Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
ble 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:
>>> >
>>> > 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 >> > /> ... 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
>>>
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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 = 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 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 comp
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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 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 so
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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 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: >> > < >> caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@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
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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:g...@bx.psu.edu]
Sent: Wednesday, July 11, 2012 7:55 AM
To: Luobin Yang
Cc: TerAvest, Emily; galaxy-...@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
mailto:g...@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
> mailto:soft...@leandrohermida.com>>
> To: Luobin Yang mailto:yangl...@isu.edu>>
> Cc: Galaxy Dev mailto:galaxy-...@bx.psu.edu>>
> Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
> queue" forever
> Message-ID:
>
> mailto:caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@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 /> ... 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
> mailto:yangl...@isu.edu>> wrote:
>> I've got the same problem and when I looked at the data_transfer.log, I saw
>> the following message:
>>
>> 2012-03-01 15:12:27,338 - datatx_13870 -
>> (u'9c17d84742cd2acb63d88b5bd41d968f',
>> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
>> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
>> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
>> 'new_status': 'Adding to data library'})
>> 2012-03-01 15:12:27,342 - datatx_13870 - Error. > "-//IETF//DTD HTML 2.0//EN">
>>
>> 405 Method Not Allowed
>>
>> Method Not Allowed
>> The requested method PUT is not allowed
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 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:
> >
> > 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 > /> ... 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
> >> fr
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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:
> > <
> caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@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 > /> ... 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 tra
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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:
>
> 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 /> ... 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/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-
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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
> 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=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 /> ... 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/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/ga
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
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=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 ... 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/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"
>> "
>> 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?
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
Dear Galaxy Dev,
The malformed library folder error on the latest galaxy-dist I am
gettting (shown below) right after data transfer I am pretty sure is a
bug and regression.
I was just able to do the exact same sample tracking setup on one of
my other Galaxy servers which is an older galaxy-dist version from
last year and everything works ok during library folder association.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida
wrote:
> Dear Galaxy Dev,
>
> Now I have another problem with the Galaxy sample tracking data
> transfer. Galaxy is not able to transfer the datasets but when it
> attempts to associate the datasets with the library and folder
> specified in the sequencing request I get this:
>
> 2012-03-28 13:07:02,706 - datatx_18327 - Setting status "Adding to
> data library" for dataset "All" of sample "16"
> 2012-03-28 13:07:02,706 - datatx_18327 -
> (u'c969d2e16ec64867a127d6e3a4018b12',
> u'http://galaxydev/api/samples/1e8ab44153008be8',
> {'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
> 'new_status': 'Adding to data library'})
> 2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
> 2012-03-28 13:07:02,818 - datatx_18327 -
> (u'c969d2e16ec64867a127d6e3a4018b12',
> u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
> {'file_type': 'auto', 'server_dir':
> '/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
> 'create_type': 'file', 'folder_id':
> '994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
> 'upload_directory'})
> 2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
> The server could not comply with the request since
> it is either malformed or otherwise incorrect.
>
> Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
> specified, unable to decode
>
> What could be the problem here? Any help would be appreciated.
>
> regards,
> Leandro
>
> On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
> wrote:
>> Dear Galaxy Dev,
>>
>> Ok I have gotten further found out what was going on, in my
>> data_transfer.log I was getting HTTP 404 Not Authorized when the data
>> transfer was trying to access Galaxy API URLs
>> http://galaxyserver/api/... This is because we are using external user
>> authentication as documented in
>> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
>> all of Galaxy behind this authentication. Since the Galaxy API uses
>> API keys to essentially authenticate you have to change you > /> ... 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/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"
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
Dear Galaxy Dev,
Now I have another problem with the Galaxy sample tracking data
transfer. Galaxy is not able to transfer the datasets but when it
attempts to associate the datasets with the library and folder
specified in the sequencing request I get this:
2012-03-28 13:07:02,706 - datatx_18327 - Setting status "Adding to
data library" for dataset "All" of sample "16"
2012-03-28 13:07:02,706 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/samples/1e8ab44153008be8',
{'sample_dataset_ids': ['2f94e8ae9edff68a', '8237ee2988567c1c'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-28 13:07:02,817 - datatx_18327 - [200, 'Done']
2012-03-28 13:07:02,818 - datatx_18327 -
(u'c969d2e16ec64867a127d6e3a4018b12',
u'http://galaxydev/api/libraries/1e8ab44153008be8/contents',
{'file_type': 'auto', 'server_dir':
'/gpfshpc/data/pmrdcdb/galaxy/datatx_18327_28Mar2012', 'dbkey': '',
'create_type': 'file', 'folder_id':
'994debf9f6ab02b99d7cff57c04c6b7c', 'upload_option':
'upload_directory'})
2012-03-28 13:07:02,906 - datatx_18327 - 400 Bad Request
The server could not comply with the request since
it is either malformed or otherwise incorrect.
Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c )
specified, unable to decode
What could be the problem here? Any help would be appreciated.
regards,
Leandro
On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida
wrote:
> Dear Galaxy Dev,
>
> Ok I have gotten further found out what was going on, in my
> data_transfer.log I was getting HTTP 404 Not Authorized when the data
> transfer was trying to access Galaxy API URLs
> http://galaxyserver/api/... This is because we are using external user
> authentication as documented in
> http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
> all of Galaxy behind this authentication. Since the Galaxy API uses
> API keys to essentially authenticate you have to change you /> ... 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/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"
>>> "
>>> 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
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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/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"
>> "
>> 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/
>
>
___
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/
Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever
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.
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/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"
> "
> 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/
>
___
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/
[galaxy-dev] Sample tracking data transfer hangs "in queue" forever
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py"
"
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/
