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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 17 Jun '13

17 Jun '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0705fc913ef5/ Changeset: 0705fc913ef5 Branch: provenance User: kellrott Date: 2013-05-27 22:03:58 Summary: Starting the provenance API. Provides information about the source of datasets. Affected #: 2 files diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 0705fc913ef53e19f41ca6b0b8351f1335bcc597 lib/galaxy/webapps/galaxy/api/provenance.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -0,0 +1,92 @@ +""" +API operations provenance +""" +import logging +from galaxy import web +from galaxy.web.base.controller import BaseAPIController +from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest + +log = logging.getLogger( __name__ ) + + +class BaseProvenanceController( BaseAPIController ): + """ + """ + @web.expose_api + def index( self, trans, **kwd ): + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id] ) + return value + + @web.expose_api + def show( self, trans, elem_name, **kwd ): + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id] ) + return value + + @web.expose_api + def create( self, trans, tag_name, payload={}, **kwd ): + raise HTTPNotImplemented() + + @web.expose_api + def delete( self, trans, tag_name, **kwd ): + raise HTTPBadRequest("Cannot Delete Provenance") + + def _get_provenance(self, trans, item_class_name, item_id, follow=True): + out = [] + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + out.append( + { + "dataset" : { + "id" : trans.security.encode_id(provenance_item.id), + "uuid" : provenance_item.dataset.uuid + }, + "tool_id" : provenance_item.creating_job.tool_id, + "parameters" : self._get_job_record(trans, provenance_item.creating_job) + } + ) + if follow: + depends = self._get_dataset_depends(provenance_item) + recorded = {} + for rec in depends: + if rec.id not in recorded: + recorded[rec.id] = True + out.append( + { + "dataset" : { + "id" : trans.security.encode_id(rec.id), + "uuid" : rec.dataset.uuid + }, + "tool_id" : rec.creating_job.tool_id, + "parameters" : self._get_job_record(trans, rec.creating_job) + } + ) + return out + + def _get_dataset_depends(self, item): + out = [] + for d in item.creating_job.input_datasets: + out.append(d.dataset) + for c in self._get_dataset_depends(d.dataset): + out.append(c) + return out + + def _get_job_record(self, trans, job): + out = {} + for p in job.parameters: + out[p.name] = p.value + for in_d in job.input_datasets: + out[in_d.name] = { "dataset_id" : trans.security.encode_id(in_d.dataset.id), "uuid" : in_d.dataset.dataset.uuid } + return out + + +class HDAProvenanceController( BaseProvenanceController ): + controller_name = "history_content_provenance" + provenance_item_class = "HistoryDatasetAssociation" + provenance_item_id = "history_content_id" + + +class LDDAProvenanceController( BaseProvenanceController ): + controller_name = "ldda_provenance" + provenance_item_class = "LibraryDatasetDatasetAssociation" + provenance_item_id = "library_content_id" + + diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 0705fc913ef53e19f41ca6b0b8351f1335bcc597 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -128,6 +128,10 @@ name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + _add_item_provenance_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -234,6 +238,12 @@ name = "%sannotation" % name_prefix webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) +def _add_item_provenance_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sprovenance" % name_prefix + name = "%sprovenance" % name_prefix + webapp.mapper.resource(name, "provenance", path_prefix=path_prefix, controller=controller) + + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful https://bitbucket.org/galaxy/galaxy-central/commits/cc89e2320856/ Changeset: cc89e2320856 Branch: provenance User: kellrott Date: 2013-05-28 09:05:35 Summary: Adding source following in provenance tracing Affected #: 1 file diff -r 0705fc913ef53e19f41ca6b0b8351f1335bcc597 -r cc89e2320856b256e224fd08b38b43782d0659d6 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -14,12 +14,14 @@ """ @web.expose_api def index( self, trans, **kwd ): - value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id] ) + follow = kwd.get('follow', False) + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id], follow ) return value @web.expose_api def show( self, trans, elem_name, **kwd ): - value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id] ) + follow = kwd.get('follow', False) + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id], follow ) return value @web.expose_api @@ -31,50 +33,35 @@ raise HTTPBadRequest("Cannot Delete Provenance") def _get_provenance(self, trans, item_class_name, item_id, follow=True): - out = [] provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) - out.append( - { - "dataset" : { - "id" : trans.security.encode_id(provenance_item.id), - "uuid" : provenance_item.dataset.uuid - }, - "tool_id" : provenance_item.creating_job.tool_id, - "parameters" : self._get_job_record(trans, provenance_item.creating_job) - } - ) - if follow: - depends = self._get_dataset_depends(provenance_item) - recorded = {} - for rec in depends: - if rec.id not in recorded: - recorded[rec.id] = True - out.append( - { - "dataset" : { - "id" : trans.security.encode_id(rec.id), - "uuid" : rec.dataset.uuid - }, - "tool_id" : rec.creating_job.tool_id, - "parameters" : self._get_job_record(trans, rec.creating_job) - } - ) + out = self._get_record(trans, provenance_item, follow) return out - def _get_dataset_depends(self, item): - out = [] - for d in item.creating_job.input_datasets: - out.append(d.dataset) - for c in self._get_dataset_depends(d.dataset): - out.append(c) - return out + def _get_record(self, trans, item, follow): + if item is not None: + if follow: + if item.copied_from_library_dataset_dataset_association: + item = item.copied_from_library_dataset_dataset_association + return { + "id" : trans.security.encode_id(item.id), + "uuid" : item.dataset.uuid, + "tool_id" : item.creating_job.tool_id, + "parameters" : self._get_job_record(trans, item.creating_job, follow) + } + else: + return { + "id" : trans.security.encode_id(item.id), + "uuid" : item.dataset.uuid + } + return None - def _get_job_record(self, trans, job): + def _get_job_record(self, trans, job, follow): out = {} for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: - out[in_d.name] = { "dataset_id" : trans.security.encode_id(in_d.dataset.id), "uuid" : in_d.dataset.dataset.uuid } + if follow: + out[in_d.name] = self._get_record(trans, in_d.dataset, follow) return out https://bitbucket.org/galaxy/galaxy-central/commits/fb220d538abb/ Changeset: fb220d538abb Branch: provenance User: Kyle Ellrott Date: 2013-05-28 19:22:01 Summary: Fixing provenance output Affected #: 1 file diff -r cc89e2320856b256e224fd08b38b43782d0659d6 -r fb220d538abb5d3e34e36149779758b0384bfc33 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -39,20 +39,14 @@ def _get_record(self, trans, item, follow): if item is not None: - if follow: - if item.copied_from_library_dataset_dataset_association: - item = item.copied_from_library_dataset_dataset_association - return { - "id" : trans.security.encode_id(item.id), - "uuid" : item.dataset.uuid, - "tool_id" : item.creating_job.tool_id, - "parameters" : self._get_job_record(trans, item.creating_job, follow) - } - else: - return { - "id" : trans.security.encode_id(item.id), - "uuid" : item.dataset.uuid - } + if item.copied_from_library_dataset_dataset_association: + item = item.copied_from_library_dataset_dataset_association + return { + "id" : trans.security.encode_id(item.id), + "uuid" : item.dataset.uuid, + "tool_id" : item.creating_job.tool_id, + "parameters" : self._get_job_record(trans, item.creating_job, follow) + } return None def _get_job_record(self, trans, job, follow): @@ -62,6 +56,11 @@ for in_d in job.input_datasets: if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) + else: + out[in_d.name] = { + "id" : trans.security.encode_id(in_d.dataset.id), + "uuid" : in_d.dataset.dataset.uuid + } return out https://bitbucket.org/galaxy/galaxy-central/commits/5b1f643e9ea4/ Changeset: 5b1f643e9ea4 User: dannon Date: 2013-06-17 18:07:20 Summary: Merged in kellrott/galaxy-central/provenance (pull request #174) Adding provenance output to the API Affected #: 2 files diff -r cac2f16e960c698101f16f9cb6191f63eb03e6a8 -r 5b1f643e9ea4da1dfda2859ef96d734f455c8972 lib/galaxy/webapps/galaxy/api/provenance.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -0,0 +1,78 @@ +""" +API operations provenance +""" +import logging +from galaxy import web +from galaxy.web.base.controller import BaseAPIController +from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest + +log = logging.getLogger( __name__ ) + + +class BaseProvenanceController( BaseAPIController ): + """ + """ + @web.expose_api + def index( self, trans, **kwd ): + follow = kwd.get('follow', False) + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id], follow ) + return value + + @web.expose_api + def show( self, trans, elem_name, **kwd ): + follow = kwd.get('follow', False) + value = self._get_provenance( trans, self.provenance_item_class, kwd[self.provenance_item_id], follow ) + return value + + @web.expose_api + def create( self, trans, tag_name, payload={}, **kwd ): + raise HTTPNotImplemented() + + @web.expose_api + def delete( self, trans, tag_name, **kwd ): + raise HTTPBadRequest("Cannot Delete Provenance") + + def _get_provenance(self, trans, item_class_name, item_id, follow=True): + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + