Sample tracking data transfer hangs "in queue" forever
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
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:
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:
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 <softdev@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 <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:
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 <softdev@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 <softdev@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 <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:
participants (2)
-
Leandro Hermida -
Luobin Yang