From Emily.TerAvest@codexis.com Thu Mar 29 13:53:32 2012 From: "TerAvest, Emily" To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Thu, 29 Mar 2012 17:49:09 +0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6540884820400674983==" --===============6540884820400674983== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Leandro,=20 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 no= t have an older version of galaxy to test and compare to see if it works in e= arlier versions. I am able to transfer data from the sequence to the import d= irectory, however it is not moved to the data library. My data_transfer.log a= lso has the same error.=20 "The server could not comply with the request since it is either malformed or= otherwise incorrect." =20 Does anyone have a solution for this?=20 Thanks Emily=20 ------------------------------ Message: 17 Date: Wed, 28 Mar 2012 13:15:47 +0200 From: Leandro Hermida To: Luobin Yang Cc: Galaxy Dev Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Message-ID: Content-Type: text/plain; charset=3DISO-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 ... container to not match URLs starting with /api. To do this you have to change it to .... . best, leandro On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. "-//IETF//DTD HTML 2.0//EN"> > > 405 Method Not Allowed > >

Method Not Allowed

The requested method PUT is not allowed for the URL > /api/samples/2d9035b3fc152403.

> > 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 > 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/rabb= itmqctl', >> '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" >> " >> rd-galaxydev.app.pmi >> 69bbd1a9b18eda2a888e9963820d8ef0 >> chp723 >> galaxy >> mypassword >> 12 >> 12 >> 15 >> 52 ? ? ? ? ? ? ? ? ? ? >> ?10 >> ttt_2.fastq.gz >> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >> ? ? ? ? ? >> 9 >> ttt_1.fastq.gz >> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >> ? ? ? ? ? ? ? ? ? ? ? ? ?" >> "universe_wsgi.ini" >> >> The FASTQ files are for testing and aren't very big (7.6 MB), what >> could be going wrong? >> >> regards, >> Leandro >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. ?To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> ?http://lists.bx.psu.edu/ > > ************ This email message and any electronic files transmitted with it relating to t= he official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privile= ged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you hav= e received this email in error, please delete this email from your system and notify the sender immediately. If you are no= t the intended recipient, you should not disclose, distribute, use or copy this email or take any action in reliance o= n its contents. --===============6540884820400674983==-- From greg@bx.psu.edu Thu Mar 29 13:59:19 2012 From: Greg Von Kuster To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Thu, 29 Mar 2012 13:59:21 -0400 Message-ID: <7C0A8F08-25F3-4823-8F2D-12BF61C496E8@bx.psu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============9000869502729368158==" --===============9000869502729368158== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable We know what the problem is and it is being fixed. We'll have the fix availa= ble shortly and let everyone know. Thanks for reporting this! Greg Von Kuster On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: >=20 > Hi Leandro,=20 >=20 > 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.=20 > "The server could not comply with the request since it is either malformed = or otherwise incorrect." >=20 > Does anyone have a solution for this?=20 >=20 > Thanks > Emily=20 >=20 >=20 >=20 > ------------------------------ >=20 > Message: 17 > Date: Wed, 28 Mar 2012 13:15:47 +0200 > From: Leandro Hermida > To: Luobin Yang > Cc: Galaxy Dev > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in > queue" forever > Message-ID: > > Content-Type: text/plain; charset=3DISO-8859-1 >=20 > Dear Galaxy Dev, >=20 > 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 /> ... container to not match URLs starting with /api. To > do this you have to change it to .... > . >=20 > best, > leandro >=20 > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang wrote: >> I've got the same problem and when I looked at the data_transfer.log, I saw >> the following message: >>=20 >> 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. > "-//IETF//DTD HTML 2.0//EN"> >> >> 405 Method Not Allowed >> >>

Method Not Allowed

The requested method PUT is not allowed for the URL >> /api/samples/2d9035b3fc152403.

