I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know: - the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/; - the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts; - even some of the blend4j unit tests are failing.
One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb9...
Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
Cheers, Freek
________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of galaxy-dev-request@lists.galaxyproject.org [galaxy-dev-request@lists.galaxyproject.org] Sent: Tuesday, December 16, 2014 18:00 To: galaxy-dev@lists.galaxyproject.org Subject: galaxy-dev Digest, Vol 102, Issue 17
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Today's Topics:
1. Re: How galaxy workflow work ? (John Chilton) 2. Re: Metadata error in uploading files to data libraries (John Chilton) 3. Re: package_numpy_1_7 can't be installed (Wang, Yu) 4. Re: "join" produces an import error (Wang, Yu) 5. Re: package_numpy_1_7 can't be installed (Björn Grüning)
----------------------------------------------------------------------
Message: 1 Date: Mon, 15 Dec 2014 14:24:13 -0500 From: John Chilton jmchilton@gmail.com To: Bongsoo Park bxp12@psu.edu Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How galaxy workflow work ? Message-ID: CANwbokcggD3W7Tkyd5fy-9d6qedLT+ta1gzzmkfE1Apa2R8w1A@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Somehow your user object is not being set. Are you sure you have initialized bioblend with the correct API key? Do other operations work with that key?
-John
On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park bxp12@psu.edu wrote:
Hi All,
I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks!
(GALAXY User Interface)
=======================================================
"xhr": {
"readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
method:", "err_code": 0}",
"responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r", "cache-control": "max-age=0,no-cache,no-store\r", "Server": "PasteWSGIServer/0.5 Python/2.7.8\r", "Connection": "close\r", "content-type": "application/json\r" }
=======================================================
I found the error message in the Galaxy instance shell interface.
=======================================================
galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator
rval = func( self, trans, *args, **kwargs)
File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index
and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
AttributeError: 'NoneType' object has no attribute 'id'
=======================================================
Best,
Bongsoo
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------------------------------
Message: 2 Date: Mon, 15 Dec 2014 14:31:20 -0500 From: John Chilton jmchilton@gmail.com To: Jelle Scholtalbers j.scholtalbers@gmail.com Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Metadata error in uploading files to data libraries Message-ID: CANwbokdzjumt4abseN3b6rxOkaXH+9fB23+_OhqmUtFqnxbxWw@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Hello,
Sorry we haven't made progress on this - and thanks for creating a Trello card (https://trello.com/c/tw75nq1U).
It looks like samtools is not on your path, can you use it from the command-line? If not you should probably install it - I would suggest install samtools 0.1.19 with homebrew (looks like you are a on Mac). If you can run samtools from the command-line - can you do a which `samtools` from your command-line and see where it is coming from and then add that directory explicitly to your Galaxy PATH - say at the top of run.sh in your Galaxy root (let me know if you need more details on that).
-John
On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers j.scholtalbers@gmail.com wrote:
Hi all,
after an update to the following changeset(14859:7ba05957588a, stable, 05.12.14), our bam files that are uploaded(linked) to a data library, are no longer indexed. The metadata_xxx.dat is created, but it stays empty. The following error message appears in the log, although the state of the dataset is 'ok':
galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam' galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
All file permissions are correct (i.e. galaxy owns them). Furthermore, executing samtools index, just works on those files: samtools index /g/K/K2.bam /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
When uploading the file - "copy files into galaxy" - the samtools index just works.
==============
Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and samtools installed globally and with the bam file sorted, I get the following situation: When I try to upload this bam to a data library by linking the following error is shown on the dataset (note: here the dataset is set in error state, which does not happen on our server)
Uploaded by: scholtal@embl.de Date uploaded: Mon Dec 8 17:42:39 2014 (UTC) File size: 2.6 GB UUID: d23cf11a-0372-41cb-939a-7c8761d78b73 Data type: auto Build: ? Miscellaneous information: Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in _ Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 294, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
=============================== When uploading the bam without linking, I see the following processes: Upload->set meta->samtools index->'error state'
Miscellaneous information: uploaded bam file Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
=================================
Although the error messages are different, it might be related?
