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commit/galaxy-central: greg: Migration script to alter the tool_dependency.version database table column type to Text.
by Bitbucket 12 Jun '12

12 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b762062399b3/ changeset: b762062399b3 user: greg date: 2012-06-12 21:09:39 summary: Migration script to alter the tool_dependency.version database table column type to Text. affected #: 2 files diff -r 9a3ab5009e8e70596a07283e3611661410f92c4d -r b762062399b3cab0a4139dc3fcd33f30945e49ac lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -397,7 +397,7 @@ Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ), Column( "installed_changeset_revision", TrimmedString( 255 ) ), Column( "name", TrimmedString( 255 ) ), - Column( "version", TrimmedString( 40 ) ), + Column( "version", Text ), Column( "type", TrimmedString( 40 ) ), Column( "uninstalled", Boolean, default=False ) ) diff -r 9a3ab5009e8e70596a07283e3611661410f92c4d -r b762062399b3cab0a4139dc3fcd33f30945e49ac lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py @@ -0,0 +1,53 @@ +""" +Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) + # Change the tool_dependency table's version column from TrimmedString to Text. + if migrate_engine.name == 'postgres': + cmd = "ALTER TABLE tool_dependency ALTER COLUMN version TYPE Text;" + elif migrate_engine.name == 'mysql': + cmd = "ALTER TABLE tool_dependency MODIFY COLUMN version Text;" + else: + # We don't have to do anything for sqlite tables. From the sqlite documentation at http://sqlite.org/datatype3.html: + # 1.0 Storage Classes and Datatypes + # Each value stored in an SQLite database (or manipulated by the database engine) has one of the following storage classes: + # NULL. The value is a NULL value. + # INTEGER. The value is a signed integer, stored in 1, 2, 3, 4, 6, or 8 bytes depending on the magnitude of the value. + # REAL. The value is a floating point value, stored as an 8-byte IEEE floating point number. + # TEXT. The value is a text string, stored using the database encoding (UTF-8, UTF-16BE or UTF-16LE). + # BLOB. The value is a blob of data, stored exactly as it was input. + cmd = None + if cmd: + try: + db_session.execute( cmd ) + except Exception, e: + log.debug( "Altering tool_dependency.version column from TrimmedString(40) to Text failed: %s" % str( e ) ) +def downgrade(): + # Not necessary to change column type Text to TrimmedString(40). + pass 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: dan: Allow OpenID to work when require_login is set to True.
by Bitbucket 12 Jun '12

12 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9a3ab5009e8e/ changeset: 9a3ab5009e8e user: dan date: 2012-06-12 20:12:46 summary: Allow OpenID to work when require_login is set to True. affected #: 1 file diff -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 -r 9a3ab5009e8e70596a07283e3611661410f92c4d lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -435,6 +435,9 @@ url_for( controller='user', action='manage_user_info' ), url_for( controller='user', action='set_default_permissions' ), url_for( controller='user', action='reset_password' ), + url_for( controller='user', action='openid_auth' ), + url_for( controller='user', action='openid_process' ), + url_for( controller='user', action='openid_associate' ), url_for( controller='library', action='browse' ), url_for( controller='history', action='list' ), url_for( controller='dataset', action='list' ) 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: jgoecks: Have Bowtie2 wrapper produce BAM rather than SAM output.
by Bitbucket 11 Jun '12

11 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36c540d788c3/ changeset: 36c540d788c3 user: jgoecks date: 2012-06-11 21:52:36 summary: Have Bowtie2 wrapper produce BAM rather than SAM output. affected #: 2 files diff -r 17302ca3be4e7b3d987733ea6e61982f9520996d -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -65,7 +65,7 @@ index_path = options.index_path # Build bowtie command. - cmd = 'bowtie2 %s -x %s %s -S %s' + cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s' # Set up reads. if options.single_paired == 'paired': diff -r 17302ca3be4e7b3d987733ea6e61982f9520996d -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -112,7 +112,7 @@ </inputs><outputs> - <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> + <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed"> 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: jgoecks: Put myExperiment URL in config's Beta features location.
