May 2011 - galaxy-dev - lists.galaxyproject.org

Error when adding datasets
by Louise-Amélie Schmitt 03 Jun '11

03 Jun '11

Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html Here is the error message I get when clicking the "Add datasets" button in a library, in the admin's "Manage data libraries" panel: UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped URL: http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db41… File '/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 109 in __call__ return self.app( environ, start_response ) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/g/funcgen/galaxy/lib/galaxy/web/controllers/library_common.py', line 907 in upload_library_dataset trans.sa_session.refresh( history ) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py', line 127 in do return getattr(self.registry(), name)(*args, **kwargs) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py', line 925 in refresh raise exc.UnmappedInstanceError(instance) UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped Now when does it occur: I have two databases. One test database I created a month ago which works fine, even now. The other one I created recently which is supposed to be the final database. But the latter keeps triggering the above message, even when I drop it and create it all over again. I even tried to create a third one, all clean and new but the problem remains. I tried to trash all the eggs so Galaxy gets fresh new eggs, with no effect at all. The error's still there. If you have any clue, I'll be forever grateful. Cheers, L-A

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how can i get all the output file names in local.py file
by shashi shekhar 03 Jun '11

03 Jun '11

Hi All, I am using standalone system for galaxy and am doing some modification in galaxy .i need the all output file names in local.py .How can i get all the output file names in local.py file. Regards shashi shekhar

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Appropriate place to ask questions about your NGLIMS for Galaxy
by scott.coutts＠monash.edu 03 Jun '11

03 Jun '11

Hi, I'm a newbie when it comes to this kind of thing, so I was wondering whether you can tell me the most appropriate place to ask questions about making some modifications to your nglims extension for galaxy? Should they be posted to the normal galaxy development list? Should I ask you directly? Cheers, Scott.

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library_upload_from_import_dir
by George, David 03 Jun '11

03 Jun '11

Hi, I'm a Galaxy and Python newbie and I'm working on project that desires to upload files from a directory to the Galaxy server. We'd like to physically copy the files rather than maintain references to them. I'm starting by following the examples in scripts/api/README. All the display and library_create_library examples work. However, the library_upload_from_import_dir fails. In my universe...ini, library_import_dir is defined to be /home/dgeorge/galaxy/import and there is a bed directory under that with a short file, bed1.bed in the correct format. I'm not sure what to provide for the last parameter, the dbkey - maybe that's my problem? I ran: ./library_upload_from_import_dir.py 59d2fd4e020e178f8c48e61150e513c2 http://localhost:8080/api/libraries/f597429621d6eb2b/contents c6ca0ddb55be603a10e891fff2e902c3 bed bed hg19 And I get the error: Exception happened during processing of request from ('127.0.0.1', 38857) Traceback (most recent call last): File "/home/dgeorge/galaxy/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/http server.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ self.finish() File "/usr/lib/python2.6/SocketServer.py", line 661, in finish self.wfile.flush() File "/usr/lib/python2.6/socket.py", line 297, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe Any ideas or suggestions? Thanks! David George Staff Software Engineer Illumina, Inc. 25861 Industrial Blvd. Hayward, CA 94545 Tel: 510-670-9326 Fax: 510-670-9302 Email: dgeorge(a)illumina.com <mailto:dgeorge@illumina.com>

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Uploading Zip Files
by SHAUN WEBB 03 Jun '11

03 Jun '11

Hi, I have a tool that takes a zipped archive as input, finds all the sequence files (~90 of them), separates them by barcode, does a little extra processing and outputs a single fasta file. I would like this to run on Galaxy in a workflow with a few other tools. I know there have been discussions about uploading zip files to Galaxy before and that currently Galaxy automatically unzips a file and uploads the first file in the archive. Are there any plans to change this behaviour and be able to upload a zipped file without decompressing. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Problem with Torque/Maui
by Marco Moretto 02 Jun '11