out = self._get_record(trans, provenance_item, follow) + return out + + def _get_record(self, trans, item, follow): + if item is not None: + if item.copied_from_library_dataset_dataset_association: + item = item.copied_from_library_dataset_dataset_association + return { + "id" : trans.security.encode_id(item.id), + "uuid" : item.dataset.uuid, + "tool_id" : item.creating_job.tool_id, + "parameters" : self._get_job_record(trans, item.creating_job, follow) + } + return None + + def _get_job_record(self, trans, job, follow): + out = {} + for p in job.parameters: + out[p.name] = p.value + for in_d in job.input_datasets: + if follow: + out[in_d.name] = self._get_record(trans, in_d.dataset, follow) + else: + out[in_d.name] = { + "id" : trans.security.encode_id(in_d.dataset.id), + "uuid" : in_d.dataset.dataset.uuid + } + return out + + +class HDAProvenanceController( BaseProvenanceController ): + controller_name = "history_content_provenance" + provenance_item_class = "HistoryDatasetAssociation" + provenance_item_id = "history_content_id" + + +class LDDAProvenanceController( BaseProvenanceController ): + controller_name = "ldda_provenance" + provenance_item_class = "LibraryDatasetDatasetAssociation" + provenance_item_id = "library_content_id" + + diff -r cac2f16e960c698101f16f9cb6191f63eb03e6a8 -r 5b1f643e9ea4da1dfda2859ef96d734f455c8972 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -128,6 +128,10 @@ name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + _add_item_provenance_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -234,6 +238,12 @@ name = "%sannotation" % name_prefix webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) +def _add_item_provenance_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sprovenance" % name_prefix + name = "%sprovenance" % name_prefix + webapp.mapper.resource(name, "provenance", path_prefix=path_prefix, controller=controller) + + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Jun '13

16 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3544960e8928/ Changeset: 3544960e8928 User: jmchilton Date: 2013-05-28 04:40:36 Summary: Improved exception and error handling conditions for the LWR job runner. PEP-8 fixes. Affected #: 2 files diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 3544960e892875f29ad9d64c8e99141bc4da4052 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -14,6 +14,7 @@ __all__ = [ 'LwrJobRunner' ] + class LwrJobRunner( AsynchronousJobRunner ): """ LWR Job Runner @@ -49,18 +50,17 @@ return job_state def queue_job(self, job_wrapper): - stderr = stdout = command_line = '' - + command_line = '' job_destination = job_wrapper.job_destination try: job_wrapper.prepare() if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files + for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files #log.debug( 'executing: %s' % cmd ) if 0 != os.system(cmd): raise Exception('Error running file staging command: %s' % cmd) - job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False ) except: job_wrapper.fail( "failure preparing job", exception=True ) @@ -73,7 +73,6 @@ return try: - #log.debug( 'executing: %s' % command_line ) client = self.get_client_from_wrapper(job_wrapper) output_files = self.get_output_files(job_wrapper) input_files = job_wrapper.get_input_fnames() @@ -85,8 +84,7 @@ client.launch( rebuilt_command_line ) job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.QUEUED ) - - except Exception, exc: + except: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return @@ -124,23 +122,36 @@ client = self.get_client_from_state(job_state) run_results = client.raw_check_complete() - log.debug('run_results %s' % run_results ) stdout = run_results['stdout'] stderr = run_results['stderr'] + download_failure_exceptions = [] if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: work_dir_outputs = self.get_work_dir_outputs(job_wrapper) output_files = self.get_output_files(job_wrapper) for source_file, output_file in work_dir_outputs: - client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + try: + client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + except Exception, e: + download_failure_exceptions.append(e) # Remove from full output_files list so don't try to download directly. output_files.remove(output_file) for output_file in output_files: - client.download_output(output_file, working_directory=job_wrapper.working_directory) - client.clean() + try: + client.download_output(output_file, working_directory=job_wrapper.working_directory) + except Exception, e: + download_failure_exceptions.append(e) + if download_failure_exceptions or self.app.config.cleanup_job == "always": + try: + client.clean() + except: + log.warn("Failed to cleanup remote LWR job") + if download_failure_exceptions: + job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) log.debug('execution