Use client-logic to run upload tool

It is pretty cool to use hooks and an alternative tool submission
endpoint, but this is less invasive. We'd have to do this anyway for
cases where the upload is already on the server and the pre-finish hook
doesn't fire.

scripts/resumable_upload.py

@@ -1,9 +1,15 @@
+import json
 import os
 
-import aiotus
-import asyncclick as click
+import click
+import requests
+from tusclient import client
+from tusclient.storage import filestorage
+
 
 UPLOAD_ENDPOINT = '/api/upload/resumable_upload'
+TOOLS_ENDPOINT = '/api/tools'
+CHUNK_SIZE = 10 ** 7
 
 
 @click.command()
@@ -13,25 +19,43 @@ UPLOAD_ENDPOINT = '/api/upload/resumable_upload'
 @click.option('--file_type', default="auto", type=str, help="Galaxy file type to use")
 @click.option('--dbkey', default="?", type=str, help="Genome Build for dataset")
 @click.option('--filename', type=str, help="Filename to use in Galaxy history, if different from path")
+@click.option('--storage', type=click.Path(), required=False, help="Store URLs to resume here")
 @click.argument('path', type=click.Path())
-async def upload_file(url, path, api_key, history_id, file_type='auto', dbkey='?', filename=None):
+def upload_file(url, path, api_key, history_id, file_type='auto', dbkey='?', filename=None, storage=None):
+    headers = {'x-api-key': api_key}
+    my_client = client.TusClient(f"{url}{UPLOAD_ENDPOINT}", headers=headers)
     filename = filename or os.path.basename(path)
     metadata = {
-        'filename': filename.encode(),
-        'history_id': history_id.encode(),
-        'file_type': file_type.encode(),
-        'dbkey': dbkey.encode(),
+        'filename': filename,
+        'history_id': history_id,
+        'file_type': file_type,
+        'dbkey': dbkey,
     }
-    headers = {'x-api-key': api_key}
 
     # Upload a file to a tus server.
-    with open(path, "rb") as f:
-        location = await aiotus.upload(f"{url}{UPLOAD_ENDPOINT}", f, metadata, headers=headers)
-        # 'location' is the URL where the file was uploaded to.
+    if storage:
+        storage = filestorage.FileStorage(storage)
+    uploader = my_client.uploader(path, metadata=metadata, url_storage=storage)
+    uploader.chunk_size = CHUNK_SIZE
+    uploader.upload()
 
-    # Read back the metadata from the server.
-    metadata = await aiotus.metadata(location, headers=headers)
-    print(metadata)
+    # Extract session from created upload URL
+    session_id = uploader.url.rsplit('/', 1)[1]
+    # This feels a bit more user-friendly ?
+    tool_id = 'upload1'
+    inputs = {
+        "file_count": 1,
+        "dbkey": dbkey,
+        "file_type": "auto",
+        "files_0|type": "upload_dataset",
+        "files_0|NAME": filename,
+        "files_0|to_posix_lines": "Yes",
+        "files_0|dbkey": dbkey,
+        "files_0|file_type": file_type,
+        "files_0|file_data": {"session_id": session_id, "name": filename}}
+    tool_payload = {'tool_id': tool_id, 'inputs': inputs, 'history_id': history_id}
+    response = requests.post(f"{url}{TOOLS_ENDPOINT}", data=json.dumps(tool_payload), headers=headers)
+    response.raise_for_status()
 
 
 if __name__ == '__main__':