Cheers,
Jelle
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------------------------------
Message: 3 Date: Mon, 15 Dec 2014 17:16:41 +0000 From: "Wang, Yu" Yu.Wang@lrz.de To: John Chilton jmchilton@gmail.com Cc: "Wang, Yu" Yu.Wang@lrz.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: f4c6170a-5f28-4871-971b-2881fc739510@BADWLRZ-SW13MB1.ads.mwn.de Content-Type: text/plain; charset="utf-8"
Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found. I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@gmail.com> wrote:
Looks like this - https://github.com/clarete/curdling/issues/19
I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
Hope this helps,
-John
On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <Yu.Wang@lrz.demailto:Yu.Wang@lrz.de> wrote: Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error. Can anyone point what goes wrong here?
Error Running from numpy source directory. /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) error: must supply either home or prefix/exec-prefix -- not both
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
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There have been a ton of changes to the workflow API - I have been trying to preserve backward compatibility though - e.g. I have API tests in Galaxy for a bunch of legacy/deprecated features related to workflows now.
Do you have a stack trace on the Galaxy side for the "Uncaught exception in exposed API method"?
I will run through the blend4j test cases and see they turn up.
-John
On Thu, Dec 18, 2014 at 9:44 AM, Bruijn, Freek de f.debruijn@vumc.nl wrote:
I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
- the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
- the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
- even some of the blend4j unit tests are failing.
One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb9...
Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
Cheers, Freek
From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of galaxy-dev-request@lists.galaxyproject.org [galaxy-dev-request@lists.galaxyproject.org] Sent: Tuesday, December 16, 2014 18:00 To: galaxy-dev@lists.galaxyproject.org Subject: galaxy-dev Digest, Vol 102, Issue 17
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When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..."
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- Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
- Strip out everything else in the digest that is not part of the thread you are responding to.
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- This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not.
- Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
Today's Topics:
- Re: How galaxy workflow work ? (John Chilton)
- Re: Metadata error in uploading files to data libraries (John Chilton)
- Re: package_numpy_1_7 can't be installed (Wang, Yu)
- Re: "join" produces an import error (Wang, Yu)
- Re: package_numpy_1_7 can't be installed (Björn Grüning)
Message: 1 Date: Mon, 15 Dec 2014 14:24:13 -0500 From: John Chilton jmchilton@gmail.com To: Bongsoo Park bxp12@psu.edu Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How galaxy workflow work ? Message-ID: CANwbokcggD3W7Tkyd5fy-9d6qedLT+ta1gzzmkfE1Apa2R8w1A@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Somehow your user object is not being set. Are you sure you have initialized bioblend with the correct API key? Do other operations work with that key?
-John
On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park bxp12@psu.edu wrote:
Hi All,
I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks!
(GALAXY User Interface)
=======================================================
"xhr": {
"readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
method:", "err_code": 0}",
"responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r", "cache-control": "max-age=0,no-cache,no-store\r", "Server": "PasteWSGIServer/0.5 Python/2.7.8\r", "Connection": "close\r", "content-type": "application/json\r" }
=======================================================
I found the error message in the Galaxy instance shell interface.
=======================================================
galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator
rval = func( self, trans, *args, **kwargs)
File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index
and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
AttributeError: 'NoneType' object has no attribute 'id'
=======================================================
Best,
Bongsoo
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Message: 2 Date: Mon, 15 Dec 2014 14:31:20 -0500 From: John Chilton jmchilton@gmail.com To: Jelle Scholtalbers j.scholtalbers@gmail.com Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Metadata error in uploading files to data libraries Message-ID: CANwbokdzjumt4abseN3b6rxOkaXH+9fB23+_OhqmUtFqnxbxWw@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Hello,
Sorry we haven't made progress on this - and thanks for creating a Trello card (https://trello.com/c/tw75nq1U).
It looks like samtools is not on your path, can you use it from the command-line? If not you should probably install it - I would suggest install samtools 0.1.19 with homebrew (looks like you are a on Mac). If you can run samtools from the command-line - can you do a which `samtools` from your command-line and see where it is coming from and then add that directory explicitly to your Galaxy PATH - say at the top of run.sh in your Galaxy root (let me know if you need more details on that).