by Bitbucket 11 Jun '12

11 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/17302ca3be4e/ changeset: 17302ca3be4e user: jgoecks date: 2012-06-11 21:22:51 summary: Put myExperiment URL in config's Beta features location. affected #: 1 file diff -r 0f32c2fc37cdc2959c86d2fdb0debe9a4c66282b -r 17302ca3be4e7b3d987733ea6e61982f9520996d universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -527,6 +527,9 @@ # be used for each "Set at Runtime" input, independent of others in the Workflow #enable_unique_workflow_defaults = False +# The URL to the myExperiment instance being used (omit scheme but include port) +#myexperiment_url = www.myexperiment.org:80 + # Enable Galaxy's "Upload via FTP" interface. You'll need to install and # configure an FTP server (we've used ProFTPd since it can use Galaxy's # database for authentication) and set the following two options. @@ -681,9 +684,6 @@ #pbs_stage_path = #pbs_dataset_server = -# The URL to the myExperiment instance being used (omit scheme but include port) -myexperiment_url = www.myexperiment.org:80 - # This option allows users to see the full path of datasets via the "View # Details" option in the history. Administrators can always see this. #expose_dataset_path = False 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: 3 new changesets
by Bitbucket 11 Jun '12

11 Jun '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/66395a9d870f/ changeset: 66395a9d870f user: jmchilton date: 2012-06-06 03:35:33 summary: First attempt at updated dynamic job runners. affected #: 3 files diff -r 1890cb0d1cfbb3ef5a09affcdd18d2b8acf7d811 -r 66395a9d870fbe48660dbf75cc0a59264bb862f6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -21,6 +21,7 @@ from galaxy.util.expressions import ExpressionContext from galaxy.jobs.actions.post import ActionBox from galaxy.exceptions import ObjectInvalid +from galaxy.jobs.mapper import JobRunnerMapper log = logging.getLogger( __name__ ) @@ -80,6 +81,7 @@ self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) + self.job_runner_mapper = JobRunnerMapper( self ) self.params = None if job.params: self.params = from_json_string( job.params ) @@ -88,7 +90,8 @@ self.__galaxy_system_pwent = None def get_job_runner( self ): - return self.tool.get_job_runner( self.params ) + job_runner = self.job_runner_mapper.get_job_runner( self.params ) + return job_runner def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) diff -r 1890cb0d1cfbb3ef5a09affcdd18d2b8acf7d811 -r 66395a9d870fbe48660dbf75cc0a59264bb862f6 lib/galaxy/jobs/mapper.py --- /dev/null +++ b/lib/galaxy/jobs/mapper.py @@ -0,0 +1,82 @@ +import inspect, sys + +import galaxy.jobs.rules + +DYNAMIC_RUNNER_PREFIX = "dynamic:///" + +class JobRunnerMapper( object ): + + def __init__( self, job_wrapper ): + self.job_wrapper = job_wrapper + + def __invoke_expand_function( self, expand_function ): + function_arg_names = inspect.getargspec( expand_function ).args + + possible_args = { "job_id" : self.job_wrapper.job_id, + "tool" : self.job_wrapper.tool, + "tool_id" : self.job_wrapper.tool.id, + "job_wrapper" : self.job_wrapper, + "app" : self.job_wrapper.app } + + actual_args = {} + + # Populate needed args + for possible_arg_name in possible_args: + if possible_arg_name in function_arg_names: + actual_args[ possible_arg_name ] = possible_args[ possible_arg_name ] + + # Don't hit the DB to load the job object is not needed + if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names: + job = self.job_wrapper.get_job() + history = job.history + user = history and history.user + user_email = user and str(user.email) + + if "job" in function_arg_names: + actual_args[ "job" ] = job + + if "user" in function_arg_names: + actual_args[ "user" ] = user + + if "user_email" in function_arg_names: + actual_args[ "user_email" ] = user_email + + return expand_function( **actual_args ) + + def __determine_expand_function_name( self, option_parts ): + # default look for function with same name as tool, unless one specified + expand_function_name = self.job_wrapper.tool.id + if len( option_parts ) > 1: + expand_function_name = option_parts[ 1 ] + return expand_function_name + + def __get_expand_function( self, expand_function_name ): + rules_module = sys.modules[ "galaxy.jobs.rules" ] + if hasattr( rules_module, expand_function_name ): + expand_function = getattr( rules_module, expand_function_name ) + return expand_function + else: + raise Exception( "Dynamic job runner cannot find function to expand job runner type - %s" % expand_function_name ) + + def __expand_dynamic_job_runner( self, options_str ): + option_parts = options_str.split( '/' ) + expand_type = option_parts[ 0 ] + if expand_type == "python": + expand_function_name = self.