>>=20 >> 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. >>=20 >> Luobin >>=20 >> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida >> wrote: >>>=20 >>> Dear Galaxy Dev, >>>=20 >>> 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. >>>=20 >>> The galaxy_listener.log shows: >>>=20 >>> 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': >>>=20 >>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rab= bitmqctl', >>> '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 >>>=20 >>> "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messagin= g/server/data_transfer.py" >>> " >>> rd-galaxydev.app.pmi >>> 69bbd1a9b18eda2a888e9963820d8ef0 >>> chp723 >>> galaxy >>> mypassword >>> 12 >>> 12 >>> 15 >>> 52 ? ? ? ? ? ? ? ? ? ? >>> ?10 >>> ttt_2.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >>> ? ? ? ? ? >>> 9 >>> ttt_1.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >>> "universe_wsgi.ini" >>>=20 >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >>> could be going wrong? >>>=20 >>> 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: >>>=20 >>> ?http://lists.bx.psu.edu/ >>=20 >>=20 >=20 >=20 > ************ > 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 privi= leged. This email message is intended solely for > the use of the individual(s) to whom it is addressed. If you believe you h= ave 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. >=20 >=20 > ___________________________________________________________ > 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: >=20 > http://lists.bx.psu.edu/ --===============9000869502729368158==-- From greg@bx.psu.edu Fri Mar 30 10:30:58 2012 From: Greg Von Kuster To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Fri, 30 Mar 2012 10:30:45 -0400 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0185146230717468062==" --===============0185146230717468062== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello Emily, This issue should be resolved in change set 6924:12b14f3e78e9, which is curre= ntly 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 cen= tral (https://bitbucket.org/galaxy/galaxy-central) if you want it now. Thanks very much for reporting this problem, and we apologize for the inconve= nience it caused. Greg Von Kuster On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: >=20 > Hi Leandro,=20 >=20 > 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.=20 > "The server could not comply with the request since it is either malformed = or otherwise incorrect." >=20 > Does anyone have a solution for this?=20 >=20 > Thanks > Emily=20 >=20 >=20 >=20 > ------------------------------ >=20 > Message: 17 > Date: Wed, 28 Mar 2012 13:15:47 +0200 > From: Leandro Hermida > To: Luobin Yang > Cc: Galaxy Dev > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in > queue" forever > Message-ID: > > Content-Type: text/plain; charset=3DISO-8859-1 >=20 > Dear Galaxy Dev, >=20 > 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 /> ... container to not match URLs starting with /api. To > do this you have to change it to .... > . >=20 > best, > leandro >=20 > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang wrote: >> I've got the same problem and when I looked at the data_transfer.log, I saw >> the following message: >>=20 >> 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. > "-//IETF//DTD HTML 2.0//EN"> >> >> 405 Method Not Allowed >> >>

Method Not Allowed

The requested method PUT is not allowed for the URL >> /api/samples/2d9035b3fc152403.

>>=20 >> 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. >>=20 >> Luobin >>=20 >> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida >> wrote: >>>=20 >>> Dear Galaxy Dev, >>>=20 >>> 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. >>>=20 >>> The galaxy_listener.log shows: >>>=20 >>> 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': >>>=20 >>> '/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rab= bitmqctl', >>> '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 >>>=20 >>> "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messagin= g/server/data_transfer.py" >>> " >>> rd-galaxydev.app.pmi >>> 69bbd1a9b18eda2a888e9963820d8ef0 >>> chp723 >>> galaxy >>> mypassword >>> 12 >>> 12 >>> 15 >>> 52 ? ? ? ? ? ? ? ? ? ? >>> ?10 >>> ttt_2.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >>> ? ? ? ? ? >>> 9 >>> ttt_1.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >>> "universe_wsgi.ini" >>>=20 >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >>> could be going wrong? >>>=20 >>> 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: >>>=20 >>> ?http://lists.bx.psu.edu/ >>=20 >>=20 >=20 >=20 > ************ > 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 privi= leged. This email message is intended solely for > the use of the individual(s) to whom it is addressed. If you believe you h= ave 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. >=20 >=20 > ___________________________________________________________ > 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: >=20 > http://lists.bx.psu.edu/ --===============0185146230717468062==-- From yangluob@isu.edu Mon Jul 9 13:25:06 2012 From: Luobin Yang To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Mon, 09 Jul 2012 11:24:57 -0600 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============5730426276564471710==" --===============5730426276564471710== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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 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 > > To: Luobin Yang > > Cc: Galaxy Dev > > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in > > queue" forever > > Message-ID: > > < > CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA(a)mail.gmail.com> > > Content-Type: text/plain; charset=3DISO-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 > /> ... container to not match URLs starting with /api. To > > do this you have to change it to .... > > . > > > > best, > > leandro > > > > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. >> "-//IETF//DTD HTML 2.0//EN"> > >> > >> 405 Method Not Allowed > >> > >>

Method Not Allowed

> >>

The requested method PUT is not allowed for the URL > >> /api/samples/2d9035b3fc152403.