02 Jun '11

Hi all, first of all, thanks to the Galaxy Team for this really useful software. Actually I don't really know if my problem is related with Galaxy or with Torque/Maui but I didn't find any solution looking in both Torque and Maui user lists, so I hope that some of you with more experience could give me some good advices. I'm trying to set up Galaxy in a small local virtual environment in order to test it. I started with 2 virtual ubuntu servers called galaxy1 and galaxy2. On galaxy1 I succesfully installed Galaxy, Apache, Torque and Maui. I'm using Postgres ad DBMS. It is installed on another "real" DB server. The virtual server galaxy2 is used as node. Galaxy is working like a charm locally but when I try to use Torque problems arise. Torque alone works correctly. That means that I can submit a job with qsub and everything works. The 2 virtual server (galaxy1 and galaxy2) share a directory (through NFS) in which I installed Galaxy following the "unified method" from the documentation. Now, as I said, Galaxy alone works, Torque/Maui alone works. When I put the two together nothing works. As a test I upload (using local runner) a gff file. Then I try to make a filter to the gff using "Filter and sort -> Extract features". When I run this tool the corresponding job on the Torque queue runs forever in Hold state. I report some output from diagnose programs: The diagnose -j reports the following: Name State Par Proc QOS WCLimit R Min User Group Account QueuedTime Network Opsys Arch Mem Disk Procs Class Features 29 Hold DEF 1 DEF 1:00:00 0 1 galaxy galaxy - 00:02:36 [NONE] [NONE] [NONE] >=0 >=0 NC0 [batch:1] [NONE] While the showq command reports ACTIVE JOBS-------------------- JOBNAME USERNAME STATE PROC REMAINING STARTTIME 0 Active Jobs 0 of 1 Processors Active (0.00%) IDLE JOBS---------------------- JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME 0 Idle Jobs BLOCKED JOBS---------------- JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME 29 galaxy Hold 1 1:00:00 Wed May 4 03:56:40 The checkjob reports: checking job 29 State: Hold Creds: user:galaxy group:galaxy class:batch qos:DEFAULT WallTime: 00:00:00 of 1:00:00 SubmitTime: Wed May 4 03:56:40 (Time Queued Total: 00:03:07 Eligible: 00:00:01) The qstat -f reports Job Id: 33.galaxy1.research.intra.ismaa.it Job_Name = 27_Extract_features1_marco.moretto(a)iasma.it Job_Owner = galaxy(a)galaxy1.research.intra.ismaa.it job_state = W queue = batch server = galaxy1.research.intra.ismaa.it ctime = Wed May 4 04:56:36 2011 Error_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.e exec_host = galaxy2/0 exec_port = 15003 Execution_Time = Wed May 4 05:26:41 2011 mtime = Wed May 4 04:56:37 2011 Output_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27. o qtime = Wed May 4 04:56:36 2011 Resource_List.neednodes = 1 Resource_List.nodect = 1 Resource_List.nodes = 1 Resource_List.walltime = 01:00:00 stagein = /mnt/equallogic1/galaxy/tmp/dataset_18.dat@galaxy1 :/mnt/equallog ic1/galaxy/galaxy-dist/database/files/000/dataset_18.dat, /mnt/equallogic1/galaxy/tmp/dataset_30.dat@galaxy1 :/mnt/equallogic1/g alaxy/galaxy-dist/database/files/000/dataset_30.dat stageout = /mnt/equallogic1/galaxy/galaxy-dist/database/files/000/dataset_ 30.dat@galaxy1 :/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/ dataset_30.dat substate = 37 Variable_List = PBS_O_QUEUE=batch, PBS_O_HOST=galaxy1.research.intra.ismaa.it euser = galaxy egroup = galaxy hashname = 33.galaxy1.research.intra.ismaa.it queue_rank = 33 queue_type = E StartDate: -00:03:06 Wed May 4 03:56:41 Total Tasks: 1 Req[0] TaskCount: 1 Partition: DEFAULT Network: [NONE] Memory >= 0 Disk >= 0 Swap >= 0 Opsys: [NONE] Arch: [NONE] Features: [NONE] IWD: [NONE] Executable: [NONE] Bypass: 0 StartCount: 1 PartitionMask: [ALL] PE: 1.00 StartPriority: 1 cannot select job 29 for partition DEFAULT (non-idle state 'Hold') and finally the tracejob reports /var/spool/torque/server_priv/accounting/20110504: Permission denied /var/spool/torque/mom_logs/20110504: No such file or directory /var/spool/torque/sched_logs/20110504: No such file or directory Job: 33.galaxy1.research.intra.ismaa.it 05/04/2011 04:56:36 S enqueuing into batch, state 1 hop 1 05/04/2011 04:56:36 S Job Queued at request of galaxy(a)galaxy1.research.intra.ismaa.it, owner = galaxy(a)galaxy1.research.intra.ismaa.it, job name = 27_Extract_features1_marco.moretto(a)iasma.it, queue = batch 05/04/2011 04:56:37 S Job Run at request of galaxy(a)galaxy1.research.intra.ismaa.it 05/04/2011 04:56:41 S Email 's' to galaxy(a)galaxy1.research.intra.ismaa.it failed: Child process 'sendmail -f adm galaxy(a)galaxy1.research.intra.ismaa.it' returned 127 (errno 10:No child processes) The only clear thing to me is that after the submission the scheduler puts it in a Hold state. But I cannot understand why. I also try to run the Galaxy-generated sh script with qsub. Following the Galaxy log: galaxy.jobs.runners.pbs DEBUG 2011-05-04 04:56:36,748 (27) submitting file /mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.sh I copied and run the 27.sh script with the command: qsub 27.sh And the job runs correctly. So what it is not clear to me is if the problem is related to Torque/Maui or is related to the way in which the job is submitted from Galaxy. Sorry for the very long e-mail and thank you very much for any help. --- Marco