__determine_expand_function_name( option_parts ) + expand_function = self.__get_expand_function( expand_function_name ) + return self.__invoke_expand_function( expand_function ) + else: + raise Exception( "Unhandled dynamic job runner type specified - %s" % calculation_type ) + + def __cache_job_runner( self, params ): + raw_job_runner = self.job_wrapper.tool.get_job_runner( params ) + if raw_job_runner.startswith( DYNAMIC_RUNNER_PREFIX ): + job_runner = self.__expand_dynamic_job_runner( raw_job_runner[ len( DYNAMIC_RUNNER_PREFIX ) : ] ) + else: + job_runner = raw_job_runner + self.cached_job_runner = job_runner + + def get_job_runner( self, params ): + if not hasattr( self, 'cached_job_runner' ): + self.__cache_job_runner( params ) + return self.cached_job_runner diff -r 1890cb0d1cfbb3ef5a09affcdd18d2b8acf7d811 -r 66395a9d870fbe48660dbf75cc0a59264bb862f6 lib/galaxy/jobs/rules.py --- /dev/null +++ b/lib/galaxy/jobs/rules.py @@ -0,0 +1,9 @@ +import logging + +log = logging.getLogger( __name__ ) + +# Add functions to dynamically map job descriptions to job runners in +# this file. These functions can optionally take in any of the +# following arguments - job_wrapper, app, user_email, job, tool, +# email, tool_id, and job_id. + https://bitbucket.org/galaxy/galaxy-central/changeset/f54b848298d4/ changeset: f54b848298d4 user: jmchilton date: 2012-06-10 06:00:16 summary: Rework dynamic job runner config so that instead using a rules.py file for storing rules, they should be placed in lib/galaxy/jobs/rules/. The rules submodules are "searched" in lexiographically allowing for hierarchical configuration overrides (e.g. naming schemes like: 000_galaxy_rules.py, 100_site_rules.py, 200_instance_rules.py) affected #: 3 files diff -r 66395a9d870fbe48660dbf75cc0a59264bb862f6 -r f54b848298d4d78d6fbcc85e9887960f21b5c239 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -1,13 +1,50 @@ -import inspect, sys +import logging +import inspect +import os + +log = logging.getLogger( __name__ ) import galaxy.jobs.rules DYNAMIC_RUNNER_PREFIX = "dynamic:///" class JobRunnerMapper( object ): - + """ + This class is responsible to managing the mapping of jobs + (in the form of job_wrappers) to job runner strings. + """ + def __init__( self, job_wrapper ): self.job_wrapper = job_wrapper + self.rule_modules = self.__get_rule_modules( ) + + def __get_rule_modules( self ): + unsorted_module_names = self.__get_rule_module_names( ) + ## Load modules in reverse order to allow hierarchical overrides + ## i.e. 000_galaxy_rules.py, 100_site_rules.py, 200_instance_rules.py + module_names = sorted( unsorted_module_names, reverse=True ) + modules = [] + for rule_module_name in module_names: + try: + module = __import__( rule_module_name ) + for comp in rule_module_name.split( "." )[1:]: + module = getattr( module, comp ) + modules.append( module ) + except BaseException, exception: + exception_str = str( exception ) + message = "%s rule module could not be loaded: %s" % ( rule_module_name, exception_str ) + log.debug( message ) + continue + return modules + + def __get_rule_module_names( self ): + rules_dir = galaxy.jobs.rules.__path__[0] + names = [] + for fname in os.listdir( rules_dir ): + if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): + rule_module_name = "galaxy.jobs.rules.