> >>

> >> > >> 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 > >> 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/rabbi= tmqctl', > >>> '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" > >>> " > >>> rd-galaxydev.app.pmi > >>> 69bbd1a9b18eda2a888e9963820d8ef0 > >>> chp723 > >>> galaxy > >>> mypassword > >>> 12 > >>> 12 > >>> 15 > >>> 52 ? ? ? ? ? ? ? ? ? ? > >>> ?10 > >>> ttt_2.fastq.gz > >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz > >>> ? ? ? ? ? > >>> 9 > >>> ttt_1.fastq.gz > >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz > >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" > >>> "universe_wsgi.ini" > >>> > >>> The FASTQ files are for testing and aren't very big (7.6 MB), what > >>> could be going wrong? > >>> > >>> regards, > >>> Leandro > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. ?To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> > >>> ?http://lists.bx.psu.edu/ > >> > >> > > > > > > ************ > > 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: > > > > http://lists.bx.psu.edu/ > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX188YnI+ClBsZWFzZSBrZWVw IGFsbCByZXBsaWVzIG9uIHRoZSBsaXN0IGJ5IHVzaW5nICZxdW90O3JlcGx5IGFsbCZxdW90Ozxi cj4KaW4geW91ciBtYWlsIGNsaWVudC4goFRvIG1hbmFnZSB5b3VyIHN1YnNjcmlwdGlvbnMgdG8g dGhpczxicj4KYW5kIG90aGVyIEdhbGF4eSBsaXN0cywgcGxlYXNlIHVzZSB0aGUgaW50ZXJmYWNl IGF0Ojxicj4KPGJyPgqgIDxhIGhyZWY9Imh0dHA6Ly9saXN0cy5ieC5wc3UuZWR1LyIgdGFyZ2V0 PSJfYmxhbmsiPmh0dHA6Ly9saXN0cy5ieC5wc3UuZWR1LzwvYT48YnI+CjwvZGl2PjwvZGl2Pjwv YmxvY2txdW90ZT48L2Rpdj48YnI+Cg== --===============5730426276564471710==-- From greg@bx.psu.edu Wed Jul 11 10:54:49 2012 From: Greg Von Kuster To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Wed, 11 Jul 2012 10:54:45 -0400 Message-ID: <65277377-CE48-4806-9AF8-9A697B248BF2@bx.psu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2301196253733323463==" --===============2301196253733323463== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello Luobin, I'm on my way to ISMB for a week, and then will be at the Galaxy Community Co= nference the following week, so I won't have time to help you track this prob= lem down until some time in August unless you will be at either of these 2 co= nferences. Sorry for the inconvenience on this, but my schedule over the nex= t few weeks is very hectic. If you'll be at either ISMB or the GCC, we can c= ertainly get together to look at this. Greg Von Kuster On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote: > Hi, Greg, >=20 > I've still got issues after I downloaded the latest version from the dist r= epository. So after I selected the datasets that I would like to transfer fro= m the sequencer and click the "Transfer" button, Galaxy generates an error me= ssage : "Invalid sample id (None)"... I tried to delete this dataset using th= e "manage datasets" menu, and Galaxy generates the same error message: "Inval= id sample id (None)". It seems galaxy system generates the sample id automati= cally (the first one is sample_1), not sure why this happens... >=20 > Luobin >=20 >=20 > On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster wrote: > Hello Emily, >=20 > This issue should be resolved in change set 6924:12b14f3e78e9, which is cur= rently 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 c= entral (https://bitbucket.org/galaxy/galaxy-central) if you want it now. >=20 > Thanks very much for reporting this problem, and we apologize for the incon= venience it caused. >=20 > Greg Von Kuster >=20 >=20 > On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: >=20 > > > > 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 d= o 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 impo= rt directory, however it is not moved to the data library. My data_transfer.l= og also has the same error. > > "The server could not comply with the request since it is either malforme= d 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 > > To: Luobin Yang > > Cc: Galaxy Dev > > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in > > queue" forever > > Message-ID: > > > > Content-Type: text/plain; charset=3DISO-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 > /> ... container to not match URLs starting with /api. To > > do this you have to change it to .... > > . > > > > best, > > leandro > > > > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. >> "-//IETF//DTD HTML 2.0//EN"> > >> > >> 405 Method Not Allowed > >> > >>

Method Not Allowed

> >>

The requested method PUT is not allowed for the URL > >> /api/samples/2d9035b3fc152403.

