test: add integration tests

.travis.yml

@@ -7,7 +7,10 @@ language: python
 # this ensures that the pipeline is triggered for internal pushes,
 # PRs from forks and pushes to existing PRs from forks
 if: (type == push) OR (type == pull_request AND fork == true)
-
+branches:
+  only:
+    - master
+    - dev
 
 stages:
 - name: test
@@ -27,6 +30,9 @@ jobs:
         - flake8
         - coverage run --source drs_filer -m pytest
         - coveralls
+        - docker-compose up --build -d
+        - sleep 10
+        - pytest "${TRAVIS_BUILD_DIR}/tests/integration_tests.py"
     - <<: *test
       python: 3.7
     - <<: *test

tests/integration_tests.py

@@ -0,0 +1,174 @@
+import json
+import requests
+
+base_url = "http://localhost:8080/ga4gh/drs/v1"
+data_objects_path = "data_objects.json"
+headers = {
+    'accept': 'application/json',
+    'Content-Type': 'application/json'
+}
+payload_objects = json.dumps({
+    "name": "Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz",
+    "size": 16700000,
+    "created_time": "2021-05-04T11:59:56.400Z",
+    "updated_time": "2021-05-04T11:59:56.400Z",
+    "version": "38",
+    "mime_type": "application/json",
+    "checksums": [
+        {
+            "checksum": "18c2f5517e4ddc02cd57f6c7554b8e88",
+            "type": "md5"
+        }
+    ],
+    "access_methods": [
+        {
+            "type": "ftp",
+            "access_url": {
+                "url": "ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapien"
+                "s/dna//Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz",
+                "headers": [
+                    "None"
+                ]
+            },
+            "region": "us-east-1"
+        },
+        {
+            "type": "ftp",
+            "access_url": {
+                "url": "ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapien"
+                "s/dna//Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz",
+                "headers": [
+                    "None"
+                ]
+            },
+            "region": "us-east-1"
+        },
+    ],
+    "contents": [
+        {
+            "name": "Homo_sapiens",
+            "id": "b001",
+            "drs_uri": [
+                "drs://drs.example.org/314159",
+                "drs://drs.example.org/213512"
+            ],
+            "contents": []
+        }
+    ],
+    "description": "description",
+    "aliases": [
+        "alias1"
+    ]
+})
+payload_service_info = json.dumps({
+    "contactUrl": "mailto:[email protected]",
+    "createdAt": "2019-06-04T12:58:19Z",
+    "description": "This service provides...",
+    "documentationUrl": "https://docs.myservice.example.com",
+    "environment": "test",
+    "id": "org.ga4gh.myservice",
+    "name": "My project",
+    "organization": {
+        "name": "My organization",
+        "url": "https://example.com"
+    },
+    "type": {
+        "artifact": "beacon",
+        "group": "org.ga4gh",
+        "version": "1.0.0"
+    },
+    "updatedAt": "2019-06-04T12:58:19Z",
+    "version": "1.0.0"
+})
+access_id = ""
+object_id = ""
+
+
+def test_post_service_info():
+    """Test `POST /service-info` for successfully creating or updating a new
+    service-info.
+    """
+    endpoint = "/service-info"
+    response = requests.request("POST", base_url + endpoint, headers=headers,
+                                data=payload_service_info)
+    assert response.status_code == 201
+
+
+def test_get_service_info():
+    """Test `GET /service-info` for fetching service info."""
+    endpoint = "/service-info"
+    response = requests.request("GET", base_url + endpoint, headers=headers)
+    assert response.status_code == 200
+    assert json.loads(response.content) == json.loads(payload_service_info)
+
+
+def test_post_objects():
+    """Test `POST /objects` for successfully registering an DrsObject."""
+    global object_id
+    endpoint = "/objects"
+    response = requests.request("POST", base_url + endpoint, headers=headers,
+                                data=payload_objects)
+    object_id = response.text.replace("\"", "").replace("\n", "")
+    assert response.status_code == 200
+
+
+def test_get_objects():
+    """Test `GET /objects/{object_id}` for fetching info about DrsObject."""
+    global access_id
+    is_expand = "True"
+    endpoint = "/objects/" + object_id + "?expand=" + is_expand
+    response = requests.request("GET", base_url + endpoint, headers=headers)
+    response_content = json.loads(response.text)
+    access_id = response_content['access_methods'][0]['access_id']
+    assert response.status_code == 200
+    assert response_content['name'] == json.loads(payload_objects)['name']
+
+
+def test_get_objects_access():
+    """Test `GET /objects/{object_id}/access/{access_id}` for fetching URL to
+    fetch the bytes of a DrsObject
+    """
+    endpoint = "/objects/" + object_id + "/access/" + access_id
+    response = requests.request("GET", base_url + endpoint, headers=headers)
+    response_content = json.loads(response.text)
+    assert response.status_code == 200
+    assert response_content['url'] == \
+        json.loads(payload_objects)['access_methods'][0]['access_url']['url']
+
+
+def test_put_objects():
+    """Test `PUT /objects/{object_id}` to modify or update a DrsObject"""
+    global access_id
+    endpoint = "/objects/" + object_id
+    object_put_payload = json.loads(payload_objects)
+    object_put_payload['name'] = "gerp_constrained_elements.tetraodon_" + \
+        "nigroviridis.bed.gz"
+    response = requests.request("PUT", base_url + endpoint, headers=headers,
+                                data=json.dumps(object_put_payload))
+    assert response.status_code == 200
+    is_expand = "True"
+    endpoint = "/objects/" + object_id + "?expand=" + is_expand
+    response = requests.request("GET", base_url + endpoint, headers=headers)
+    response_content = json.loads(response.text)
+    access_id = response_content['access_methods'][0]['access_id']
+    assert response.status_code == 200
+    assert response_content['name'] == \
+        "gerp_constrained_elements.tetraodon_nigroviridis.bed.gz"
+
+
+def test_delete_objects_access():
+    """Test `DELETE /objects/{object_id}/access/{access_id}` to delete
+    DrsObject's access method.
+    """
+    endpoint = "/objects/" + object_id + "/access/" + access_id
+    response = requests.request("DELETE", base_url + endpoint, headers=headers)
+    assert response.status_code == 200
+    assert response.text.replace("\"", "").replace("\n", "") == access_id
+
+
+def test_delete_objects():
+    """Test `DELETE /objects/{object_id}` to delete existing DrsObject"""
+    endpoint = "/objects/" + object_id
+    response = requests.request("DELETE", base_url + endpoint, headers=headers)
+    assert response.status_code == 200
+    assert response.text.replace("\"", "").replace("\n", "") == object_id