%s" % fname[:-len(".py")] + names.append( rule_module_name ) + return names def __invoke_expand_function( self, expand_function ): function_arg_names = inspect.getargspec( expand_function ).args @@ -15,7 +52,7 @@ possible_args = { "job_id" : self.job_wrapper.job_id, "tool" : self.job_wrapper.tool, "tool_id" : self.job_wrapper.tool.id, - "job_wrapper" : self.job_wrapper, + "job_wrapper" : self.job_wrapper, "app" : self.job_wrapper.app } actual_args = {} @@ -25,7 +62,7 @@ if possible_arg_name in function_arg_names: actual_args[ possible_arg_name ] = possible_args[ possible_arg_name ] - # Don't hit the DB to load the job object is not needed + # Don't hit the DB to load the job object if not needed if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names: job = self.job_wrapper.get_job() history = job.history @@ -51,13 +88,21 @@ return expand_function_name def __get_expand_function( self, expand_function_name ): - rules_module = sys.modules[ "galaxy.jobs.rules" ] - if hasattr( rules_module, expand_function_name ): - expand_function = getattr( rules_module, expand_function_name ) + matching_rule_module = self.__last_rule_module_with_function( expand_function_name ) + if matching_rule_module: + expand_function = getattr( matching_rule_module, expand_function_name ) return expand_function else: raise Exception( "Dynamic job runner cannot find function to expand job runner type - %s" % expand_function_name ) - + + def __last_rule_module_with_function( self, function_name ): + # self.rule_modules is sorted in reverse order, so find first + # wiht function + for rule_module in self.rule_modules: + if hasattr( rule_module, function_name ): + return rule_module + return None + def __expand_dynamic_job_runner( self, options_str ): option_parts = options_str.split( '/' ) expand_type = option_parts[ 0 ] @@ -77,6 +122,9 @@ self.cached_job_runner = job_runner def get_job_runner( self, params ): + """ + Cache the job_runner string to avoid recalculation. + """ if not hasattr( self, 'cached_job_runner' ): self.__cache_job_runner( params ) return self.cached_job_runner diff -r 66395a9d870fbe48660dbf75cc0a59264bb862f6 -r f54b848298d4d78d6fbcc85e9887960f21b5c239 lib/galaxy/jobs/rules.py --- a/lib/galaxy/jobs/rules.py +++ /dev/null @@ -1,9 +0,0 @@ -import logging - -log = logging.getLogger( __name__ ) - -# Add functions to dynamically map job descriptions to job runners in -# this file. These functions can optionally take in any of the -# following arguments - job_wrapper, app, user_email, job, tool, -# email, tool_id, and job_id. - https://bitbucket.org/galaxy/galaxy-central/changeset/0f32c2fc37cd/ changeset: 0f32c2fc37cd user: natefoo date: 2012-06-11 16:26:12 summary: Merged in jmchilton/umn-galaxy-central (pull request #47) affected #: 3 files diff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 -r 0f32c2fc37cdc2959c86d2fdb0debe9a4c66282b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -21,6 +21,7 @@ from galaxy.util.expressions import ExpressionContext from galaxy.jobs.actions.post import ActionBox from galaxy.exceptions import ObjectInvalid +from galaxy.jobs.mapper import JobRunnerMapper log = logging.getLogger( __name__ ) @@ -80,6 +81,7 @@ self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) + self.job_runner_mapper = JobRunnerMapper( self ) self.params = None if job.params: self.params = from_json_string( job.params ) @@ -88,7 +90,8 @@ self.__galaxy_system_pwent = None def get_job_runner( self ): - return self.tool.get_job_runner( self.params ) + job_runner = self.job_runner_mapper.get_job_runner( self.params ) + return job_runner def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) diff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 -r 0f32c2fc37cdc2959c86d2fdb0debe9a4c66282b lib/galaxy/jobs/mapper.py --- /dev/null +++ b/lib/galaxy/jobs/mapper.py @@ -0,0 +1,130 @@ +import logging +import inspect +import os + +log = logging.getLogger( __name__ ) + +import galaxy.jobs.rules + +DYNAMIC_RUNNER_PREFIX = "dynamic:///" + +class JobRunnerMapper( object ): + """ + This class is responsible to managing the mapping of jobs + (in the form of job_wrappers) to job runner strings. + """ + + def __init__( self, job_wrapper ): + self.job_wrapper = job_wrapper + self.rule_modules = self.__get_rule_modules( ) + + def __get_rule_modules( self ): + unsorted_module_names = self.