Hello Emily,
This issue should be resolved in change set 6924:12b14f3e78e9, which is
currently only available from our central repository. It will not be available
in the dist repository fro some time, so you'll have to pull it from Galaxy
central (https://bitbucket.org/galaxy/galaxy-central) if you want it now.
Thanks very much for reporting this problem, and we apologize for the
inconvenience it caused.
Greg Von Kuster
On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
Hi Leandro,
I am also experiencing the same problem with the latest version of galaxy. I
just attempted to connect our sequencer for the first time yesterday. I do
not have an older version of galaxy to test and compare to see if it works in
earlier versions. I am able to transfer data from the sequence to the import
directory, however it is not moved to the data library. My data_transfer.log
also has the same error.
The server could not comply with the request since it is either malformed or
otherwise incorrect.
Does anyone have a solution for this?
Thanks
Emily
--
Message: 17
Date: Wed, 28 Mar 2012 13:15:47 +0200
From: Leandro Hermida soft...@leandrohermida.com
To: Luobin Yang yangl...@isu.edu
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in
queue forever
Message-ID:
caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you Location
/ ... /Location container to not match URLs starting with /api. To
do this you have to change it to LocationMatch ^/(?!api)
/LocationMatch.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote:
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f',
u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample status
from in queue to complete but didn't add the downloaded files to the data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
api_key69bbd1a9b18eda2a888e9963820d8ef0/api_key
data_hostchp723/data_host
data_usergalaxy/data_user
data_passwordmypassword/data_password
request_id12/request_id
sample_id12/sample_id
library_id15/library_id
folder_id52/folder_id ? ? ? ? ? ? ? ? ? ?dataset
?dataset_id10/dataset_id
namettt_2.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz/file
? ? ? ? ?/datasetdataset
dataset_id9/dataset_id
namettt_1.fastq.gz/name
