Hi, Greg,

Unfortunately I won't be able to attend these two conference. I spent a bit
time looking at the codes that are related to the issue and I found why
this issue is happening, even though I am not sure how this happened.
Basically this happens on line 755 of requests_admin.py, which is this
statement:

       sample_id = params.get( 'sample_id', None )

It seems this statement is executed twice for each dataset operation. For
the first time of execution, sample_id contains the right ID but for the
second time, sample_id contains None. Based on this observation, I have
come up with a quick fix : I just added the following two lines after above
line:

        if sample_id == None:
            sample_id = params.get( 'id', None )

This fixed the problem and I am able to transfer, delete, or rename sample
datasets even though it doesn't eliminate the source that causes sample_id
to have a value of None.

Another small issue is that I can only transfer one dataset at a time. If I
select two datasets and then click "Transfer" button, the system shows an
error message of invalid sample_id, and the value of sample_id is actually
a tuple instead of a single sample_id. I am not very sure if this is
because the system is designed to handle just one dataset at a time or it's
a bug in the code.

Best,
Luobin

On Wed, Jul 11, 2012 at 8:54 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> 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> 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/. <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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