__get_rule_module_names( ) + ## Load modules in reverse order to allow hierarchical overrides + ## i.e. 000_galaxy_rules.py, 100_site_rules.py, 200_instance_rules.py + module_names = sorted( unsorted_module_names, reverse=True ) + modules = [] + for rule_module_name in module_names: + try: + module = __import__( rule_module_name ) + for comp in rule_module_name.split( "." )[1:]: + module = getattr( module, comp ) + modules.append( module ) + except BaseException, exception: + exception_str = str( exception ) + message = "%s rule module could not be loaded: %s" % ( rule_module_name, exception_str ) + log.debug( message ) + continue + return modules + + def __get_rule_module_names( self ): + rules_dir = galaxy.jobs.rules.__path__[0] + names = [] + for fname in os.listdir( rules_dir ): + if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ): + rule_module_name = "galaxy.jobs.rules.%s" % fname[:-len(".py")] + names.append( rule_module_name ) + return names + + def __invoke_expand_function( self, expand_function ): + function_arg_names = inspect.getargspec( expand_function ).args + + possible_args = { "job_id" : self.job_wrapper.job_id, + "tool" : self.job_wrapper.tool, + "tool_id" : self.job_wrapper.tool.id, + "job_wrapper" : self.job_wrapper, + "app" : self.job_wrapper.app } + + actual_args = {} + + # Populate needed args + for possible_arg_name in possible_args: + if possible_arg_name in function_arg_names: + actual_args[ possible_arg_name ] = possible_args[ possible_arg_name ] + + # Don't hit the DB to load the job object if not needed + if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names: + job = self.job_wrapper.get_job() + history = job.history + user = history and history.user + user_email = user and str(user.email) + + if "job" in function_arg_names: + actual_args[ "job" ] = job + + if "user" in function_arg_names: + actual_args[ "user" ] = user + + if "user_email" in function_arg_names: + actual_args[ "user_email" ] = user_email + + return expand_function( **actual_args ) + + def __determine_expand_function_name( self, option_parts ): + # default look for function with same name as tool, unless one specified + expand_function_name = self.job_wrapper.tool.id + if len( option_parts ) > 1: + expand_function_name = option_parts[ 1 ] + return expand_function_name + + def __get_expand_function( self, expand_function_name ): + matching_rule_module = self.__last_rule_module_with_function( expand_function_name ) + if matching_rule_module: + expand_function = getattr( matching_rule_module, expand_function_name ) + return expand_function + else: + raise Exception( "Dynamic job runner cannot find function to expand job runner type - %s" % expand_function_name ) + + def __last_rule_module_with_function( self, function_name ): + # self.rule_modules is sorted in reverse order, so find first + # wiht function + for rule_module in self.rule_modules: + if hasattr( rule_module, function_name ): + return rule_module + return None + + def __expand_dynamic_job_runner( self, options_str ): + option_parts = options_str.split( '/' ) + expand_type = option_parts[ 0 ] + if expand_type == "python": + expand_function_name = self.__determine_expand_function_name( option_parts ) + expand_function = self.__get_expand_function( expand_function_name ) + return self.__invoke_expand_function( expand_function ) + else: + raise Exception( "Unhandled dynamic job runner type specified - %s" % calculation_type ) + + def __cache_job_runner( self, params ): + raw_job_runner = self.job_wrapper.tool.get_job_runner( params ) + if raw_job_runner.startswith( DYNAMIC_RUNNER_PREFIX ): + job_runner = self.__expand_dynamic_job_runner( raw_job_runner[ len( DYNAMIC_RUNNER_PREFIX ) : ] ) + else: + job_runner = raw_job_runner + self.cached_job_runner = job_runner + + def get_job_runner( self, params ): + """ + Cache the job_runner string to avoid recalculation. + """ + if not hasattr( self, 'cached_job_runner' ): + self.__cache_job_runner( params ) + return self.cached_job_runner Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Handle Tophat2 fusion-ignore-chromosome parameter correctly.
