> 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 <
softdev@leandrohermida.com>
> To: Luobin Yang <
yangluob@isu.edu>
> Cc: Galaxy Dev <
galaxy-dev@bx.psu.edu>
> Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
> queue" forever
> Message-ID:
> <
CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA@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 <
yangluob@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
>> <
softdev@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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>>> ?
http://lists.bx.psu.edu/
>>
>>
>
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