Merge pull request #53 from common-workflow-language/directClientCalls

Direct client calls.

Author: tetron

setup.py

@@ -25,7 +25,6 @@
       install_requires=[
           'future',
           'connexion==1.4.2',
-          'bravado==10.1.0',
           'ruamel.yaml >= 0.12.4, < 0.15',
           'cwlref-runner==1.0',
           'schema-salad>=2.6, <3',

test/test_client_util.py

@@ -0,0 +1,39 @@
+from __future__ import absolute_import
+
+import unittest
+import os
+import logging
+import subprocess
+
+from wes_client.util import expand_globs
+
+logging.basicConfig(level=logging.INFO)
+
+
+class IntegrationTest(unittest.TestCase):
+    def setUp(self):
+        dirname, filename = os.path.split(os.path.abspath(__file__))
+        self.testdata_dir = dirname + 'data'
+
+    def tearDown(self):
+        unittest.TestCase.tearDown(self)
+
+    def test_expand_globs(self):
+        """Asserts that wes_client.expand_globs() sees the same files in the cwd as 'ls'."""
+        files = subprocess.check_output(['ls', '-1', '.'])
+
+        # python 2/3 bytestring/utf-8 compatibility
+        if isinstance(files, str):
+            files = files.split('\n')
+        else:
+            files = files.decode('utf-8').split('\n')
+
+        if '' in files:
+            files.remove('')
+        files = ['file://' + os.path.abspath(f) for f in files]
+        glob_files = expand_globs('*')
+        assert set(files) == glob_files, '\n' + str(set(files)) + '\n' + str(glob_files)
+
+
+if __name__ == '__main__':
+    unittest.main()  # run all tests

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)
 
@@ -28,7 +27,10 @@ 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')]
-        
+
+        # client for the swagger API methods
+        cls.client = WESClient({'auth': '', 'proto': 'http', 'host': 'localhost:8080'})
+
         # manual test (wdl only working locally atm)
         cls.manual = False
 
@@ -52,44 +54,68 @@ 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 test_get_service_info(self):
+        """
+        Test wes_client.util.WESClient.get_service_info()
+
+        This method will exit(1) if the response is not 200.
+        """
+        r = self.client.get_service_info()
+        assert 'workflow_type_versions' in r
+        assert 'supported_wes_versions' in r
+        assert 'supported_filesystem_protocols' in r
+        assert 'engine_versions' in r
+
+    def test_list_runs(self):
+        """
+        Test wes_client.util.WESClient.list_runs()
 
-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']
+        This method will exit(1) if the response is not 200.
+        """
+        r = self.client.list_runs()
+        assert 'workflows' in r
 
+    def test_get_run_status(self):
+        """
+        Test wes_client.util.WESClient.run_status()
 
-def get_log_request(run_id):
-    endpoint = 'http://localhost:8080/ga4gh/wes/v1/runs/{}'.format(run_id)
-    return requests.get(endpoint).json()
+        This method will exit(1) if the response is not 200.
+        """
+        outfile_path, run_id = self.run_md5sum(wf_input=self.cwl_local_path,
+                                               json_input=self.cwl_json_input,
+                                               workflow_attachment=self.cwl_attachments)
+        r = self.client.get_run_status(run_id)
+        assert 'state' in r
+        assert 'run_id' in r
+
+    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():
@@ -143,14 +169,15 @@ def test_local_wdl(self):
         """LOCAL md5sum wdl to the wes-service server, and check for the correct output."""
         # Working locally but not on travis... >.<;
         if self.manual:
-            outfile_path, run_id = run_md5sum(wf_input=self.wdl_local_path,
-                                              json_input=self.wdl_json_input,
-                                              workflow_attachment=self.wdl_attachments)
+            outfile_path, run_id = self.run_md5sum(wf_input=self.wdl_local_path,
+                                                   json_input=self.wdl_json_input,
+                                                   workflow_attachment=self.wdl_attachments)
             self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
 
 # Prevent pytest/unittest's discovery from attempting to discover the base test class.
 del IntegrationTest
 
+
 if __name__ == '__main__':
     unittest.main()  # run all tests