Thanks for the report, I suspect the breaking change would be this - https://github.com/galaxyproject/galaxy/pull/4563. I added a bunch of tests for these API changes that I though would ensure backward compatibility but perhaps there is some sort of breakage here. I opened a PR in response to this thread against bioblend to ensure setting the dbkey still works (https://github.com/galaxyproject/bioblend/pull/252) and it seems to work for me.
Does that dbkey not properly exist for that user? Maybe there is a change in behavior for non-existent dbkeys? Or is the dbkey a custom build for that user? I could write some tests for that if that is the case. -John On Mon, Nov 20, 2017 at 7:38 AM, Hans-Rudolf Hotz <[email protected]> wrote: > 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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
