We know what the problem is and it is being fixed. We'll have the fix available shortly and let everyone know. Thanks for reporting this! 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 <softdev@leandrohermida.com> To: Luobin Yang <yangluob@isu.edu> Cc: Galaxy Dev <galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Message-ID: <CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA@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 <yangluob@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 <softdev@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:
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