finished: %s' % command_line) - except Exception, exc: - job_wrapper.fail( "failure running job", exception=True ) + except: + message = "Failed to communicate with remote job server." + job_wrapper.fail( message, exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return self._handle_metadata_externally( job_wrapper ) @@ -166,14 +177,14 @@ if e.errno == errno.ESRCH: log.debug( "check_pid(): PID %d is dead" % pid ) else: - log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" %( errno.errorcode[e.errno], pid, e.strerror ) ) + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" % ( errno.errorcode[e.errno], pid, e.strerror ) ) return False def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished job_ext_output_metadata = job.get_external_output_metadata() if job_ext_output_metadata: - pid = job_ext_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return @@ -189,10 +200,10 @@ return # give up sleep( 2 ) if not self.check_pid( pid ): - log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" %( job.id, pid, sig ) ) + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" % ( job.id, pid, sig ) ) return else: - log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" %( job.id, pid ) ) + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % ( job.id, pid ) ) else: # Remote kill lwr_url = job.job_runner_name @@ -201,7 +212,6 @@ client = self.get_client(job.destination_params, job_id) client.kill() - def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_state = AsynchronousJobState() diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 3544960e892875f29ad9d64c8e99141bc4da4052 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -19,6 +19,15 @@ return replacement +class OutputNotFoundException(Exception): + + def __init__(self, path): + self.path = path + + def __str__(self): + return "No remote output found for path %s" % self.path + + class Client(object): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -163,7 +172,7 @@ elif output_type == "task": output_path = os.path.join(working_directory, name) else: - raise Exception("No remote output found for dataset with path %s" % path) + raise OutputNotFoundException(path) self.__raw_download_output(name, self.job_id, output_type, output_path) def __raw_download_output(self, name, job_id, output_type, output_path): https://bitbucket.org/galaxy/galaxy-central/commits/cac2f16e960c/ Changeset: cac2f16e960c User: dannon Date: 2013-06-16 20:09:39 Summary: Merged in jmchilton/galaxy-central-lwr (pull request #173) Improved exception and error handling conditions for the LWR job runner. PEP-8 fixes. Affected #: 2 files diff -r eb910f78fa5bb75eed2b967d1bdac69b2ae47894 -r cac2f16e960c698101f16f9cb6191f63eb03e6a8 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -14,6 +14,7 @@ __all__ = [ 'LwrJobRunner' ] + class LwrJobRunner( AsynchronousJobRunner ): """ LWR Job Runner @@ -49,18 +50,17 @@ return job_state def queue_job(self, job_wrapper): - stderr = stdout = command_line = '' - + command_line = '' job_destination = job_wrapper.job_destination try: job_wrapper.prepare() if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: - for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files + for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files #log.debug( 'executing: %s' % cmd ) if 0 != os.system(cmd): raise Exception('Error running file staging command: %s' % cmd) - job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False ) except: job_wrapper.fail( "failure preparing job", exception=True ) @@ -73,7 +73,6 @@ return try: - #log.debug( 'executing: %s' % command_line ) client = self.get_client_from_wrapper(job_wrapper) output_files = self.get_output_files(job_wrapper) input_files = job_wrapper.get_input_fnames() @@ -85,8 +84,7 @@ client.launch( rebuilt_command_line ) job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.QUEUED ) - - except Exception, exc: + except: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return @@ -124,23 +122,36 @@ client = self.get_client_from_state(job_state) run_results = client.raw_check_complete() - log.debug('run_results %s' % run_results ) stdout = run_results['stdout'] stderr = run_results['stderr'] + download_failure_exceptions = [] if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ]: work_dir_outputs = self.get_work_dir_outputs(job_wrapper) output_files = self.get_output_files(job_wrapper) for source_file, output_file in work_dir_outputs: - client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + try: + client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) + except Exception, e: + download_failure_exceptions.append(e) # Remove from full output_files list so don't try to download directly. output_files.remove(output_file) for output_file in output_files: - client.download_output(output_file, working_directory=job_wrapper.working_directory) - client.clean() + try: + client.download_output(output_file, working_directory=job_wrapper.working_directory) + except Exception, e: + download_failure_exceptions.append(e) + if download_failure_exceptions or self.app.config.cleanup_job == "always": + try: + client.clean() + except: + log.warn("Failed to cleanup remote LWR job") + if download_failure_exceptions: + job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True) log.debug('execution finished: %s' % command_line) - except Exception, exc: - job_wrapper.fail( "failure running job", exception=True ) + except: + message = "Failed to communicate with remote job server." + job_wrapper.fail( message, exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return self._handle_metadata_externally( job_wrapper ) @@ -166,14 +177,14 @@ if e.errno == errno.ESRCH: log.debug( "check_pid(): PID %d is dead" % pid ) else: - log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" %( errno.errorcode[e.errno], pid, e.strerror ) ) + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" % ( errno.errorcode[e.errno], pid, e.strerror ) ) return False def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished job_ext_output_metadata = job.get_external_output_metadata() if job_ext_output_metadata: - pid = job_ext_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return @@ -189,10 +200,10 @@ return # give up sleep( 2 ) if not self.check_pid( pid ): - log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" %( job.id, pid, sig ) ) + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" % ( job.id, pid, sig ) ) return else: - log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" %( job.id, pid ) ) + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % ( job.id, pid ) ) else: # Remote kill lwr_url = job.job_runner_name @@ -201,7 +212,6 @@ client = self.get_client(job.destination_params, job_id) client.kill() - def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_state = AsynchronousJobState() diff -r eb910f78fa5bb75eed2b967d1bdac69b2ae47894 -r cac2f16e960c698101f16f9cb6191f63eb03e6a8 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -19,6 +19,15 @@ return replacement +class OutputNotFoundException(Exception): + + def __init__(self, path): + self.path = path + + def __str__(self): + return "No remote output found for path %s" % self.path + + class Client(object): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -163,7 +172,7 @@ elif output_type == "task": output_path = os.path.join(working_directory, name) else: - raise Exception("No remote output found for dataset with path %s" % path) + raise OutputNotFoundException(path) self.__raw_download_output(name, self.job_id, output_type, output_path) def __raw_download_output(self, name, job_id, output_type, output_path): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jun '13

15 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/723bd4c7197a/ Changeset: 723bd4c7197a Branch: twobit_upload User: ghuls Date: 2013-05-27 15:02:06 Summary: Fix detection of 2bit files when uploading them. When 2bit files are uploaded, they were not detected as 2bit files: Example: test.2bit empty format: twobit, database: hg19 The uploaded binary file contains inappropriate content This issue is solved by registering the TwoBit file format in: ./lib/galaxy/datatypes/binary.py Affected #: 1 file diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 723bd4c7197aec7ac42a20f07f48112cd5654a29 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -399,3 +399,5 @@ return dataset.peek except: return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size())) + +Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) https://bitbucket.org/galaxy/galaxy-central/commits/eb910f78fa5b/ Changeset: eb910f78fa5b User: dannon Date: 2013-06-15 19:25:44 Summary: Merged in ghuls/galaxy-central/twobit_upload (pull request #170) Fix detection of 2bit files when uploading them. Affected #: 1 file diff -r b186609ec0cd60c8401b18b1c849745ce17ef0bd -r eb910f78fa5bb75eed2b967d1bdac69b2ae47894 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -399,3 +399,5 @@ return dataset.peek except: return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size())) + +Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jun '13