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Migration error: fields in MySQL
by John Eppley 02 Jun '11

02 Jun '11

I had an error upgrading my galaxy instance. I got the following exception while migrating the db (during step 64->65): sqlalchemy.exc.ProgrammingError: (ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'fields FROM form_definition' at line 1") u'SELECT id, fields FROM form_definition' [] It seems my version (4.1.22-log) of MySQL did not like 'fields' as a column name. If I alias the formdefinition as f and us f.fields, the error goes away. I also had to modify migration 76 for the same reason. Here is my diff of the migrations dir: diff -r 50e249442c5a lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py --- a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py Thu Apr 07 08:39:07 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py Fri Apr 15 11:09:26 2011 -0400 @@ -39,7 +39,7 @@ return '' # Go through the entire table and add a 'name' attribute for each field # in the list of fields for each form definition - cmd = "SELECT id, fields FROM form_definition" + cmd = "SELECT f.id, f.fields FROM form_definition f" result = db_session.execute( cmd ) for row in result: form_definition_id = row[0] @@ -53,7 +53,7 @@ field[ 'helptext' ] = field[ 'helptext' ].replace("'", "''").replace('"', "") field[ 'label' ] = field[ 'label' ].replace("'", "''") fields_json = to_json_string( fields_list ) - cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( fields_json, form_definition_id ) + cmd = "UPDATE form_definition f SET f.fields='%s' WHERE f.id=%i" %( fields_json, form_definition_id ) db_session.execute( cmd ) # replace the values list in the content field of the form_values table with a name:value dict cmd = "SELECT form_values.id, form_values.content, form_definition.fields" \ @@ -112,7 +112,7 @@ cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_list ), form_values_id ) db_session.execute( cmd ) # remove name attribute from the field column of the form_definition table - cmd = "SELECT id, fields FROM form_definition" + cmd = "SELECT f.id, f.fields FROM form_definition f" result = db_session.execute( cmd ) for row in result: form_definition_id = row[0] @@ -124,5 +124,5 @@ for index, field in enumerate( fields_list ): if field.has_key( 'name' ): del field[ 'name' ] - cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( to_json_string( fields_list ), form_definition_id ) + cmd = "UPDATE form_definition f SET f.fields='%s' WHERE id=%i" %( to_json_string( fields_list ), form_definition_id ) db_session.execute( cmd ) diff -r 50e249442c5a lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Thu Apr 07 08:39:07 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Fri Apr 15 11:09:26 2011 -0400 @@ -32,7 +32,7 @@ def upgrade(): print __doc__ metadata.reflect() - cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields " \ + cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fdfields " \ + " FROM form_definition, form_values " \ + " WHERE form_values.form_definition_id=form_definition.id " \ + " ORDER BY form_values.id" @@ -46,7 +46,7 @@ except Exception, e: corrupted_rows = corrupted_rows + 1 # content field is corrupted - fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) ) + fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) try: #Encoding errors? Just to be safe. -j

