Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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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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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
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 <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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
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 <greg@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
"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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally
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. privileged. This email message is intended solely for
the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
___________________________________________________________ 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:
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 <greg@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 <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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
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___________________________________________________________ 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:
Hi Greg, I will be at the galaxy conference and am experiencing the same problem. I would love to meet with you to look at this together. Emily From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Wednesday, July 11, 2012 7:55 AM To: Luobin Yang Cc: TerAvest, Emily; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever 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 <greg@bx.psu.edu<mailto:greg@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 <softdev@leandrohermida.com<mailto:softdev@leandrohermida.com>> To: Luobin Yang <yangluob@isu.edu<mailto:yangluob@isu.edu>> Cc: Galaxy Dev <galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>> Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Message-ID: <CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA@mail.gmail.com<mailto: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/.<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<mailto: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<mailto: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<http://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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
___________________________________________________________ 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/ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
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 <greg@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 <greg@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
"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/. <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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally
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. privileged. This email message is intended solely for
the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
___________________________________________________________ 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:
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 <greg@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 <greg@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 <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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
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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 <greg@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 <greg@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 <greg@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
"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/. <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
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):
"/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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally
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 data python privileged. This email message is intended solely for
the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
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 <greg@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 <greg@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 <greg@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 <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:
************ This email message and any electronic files transmitted with it relating to the official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privileged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you have received this email in error, please delete this email from your system and notify the sender immediately. If you are not the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance on its contents.
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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 (4)
-
Greg Von Kuster -
Luobin Yang -
Nate Coraor -
TerAvest, Emily