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
>> ___________________________________________________________
>> 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:
>>
>>  http://lists.bx.psu.edu/
>
>

___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to