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> 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>
> > 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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