by Bitbucket 11 Jun '12

11 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1df26d9240bb/ changeset: 1df26d9240bb user: jgoecks date: 2012-06-11 14:49:31 summary: Handle Tophat2 fusion-ignore-chromosome parameter correctly. affected #: 2 files diff -r 0edd1d65d746a806de155d3d37428ac84b4265ff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -200,10 +200,12 @@ # Fusion search options. if options.fusion_search: - opts += ' --fusion-search --fusion-anchor-length %i --fusion-min-dist %i --fusion-read-mismatches %i --fusion-multireads %i --fusion-multipairs %i --fusion-ignore-chromosomes %s' % \ + opts += ' --fusion-search --fusion-anchor-length %i --fusion-min-dist %i --fusion-read-mismatches %i --fusion-multireads %i --fusion-multipairs %i' % \ ( int( options.fusion_anchor_length ), int( options.fusion_min_dist ), int( options.fusion_read_mismatches ), int( options.fusion_multireads ), - int( options.fusion_multipairs ), options.fusion_ignore_chromosomes ) + int( options.fusion_multipairs ) ) + if options.fusion_ignore_chromosomes: + opts += ' --fusion-ignore-chromosomes %s' % options.fusion_ignore_chromosomes # Bowtie2 options. if options.b2_very_fast: diff -r 0edd1d65d746a806de155d3d37428ac84b4265ff -r 1df26d9240bb4e115cdd8cd019673c56c8e4ad67 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -103,7 +103,7 @@ --fusion-read-mismatches $params.fusion_search.read_mismatches --fusion-multireads $params.fusion_search.multireads --fusion-multipairs $params.fusion_search.multipairs - --fusion-ignore-chromosomes $params.fusion_search.ignore_chromosomes + --fusion-ignore-chromosomes "$params.fusion_search.ignore_chromosomes" #end if #if $params.bowtie2_settings.b2_settings == "Yes": 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: jgoecks: Backbone-ify server-state deferred and use when running tools in Trackster.
by Bitbucket 08 Jun '12

08 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0edd1d65d746/ changeset: 0edd1d65d746 user: jgoecks date: 2012-06-08 21:36:02 summary: Backbone-ify server-state deferred and use when running tools in Trackster. affected #: 3 files diff -r be2577bfdbac49309f962b0b9a48ab11bac6159b -r 0edd1d65d746a806de155d3d37428ac84b4265ff static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -244,8 +244,17 @@ .attr("class", "node") .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }); + // Set up behavior when node is clicked. node.on("click", function(d, i) { - console.log(d, i); + console.log(d, i); + + // Gather: (a) dataset of interest; (b) region(s) of interest and (c) sets of parameters based on node clicked. + + // Run job by submitting parameters + dataset as job inputs; get dataset ids as result. + + // Create tracks for all resulting dataset ids. + + // Display tiles for region(s) of interest. }); node.append("circle") diff -r be2577bfdbac49309f962b0b9a48ab11bac6159b -r 0edd1d65d746a806de155d3d37428ac84b4265ff static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -25,28 +25,6 @@ }; /** - * Provides support for server-state based deferred. Server is repeatedly polled, and when - * condition is met, deferred is resolved. - */ -var server_state_deferred = function(url, url_params, interval, success_fn) { - var deferred = $.Deferred(), - go = function() { - $.getJSON(url, url_params, function(result) { - if (success_fn(result)) { - // Result is good, so resolve. - deferred.resolve(result); - } - else { - // Result not good, try again. - setTimeout(go, interval); - } - }); - }; - go(); - return deferred; -}; - -/** * Find browser's requestAnimationFrame method or fallback on a setTimeout */ var requestAnimationFrame = (function(){ @@ -1950,7 +1928,10 @@ this.run(url_params, new_track, // Success callback. function(track_data) { - new_track.dataset_id = track_data.dataset_id; + new_track.set_dataset(new Dataset({ + id: track_data.dataset_id, + hda_ldda: track_data.hda_ldda + })); new_track.tiles_div.text("Running job."); new_track.init(); } @@ -1960,36 +1941,36 @@ * Run tool using a set of URL params and a success callback. */ run: function(url_params, new_track, success_callback) { - // Add tool params to URL params. - $.extend(url_params, this.get_param_values_dict()); + // Run tool. + var ss_deferred = new ServerStateDeferred({ + url: rerun_tool_url, + url_params: $.extend(url_params, this.get_param_values_dict()), + interval: 2000, + success_fn: function(response) { + return response !