> >>

> >> > >> Using Galaxy instead of Apache as the web server changed the sample stat= us > >> from "in queue" to complete but didn't add the downloaded files to the d= ata > >> library. > >> > >> Luobin > >> > >> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida > >> 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/r= abbitmqctl', > >>> '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_messag= ing/server/data_transfer.py" > >>> " > >>> rd-galaxydev.app.pmi > >>> 69bbd1a9b18eda2a888e9963820d8ef0 > >>> chp723 > >>> galaxy > >>> mypassword > >>> 12 > >>> 12 > >>> 15 > >>> 52 ? ? ? ? ? ? ? ? ? ? > >>> ?10 > >>> ttt_2.fastq.gz > >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz > >>> ? ? ? ? ? > >>> 9 > >>> ttt_1.fastq.gz > >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz > >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" > >>> "universe_wsgi.ini" > >>> > >>> The FASTQ files are for testing and aren't very big (7.6 MB), what > >>> could be going wrong? > >>> > >>> regards, > >>> Leandro > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. ?To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> > >>> ?http://lists.bx.psu.edu/ > >> > >> > > > > > > ************ > > 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 pri= vileged. 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 ar= e not the intended recipient, you should not > > disclose, distribute, use or copy this email or take any action in relian= ce 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: > > > > http://lists.bx.psu.edu/ >=20 >=20 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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YT48YnI+CjwvZGl2PjwvZGl2PjwvYmxvY2txdW90ZT48L2Rpdj48YnI+CjwvYmxvY2txdW90ZT48 L2Rpdj48YnI+PC9kaXY+PC9ib2R5PjwvaHRtbD4= --===============2301196253733323463==-- From Emily.TerAvest@codexis.com Wed Jul 11 10:57:26 2012 From: "TerAvest, Emily" To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Wed, 11 Jul 2012 14:57:19 +0000 Message-ID: In-Reply-To: <65277377-CE48-4806-9AF8-9A697B248BF2@bx.psu.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1865697826590576087==" --===============1865697826590576087== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Greg, I will be at the galaxy conference and am experiencing the same problem. I w= ould love to meet with you to look at this together. Emily From: Greg Von Kuster [mailto:greg(a)bx.psu.edu] Sent: Wednesday, July 11, 2012 7:55 AM To: Luobin Yang Cc: TerAvest, Emily; galaxy-dev(a)bx.psu.edu Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" fore= ver Hello Luobin, I'm on my way to ISMB for a week, and then will be at the Galaxy Community Co= nference the following week, so I won't have time to help you track this prob= lem down until some time in August unless you will be at either of these 2 co= nferences. Sorry for the inconvenience on this, but my schedule over the nex= t few weeks is very hectic. If you'll be at either ISMB or the GCC, we can c= ertainly 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 rep= ository. So after I selected the datasets that I would like to transfer from = the sequencer and click the "Transfer" button, Galaxy generates an error mess= age : "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 automatica= lly (the first one is sample_1), not sure why this happens... Luobin On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster > wrote: Hello Emily, This issue should be resolved in change set 6924:12b14f3e78e9, which is curre= ntly 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 cen= tral (https://bitbucket.org/galaxy/galaxy-central) if you want it now. Thanks very much for reporting this problem, and we apologize for the inconve= nience 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 > > To: Luobin Yang > > Cc: Galaxy Dev > > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in > queue" forever > Message-ID: > > > Content-Type: text/plain; charset=3DISO-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 ar= e 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 /> ... container to not match URLs starting with /api. To > do this you have to change it to .... > . > > best, > leandro > > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang > 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. > "-//IETF//DTD HTML 2.0//EN"> >> >> 405 Method Not Allowed >> >>

Method Not Allowed

The requested method PUT is not allowed for the URL >> /api/samples/2d9035b3fc152403.

