Merge pull request #8 from ga4gh/release/0.2.0

Release/0.2.0 into main

.github/workflows/test.yml

@@ -25,6 +25,18 @@ jobs:
     - name: Install dependencies
       run: pip install -r requirements.txt
 
+    - name: Run Testbed API
+      run: docker run -d -p 4500:4500 ga4gh/ga4gh-testbed-api:0.1.0
+
+    - name: Service Health Check
+      uses: jtalk/url-health-check-action@v2
+      with:
+        url: http://localhost:4500/reports
+        follow-redirect: false
+        max-attempts: 6
+        retry-delay: 10s
+        retry-all: true
+
     - name: Run Tests
       run: python -m pytest --cov
 

README.md

@@ -57,5 +57,8 @@ python -m pytest --cov
 
 ## Changelog
 
+### v0.2.0
+* Able to submit reports to Testbed API via standard `POST` request
+
 ### v0.1.2
 * Test level entity now has a `message` attribute for capturing test result summary in a single message

ga4gh/testbed/submit/report_submitter.py

@@ -0,0 +1,32 @@
+from re import sub
+import requests
+
+
+class ReportSubmitter():
+
+    def submit_report(series_id, series_token, report, url="http://localhost:4500/reports"):
+        '''
+        Submits a report to the GA4GH testbed api.
+        
+        Required arguments:
+            series_id - A series ID is needed by server to group the report
+            series_token - A token is needed to verify authenticity
+            report - GA4GH report in JSON format
+            url - URL of the testbed server
+        '''
+        header = {"GA4GH-TestbedReportSeriesId": series_id, "GA4GH-TestbedReportSeriesToken": series_token}
+        submit_request = requests.post(url, headers=header ,json=report)
+
+        results = {
+            "status_code": submit_request.status_code,
+            "error_message": None,
+            "report_id": None
+        }
+
+        if submit_request.status_code == 200:
+            results["report_id"] = submit_request.json()["id"]
+        else:
+            if "message" in submit_request.json().keys():
+                results["error_message"] = submit_request.json()["message"]
+
+        return results

setup.py

@@ -1,7 +1,7 @@
 import setuptools
 
 NAME = "ga4gh-testbed-lib"
-VERSION = "0.1.2"
+VERSION = "0.2.0"
 AUTHOR = "Jeremy Adams"
 EMAIL = "[email protected]"
 

tests/test_unit/test_ga4gh/test_testbed/test_submit/test_report_submitter.py

@@ -0,0 +1,56 @@
+import pytest
+from ga4gh.testbed.submit.report_submitter import ReportSubmitter
+
+sample_report = {"schema_name":"ga4gh-testbed-report","schema_version":"0.1.0","testbed_name":"refget-compliance-suite","testbed_version":"","testbed_description":"","platform_name":"","platform_description":"","input_parameters":{},"start_time":"2022-03-22T17:45:37Z","end_time":"2022-03-22T17:46:32Z","status":"PASS","summary":{"unknown":0,"passed":49,"warned":0,"failed":0,"skipped":20},"phases":[]}
+
+submit_report_inputs = "series_id,series_token,report,url,status_code"
+submit_report_cases = [
+    (
+        "1edb5213-52a2-434f-a7b8-b101fea8fb30",
+        "K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn",
+        sample_report,
+        "http://localhost:4500/reports",
+        200
+    ),
+    (
+        "483382e9-f92b-466d-9427-154d56a75fcf",
+        "l0HiRbbpjVDKc6k3tQ2skzROB1oAP2IV",
+        sample_report,
+        "http://localhost:4500/reports",
+        200
+    ),
+    (
+        "1edb5213-52a2-434f-a7b8-b101fea8fb30",
+        "K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn",
+        "",
+        "http://localhost:4500/reports",
+        400
+    ),
+    (
+        "1edb5213-52a2-434f-a7b8-b101fea8fb30",
+        "K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn",
+        {},
+        "http://localhost:4500/reports",
+        500
+    ),
+    (
+        "",
+        "K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn",
+        sample_report,
+        "http://localhost:4500/reports",
+        404
+    ),
+    (
+        "1edb5213-52a2-434f-a7b8-b101fea8fb30",
+        "",
+        sample_report,
+        "http://localhost:4500/reports",
+        401
+    ),
+]
+
+@pytest.mark.parametrize(submit_report_inputs, submit_report_cases)
+def test_case_submit_report(series_id,series_token,report,url, status_code):
+    submitter = ReportSubmitter
+    assert submitter.submit_report(series_id, series_token, report, url)["status_code"] == status_code
+