to the ``sodar_uuid`` field of each model unless otherwise noted.
+
+For permissions the API uses the same rules which are in effect in the SODAR GUI.
+That means you need to have appropriate project access for each operation.
+
+Return Data
+===========
+
+The return data for each request will be a JSON document unless otherwise specified.
+
+If return data is not specified in the documentation of an API view, it will return the appropriate HTTP status code along with an optional ``detail`` JSON field upon a successfully processed request.
diff --git a/docs_manual/index.rst b/docs_manual/index.rst
@@ -117,6 +117,19 @@ Currently, the main focus is on small/sequence variants called from high-througp
     sop_supporting
     sop_filtration
 
+.. raw:: latex
+
+    \part{REST API}
+
+.. toctree::
+    :maxdepth: 1
+    :caption: REST API
+    :name: api-docs
+    :hidden:
+    :titlesonly:
+
+    api_overview
+
 .. raw:: latex
 
     \part{Developer's Manual}

diff --git a/importer/tests/test_views_api.py b/importer/tests/test_views_api.py
@@ -1,11 +1,18 @@
+from varfish import __version__ as varfish_version
+from varfish.api_utils import VARFISH_API_DEFAULT_VERSION, VARFISH_API_MEDIA_TYPE
+
 import os
 from itertools import chain
 
 from django.contrib.auth import get_user_model
 from django.urls import reverse
 from django.forms import model_to_dict
 
-from variants.tests.helpers import ApiViewTestBase
+from variants.tests.helpers import (
+    ApiViewTestBase,
+    VARFISH_INVALID_VERSION,
+    VARFISH_INVALID_MIMETYPE,
+)
 from variants.tests.test_views_api import transmogrify_pedigree
 
 from ..models import CaseImportInfo, VariantSetImportInfo, CaseVariantType, BamQcFile, GenotypeFile
@@ -16,6 +23,15 @@
     GenotypeFileFactory,
 )
 
+#: A known invalid MIME type.
+INVALID_MIMETYPE = "application/vnd.bihealth.invalid+json"
+#: A known invalid version.
+INVALID_VERSION = "0.0.0"
+#: The known valid MIME type.
+VALID_MIMETYPE = "application/vnd.bihealth.varfish+json"
+#: A known valid version.
+VALID_VERSION = varfish_version
+
 #: The User model to use.
 User = get_user_model()
 
@@ -84,11 +100,12 @@ def test_create(self):
         post_data = case_import_info_to_dict(obj, self.project, exclude=("sodar_uuid",))
 
         with self.login(self.user):
-            response = self.client.post(
+            response = self.request_knox(
                 reverse(
                     "importer:api-case-import-info-list-create",
                     kwargs={"project": self.project.sodar_uuid},
                 ),
+                method="POST",
                 data=post_data,
                 format="json",
             )
@@ -105,7 +122,7 @@ def test_create(self):
 
     def test_retrieve(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-case-import-info-retrieve-update-destroy",
                     kwargs={
@@ -138,14 +155,15 @@ def test_update(self):
         }
 
         with self.login(self.user):
-            response = self.client.patch(
+            response = self.request_knox(
                 reverse(
                     "importer:api-case-import-info-retrieve-update-destroy",
                     kwargs={
                         "project": self.project.sodar_uuid,
                         "caseimportinfo": self.case_import_info.sodar_uuid,
                     },
                 ),
+                method="PATCH",
                 data=post_data,
                 format="json",
             )
@@ -166,14 +184,15 @@ def test_update(self):
 
     def test_destroy(self):
         with self.login(self.user):
-            response = self.client.delete(
+            response = self.request_knox(
                 reverse(
                     "importer:api-case-import-info-retrieve-update-destroy",
                     kwargs={
                         "project": self.project.sodar_uuid,
                         "caseimportinfo": self.case_import_info.sodar_uuid,
                     },
-                )
+                ),
+                method="DELETE",
             )
 
             expected = None
@@ -204,7 +223,7 @@ def setUp(self):
 
     def test_list(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-variant-set-import-info-list-create",
                     kwargs={"caseimportinfo": self.case_import_info.sodar_uuid},
@@ -240,11 +259,12 @@ def test_create(self):
         )
 
