galaxy-dev July 2011

galaxy-dev@lists.galaxyproject.org

79 participants
166 discussions

Problems with Galaxy on a mapped drive
by Peter Cock 19 Aug '11

19 Aug '11

Hi all, In my recent email I mentioned problems with our setup and mapped drives. I am running a test Galaxy on a server under a CIFS mapped drive. If I map the drive with noperms then things seem to work with submitting jobs to the cluster etc, but that doesn't seem secure at all. Mounting with strict permissions seems to cause various network latency related problems in Galaxy though. Specifically during loading the converters and history export tool, Galaxy creates a temporary XML file which it then tries to parse. I was able to resolve this by switching from tempfile.TemporaryFile to tempfile.mkstemp and adding a 1s sleep, but it isn't very elegant. Couldn't you use a StringIO handle instead? Later during start up there were two errors with a similar issue - Galaxy creates a temp folder then immediately tries to write a tar ball or zip file to it. Again, adding a 1 second sleep after creating the directory before using it seems to work. See lib/galaxy/web/controllers/dataset.py After that Galaxy started, but still gives problems - like the issue reported here which Galaxy handled badly (see patch): http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-July/006213.html Here again, inserting a one second sleep between writing the cluster script file and setting its permissions made it work. If those are the only issues, that can be dealt with. But are there likely to be lots more similar problems of this nature later on? That is my worry. How are most people setting up mapped drives for Galaxy with a cluster? Thanks, Peter

3 3

job runner issue
by shashi shekhar 19 Aug '11

19 Aug '11

Hi In my galaxy instance, whatever jobs i am submitting it goes into queued state. If I restart the server then the previous submitted jobs state changes to running. but the newly submitted jobs again goes to queued state. I am at a loss to understand this behaviour of galaxy and unable to debug it. The job submission uses a customized runner. How is it actually goes into the queued state automatically when all the workers thread are free? Does galaxy_session table is_valid attribute makes jobs state true? Or what all places in tables the queued states are getting stored. I can only see that the jobs table state attribute only stores the state. The server logs points error here: galaxy.jobs ERROR 2011-07-29 11:01:28,098 failure running job 2243 Traceback (most recent call last): File "/home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py", line 202, in __monitor_step self.dispatcher.put( JobWrapper( job, self ) ) File "/home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py", line 856, in put self.job_runners[runner_name].put( job_wrapper ) File "/home/gwadmin/galaxy-central/lib/galaxy/jobs/runners/gw.py", line 375, in put job_wrapper.change_state( model.Job.states.QUEUED ) File "/home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py", line 437, in change_state self.sa_session.flush() Regards Karuna

2 1

Could anyone tell me why the result file in directary /galaxy-dist /database/files/000 do not return to the web page
by liyanhui607 19 Aug '11

19 Aug '11

Dear Sir, We have a program writen in perl. It can run nomally in linux environment with a file saved as result. After added it to galaxy system, we found that it can produce the right result file in directary "/var/we/galaxy-dist/database/files/000" , but the result file did not return to the web page where the state is always "Job is currently running". Could anyone tell me what is wrong ? why it does not work? The bagging-SVM.xml and the bagging-SVM.pl are attached. Thank you very much! Best Wishes! Yan-Hui Li

2 1

Galaxy: self-cleaning on file_path
by Sanka, Ravi 19 Aug '11

19 Aug '11

Hello, We have recently put a local installation of Galaxy on our network and connected it to a MYSQL database. In order to have more space available for uploaded and created files, we also changed the values of file_path and new_file_path in the config file. The file_path field was changed to a larger, communal location. The new_file_path was changed to a directory called "tmp" in that same communal location. This location, however, undergoes self-cleaning; deleting any files that reach 7 days old (and any directories that have no files less than 7 days old). This would include any datasets uploaded or created by Galaxy. Can the Galaxy framework and schema handle this occurrence? Or will it cause errors to occur? ----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -----------------------------------------------

2 3

database problem
by shashi shekhar 19 Aug '11

19 Aug '11

Hi ALL, I want to delete some data from history_dataset_association. Will it effect any other tables.and I want to delete records for last 3 days by sqlite query manually.How may tables will be effected by this and provide me tables name .How can i delete the records. Regards shashi shekhar

2 1

Cluster setup - shared temporary directory
by Peter Cock 19 Aug '11

19 Aug '11

Hi all, I'm reading http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster Could someone expand a little on this section please: > Create a shared temporary directory > > Some tools make use of temporary files created on the server, > but accessed on the nodes. For this, you'll need to make a > directory (galaxy_dist/database/tmp by default) ... I presume this is talking about the universe_wsgi.ini setting new_file_path = database/tmp (if so, could that be explicit)? I would like to know more about this from the tool author point of view. Could you at least give one example of a tool that uses this temporary folder? As a tool author I am unclear what the purpose is (and it would be a shock if I accidentally use this mapped folder instead of the local temp drive of a node). Thanks, Peter

4 6

Re: [galaxy-dev] galaxy-dev Digest, Vol 61, Issue 10 - Handling runner-specific (SLURM) DRMAA settings (Roman Valls)
by Mariusz Mamoński 18 Aug '11

