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">
> <html><head>
> <title>405 Method Not Allowed</title>
> </head><body>
> <h1>Method Not Allowed</h1>
> <p>The 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_host>rd-galaxydev.app.pmi</galaxy_host>
>> <api_key>69bbd1a9b18eda2a888e9963820d8ef0</api_key>
>> <data_host>chp723</data_host>
>> <data_user>galaxy</data_user>
>> <data_password>mypassword</data_password>
>> <request_id>12</request_id>
>> <sample_id>12</sample_id>
>> <library_id>15</library_id>
>> <folder_id>52</folder_id> ? ? ? ? ? ? ? ? ? ?<dataset>
>> ?<dataset_id>10</dataset_id>
>> <name>ttt_2.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz</file>
>> ? ? ? ? ?</dataset><dataset>
>> <dataset_id>9</dataset_id>
>> <name>ttt_1.fastq.gz</name>
>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz</file>
>> ? ? ? ? ?</dataset> ? ? ? ? ? ? ? ?</data_transfer>"
>> "universe_wsgi.ini"
>>
>> The FASTQ files are for testing and aren't very big (7.6 MB), what
>> could be going wrong?
>>
>> regards,
>> Leandro
>> ___________________________________________________________
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>
>


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