1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/5affe61170f7/ changeset: r5391:5affe61170f7 user: greg date: 2011-04-14 22:42:12 summary: Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0. affected #: 8 files (2.5 KB)

--- a/external_service_types/pacific_biosciences_smrt_portal.xml Thu Apr 14 14:34:39 2011 -0400 +++ b/external_service_types/pacific_biosciences_smrt_portal.xml Thu Apr 14 16:42:12 2011 -0400 @@ -2,9 +2,6 @@ <description></description><version>1</version><data_transfer_settings> - <!-- - <data_transfer protocol='scp' automatic_transfer='True' host='host' user_name='user_name' password='password' data_location='data_location' /> - --><data_transfer protocol='http' automatic_transfer='True' /></data_transfer_settings><run_details>

--- a/lib/galaxy/jobs/deferred/data_transfer.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/deferred/data_transfer.py Thu Apr 14 16:42:12 2011 -0400 @@ -4,8 +4,6 @@ import logging, urllib2, re, shutil

from galaxy import eggs -from galaxy.util import json -from string import Template from sqlalchemy import and_

from galaxy.util.odict import odict @@ -19,6 +17,8 @@

log = logging.getLogger( __name__ )

+__all__ = [ 'DataTransfer' ] + class DataTransfer( object ): check_interval = 15 dataset_name_re = re.compile( '(dataset\d+)_(name)' ) @@ -36,7 +36,10 @@ if job.params[ 'protocol' ] in [ 'http', 'https' ]: results = [] for result in job.params[ 'results' ].values(): - result[ 'transfer_job' ] = self.app.transfer_manager.new( protocol=job.params[ 'protocol' ], url=result[ 'url' ] ) + result[ 'transfer_job' ] = self.app.transfer_manager.new( protocol=job.params[ 'protocol' ], + name=result[ 'name' ], + datatype=result[ 'datatype' ], + url=result[ 'url' ] ) results.append( result ) elif job.params[ 'protocol' ] == 'scp': results = [] @@ -83,9 +86,9 @@ # Update the state of the relevant SampleDataset new_status = self.app.model.SampleDataset.transfer_status.ADD_TO_LIBRARY if protocol in [ 'http', 'https' ]: - result_dict = job.params[ 'results' ] - library_dataset_name = job.params[ 'result' ][ 'name' ] - extension = job.params[ 'result' ][ 'datatype' ] + result_dict = job.params[ 'result' ] + library_dataset_name = result_dict[ 'name' ] + extension = result_dict[ 'datatype' ] elif protocol in [ 'scp' ]: # In this case, job.params will be a dictionary that contains a key named 'result'. The value # of the result key is a dictionary that looks something like:

--- a/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Thu Apr 14 16:42:12 2011 -0400 @@ -3,6 +3,9 @@ produced by SMRT Portal. """ import logging, urllib2, re, shutil +from string import Template +from galaxy.util import json + from data_transfer import *

log = logging.getLogger( __name__ ) @@ -18,9 +21,16 @@ sample = kwd[ 'sample' ] smrt_job_id = kwd[ 'secondary_analysis_job_id' ] external_service = sample.request.type.get_external_service( 'pacific_biosciences_smrt_portal' ) + external_service.load_data_transfer_settings( trans ) + http_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.HTTP ] + if not http_configs[ 'automatic_transfer' ]: + raise Exception( "Manual data transfer using http is not yet supported." ) smrt_host = external_service.form_values.content[ 'host' ] - external_service_type_id = external_service.external_service_type_id - external_service_type = self.app.external_service_types.all_external_service_types[ external_service_type_id ] + external_service_type = external_service.get_external_service_type( trans ) + # TODO: is there a better way to store the protocol? + # external_service_type.data_transfer looks somethng like + # {'http': <galaxy.sample_tracking.data_transfer.HttpDataTransferFactory object at 0x1064239d0>} + protocol = external_service_type.data_transfer.keys()[0] results = {} for k, v in external_service.form_values.content.items(): match = self.dataset_name_re.match( k ) or self.dataset_datatype_re.match( k ) @@ -42,6 +52,7 @@ self.sa_session.add(sample) self.sa_session.flush() params = { 'type' : 'init_transfer', + 'protocol' : protocol, 'sample_id' : sample.id, 'results' : results, 'smrt_host' : smrt_host, @@ -50,6 +61,7 @@ self._associate_untransferred_datasets_with_sample( sample, external_service, results ) elif 'transfer_job_id' in kwd: params = { 'type' : 'finish_transfer', + 'protocol' : kwd[ 'result' ][ 'protocol' ], 'sample_id' : kwd[ 'sample_id' ], 'result' : kwd[ 'result' ], 'transfer_job_id' : kwd[ 'transfer_job_id' ] }