15 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b186609ec0cd/ Changeset: b186609ec0cd User: dannon Date: 2013-06-15 15:08:09 Summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… Affected #: 1 file diff -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 -r b186609ec0cd60c8401b18b1c849745ce17ef0bd lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,9 +1,9 @@ -import operator, os +import os +import logging from datetime import datetime, timedelta from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.model.orm import and_, not_, or_, desc -import logging +from galaxy.model.orm import and_, desc, eagerload log = logging.getLogger( __name__ ) class System( BaseUIController ): https://bitbucket.org/galaxy/galaxy-central/commits/f295092476c7/ Changeset: f295092476c7 Branch: stable User: dannon Date: 2013-06-15 15:08:09 Summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… Affected #: 1 file diff -r 2efb1083676b56c4a2678e43600fd707756fca27 -r f295092476c781987d5a31e44e7a19a372a461aa lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,9 +1,9 @@ -import operator, os +import os +import logging from datetime import datetime, timedelta from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.model.orm import and_, not_, or_, desc -import logging +from galaxy.model.orm import and_, desc, eagerload log = logging.getLogger( __name__ ) class System( BaseUIController ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Remove print statements from api/search, ctrl/visualization, ctrl/workflow
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2efb1083676b/ Changeset: 2efb1083676b Branch: stable User: carlfeberhard Date: 2013-06-14 21:06:56 Summary: Remove print statements from api/search, ctrl/visualization, ctrl/workflow Affected #: 3 files diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/api/search.py --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -30,7 +30,6 @@ current_user_roles = trans.get_current_user_roles() try: results = query.process(trans) - print results except Exception, e: return {'error' : str(e)} for item in results: diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -848,7 +848,6 @@ get the visualization with the given id; otherwise, create a new visualization using a given dataset and regions. """ - print 'sweepster:', id, hda_ldda, dataset_id, regions regions = regions or '{}' # Need to create history if necessary in order to create tool form. trans.get_history( create=True ) @@ -861,7 +860,6 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - print 'dataset:', dataset job = get_dataset_job( dataset ) viz_config = { 'dataset_id': dataset_id, diff -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 -r 2efb1083676b56c4a2678e43600fd707756fca27 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -132,7 +132,6 @@ @web.expose def index( self, trans ): - print trans.request.host_url return self.list( trans ) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Remove print statements from api/search, ctrl/visualization, ctrl/workflow
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12a45cc8c67f/ Changeset: 12a45cc8c67f User: carlfeberhard Date: 2013-06-14 21:01:12 Summary: Remove print statements from api/search, ctrl/visualization, ctrl/workflow Affected #: 3 files diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/api/search.py --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -30,7 +30,6 @@ current_user_roles = trans.get_current_user_roles() try: results = query.process(trans) - print results except Exception, e: return {'error' : str(e)} for item in results: diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -848,7 +848,6 @@ get the visualization with the given id; otherwise, create a new visualization using a given dataset and regions. """ - print 'sweepster:', id, hda_ldda, dataset_id, regions regions = regions or '{}' # Need to create history if necessary in order to create tool form. trans.get_history( create=True ) @@ -861,7 +860,6 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - print 'dataset:', dataset job = get_dataset_job( dataset ) viz_config = { 'dataset_id': dataset_id, diff -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 -r 12a45cc8c67f86f595f50bfcf2155892f5eafeb0 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -132,7 +132,6 @@ @web.expose def index( self, trans ): - print trans.request.host_url return self.list( trans ) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: galaxy.base.js: Remove console.debug; pack scripts
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48b7d75bbb33/ Changeset: 48b7d75bbb33 User: carlfeberhard Date: 2013-06-14 20:51:49 Summary: galaxy.base.js: Remove console.debug; pack scripts Affected #: 2 files diff -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -158,7 +158,6 @@ confirmtext = link_dom.getAttribute( "confirm" ), href = link_dom.getAttribute( "href" ), target = link_dom.getAttribute( "target" ); - console.debug( link.text(), href, target ); // no href - no function (gen. a label) if (!href) { diff -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 -r 48b7d75bbb339e27a6db906dd5b1b2a2dbbaaf71 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var 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k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Add defaults to the tool shed's config.py for the toolbox dynamic filtering feature.