== "pending"; + } + }); - // Run tool. - // TODO: rewrite to use server state deferred. - var json_run_tool = function() { - $.getJSON(rerun_tool_url, url_params, function(response) { - if (response === "no converter") { - // No converter available for input datasets, so cannot run tool. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_NOCONVERTER); - } - else if (response.error) { - // General error. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_CANNOT_RUN_TOOL + response.message); - } - else if (response === "pending") { - // Converting/indexing input datasets; show message and try again. - new_track.container_div.addClass("pending"); - new_track.content_div.text("Converting input data so that it can be used quickly with tool."); - setTimeout(json_run_tool, 2000); - } - else { - // Job submitted and running. - success_callback(response); - } - }); - }; - json_run_tool(); + // Start with this status message. + //new_track.container_div.addClass("pending"); + //new_track.content_div.text("Converting input data so that it can be used quickly with tool."); + + $.when(ss_deferred.go()).then(function(response) { + if (response === "no converter") { + // No converter available for input datasets, so cannot run tool. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_NOCONVERTER); + } + else if (response.error) { + // General error. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_CANNOT_RUN_TOOL + response.message); + } + else { + // Job submitted and running. + success_callback(response); + } + }); } }); @@ -3765,7 +3746,7 @@ init_for_tool_data: function() { // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- // is ready. - this.data_url = raw_data_url; + this.data_manager.set('data_url', raw_data_url); this.data_query_wait = 1000; this.dataset_check_url = dataset_state_url; @@ -3786,15 +3767,16 @@ self.data_query_wait = DEFAULT_DATA_QUERY_WAIT; // Reset data URL when dataset indexing has completed/when not pending. - $.when( + var ss_deferred = new ServerStateDeferred({ + url: self.dataset_state_url, + url_params: {dataset_id : self.dataset_id, hda_ldda: self.hda_ldda}, + interval: self.data_query_wait, // Set up deferred to check dataset state until it is not pending. - server_state_deferred(self.dataset_state_url, - {dataset_id : self.dataset_id, hda_ldda: self.hda_ldda}, - self.data_query_wait, - function(result) { return result !== "pending" }) - ).then(function() { + success_fn: function(result) { return result !== "pending" } + }); + $.when(ss_deferred.go()).then(function() { // Dataset is indexed, so use default data URL. - self.data_url = default_data_url; + self.data_manager.set('data_url', default_data_url); }); // Reset post-draw actions function. @@ -4371,6 +4353,12 @@ this.set_painter_from_config(); }; extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + set_dataset: function(dataset) { + this.dataset_id = dataset.get('id'); + this.hda_ldda = dataset.get('hda_ldda'); + this.data_manager.set('dataset', dataset); + }, + set_painter_from_config: function() { if ( this.config.values['connector_style'] === 'arcs' ) { this.painter = painters.ArcLinkedFeaturePainter; diff -r be2577bfdbac49309f962b0b9a48ab11bac6159b -r 0edd1d65d746a806de155d3d37428ac84b4265ff static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -9,6 +9,43 @@ // --------- Models --------- /** + * Implementation of a server-state based deferred. Server is repeatedly polled, and when + * condition is met, deferred is resolved. + */ +var ServerStateDeferred = Backbone.Model.extend({ + defaults: { + url: null, + url_params: {}, + interval: 1000, + success_fn: function(result) { return true; } + }, + + /** + * Returns a deferred that resolves when success function returns true. + */ + go: function() { + var deferred = $.Deferred(), + self = this, + success_fn = self.get('success_fn'), + interval = self.get('interval'), + _go = function() { + $.getJSON(self.get('url'), self.get('url_params'), function(result) { + if (success_fn(result)) { + // Result is good, so resolve. + deferred.resolve(result); + } + else { + // Result not good, try again. + setTimeout(_go, interval); + } + }); + }; + _go(); + return deferred; + } +}); + +/** * Generic cache that handles key/value pairs. */ var Cache = Backbone.Model.extend({ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add min, max insert size parameters to bowtie2 wrapper.