>> >> 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 >> > 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/rab= bitmqctl', >>> '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_messagin= g/server/data_transfer.py" >>> " >>> rd-galaxydev.app.pmi >>> 69bbd1a9b18eda2a888e9963820d8ef0 >>> chp723 >>> galaxy >>> mypassword >>> 12 >>> 12 >>> 15 >>> 52 ? ? ? ? ? ? ? ? ? ? >>> ?10 >>> ttt_2.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >>> ? ? ? ? ? >>> 9 >>> ttt_1.fastq.gz >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >>> "universe_wsgi.ini" >>> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >>> could be going wrong? >>> >>> regards, >>> Leandro >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. ?To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> ?http://lists.bx.psu.edu/ >> >> > > > ************ > 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 privi= leged. This email message is intended solely for > the use of the individual(s) to whom it is addressed. If you believe you h= ave 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: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ This email message and any electronic files transmitted with it relating to t= he official business of Codexis, Inc. and its affiliates are proprietary, strictly confidential, and may be legally privile= ged. This email message is intended solely for the use of the individual(s) to whom it is addressed. If you believe you hav= e received this email in error, please delete this email from your system and notify the sender immediately. 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In-Reply-To: <65277377-CE48-4806-9AF8-9A697B248BF2@bx.psu.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0407233491534442961==" --===============0407233491534442961== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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 =3D 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 =3D=3D None: sample_id =3D 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 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 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 >> > To: Luobin Yang >> > Cc: Galaxy Dev >> > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in >> > queue" forever >> > Message-ID: >> > < >> CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA(a)mail.gmail.com> >> > Content-Type: text/plain; charset=3DISO-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 > > /> ... container to not match URLs starting with /api. To >> > do this you have to change it to .... >> > . >> > >> > best, >> > leandro >> > >> > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. > >> "-//IETF//DTD HTML 2.0//EN"> >> >> >> >> 405 Method Not Allowed >> >> >> >>

Method Not Allowed

>> >>

The requested method PUT is not allowed for the URL >> >> /api/samples/2d9035b3fc152403.

>> >>

>> >> >> >> 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 >> >> 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/rabb= itmqctl', >> >>> '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" >> >>> " >> >>> rd-galaxydev.app.pmi >> >>> 69bbd1a9b18eda2a888e9963820d8ef0 >> >>> chp723 >> >>> galaxy >> >>> mypassword >> >>> 12 >> >>> 12 >> >>> 15 >> >>> 52 ? ? ? ? ? ? ? ? ? ? >> >>> ?10 >> >>> ttt_2.fastq.gz >> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >> >>> ? ? ? ? ? >> >>> 9 >> >>> ttt_1.fastq.gz >> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >> >>> "universe_wsgi.ini" >> >>> >> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >> >>> could be going wrong? >> >>> >> >>> regards, >> >>> Leandro >> >>> ___________________________________________________________ >> >>> Please keep all replies on the list by using "reply all" >> >>> in your mail client. ?To manage your subscriptions to this >> >>> and other Galaxy lists, please use the interface at: >> >>> >> >>> ?http://lists.bx.psu.edu/ >> >> >> >> >> > >> > >> > ************ >> > 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: >> > >> > http://lists.bx.psu.edu/ >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. 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Greg Von Kuster To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Fri, 13 Jul 2012 10:19:23 -0400 Message-ID: <65C82773-6989-4BB8-8244-3509B6BD2F97@bx.psu.edu> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2644415895329516718==" --===============2644415895329516718== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello Luobin, Your information really helped narrow down the problem, and I've committed wh= at I believe is a fix in change set 7388:28b3364341b6, which is currently ava= ilable 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 f= ully 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 th= e 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, >=20 > 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 t= his happens on line 755 of requests_admin.py, which is this statement:=20 >=20 > sample_id =3D params.get( 'sample_id', None ) >=20 > It seems this statement is executed twice for each dataset operation. For t= he first time of execution, sample_id contains the right ID but for the secon= d time, sample_id contains None. Based on this observation, I have come up wi= th a quick fix : I just added the following two lines after above line: >=20 > if sample_id =3D=3D None: > sample_id =3D params.get( 'id', None ) >=20 > 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. >=20 > 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 er= ror message of invalid sample_id, and the value of sample_id is actually a tu= ple 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.=20 >=20 > Best, > Luobin >=20 > On Wed, Jul 11, 2012 at 8:54 AM, Greg Von Kuster wrote: > Hello Luobin, >=20 > 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 pr= oblem 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 n= ext few weeks is very hectic. If you'll be at either ISMB or the GCC, we can= certainly get together to look at this. >=20 > Greg Von Kuster >=20 >=20 > On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote: >=20 >> Hi, Greg, >>=20 >> 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 fr= om the sequencer and click the "Transfer" button, Galaxy generates an error m= essage : "Invalid sample id (None)"... I tried to delete this dataset using t= he "manage datasets" menu, and Galaxy generates the same error message: "Inva= lid sample id (None)". It seems galaxy system generates the sample id automat= ically (the first one is sample_1), not sure why this happens... >>=20 >> Luobin >>=20 >>=20 >> On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster wrote: >> Hello Emily, >>=20 >> This issue should be resolved in change set 6924:12b14f3e78e9, which is cu= rrently 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. >>=20 >> Thanks very much for reporting this problem, and we apologize for the inco= nvenience it caused. >>=20 >> Greg Von Kuster >>=20 >>=20 >> On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: >>=20 >> > >> > Hi Leandro, >> > >> > I am also experiencing the same problem with the latest version of galax= y. 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 imp= ort 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 malform= ed 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 >> > To: Luobin Yang >> > Cc: Galaxy Dev >> > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in >> > queue" forever >> > Message-ID: >> > >> > Content-Type: text/plain; charset=3DISO-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 > > /> ... container to not match URLs starting with /api. To >> > do this you have to change it to .... >> > . >> > >> > best, >> > leandro >> > >> > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. > >> "-//IETF//DTD HTML 2.0//EN"> >> >> >> >> 405 Method Not Allowed >> >> >> >>

