fix: update request builder to allow remote params and attachments

Add logic to 'build_wes_request' to retrieve contents from params
(jsonyaml) or attachment files if paths for each are URLs (http(s))
rather than local paths. Use JSON string from params file in request
and file objects for attachments.

Author: jaeddy

wes_client/util.py

@@ -66,38 +66,6 @@ def wf_info(workflow_path):
     return version, file_type.upper()
 
 
-def build_wes_request(workflow_file, json_path, attachments=None):
-    """
-    :param str workflow_file: Path to cwl/wdl file.  Can be http/https/file.
-    :param json_path: Path to accompanying json file.  Currently must be local.
-    :param attachments: Any other files needing to be uploaded to the server.
-
-    :return: A list of tuples formatted to be sent in a post to the wes-server (Swagger API).
-    """
-    workflow_file = "file://" + workflow_file if ":" not in workflow_file else workflow_file
-    json_path = json_path[7:] if json_path.startswith("file://") else json_path
-    wf_version, wf_type = wf_info(workflow_file)
-
-    parts = [("workflow_params", json.dumps(json.load(open(json_path)))),
-             ("workflow_type", wf_type),
-             ("workflow_type_version", wf_version)]
-
-    if workflow_file.startswith("file://"):
-        parts.append(("workflow_attachment", (os.path.basename(workflow_file[7:]), open(workflow_file[7:], "rb"))))
-        parts.append(("workflow_url", os.path.basename(workflow_file[7:])))
-    else:
-        parts.append(("workflow_url", workflow_file))
-
-    if attachments:
-        for attachment in attachments:
-            attachment = attachment[7:] if attachment.startswith("file://") else attachment
-            if ':' in attachment:
-                raise TypeError('Only local files supported for attachment: %s' % attachment)
-            parts.append(("workflow_attachment", (os.path.basename(attachment), open(attachment, "rb"))))
-
-    return parts
-
-
 def modify_jsonyaml_paths(jsonyaml_file):
     """
     Changes relative paths in a json/yaml file to be relative
@@ -124,6 +92,49 @@ def fixpaths(d):
                 del d["path"]
 
     visit(input_dict, fixpaths)
+    return json.dumps(input_dict)
+
+
+def build_wes_request(workflow_file, json_path, attachments=None):
+    """
+    :param str workflow_file: Path to cwl/wdl file.  Can be http/https/file.
+    :param json_path: Path to accompanying json file.
+    :param attachments: Any other files needing to be uploaded to the server.
+
+    :return: A list of tuples formatted to be sent in a post to the wes-server (Swagger API).
+    """
+    workflow_file = "file://" + workflow_file if ":" not in workflow_file else workflow_file
+    if json_path.startswith("file://"):
+        json_path = json_path[7:]
+        with open(json_path) as f:
+            wf_params = json.dumps(json.load(f))
+    elif json_path.startswith("http"):
+        wf_params = modify_jsonyaml_paths(json_path)
+    else: 
+        wf_params = json_path
+    wf_version, wf_type = wf_info(workflow_file)
+
+    parts = [("workflow_params", wf_params),
+             ("workflow_type", wf_type),
+             ("workflow_type_version", wf_version)]
+
+    if workflow_file.startswith("file://"):
+        parts.append(("workflow_attachment", (os.path.basename(workflow_file[7:]), open(workflow_file[7:], "rb"))))
+        parts.append(("workflow_url", os.path.basename(workflow_file[7:])))
+    else:
+        parts.append(("workflow_url", workflow_file))
+
+    if attachments:
+        for attachment in attachments:
+            if attachment.startswith("file://"):
+                attachment = attachment[7:] 
+                attach_f = open(attachment, "rb")
+            elif attachment.startswith("http"):
+                attach_f = urlopen(attachment)
+
+            parts.append(("workflow_attachment", (os.path.basename(attachment), attach_f)))
+
+    return parts
 
 
 def expand_globs(attachments):