Dear Galaxy Dev, The malformed library folder error on the latest galaxy-dist I am gettting (shown below) right after data transfer I am pretty sure is a bug and regression.
I was just able to do the exact same sample tracking setup on one of my other Galaxy servers which is an older galaxy-dist version from last year and everything works ok during library folder association. regards, Leandro On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida <soft...@leandrohermida.com> wrote: > Dear Galaxy Dev, > > Now I have another problem with the Galaxy sample tracking data > transfer. Galaxy is not able to transfer the datasets but when it > attempts to associate the datasets with the library and folder > specified in the sequencing request I get this: > > 2012-03-28 13:07:02,706 - datatx_18327 - Setting status "Adding to > data library" for dataset "All" of sample "16" > 2012-03-28 13:07:02,706 - datatx_18327 - > (u'c969d2e16ec64867a127d6e3a4018b12', > u'http://galaxydev/api/samples/1e8ab44153008be8', > {'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'], > 'error_msg': '', 'update_type': 'sample_dataset_transfer_status', > 'new_status': 'Adding to data library'}) > 2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done'] > 2012-03-28 13:07:02,818 - datatx_18327 - > (u'c969d2e16ec64867a127d6e3a4018b12', > u'http://galaxydev/api/libraries/1e8ab44153008be8/contents', > {'file_type': 'auto', 'server_dir': > '/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '', > 'create_type': 'file', 'folder_id': > '994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option': > 'upload_directory'}) > 2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request > The server could not comply with the request since > it is either malformed or otherwise incorrect. > > Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c ) > specified, unable to decode > > What could be the problem here? Any help would be appreciated. > > regards, > Leandro > > On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida > <soft...@leandrohermida.com> wrote: >> 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 >>>> ___________________________________________________________ >>>> 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: >>>> >>>> http://lists.bx.psu.edu/ >>> >>> ___________________________________________________________ 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: http://lists.bx.psu.edu/