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/07fb676b0a1d/ Changeset: 07fb676b0a1d User: Dave Bouvier Date: 2013-06-14 18:16:02 Summary: Add defaults to the tool shed's config.py for the toolbox dynamic filtering feature. Affected #: 1 file diff -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 -r 07fb676b0a1d57f9352a0b9048bca9914b4095b6 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -6,7 +6,7 @@ import logging, logging.config from optparse import OptionParser import ConfigParser -from galaxy.util import string_as_bool +from galaxy.util import string_as_bool, listify from galaxy import eggs import pkg_resources @@ -44,6 +44,9 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) # Tool stuff + self.tool_filters = listify( kwargs.get( "tool_filters", [] ) ) + self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ) ) + self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Jun '13

14 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d794e30fcd1a/ Changeset: d794e30fcd1a User: jmchilton Date: 2013-06-07 22:12:09 Summary: Refactor hardcoded references to static/welcome.html to a new welcome action on the root controller. Affected #: 4 files diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -547,6 +547,10 @@ return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) @web.expose + def welcome( self, trans ): + return trans.response.send_redirect( url_for( '/static/welcome.html' ) ) + + @web.expose def bucket_proxy( self, trans, bucket=None, **kwd): if bucket: trans.response.set_content_type( 'text/xml' ) diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -52,7 +52,7 @@ def index(self, trans, tool_id=None, from_noframe=None, **kwd): # No tool id passed, redirect to main page if tool_id is None: - return trans.response.send_redirect( url_for( "/static/welcome.html" ) ) + return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -492,7 +492,7 @@ message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ ( user.email, redirect, url_for( '/' ) ) if trans.app.config.require_login: - message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( controller="root", action="welcome" ) success = True return ( message, status, user, success ) diff -r 30e8f84914bdd4ea66138f690c9df83e520d9572 -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -149,7 +149,7 @@ elif m_c is not None: center_url = h.url_for( controller=m_c, action=m_a ) else: - center_url = h.url_for( '/static/welcome.html' ) + center_url = h.url_for( controller="root", action="welcome" ) %><div style="position: absolute; width: 100%; height: 100%"> https://bitbucket.org/galaxy/galaxy-central/commits/3636ba2f4439/ Changeset: 3636ba2f4439 User: jmchilton Date: 2013-06-08 00:35:36 Summary: Add config option 'welcome_url' to allow override of relative url to welcome file. Much like the tool filter request, the driving motivation here is allowing a single CloudMan packaged cloud image to host different Galaxys based on the supplied user data. More specifically, with this changset one can override the default welcome file to point to 'static/welcome_site1.html' when launching CloudMan by adding the option 'galaxy_universe_welcome_url: "/static/welcome_site1.html"' to the launch request's user data. Affected #: 2 files diff -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -166,6 +166,7 @@ self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) + self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) # Configuration for the message box directly below the masthead. self.message_box_visible = kwargs.get( 'message_box_visible', False ) self.message_box_content = kwargs.get( 'message_box_content', None ) diff -r d794e30fcd1ac28fa84c13d3f68c86c7de5df0d4 -r 3636ba2f4439b7b61f25425698f8e0be9f0f6f07 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -548,7 +548,8 @@ @web.expose def welcome( self, trans ): - return trans.response.send_redirect( url_for( '/static/welcome.html' ) ) + welcome_url = trans.app.config.welcome_url + return trans.response.send_redirect( url_for( welcome_url ) ) @web.expose def bucket_proxy( self, trans, bucket=None, **kwd): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 Jun '13

13 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30e8f84914bd/ Changeset: 30e8f84914bd User: dannon Date: 2013-06-14 01:08:16 Summary: Fix toolshed migration 0017 to work with both postgres, postgresql dialect names Affected #: 1 file diff -r 827ff13a72914ed3ddacace717cc07af66af718e -r 30e8f84914bdd4ea66138f690c9df83e520d9572 lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -29,7 +29,7 @@ # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" - elif migrate_engine.name == 'postgres': + elif migrate_engine.name in ['postgres', 'postgresql']: default_false = "false" # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) https://bitbucket.org/galaxy/galaxy-central/commits/68c705bf0325/ Changeset: 68c705bf0325 Branch: stable User: dannon Date: 2013-06-14 01:08:16 Summary: Fix toolshed migration 0017 to work with both postgres, postgresql dialect names Affected #: 1 file diff -r aea50b1c8d9178de429e58805ca6c12e7f0465ee -r 68c705bf0325a54d2424a7b8ed44232c57a3b506 lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -29,7 +29,7 @@ # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" - elif migrate_engine.name == 'postgres': + elif migrate_engine.name in ['postgres', 'postgresql']: default_false = "false" # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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