Method Not Allowed

>> >>

The requested method PUT is not allowed for the URL >> >> /api/samples/2d9035b3fc152403.

>> >>

>> >> >> >> Using Galaxy instead of Apache as the web server changed the sample sta= tus >> >> 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 >> >> 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_messa= ging/server/data_transfer.py" >> >>> " >> >>> rd-galaxydev.app.pmi >> >>> 69bbd1a9b18eda2a888e9963820d8ef0 >> >>> chp723 >> >>> galaxy >> >>> mypassword >> >>> 12 >> >>> 12 >> >>> 15 >> >>> 52 ? ? ? ? ? ? ? ? ? ? >> >>> ?10 >> >>> ttt_2.fastq.gz >> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >> >>> ? ? ? ? ? >> >>> 9 >> >>> ttt_1.fastq.gz >> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >> >>> "universe_wsgi.ini" >> >>> >> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >> >>> could be going wrong? >> >>> >> >>> regards, >> >>> Leandro >> >>> ___________________________________________________________ >> >>> Please keep all replies on the list by using "reply all" >> >>> in your mail client. ?To manage your subscriptions to this >> >>> and other Galaxy lists, please use the interface at: >> >>> >> >>> ?http://lists.bx.psu.edu/ >> >> >> >> >> > >> > >> > ************ >> > 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 pr= ivileged. This email message is intended solely for >> > the use of the individual(s) to whom it is addressed. If you believe yo= u have received this email in error, please delete >> > this email from your system and notify the sender immediately. If you a= re not the intended recipient, you should not >> > disclose, distribute, use or copy this email or take any action in relia= nce 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: >> > >> > http://lists.bx.psu.edu/ >>=20 >>=20 >> ___________________________________________________________ >> 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: >>=20 >> http://lists.bx.psu.edu/ >>=20 >=20 >=20 > ___________________________________________________________ > 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: >=20 > http://lists.bx.psu.edu/ --===============2644415895329516718== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+PGhlYWQ+PC9oZWFkPjxib2R5IHN0eWxlPSJ3b3JkLXdyYXA6IGJyZWFrLXdvcmQ7IC13 ZWJraXQtbmJzcC1tb2RlOiBzcGFjZTsgLXdlYmtpdC1saW5lLWJyZWFrOiBhZnRlci13aGl0ZS1z cGFjZTsgIj5IZWxsbyBMdW9iaW4sPGRpdj48YnI+PC9kaXY+PGRpdj5Zb3VyIGluZm9ybWF0aW9u IHJlYWxseSBoZWxwZWQgbmFycm93IGRvd24gdGhlIHByb2JsZW0sIGFuZCBJJ3ZlIGNvbW1pdHRl ZCB3aGF0IEkgYmVsaWV2ZSBpcyBhIGZpeCBpbiBjaGFuZ2Ugc2V0Jm5ic3A7NzM4ODoyOGIzMzY0 MzQxYjYsIHdoaWNoIGlzIGN1cnJlbnRseSBhdmFpbGFibGUgaW4gdGhlIEdhbGF4eSBjZW50cmFs IHJlcG9zaXRvcnkuICZuYnNwO1RoaXMgZml4IHNob3VsZCBiZSBhdmFpbGFibGUgaW4gdGhlIG5l eHQgR2FsYXh5IGRpc3QgdXBkYXRlLCB3aGljaCBzaG91bGQgYmUgYXZhaWxhYmxlIHNvb24uICZu YnNwO0kgYW0gbm90IGFibGUgdG8gZnVsbHkgdGVzdCB0aGlzIGZpeCB0aG91Z2gsIHNvIGlmIHlv 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Y3JpcHRpb25zIHRvIHRoaXM8YnI+YW5kIG90aGVyIEdhbGF4eSBsaXN0cywgcGxlYXNlIHVzZSB0 aGUgaW50ZXJmYWNlIGF0Ojxicj48YnI+ICZuYnNwOzxhIGhyZWY9Imh0dHA6Ly9saXN0cy5ieC5w c3UuZWR1LyI+aHR0cDovL2xpc3RzLmJ4LnBzdS5lZHUvPC9hPjwvYmxvY2txdW90ZT48L2Rpdj48 YnI+PC9kaXY+PC9ib2R5PjwvaHRtbD4= --===============2644415895329516718==-- From yangluob@isu.edu Mon Jul 23 11:56:28 2012 From: Luobin Yang To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever Date: Mon, 23 Jul 2012 09:56:18 -0600 Message-ID: In-Reply-To: <65C82773-6989-4BB8-8244-3509B6BD2F97@bx.psu.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7300040879143569887==" --===============7300040879143569887== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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 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 =3D 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 =3D=3D None: > sample_id =3D 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 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 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 >>> > To: Luobin Yang >>> > Cc: Galaxy Dev >>> > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in >>> > queue" forever >>> > Message-ID: >>> > < >>> CAOhzmPJ67udRQBhfChgyxNrXsm3QcY1c7jna1kR0aJBNKEKJxA(a)mail.gmail.com> >>> > Content-Type: text/plain; charset=3DISO-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 >> > /> ... container to not match URLs starting with /api. To >>> > do this you have to change it to .... >>> > . >>> > >>> > best, >>> > leandro >>> > >>> > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. >> >> "-//IETF//DTD HTML 2.0//EN"> >>> >> >>> >> 405 Method Not Allowed >>> >> >>> >>