by Bitbucket 08 Jun '12

08 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be2577bfdbac/ changeset: be2577bfdbac user: jgoecks date: 2012-06-08 20:03:41 summary: Add min, max insert size parameters to bowtie2 wrapper. affected #: 2 files diff -r 6f15c9e850ab60fa027f0eccd445aad69c45eef9 -r be2577bfdbac49309f962b0b9a48ab11bac6159b tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -18,6 +18,8 @@ parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) parser.add_option( '', '--single-paired', dest='single_paired', help='' ) + parser.add_option( '-I', '--minins', dest='min_insert' ) + parser.add_option( '-X', '--maxins', dest='max_insert' ) parser.add_option( '', '--settings', dest='settings', help='' ) parser.add_option( '', '--end-to-end', dest='end_to_end', action="store_true" ) parser.add_option( '', '--local', dest='local', action="store_true" ) @@ -73,6 +75,11 @@ # Set up options. opts = '-p %s' % ( options.num_threads ) + if options.single_paired == 'paired': + if options.min_insert: + opts += ' -I %s' % options.min_insert + if options.max_insert: + opts += ' -X %s' % options.max_insert if options.settings == 'preSet': pass else: diff -r 6f15c9e850ab60fa027f0eccd445aad69c45eef9 -r be2577bfdbac49309f962b0b9a48ab11bac6159b tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -30,6 +30,8 @@ ## Second input only if input is paired-end. #if $singlePaired.sPaired == "paired" --input2=$singlePaired.input2 + -I $singlePaired.minInsert + -X $singlePaired.maxInsert #end if ## Set params. @@ -56,6 +58,8 @@ <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><param format="fastqsanger" name="input2" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> + <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> + <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional><conditional name="refGenomeSource"> 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: natefoo: Fix API history undelete, issue #763.
by Bitbucket 08 Jun '12

08 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6f15c9e850ab/ changeset: 6f15c9e850ab user: natefoo date: 2012-06-08 19:52:06 summary: Fix API history undelete, issue #763. affected #: 1 file diff -r d69ccbd53ea295e0a4ad0068317bf7238eb1f3b8 -r 6f15c9e850ab60fa027f0eccd445aad69c45eef9 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -153,6 +153,7 @@ POST /api/histories/deleted/{encoded_quota_id}/undelete Undeletes a quota """ + history_id = id history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) history.deleted = False trans.sa_session.add( history ) 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: jgoecks: Fix bug in setting Bowtie2 parameters.
by Bitbucket 08 Jun '12

08 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d69ccbd53ea2/ changeset: d69ccbd53ea2 user: jgoecks date: 2012-06-08 19:48:37 summary: Fix bug in setting Bowtie2 parameters. affected #: 1 file diff -r 2f2870f4f67d2198c69b44af688b5b37174459b0 -r d69ccbd53ea295e0a4ad0068317bf7238eb1f3b8 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -35,10 +35,12 @@ ## Set params. --settings=$params.settingsType - #if str($params.align_type) == "end_to_end": - --end-to-end --preset-alignment=$params.preset.align_preset_select - #else: - --local --preset-alignment=$params.preset.align_preset_select-local + #if $params.settingsType == "full": + #if str($params.align_type) == "end_to_end": + --end-to-end --preset-alignment=$params.preset.align_preset_select + #else: + --local --preset-alignment=$params.preset.align_preset_select-local + #end if #end if </command><inputs> 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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