         with self.login(self.user):
-            response = self.client.post(
+            response = self.request_knox(
                 reverse(
                     "importer:api-variant-set-import-info-list-create",
                     kwargs={"caseimportinfo": self.case_import_info.sodar_uuid},
                 ),
+                method="POST",
                 data=post_data,
                 format="json",
             )
@@ -259,7 +279,7 @@ def test_create(self):
 
     def test_retrieve(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-variant-set-import-info-retrieve-update-destroy",
                     kwargs={
@@ -287,14 +307,15 @@ def test_update(self):
         }
 
         with self.login(self.user):
-            response = self.client.patch(
+            response = self.request_knox(
                 reverse(
                     "importer:api-variant-set-import-info-retrieve-update-destroy",
                     kwargs={
                         "caseimportinfo": self.case_import_info.sodar_uuid,
                         "variantsetimportinfo": self.variant_set_import_info.sodar_uuid,
                     },
                 ),
+                method="PATCH",
                 data=post_data,
                 format="json",
             )
@@ -315,14 +336,15 @@ def test_update(self):
 
     def test_destroy(self):
         with self.login(self.user):
-            response = self.client.delete(
+            response = self.request_knox(
                 reverse(
                     "importer:api-variant-set-import-info-retrieve-update-destroy",
                     kwargs={
                         "caseimportinfo": self.case_import_info.sodar_uuid,
                         "variantsetimportinfo": self.variant_set_import_info.sodar_uuid,
                     },
-                )
+                ),
+                method="DELETE",
             )
 
             expected = None
@@ -349,7 +371,7 @@ def setUp(self):
 
     def test_list(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-bam-qc-file-list-create",
                     kwargs={"caseimportinfo": self.case_import_info.sodar_uuid},
@@ -375,11 +397,13 @@ def test_create(self):
             with open(
                 os.path.join(os.path.dirname(__file__), "data", "example.tsv"), "rb"
             ) as upload_file:
-                response = self.client.post(
+                response = self.request_knox(
                     reverse(
                         "importer:api-bam-qc-file-list-create",
                         kwargs={"caseimportinfo": self.case_import_info.sodar_uuid},
                     ),
+                    format="multipart",
+                    method="POST",
                     data={**post_data, "file": upload_file},
                 )
 
@@ -393,7 +417,7 @@ def test_create(self):
 
     def test_retrieve(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-bam-qc-file-retrieve-destroy",
                     kwargs={
@@ -411,14 +435,15 @@ def test_retrieve(self):
 
     def test_destroy(self):
         with self.login(self.user):
-            response = self.client.delete(
+            response = self.request_knox(
                 reverse(
                     "importer:api-bam-qc-file-retrieve-destroy",
                     kwargs={
                         "caseimportinfo": self.case_import_info.sodar_uuid,
                         "bamqcfile": self.bam_qc_file.sodar_uuid,
                     },
-                )
+                ),
+                method="DELETE",
             )
 
             expected = None
@@ -448,7 +473,7 @@ def setUp(self):
 
     def test_list(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-genotype-file-list-create",
                     kwargs={"variantsetimportinfo": self.variant_set_import_info.sodar_uuid},
@@ -476,11 +501,13 @@ def test_create(self):
             with open(
                 os.path.join(os.path.dirname(__file__), "data", "example.tsv"), "rb"
             ) as upload_file:
-                response = self.client.post(
+                response = self.request_knox(
                     reverse(
                         "importer:api-genotype-file-list-create",
                         kwargs={"variantsetimportinfo": self.variant_set_import_info.sodar_uuid},
                     ),
+                    method="POST",
+                    format="multipart",
                     data={**post_data, "file": upload_file},
                 )
 
@@ -494,7 +521,7 @@ def test_create(self):
 
     def test_retrieve(self):
         with self.login(self.user):
-            response = self.client.get(
+            response = self.request_knox(
                 reverse(
                     "importer:api-genotype-file-retrieve-destroy",
                     kwargs={
@@ -512,14 +539,15 @@ def test_retrieve(self):
 
     def test_destroy(self):
         with self.login(self.user):
-            response = self.client.delete(
+            response = self.request_knox(
                 reverse(
                     "importer:api-genotype-file-retrieve-destroy",
                     kwargs={
                         "variantsetimportinfo": self.variant_set_import_info.sodar_uuid,
                         "genotypefile": self.genotype_file.sodar_uuid,
                     },
-                )
+                ),
+                method="DELETE",
             )
 
             expected = None