Method Not Allowed

>>> >>

The requested method PUT is not allowed for the URL >>> >> /api/samples/2d9035b3fc152403.

>>> >>

>>> >> >>> >> 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 >>> >> 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/rab= bitmqctl', >>> >>> '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_messagin= g/server/data_transfer.py" >>> >>> " >>> >>> rd-galaxydev.app.pmi >>> >>> 69bbd1a9b18eda2a888e9963820d8ef0 >>> >>> chp723 >>> >>> galaxy >>> >>> mypassword >>> >>> 12 >>> >>> 12 >>> >>> 15 >>> >>> 52 ? ? ? ? ? ? ? ? ? ? >>> >>> ?10 >>> >>> ttt_2.fastq.gz >>> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >>> >>> ? ? ? ? ? >>> >>> 9 >>> >>> ttt_1.fastq.gz >>> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >>> >>> "universe_wsgi.ini" >>> >>> >>> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >>> >>> could be going wrong? >>> >>> >>> >>> regards, >>> >>> Leandro >>> >>> ___________________________________________________________ >>> >>> Please keep all replies on the list by using "reply all" >>> >>> in your mail client. ?To manage your subscriptions to this >>> >>> and other Galaxy lists, please use the interface at: >>> >>> >>> >>> ?http://lists.bx.psu.edu/ >>> >> >>> >> >>> > >>> > >>> > ************ >>> > 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: >>> > >>> > http://lists.bx.psu.edu/ >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >> >> >> > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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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' (w= hich is standard for grid operations), whereas when other methods redirect to= /requests_admin/manage_datasets, they use the param name 'sample_id'. So th= e fix that Luobin supplied is necessary too, and I've committed it in 7438:cd= f84aee000b. --nate On Jul 23, 2012, at 10:56 AM, Luobin Yang wrote: > Hi, Greg, >=20 > 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 wi= thout any error message.=20 >=20 > Thanks, > Luobin >=20 > On Fri, Jul 13, 2012 at 8:19 AM, Greg Von Kuster wrote: > Hello Luobin, >=20 > 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 a= vailable in the Galaxy central repository. This fix should be available in t= he 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 exis= t 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. >=20 > Thanks ver much! >=20 > Greg Von Kuster >=20 >=20 > On Jul 12, 2012, at 1:07 PM, Luobin Yang wrote: >=20 >> Hi, Greg, >>=20 >> Unfortunately I won't be able to attend these two conference. I spent a bi= t time looking at the codes that are related to the issue and I found why thi= s 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:=20 >>=20 >> sample_id =3D params.get( 'sample_id', None ) >>=20 >> 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 seco= nd time, sample_id contains None. Based on this observation, I have come up w= ith a quick fix : I just added the following two lines after above line: >>=20 >> if sample_id =3D=3D None: >> sample_id =3D params.get( 'id', None ) >>=20 >> 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 t= o have a value of None. >>=20 >> 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 e= rror message of invalid sample_id, and the value of sample_id is actually a t= uple 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.=20 >>=20 >> Best, >> Luobin >>=20 >> On Wed, Jul 11, 2012 at 8:54 AM, Greg Von Kuster wrote: >> Hello Luobin, >>=20 >> 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 p= roblem 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 ca= n certainly get together to look at this. >>=20 >> Greg Von Kuster >>=20 >>=20 >> On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote: >>=20 >>> Hi, Greg, >>>=20 >>> 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 f= rom 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: "Inv= alid sample id (None)". It seems galaxy system generates the sample id automa= tically (the first one is sample_1), not sure why this happens... >>>=20 >>> Luobin >>>=20 >>>=20 >>> On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster wrot= e: >>> Hello Emily, >>>=20 >>> This issue should be resolved in change set 6924:12b14f3e78e9, which is c= urrently only available from our central repository. It will not be availabl= e 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. >>>=20 >>> Thanks very much for reporting this problem, and we apologize for the inc= onvenience it caused. >>>=20 >>> Greg Von Kuster >>>=20 >>>=20 >>> On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: >>>=20 >>> > >>> > Hi Leandro, >>> > >>> > I am also experiencing the same problem with the latest version of gala= xy. 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 work= s in earlier versions. I am able to transfer data from the sequence to the im= port 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 malfor= med 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 >>> > To: Luobin Yang >>> > Cc: Galaxy Dev >>> > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in >>> > queue" forever >>> > Message-ID: >>> > >>> > Content-Type: text/plain; charset=3DISO-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 >> > /> ... container to not match URLs starting with /api. To >>> > do this you have to change it to .... >>> > . >>> > >>> > best, >>> > leandro >>> > >>> > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang 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. >> >> "-//IETF//DTD HTML 2.0//EN"> >>> >> >>> >> 405 Method Not Allowed >>> >> >>> >>