--- a/lib/galaxy/jobs/transfer_manager.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/jobs/transfer_manager.py Thu Apr 14 16:42:12 2011 -0400 @@ -30,14 +30,13 @@ if protocol in [ 'http', 'https' ]: if 'url' not in kwd: raise Exception( 'Missing required parameter "url".' ) - transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) elif protocol == 'scp': # TODO: add more checks here? if 'sample_dataset_id' not in kwd: raise Exception( 'Missing required parameter "sample_dataset_id".' ) if 'file_path' not in kwd: raise Exception( 'Missing required parameter "file_path".' ) - transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) + transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) self.sa_session.add( transfer_job ) self.sa_session.flush() return transfer_job

--- a/lib/galaxy/model/__init__.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/model/__init__.py Thu Apr 14 16:42:12 2011 -0400 @@ -1825,6 +1825,11 @@ scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer_obj.config.get( 'data_location', '' ), '' ) scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer_obj.config.get( 'rename_dataset', '' ), '' ) self.data_transfer[ self.data_transfer_protocol.SCP ] = scp_configs + if data_transfer_protocol == self.data_transfer_protocol.HTTP: + http_configs = {} + automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) + http_configs[ 'automatic_transfer' ] = util.string_as_bool( automatic_transfer ) + self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict )

--- a/lib/galaxy/sample_tracking/data_transfer.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/sample_tracking/data_transfer.py Thu Apr 14 16:42:12 2011 -0400 @@ -27,12 +27,23 @@ # Validate for name, value in self.config.items(): assert value, "'%s' attribute missing in 'data_transfer' element of type 'scp' in external_service_type xml config file: '%s'." % ( name, config_file ) - + +class HttpDataTransferFactory( DataTransferFactory ): + type = 'http' + def __init__( self ): + pass + def parse( self, config_file, elem ): + self.config = {} + self.config[ 'automatic_transfer' ] = elem.get( 'automatic_transfer' ) + # Validate + for name, value in self.config.items(): + assert value, "'%s' attribute missing in 'data_transfer' element of type 'http' in external_service_type xml config file: '%s'." % ( name, config_file ) + class FtpDataTransferFactory( DataTransferFactory ): type = 'ftp' def __init__( self ): pass def parse( self, elem ): pass - -data_transfer_factories = dict( [ ( data_transfer.type, data_transfer() ) for data_transfer in [ ScpDataTransferFactory, FtpDataTransferFactory ] ] ) + +data_transfer_factories = dict( [ ( data_transfer.type, data_transfer() ) for data_transfer in [ ScpDataTransferFactory, HttpDataTransferFactory, FtpDataTransferFactory ] ] )

--- a/lib/galaxy/sample_tracking/external_service_types.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/sample_tracking/external_service_types.py Thu Apr 14 16:42:12 2011 -0400 @@ -84,12 +84,16 @@ def parse_data_transfer_settings( self, root ): self.data_transfer = {} data_transfer_settings_elem = root.find( 'data_transfer_settings' ) - # Currently only data transfer using scp is supported. + # Currently only data transfer using scp or http is supported. for data_transfer_elem in data_transfer_settings_elem.findall( "data_transfer" ): if data_transfer_elem.get( 'protocol' ) == model.ExternalService.data_transfer_protocol.SCP: scp_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_protocol.SCP ] scp_data_transfer.parse( self.config_file, data_transfer_elem ) self.data_transfer[ model.ExternalService.data_transfer_protocol.SCP ] = scp_data_transfer + if data_transfer_elem.get( 'protocol' ) == model.ExternalService.data_transfer_protocol.HTTP: + http_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_protocol.HTTP ] + http_data_transfer.parse( self.config_file, data_transfer_elem ) + self.data_transfer[ model.ExternalService.data_transfer_protocol.HTTP ] = http_data_transfer def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' )

--- a/lib/galaxy/web/controllers/requests_admin.py Thu Apr 14 14:34:39 2011 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Apr 14 16:42:12 2011 -0400 @@ -671,7 +671,7 @@ if not scp_configs[ 'automatic_transfer' ]: deferred_plugin = 'ManualDataTransferPlugin' else: - raise Exception( "Automatic data transfer using scp is not yet suppored." ) + raise Exception( "Automatic data transfer using scp is not yet supported." ) trans.app.job_manager.deferred_job_queue.plugins[ deferred_plugin ].create_job( trans, sample=sample, sample_datasets=sample_datasets,

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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