-John
On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers j.scholtalbers@gmail.com wrote:
Hi all,
after an update to the following changeset(14859:7ba05957588a, stable, 05.12.14), our bam files that are uploaded(linked) to a data library, are no longer indexed. The metadata_xxx.dat is created, but it stays empty. The following error message appears in the log, although the state of the dataset is 'ok':
galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam' galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
All file permissions are correct (i.e. galaxy owns them). Furthermore, executing samtools index, just works on those files: samtools index /g/K/K2.bam /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
When uploading the file - "copy files into galaxy" - the samtools index just works.
==============
Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and samtools installed globally and with the bam file sorted, I get the following situation: When I try to upload this bam to a data library by linking the following error is shown on the dataset (note: here the dataset is set in error state, which does not happen on our server)
Uploaded by: scholtal@embl.de Date uploaded: Mon Dec 8 17:42:39 2014 (UTC) File size: 2.6 GB UUID: d23cf11a-0372-41cb-939a-7c8761d78b73 Data type: auto Build: ? Miscellaneous information: Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in _ Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 294, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
=============================== When uploading the bam without linking, I see the following processes: Upload->set meta->samtools index->'error state'
Miscellaneous information: uploaded bam file Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
=================================
Although the error messages are different, it might be related?
Cheers,
Jelle
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Message: 3 Date: Mon, 15 Dec 2014 17:16:41 +0000 From: "Wang, Yu" Yu.Wang@lrz.de To: John Chilton jmchilton@gmail.com Cc: "Wang, Yu" Yu.Wang@lrz.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: f4c6170a-5f28-4871-971b-2881fc739510@BADWLRZ-SW13MB1.ads.mwn.de Content-Type: text/plain; charset="utf-8"
Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found. I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@gmail.com> wrote:
Looks like this - https://github.com/clarete/curdling/issues/19
I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
Hope this helps,
-John
On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <Yu.Wang@lrz.demailto:Yu.Wang@lrz.de> wrote: Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error. Can anyone point what goes wrong here?
Error Running from numpy source directory. /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) error: must supply either home or prefix/exec-prefix -- not both
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
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There was definitely a bug where I broke backward compatibility on workflows in central a couple nights ago - I have patched that and blend4j's test cases for running workflows now actually cause the workflows to run again.
There are still some problems with blend4j where it is very particular about what is in the response - these are blend4j specific issues that I will try to clear up - I have created a github issue here:
https://github.com/jmchilton/blend4j/issues/26
Sorry about the problems.
-John
On Thu, Dec 18, 2014 at 9:59 AM, John Chilton jmchilton@gmail.com wrote:
There have been a ton of changes to the workflow API - I have been trying to preserve backward compatibility though - e.g. I have API tests in Galaxy for a bunch of legacy/deprecated features related to workflows now.
Do you have a stack trace on the Galaxy side for the "Uncaught exception in exposed API method"?
I will run through the blend4j test cases and see they turn up.
-John
On Thu, Dec 18, 2014 at 9:44 AM, Bruijn, Freek de f.debruijn@vumc.nl wrote:
I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
- the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
- the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
- even some of the blend4j unit tests are failing.
One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb9...
Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
Cheers, Freek
From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of galaxy-dev-request@lists.galaxyproject.org [galaxy-dev-request@lists.galaxyproject.org] Sent: Tuesday, December 16, 2014 18:00 To: galaxy-dev@lists.galaxyproject.org Subject: galaxy-dev Digest, Vol 102, Issue 17
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Today's Topics:
- Re: How galaxy workflow work ? (John Chilton)
- Re: Metadata error in uploading files to data libraries (John Chilton)
- Re: package_numpy_1_7 can't be installed (Wang, Yu)
- Re: "join" produces an import error (Wang, Yu)
- Re: package_numpy_1_7 can't be installed (Björn Grüning)
Message: 1 Date: Mon, 15 Dec 2014 14:24:13 -0500 From: John Chilton jmchilton@gmail.com To: Bongsoo Park bxp12@psu.edu Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How galaxy workflow work ? Message-ID: CANwbokcggD3W7Tkyd5fy-9d6qedLT+ta1gzzmkfE1Apa2R8w1A@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Somehow your user object is not being set. Are you sure you have initialized bioblend with the correct API key? Do other operations work with that key?
-John
On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park bxp12@psu.edu wrote:
Hi All,
I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks!