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Support for subdirs in dataset extra_files_path
by Jim Johnson 02 Jun '11

02 Jun '11

Request is issue#494 https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-e… I'm finding that some qiime metagenomics applications build HTML results with an inherent directory structure. For some other applications, e.g. FastQC, I've been able to flatten the hierarchy and edit the html, but that appears problematic for qiime. Galaxy hasn't supported a dataset extra_files_path hierarchy, though the developers don't seem opposed to the idea: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003605.html I added a route in lib/galaxy/web/buildapp.py and modified the dataset download code to traverse a hierarchy in lib/galaxy/web/controllers/dataset.py I don't think these add any security vulnerabilities, (I tried the obvious ../../ ). $ hg diff lib/galaxy/web/buildapp.py diff -r 6ae06d89fec7 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Wed Mar 16 09:01:57 2011 -0400 +++ b/lib/galaxy/web/buildapp.py Wed Mar 16 10:24:13 2011 -0500 @@ -94,6 +94,8 @@ webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) + # allow for subdirectories in extra_files_path + webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', controller='dataset', action='display_application', dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug', controller='dataset', action='display_by_username_and_slug' ) $ $ hg diff lib/galaxy/web/controllers/dataset.py diff -r 6ae06d89fec7 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Mar 16 09:01:57 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Wed Mar 16 10:24:29 2011 -0500 @@ -266,17 +266,18 @@ log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) msg = "Unable to create archive for download, please report this error" messagetype = 'error' - flist = glob.glob(os.path.join(efp,'*.*')) # glob returns full paths - for fpath in flist: - efp,fname = os.path.split(fpath) - try: - archive.add( fpath,fname ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % fname) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue if not error: if params.do_action == 'zip': archive.close()

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Sharing tool definitions between XML files
by Peter 02 Jun '11

02 Jun '11

Hi all, I'm wondering if there is any established way to share parameter definitions between tool wrapper XML files? For example, I am currently working on NCBI BLAST+ wrappers, and these tools have a lot in common. For example, the output format option will be a select parameter, and it will be the same for blastn, blastp, tblastn, etc. I can just cut and paste the definition but this seems inelegant and will be a long term maintenance burden if it ever needs updating (lots of places would need to be updated the same way). I'd like to have a shared XML snippet defining this parameter which I could then reference/include from each tool wrapper than needs it. I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible? Peter

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user and dataset management with LDAP: some questions
by Louise-Amélie Schmitt 02 Jun '11

02 Jun '11

Hello everyone I have a couple of questions regarding user and dataset management. 1) We use LDAP for user registration and logging, would it be possible to retrieve automatically the LDAP users' groups and create the groups in Galaxy accordigly? (and of course put the user in their respective groups) 2) Is it possible, still using LDAP, to delete a user and all his datasets? 3) Is it possible to automatically suppress, for instance, any dataset that was added more than a couple of months ago? 4) Is there a not-so-intrusive way to add a column in the user list showing the disk space they use respectively? 5) I tried to see how the API works but i have to admit I didn't get a thing. I read the scripts/api/README file and there I saw one needs to access the user preferences to generate an API key. What is its purpose? Is there a way to do it when you use LDAP (therefore no access to that key generator) ? Sorry, this is a bit random but I'm kinda drowning here, since I'm not used to manipulating apps this huge. Thanks for your help and patience. Cheers, L-A

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