18 Aug '11

> The general config file allows us to set a fixed project: > > default_cluster_job_runner = drmaa://-A a2010002 -p core > > And even set per-tool job settings. But we would like each user to have > the ability to change those settings. > > > What is the least intrusive way to set per-user native (site-specific) > job manager settings ? you may try to use an user's local DRMAA configuration file: ~/.slurm_drmaa.conf ". If multiple configuration sources are present then all configurations are merged with values from user-defined files taking precedence (in following order: $SLURM_DRMAA_CONF, ~/.slurm_drmaa.conf, /etc/slurm_drmaa.conf)" there you can put any user's specific settings, e.g.: job_categories: { default: "-A a2010002 -p core", } Cheers, -- Mariusz

3 4

Database scheme migration.
by michael burrell (TSL) 17 Aug '11

17 Aug '11

Good afternoon I am having some trouble updating our local galaxy, in summary it seems to fail. I have included the errors below and would really appreciate any assistance that could be offered. galaxy@jic55119:~/software/galaxy-ceneral$ sh manage_db.sh upgrade 57 -> 58... Migration script to create table for exporting histories to archives. (ProgrammingError) there is no unique constraint matching given keys for referenced table "job" '\nCREATE TABLE job_export_history_archive (\n\tid SERIAL NOT NULL, \n\tjob_id INTEGER, \n\thistory_id INTEGER, \n\tdataset_id INTEGER, \n\tcompressed BOOLEAN, \n\thistory_attrs_filename TEXT, \n\tdatasets_attrs_filename TEXT, \n\tjobs_attrs_filename TEXT, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(job_id) REFERENCES job (id), \n\t FOREIGN KEY(history_id) REFERENCES history (id), \n\t FOREIGN KEY(dataset_id) REFERENCES dataset (id)\n)\n\n' {} done 58 -> 59... ….INTERMEDIATE STEPS REMOVED NO ERRORS REPORTED…… 78 -> 79... Migration script to add the job_to_input_library_dataset table. Creating job_to_input_library_dataset table failed: (ProgrammingError) there is no unique constraint matching given keys for referenced table "job" '\nCREATE TABLE job_to_input_library_dataset (\n\tid SERIAL NOT NULL, \n\tjob_id INTEGER, \n\tldda_id INTEGER, \n\tname VARCHAR(255), \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(job_id) REFERENCES job (id), \n\t FOREIGN KEY(ldda_id) REFERENCES library_dataset_dataset_association (id)\n)\n\n' {} Done Further information galaxy@jic55119:~/software/galaxy-ceneral$ hg tip changeset: 5793:f2638528e904 tag: tip user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jul 14 22:54:43 2011 +0200 summary: Fix bug in trackster filtering of GFF datasets. galaxy@jic55119:~/software/galaxy-ceneral$ python -V Python 2.6.6 galaxy@jic55119:~/software/galaxy-ceneral$ psql --version psql (PostgreSQL) 8.4.8

2 1

Python bug?
by David Hoover 17 Aug '11

17 Aug '11

We've run into an error with the SAM to BAM converter. An error occurred running this job: Samtools Version: 0.1.15 (r949:203) Error extracting alignments from (/gs1/users/galaxy/pro/database/files/000/dataset_285.dat), requested number of bytes is more than a Python string can hold We are running 32-bit Python. Would this be the problem, or do we need a newer version of samtools? David Hoover Helix Systems Staff http://helix.nih.gov

2 1

Error after migrating to latest changeset
by michael burrell (TSL) 16 Aug '11

16 Aug '11

Good Morning, I am getting a big problem with our production server when I upgrade to the latest change set (it was quite out of date). I have attached quite a long paster output to try and show whats going on, Our galaxy instance no longer seems to run jobs at all, they are not allocated a job runner and the following is given in the paster log I look forwards to your assistance. Thanks Michael. ====== galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: INDEXER_Interval_0 galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in new state, adding to the jobs queue galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in new state, adding to the jobs queue galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,872 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,875 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling 'tracks' controller, class: TracksController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,022 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,107 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,110 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,112 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,115 Enabling 'request_type' controller, class: RequestType galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,146 Enabling 'httpexceptions' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,148 Enabling 'recursive' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,169 Enabling 'error' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,174 Enabling 'x-forwarded-host' middleware Starting server in PID 3738. serving on http://127.0.0.1:8080 sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,942 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,942 failure running job 4400 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4400} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,978 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,979 failure running job 4401 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4401} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,999 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:00,999 failure running job 4403 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4403} sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:01,027 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:01,028 failure running job 4404 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4404} 149.155.218.28 - - [12/Jul/2011:11:47:31 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.116 - - [12/Jul/2011:11:47:33 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /root/tool_menu HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:35 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.116 - - [12/Jul/2011:11:47:37 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:36 +0100] "GET /tool_runner/rerun?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:38 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:39 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1" 149.155.221.194 - - [12/Jul/2011:11:47:39 +0100] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/rerun?id=6014" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:40,371 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block galaxy.jobs ERROR 2011-07-12 11:47:40,372 failure running job 4405 Traceback (most recent call last): File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run for dataset_assoc in job.input_datasets + job.input_library_datasets: File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__ return self.impl.get(instance_state(instance), instance_dict(instance)) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get value = callable_() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__ result = q.all() File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) relation "job_to_input_library_dataset" does not exist 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4405} 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /user/get_most_recently_used_tool_async HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.221.116 - - [12/Jul/2011:11:47:41 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19" 149.155.221.194 - - [12/Jul/2011:11:47:42 +0100] "GET /root/delete_async?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0" 149.155.218.28 - - [12/Jul/2011:11:47:43 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"

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galaxy-dev July 2011