Method Not Allowed

>>> >>

The requested method PUT is not allowed for the URL >>> >> /api/samples/2d9035b3fc152403.

>>> >>

>>> >> >>> >> Using Galaxy instead of Apache as the web server changed the sample st= atus >>> >> 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 >>> >> 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_mess= aging/server/data_transfer.py" >>> >>> " >>> >>> rd-galaxydev.app.pmi >>> >>> 69bbd1a9b18eda2a888e9963820d8ef0 >>> >>> chp723 >>> >>> galaxy >>> >>> mypassword >>> >>> 12 >>> >>> 12 >>> >>> 15 >>> >>> 52 ? ? ? ? ? ? ? ? ? ? >>> >>> ?10 >>> >>> ttt_2.fastq.gz >>> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz >>> >>> ? ? ? ? ? >>> >>> 9 >>> >>> ttt_1.fastq.gz >>> >>> /gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?" >>> >>> "universe_wsgi.ini" >>> >>> >>> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what >>> >>> could be going wrong? >>> >>> >>> >>> regards, >>> >>> Leandro >>> >>> ___________________________________________________________ >>> >>> Please keep all replies on the list by using "reply all" >>> >>> in your mail client. ?To manage your subscriptions to this >>> >>> and other Galaxy lists, please use the interface at: >>> >>> >>> >>> ?http://lists.bx.psu.edu/ >>> >> >>> >> >>> > >>> > >>> > ************ >>> > This email message and any electronic files transmitted with it relatin= g to the official business of Codexis, Inc. and its >>> > affiliates are proprietary, strictly confidential, and may be legally p= rivileged. This email message is intended solely for >>> > the use of the individual(s) to whom it is addressed. If you believe y= ou 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 reli= ance 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: >>> > >>> > http://lists.bx.psu.edu/ >>>=20 >>>=20 >>> ___________________________________________________________ >>> 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: >>>=20 >>> http://lists.bx.psu.edu/ >>>=20 >>=20 >>=20 >> ___________________________________________________________ >> 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: >>=20 >> http://lists.bx.psu.edu/ >=20 >=20 > ___________________________________________________________ > 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: >=20 > http://lists.bx.psu.edu/ --===============0182989334446225516==--