Emily is still running in to this error, even after 7388, and I'm able to 
duplicate it.  It looks like what's happening is that when the grid operation 
on /requests_admin/manage_datasets is submitted, it uses the param name 'id' 
(which is standard for grid operations), whereas when other methods redirect to 
/requests_admin/manage_datasets, they use the param name 'sample_id'.  So the 
fix that Luobin supplied is necessary too, and I've committed it in 
7438:cdf84aee000b.

--nate

On Jul 23, 2012, at 10:56 AM, Luobin Yang wrote:

> Hi, Greg,
> 
> I tested your fix in changeset 7388:28b3364341b6, it works fine on my local 
> copy of Galaxy. I am able to transfer, delete, and rename sample datasets 
> without any error message. 
> 
> Thanks,
> Luobin
> 
> On Fri, Jul 13, 2012 at 8:19 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Luobin,
> 
> Your information really helped narrow down the problem, and I've committed 
> what I believe is a fix in change set 7388:28b3364341b6, which is currently 
> available in the Galaxy central repository.  This fix should be available in 
> the next Galaxy dist update, which should be available soon.  I am not able 
> to fully test this fix though, so if you can let me know if problems still 
> exist when you get a chance to test it, I'll look further into the problem 
> after the GCC.  Sorry for the inconvenience this has caused.
> 
> Thanks ver much!
> 
> Greg Von Kuster
> 
> 
> On Jul 12, 2012, at 1:07 PM, Luobin Yang wrote:
> 
>> 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/... 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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