Dear All
If I execute the following command:
python import_with_dbkey.py *** file.bam hg19sub
the bam files will be added to the user's history
the code (import_with_dbkey.py) is as follows:
import sys
sys.path.append('***/bioblend-0.10.0-py2.7.egg')
sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg')
from bioblend.galaxy import GalaxyInstance
from bioblend.galaxy.tools import ToolClient
url = "http://galaxy-dev.fmi.ch";
key = "***"
history_id = sys.argv[1]
file_path = sys.argv[2]
dbkey= sys.argv[3]
gi = GalaxyInstance(url=url, key=key)
toolClient = ToolClient(gi)
uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey)
Now, if I use the virtual environment from Galaxy, I get:
(.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub
Traceback (most recent call last):
File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line
40, in <module>
uploadedFile = toolClient.upload_file(file_path, history_id,
dbkey=dbkey)
File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py",
line 148, in upload_file
return self._tool_post(payload, files_attached=True)
File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py",
line 218, in _tool_post
return Client._post(self, payload, files_attached=files_attached)
File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py",
line 171, in _post
files_attached=files_attached)
File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py", line
131, in make_post_request
r.status_code, body=r.text)
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:
400: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>400 Bad Request</title>
</head><body>
<h1>Bad Request</h1>
<p>Your browser sent a request that this server could not understand.<br />
</p>
</body></html>
(.venv)-bash-4.2$
...and the file does not get uploaded.
I will continue investigating the difference between the python modules
used, but maybe someone has a clue and could help me
Thank you very much
Hans-Rudolf
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