Change tests to use new client.

Author: DailyDreaming

test/test_integration.py

@@ -5,11 +5,10 @@
 import os
 import subprocess32 as subprocess
 import signal
-import requests
 import shutil
 import logging
 
-from wes_client.util import build_wes_request
+from wes_client.util import WESClient
 
 logging.basicConfig(level=logging.INFO)
 
@@ -28,6 +27,9 @@ def setUpClass(cls):
         cls.wdl_local_path = os.path.abspath('testdata/md5sum.wdl')
         cls.wdl_json_input = "file://" + os.path.abspath('testdata/md5sum.wdl.json')
         cls.wdl_attachments = ['file://' + os.path.abspath('testdata/md5sum.input')]
+
+        # houses the API methods
+        cls.client = WESClient({'auth': '', 'proto': 'http', 'host': 'localhost:8080'})
 
         # manual test (wdl only working locally atm)
         cls.manual = False
@@ -52,44 +54,35 @@ def tearDown(self):
 
     def test_dockstore_md5sum(self):
         """HTTP md5sum cwl (dockstore), run it on the wes-service server, and check for the correct output."""
-        outfile_path, _ = run_md5sum(wf_input=self.cwl_dockstore_url,
-                                     json_input=self.cwl_json_input,
-                                     workflow_attachment=self.cwl_attachments)
+        outfile_path, _ = self.run_md5sum(wf_input=self.cwl_dockstore_url,
+                                          json_input=self.cwl_json_input,
+                                          workflow_attachment=self.cwl_attachments)
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
     def test_local_md5sum(self):
         """LOCAL md5sum cwl to the wes-service server, and check for the correct output."""
-        outfile_path, run_id = run_md5sum(wf_input=self.cwl_local_path,
-                                          json_input=self.cwl_json_input,
-                                          workflow_attachment=self.cwl_attachments)
+        outfile_path, run_id = self.run_md5sum(wf_input=self.cwl_local_path,
+                                               json_input=self.cwl_json_input,
+                                               workflow_attachment=self.cwl_attachments)
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
     def test_run_attachments(self):
         """LOCAL md5sum cwl to the wes-service server, check for attachments."""
-        outfile_path, run_id = run_md5sum(wf_input=self.cwl_local_path,
-                                          json_input=self.cwl_json_input,
-                                          workflow_attachment=self.cwl_attachments)
-        get_response = get_log_request(run_id)["request"]
+        outfile_path, run_id = self.run_md5sum(wf_input=self.cwl_local_path,
+                                               json_input=self.cwl_json_input,
+                                               workflow_attachment=self.cwl_attachments)
+        get_response = self.client.get_run_log(run_id)["request"]
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + get_response["workflow_attachment"])
         attachment_tool_path = get_response["workflow_attachment"][7:] + "/dockstore-tool-md5sum.cwl"
         self.assertTrue(check_for_file(attachment_tool_path), 'Attachment file was not found: ' + get_response["workflow_attachment"])
 
 
-def run_md5sum(wf_input, json_input, workflow_attachment=None):
-    """Pass a local md5sum cwl to the wes-service server, and return the path of the output file that was created."""
-    endpoint = 'http://localhost:8080/ga4gh/wes/v1/runs'
-    parts = build_wes_request(wf_input,
-                              json_input,
-                              attachments=workflow_attachment)
-    response = requests.post(endpoint, files=parts).json()
-    assert 'run_id' in response, str(response.json())
-    output_dir = os.path.abspath(os.path.join('workflows', response['run_id'], 'outdir'))
-    return os.path.join(output_dir, 'md5sum.txt'), response['run_id']
-
-
-def get_log_request(run_id):
-    endpoint = 'http://localhost:8080/ga4gh/wes/v1/runs/{}'.format(run_id)
-    return requests.get(endpoint).json()
+    def run_md5sum(self, wf_input, json_input, workflow_attachment=None):
+        """Pass a local md5sum cwl to the wes-service server, and return the path of the output file that was created."""
+        response = self.client.run(wf_input, json_input, workflow_attachment)
+        assert 'run_id' in response, str(response.json())
+        output_dir = os.path.abspath(os.path.join('workflows', response['run_id'], 'outdir'))
+        return os.path.join(output_dir, 'md5sum.txt'), response['run_id']
 
 
 def get_server_pids():

wes_client/util.py

@@ -1,6 +1,6 @@
 import os
 import json
-from bravado.requests_client import RequestsClient
+import requests
 import urllib
 import logging
 import schema_salad.ref_resolver
@@ -102,7 +102,6 @@ def __init__(self, service):
         self.auth = service['auth']
         self.proto = service['proto']
         self.host = service['host']
-        self.http_client = RequestsClient()
 
     def get_service_info(self):
         """
@@ -118,8 +117,8 @@ def get_service_info(self):
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the get result as a dictionary.
         """
-        postresult = self.http_client.session.get("%s://%s/ga4gh/wes/v1/service-info" % (self.proto, self.host),
-                                                  headers={"Authorization": self.auth})
+        postresult = requests.get("%s://%s/ga4gh/wes/v1/service-info" % (self.proto, self.host),
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def list_runs(self):
@@ -135,8 +134,8 @@ def list_runs(self):
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the get result as a dictionary.
         """
-        postresult = self.http_client.session.get("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
-                                                  headers={"Authorization": self.auth})
+        postresult = requests.get("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def run(self, wf, jsonyaml, attachments):
@@ -154,52 +153,52 @@ def run(self, wf, jsonyaml, attachments):
         :return: The body of the post result as a dictionary.
         """
         parts = build_wes_request(wf, jsonyaml, attachments)
-        postresult = self.http_client.session.post("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
-                                                   files=parts,
-                                                   headers={"Authorization": self.auth})
+        postresult = requests.post("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
+                                   files=parts,
+                                   headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def cancel(self, run_id):
         """
         Cancel a running workflow.
 
-        :param run_id:
+        :param run_id: String (typically a uuid) identifying the run.
         :param object http_client: bravado.requests_client.RequestsClient
         :param str auth: String to send in the auth header.
         :param proto: Schema where the server resides (http, https)
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the delete result as a dictionary.
         """
-        postresult = self.http_client.session.delete("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
-                                                     headers={"Authorization": self.auth})
+        postresult = requests.delete("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
+                                     headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def get_run_log(self, run_id):
         """
         Get detailed info about a running workflow.
 
-        :param run_id:
+        :param run_id: String (typically a uuid) identifying the run.
         :param object http_client: bravado.requests_client.RequestsClient
         :param str auth: String to send in the auth header.
         :param proto: Schema where the server resides (http, https)
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the get result as a dictionary.
         """
-        postresult = self.http_client.session.get("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
-                                                  headers={"Authorization": self.auth})
+        postresult = requests.get("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)
 
     def get_run_status(self, run_id):
         """
         Get quick status info about a running workflow.
 
-        :param run_id:
+        :param run_id: String (typically a uuid) identifying the run.
         :param object http_client: bravado.requests_client.RequestsClient
         :param str auth: String to send in the auth header.
         :param proto: Schema where the server resides (http, https)
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the get result as a dictionary.
         """
-        postresult = self.http_client.session.get("%s://%s/ga4gh/wes/v1/runs/%s/status" % (self.proto, self.host, run_id),
-                                             headers={"Authorization": self.auth})
+        postresult = requests.get("%s://%s/ga4gh/wes/v1/runs/%s/status" % (self.proto, self.host, run_id),
+                                  headers={"Authorization": self.auth})
         return wes_reponse(postresult)