Hi Greg,

I will be at the galaxy conference and am experiencing the same problem.  I 
would love to meet with you to look at this together.

Emily

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Wednesday, July 11, 2012 7:55 AM
To: Luobin Yang
Cc: TerAvest, Emily; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

Hello Luobin,

I'm on my way to ISMB for a week, and then will be at the Galaxy Community 
Conference the following week, so I won't have time to help you track this 
problem down until some time in August unless you will be at either of these 2 
conferences.  Sorry for the inconvenience on this, but my schedule over the 
next few weeks is very hectic.  If you'll be at either ISMB or the GCC, we can 
certainly get together to look at this.

Greg Von Kuster


On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote:


Hi, Greg,

I've still got issues after I downloaded the latest version from the dist 
repository. So after I selected the datasets that I would like to transfer from 
the sequencer and click the "Transfer" button, Galaxy generates an error 
message : "Invalid sample id (None)"... I tried to delete this dataset using 
the "manage datasets" menu, and Galaxy generates the same error message: 
"Invalid sample id (None)". It seems galaxy system generates the sample id 
automatically (the first one is sample_1), not sure why this happens...

Luobin

On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster 
<g...@bx.psu.edu<mailto:g...@bx.psu.edu>> wrote:
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<mailto:soft...@leandrohermida.com>>
> To: Luobin Yang <yangl...@isu.edu<mailto:yangl...@isu.edu>>
> Cc: Galaxy Dev <galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>>
> Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
>       queue"  forever
> Message-ID:
>       
> <caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com<mailto: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/.<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<mailto: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<mailto: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<http://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"
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>>>
>>> ?http://lists.bx.psu.edu/
>>
>>
>
>
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