(GALAXY User Interface)
=======================================================
"xhr": {
"readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
method:", "err_code": 0}",
"responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r", "cache-control": "max-age=0,no-cache,no-store\r", "Server": "PasteWSGIServer/0.5 Python/2.7.8\r", "Connection": "close\r", "content-type": "application/json\r" }
=======================================================
I found the error message in the Galaxy instance shell interface.
=======================================================
galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator
rval = func( self, trans, *args, **kwargs)
File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index
and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
AttributeError: 'NoneType' object has no attribute 'id'
=======================================================
Best,
Bongsoo
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Message: 2 Date: Mon, 15 Dec 2014 14:31:20 -0500 From: John Chilton jmchilton@gmail.com To: Jelle Scholtalbers j.scholtalbers@gmail.com Cc: galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Metadata error in uploading files to data libraries Message-ID: CANwbokdzjumt4abseN3b6rxOkaXH+9fB23+_OhqmUtFqnxbxWw@mail.gmail.com Content-Type: text/plain; charset=UTF-8
Hello,
Sorry we haven't made progress on this - and thanks for creating a Trello card (https://trello.com/c/tw75nq1U).
It looks like samtools is not on your path, can you use it from the command-line? If not you should probably install it - I would suggest install samtools 0.1.19 with homebrew (looks like you are a on Mac). If you can run samtools from the command-line - can you do a which `samtools` from your command-line and see where it is coming from and then add that directory explicitly to your Galaxy PATH - say at the top of run.sh in your Galaxy root (let me know if you need more details on that).
-John
On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers j.scholtalbers@gmail.com wrote:
Hi all,
after an update to the following changeset(14859:7ba05957588a, stable, 05.12.14), our bam files that are uploaded(linked) to a data library, are no longer indexed. The metadata_xxx.dat is created, but it stays empty. The following error message appears in the log, although the state of the dataset is 'ok':
galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam' galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam, will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
All file permissions are correct (i.e. galaxy owns them). Furthermore, executing samtools index, just works on those files: samtools index /g/K/K2.bam /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
When uploading the file - "copy files into galaxy" - the samtools index just works.
==============
Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and samtools installed globally and with the bam file sorted, I get the following situation: When I try to upload this bam to a data library by linking the following error is shown on the dataset (note: here the dataset is set in error state, which does not happen on our server)
Uploaded by: scholtal@embl.de Date uploaded: Mon Dec 8 17:42:39 2014 (UTC) File size: 2.6 GB UUID: d23cf11a-0372-41cb-939a-7c8761d78b73 Data type: auto Build: ? Miscellaneous information: Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in _ Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 294, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
=============================== When uploading the bam without linking, I see the following processes: Upload->set meta->samtools index->'error state'
Miscellaneous information: uploaded bam file Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p Job Standard Error
Traceback (most recent call last): File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 407, in __main__() File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 396, in __main__ add_file( dataset, registry, json_file, output_path ) File "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py", line 324, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 147, in dataset_content_needs_grooming version = self._get_samtools_version() File "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py", line 129, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
error Database/Build: ? Number of data lines: None Disk file: /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
=================================
Although the error messages are different, it might be related?
Cheers,
Jelle
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Message: 3 Date: Mon, 15 Dec 2014 17:16:41 +0000 From: "Wang, Yu" Yu.Wang@lrz.de To: John Chilton jmchilton@gmail.com Cc: "Wang, Yu" Yu.Wang@lrz.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed Message-ID: f4c6170a-5f28-4871-971b-2881fc739510@BADWLRZ-SW13MB1.ads.mwn.de Content-Type: text/plain; charset="utf-8"
Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found. I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
On 15 Dec 2014, at 16:12, John Chilton <jmchilton@gmail.commailto:jmchilton@gmail.com> wrote:
Looks like this - https://github.com/clarete/curdling/issues/19
I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
Hope this helps,
-John
On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <Yu.Wang@lrz.demailto:Yu.Wang@lrz.de> wrote: Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error. Can anyone point what goes wrong here?
Error Running from numpy source directory. /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) /bin/sh: svnversion: command not found /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) error: must supply either home or prefix/exec-prefix -- not both
Cheers, Yu
di29her wang@lrz.demailto:wang@lrz.de
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