def trackster(self, trans, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# define app configuration
app = { 'jscript' : "viz/trackster" }
# get dataset to add
id = kwargs.get( "id", None )
# get dataset to add
new_dataset_id = kwargs.get( "dataset_id", None )
# set up new browser if no id provided
if not id:
# use dbkey from dataset to be added or from incoming parameter
dbkey = None
if new_dataset_id:
decoded_id = self.decode_id( new_dataset_id )
hda = self.hda_manager.get_owned( decoded_id, trans.user, current_history=trans.user )
dbkey = hda.dbkey
if dbkey == '?':
dbkey = kwargs.get( "dbkey", None )
# save database key
app['default_dbkey'] = dbkey
else:
# load saved visualization
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
app['viz_config'] = self.get_visualization_config( trans, vis )
# backup id
app['id'] = id;
# add dataset id
app['add_dataset'] = new_dataset_id
# check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
app['gene_region'] = {
'chrom' : gene_region.chrom,
'start' : gene_region.start,
'end' : gene_region.end
}
# fill template
return trans.fill_template('galaxy.panels.mako', config = {'right_panel' : True, 'app' : app})
def trackster(self, trans, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# define app configuration
app = {'jscript' : "viz/trackster"}
# get dataset to add
id = kwargs.get("id", None)
# get dataset to add
new_dataset_id = kwargs.get("dataset_id", None)
# set up new browser if no id provided
if not id:
# use dbkey from dataset to be added or from incoming parameter
dbkey = None
if new_dataset_id:
decoded_id = self.decode_id(new_dataset_id)
hda = self.hda_manager.get_owned(decoded_id, trans.user, current_history=trans.user)
dbkey = hda.dbkey
if dbkey == '?':
dbkey = kwargs.get("dbkey", None)
# save database key
app['default_dbkey'] = dbkey
else:
# load saved visualization
vis = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
app['viz_config'] = self.get_visualization_config(trans, vis)
# backup id
app['id'] = id
# add dataset id
app['add_dataset'] = new_dataset_id
# check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
app['gene_region'] = {
'chrom' : gene_region.chrom,
'start' : gene_region.start,
'end' : gene_region.end
}
# fill template
return trans.fill_template('galaxy.panels.mako', config={'right_panel': True, 'app': app})
def trackster(self, trans, id=None, **kwargs):
"""
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
# Get dataset to add.
new_dataset_id = kwargs.get( "dataset_id", None )
# Check for gene region
gene_region = GenomeRegion.from_str(kwargs.get("gene_region", ""))
# Set up new browser if no id provided.
if not id:
# Use dbkey from dataset to be added or from incoming parameter.
dbkey = None
if new_dataset_id:
dbkey = self.get_dataset( trans, new_dataset_id ).dbkey
if dbkey == '?':
dbkey = kwargs.get( "dbkey", None )
# fill template
return trans.fill_template( "tracks/browser.mako", viewport_config=gene_region.__dict__, add_dataset=new_dataset_id, default_dbkey=dbkey )
# Display saved visualization.
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
viz_config = self.get_visualization_config( trans, vis )
# Update gene region of saved visualization if user parses a new gene region in the url
if gene_region.chrom is not None:
viz_config['viewport']['chrom'] = gene_region.chrom
viz_config['viewport']['start'] = gene_region.start
viz_config['viewport']['end'] = gene_region.end
'''
FIXME:
if new_dataset is not None:
if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]:
new_dataset = None # Already in browser, so don't add
'''
# fill template
return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset_id )
def _rerun_tool(self, trans, payload, **kwargs):
"""
Rerun a tool to produce a new output dataset that corresponds to a
dataset that a user is currently viewing.
"""
#
# TODO: refactor to use same code as run_tool.
#
# Run tool on region if region is specificied.
run_on_regions = False
regions = payload.get('regions', None)
if regions:
if isinstance(regions, dict):
# Regions is a single region.
regions = [GenomeRegion.from_dict(regions)]
elif isinstance(regions, list):
# There is a list of regions.
regions = [GenomeRegion.from_dict(r) for r in regions]
if len(regions) > 1:
# Sort by chrom name, start so that data is not fetched out of order.
regions = sorted(regions,
key=lambda r: (r.chrom.lower(), r.start))
# Merge overlapping regions so that regions do not overlap
# and hence data is not included multiple times.
prev = regions[0]
cur = regions[1]
index = 1
while True:
if cur.chrom == prev.chrom and cur.start <= prev.end:
# Found overlapping regions, so join them into prev.
prev.end = cur.end
del regions[index]
else:
# No overlap, move to next region.
prev = cur
index += 1
# Get next region or exit.
if index == len(regions):
# Done.
break
else:
cur = regions[index]
run_on_regions = True
# Dataset check.
decoded_dataset_id = self.decode_id(payload.get('target_dataset_id'))
original_dataset = self.hda_manager.get_accessible(decoded_dataset_id,
user=trans.user)
original_dataset = self.hda_manager.error_if_uploading(
original_dataset)
msg = self.hda_manager.data_conversion_status(original_dataset)
if msg:
return msg
# Set tool parameters--except non-hidden dataset parameters--using combination of
# job's previous parameters and incoming parameters. Incoming parameters
# have priority.
#
original_job = self.hda_manager.creating_job(original_dataset)
tool = trans.app.toolbox.get_tool(original_job.tool_id)
if not tool or not tool.allow_user_access(trans.user):
return trans.app.model.Dataset.conversion_messages.NO_TOOL
tool_params = dict([(p.name, p.value)
for p in original_job.parameters])
# TODO: rather than set new inputs using dict of json'ed value, unpack parameters and set using set_param_value below.
# TODO: need to handle updates to conditional parameters; conditional
# params are stored in dicts (and dicts within dicts).
new_inputs = payload['inputs']
tool_params.update(
dict([(key, dumps(value)) for key, value in new_inputs.items()
if key in tool.inputs and value is not None]))
tool_params = tool.params_from_strings(tool_params, self.app)
#
# If running tool on region, convert input datasets (create indices) so
# that can regions of data can be quickly extracted.
#
data_provider_registry = trans.app.data_provider_registry
messages_list = []
if run_on_regions:
for jida in original_job.input_datasets:
input_dataset = jida.dataset
data_provider = data_provider_registry.get_data_provider(
trans, original_dataset=input_dataset, source='data')
if data_provider and (not data_provider.converted_dataset
or data_provider.converted_dataset.state
!= trans.app.model.Dataset.states.OK):
# Can convert but no converted dataset yet, so return message about why.
data_sources = input_dataset.datatype.data_sources
msg = input_dataset.convert_dataset(
trans, data_sources['data'])
if msg is not None:
messages_list.append(msg)
# Return any messages generated during conversions.
return_message = self._get_highest_priority_msg(messages_list)
if return_message:
return return_message
#
# Set target history (the history that tool will use for inputs/outputs).
# If user owns dataset, put new data in original dataset's history; if
# user does not own dataset (and hence is accessing dataset via sharing),
# put new data in user's current history.
#
if original_dataset.history.user == trans.user:
target_history = original_dataset.history
else:
target_history = trans.get_history(create=True)
hda_permissions = trans.app.security_agent.history_get_default_permissions(
target_history)
def set_param_value(param_dict, param_name, param_value):
"""
Set new parameter value in a tool's parameter dictionary.
"""
# Recursive function to set param value.
def set_value(param_dict, group_name, group_index, param_name,
param_value):
if group_name in param_dict:
param_dict[group_name][group_index][
param_name] = param_value
return True
elif param_name in param_dict:
param_dict[param_name] = param_value
return True
else:
# Recursive search.
return_val = False
for value in param_dict.values():
if isinstance(value, dict):
return_val = set_value(value, group_name,
group_index, param_name,
param_value)
if return_val:
return return_val
return False
# Parse parameter name if necessary.
if param_name.find("|") == -1:
# Non-grouping parameter.
group_name = group_index = None
else:
# Grouping parameter.
group, param_name = param_name.split("|")
index = group.rfind("_")
group_name = group[:index]
group_index = int(group[index + 1:])
return set_value(param_dict, group_name, group_index, param_name,
param_value)
# Set parameters based tool's trackster config.
params_set = {}
for action in tool.trackster_conf.actions:
success = False
for joda in original_job.output_datasets:
if joda.name == action.output_name:
set_param_value(tool_params, action.name, joda.dataset)
params_set[action.name] = True
success = True
break
if not success:
return trans.app.model.Dataset.conversion_messages.ERROR
#
# Set input datasets for tool. If running on regions, extract and use subset
# when possible.
#
if run_on_regions:
regions_str = ",".join([str(r) for r in regions])
for jida in original_job.input_datasets:
# If param set previously by config actions, do nothing.
if jida.name in params_set:
continue
input_dataset = jida.dataset
if input_dataset is None: # optional dataset and dataset wasn't selected
tool_params[jida.name] = None
elif run_on_regions and 'data' in input_dataset.datatype.data_sources:
# Dataset is indexed and hence a subset can be extracted and used
# as input.
# Look for subset.
subset_dataset_association = trans.sa_session.query(trans.app.model.HistoryDatasetAssociationSubset) \
.filter_by(hda=input_dataset, location=regions_str) \
.first()
if subset_dataset_association:
# Data subset exists.
subset_dataset = subset_dataset_association.subset
else:
# Need to create subset.
data_source = input_dataset.datatype.data_sources['data']
input_dataset.get_converted_dataset(trans, data_source)
input_dataset.get_converted_dataset_deps(
trans, data_source)
# Create new HDA for input dataset's subset.
new_dataset = trans.app.model.HistoryDatasetAssociation(
extension=input_dataset.ext,
dbkey=input_dataset.dbkey,
create_dataset=True,
sa_session=trans.sa_session,
name="Subset [%s] of data %i" %
(regions_str, input_dataset.hid),
visible=False)
target_history.add_dataset(new_dataset)
trans.sa_session.add(new_dataset)
trans.app.security_agent.set_all_dataset_permissions(
new_dataset.dataset, hda_permissions)
# Write subset of data to new dataset
data_provider = data_provider_registry.get_data_provider(
trans, original_dataset=input_dataset, source='data')
trans.app.object_store.create(new_dataset.dataset)
data_provider.write_data_to_file(regions,
new_dataset.file_name)
# TODO: (a) size not working; (b) need to set peek.
new_dataset.set_size()
new_dataset.info = "Data subset for trackster"
new_dataset.set_dataset_state(
trans.app.model.Dataset.states.OK)
# Set metadata.
# TODO: set meta internally if dataset is small enough?
trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
trans.app.datatypes_registry.
set_external_metadata_tool,
trans,
incoming={'input1': new_dataset},
overwrite=False,
job_params={"source": "trackster"})
# Add HDA subset association.
subset_association = trans.app.model.HistoryDatasetAssociationSubset(
hda=input_dataset,
subset=new_dataset,
location=regions_str)
trans.sa_session.add(subset_association)
subset_dataset = new_dataset
trans.sa_session.flush()
# Add dataset to tool's parameters.
if not set_param_value(tool_params, jida.name, subset_dataset):
return {
"error": True,
"message": "error setting parameter %s" % jida.name
}
#
# Execute tool and handle outputs.
#
try:
subset_job, subset_job_outputs = tool.execute(
trans,
incoming=tool_params,
history=target_history,
job_params={"source": "trackster"})
except Exception as e:
# Lots of things can go wrong when trying to execute tool.
return {
"error": True,
"message": e.__class__.__name__ + ": " + str(e)
}
if run_on_regions:
for output in subset_job_outputs.values():
output.visible = False
trans.sa_session.flush()
#
# Return new track that corresponds to the original dataset.
#
output_name = None
for joda in original_job.output_datasets:
if joda.dataset == original_dataset:
output_name = joda.name
break
for joda in subset_job.output_datasets:
if joda.name == output_name:
output_dataset = joda.dataset
dataset_dict = output_dataset.to_dict()
dataset_dict['id'] = trans.security.encode_id(dataset_dict['id'])
dataset_dict['track_config'] = self.get_new_track_config(
trans, output_dataset)
return dataset_dict
def _rerun_tool( self, trans, payload, **kwargs ):
"""
Rerun a tool to produce a new output dataset that corresponds to a
dataset that a user is currently viewing.
"""
#
# TODO: refactor to use same code as run_tool.
#
# Run tool on region if region is specificied.
run_on_regions = False
regions = payload.get( 'regions', None )
if regions:
if isinstance( regions, dict ):
# Regions is a single region.
regions = [ GenomeRegion.from_dict( regions ) ]
elif isinstance( regions, list ):
# There is a list of regions.
regions = [ GenomeRegion.from_dict( r ) for r in regions ]
if len( regions ) > 1:
# Sort by chrom name, start so that data is not fetched out of order.
regions = sorted(regions, key=lambda r: (r.chrom.lower(), r.start))
# Merge overlapping regions so that regions do not overlap
# and hence data is not included multiple times.
prev = regions[0]
cur = regions[1]
index = 1
while True:
if cur.chrom == prev.chrom and cur.start <= prev.end:
# Found overlapping regions, so join them into prev.
prev.end = cur.end
del regions[ index ]
else:
# No overlap, move to next region.
prev = cur
index += 1
# Get next region or exit.
if index == len( regions ):
# Done.
break
else:
cur = regions[ index ]
run_on_regions = True
# Dataset check.
original_dataset = self.get_dataset( trans, payload[ 'target_dataset_id' ], check_ownership=False, check_accessible=True )
msg = self.check_dataset_state( trans, original_dataset )
if msg:
return msg
#
# Set tool parameters--except non-hidden dataset parameters--using combination of
# job's previous parameters and incoming parameters. Incoming parameters
# have priority.
#
original_job = self.get_hda_job( original_dataset )
tool = trans.app.toolbox.get_tool( original_job.tool_id )
if not tool:
return trans.app.model.Dataset.conversion_messages.NO_TOOL
tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] )
# TODO: rather than set new inputs using dict of json'ed value, unpack parameters and set using set_param_value below.
# TODO: need to handle updates to conditional parameters; conditional
# params are stored in dicts (and dicts within dicts).
new_inputs = payload[ 'inputs' ]
tool_params.update( dict( [ ( key, to_json_string( value ) ) for key, value in new_inputs.items() if key in tool.inputs and new_inputs[ key ] is not None ] ) )
tool_params = tool.params_from_strings( tool_params, self.app )
#
# If running tool on region, convert input datasets (create indices) so
# that can regions of data can be quickly extracted.
#
data_provider_registry = trans.app.data_provider_registry
messages_list = []
if run_on_regions:
for jida in original_job.input_datasets:
input_dataset = jida.dataset
data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' )
if data_provider and ( not data_provider.converted_dataset
or data_provider.converted_dataset.state != trans.app.model.Dataset.states.OK ):
# Can convert but no converted dataset yet, so return message about why.
data_sources = input_dataset.datatype.data_sources
msg = input_dataset.convert_dataset( trans, data_sources[ 'data' ] )
if msg is not None:
messages_list.append( msg )
# Return any messages generated during conversions.
return_message = self._get_highest_priority_msg( messages_list )
if return_message:
return return_message
#
# Set target history (the history that tool will use for inputs/outputs).
# If user owns dataset, put new data in original dataset's history; if
# user does not own dataset (and hence is accessing dataset via sharing),
# put new data in user's current history.
#
if original_dataset.history.user == trans.user:
target_history = original_dataset.history
else:
target_history = trans.get_history( create=True )
hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history )
def set_param_value( param_dict, param_name, param_value ):
"""
Set new parameter value in a tool's parameter dictionary.
"""
# Recursive function to set param value.
def set_value( param_dict, group_name, group_index, param_name, param_value ):
if group_name in param_dict:
param_dict[ group_name ][ group_index ][ param_name ] = param_value
return True
elif param_name in param_dict:
param_dict[ param_name ] = param_value
return True
else:
# Recursive search.
return_val = False
for value in param_dict.values():
if isinstance( value, dict ):
return_val = set_value( value, group_name, group_index, param_name, param_value)
if return_val:
return return_val
return False
# Parse parameter name if necessary.
if param_name.find( "|" ) == -1:
# Non-grouping parameter.
group_name = group_index = None
else:
# Grouping parameter.
group, param_name = param_name.split( "|" )
index = group.rfind( "_" )
group_name = group[ :index ]
group_index = int( group[ index + 1: ] )
return set_value( param_dict, group_name, group_index, param_name, param_value )
# Set parameters based tool's trackster config.
params_set = {}
for action in tool.trackster_conf.actions:
success = False
for joda in original_job.output_datasets:
if joda.name == action.output_name:
set_param_value( tool_params, action.name, joda.dataset )
params_set[ action.name ] = True
success = True
break
if not success:
return trans.app.model.Dataset.conversion_messages.ERROR
#
# Set input datasets for tool. If running on regions, extract and use subset
# when possible.
#
if run_on_regions:
regions_str = ",".join( [ str( r ) for r in regions ] )
for jida in original_job.input_datasets:
# If param set previously by config actions, do nothing.
if jida.name in params_set:
continue
input_dataset = jida.dataset
if input_dataset is None: # optional dataset and dataset wasn't selected
tool_params[ jida.name ] = None
elif run_on_regions and 'data' in input_dataset.datatype.data_sources:
# Dataset is indexed and hence a subset can be extracted and used
# as input.
# Look for subset.
subset_dataset_association = trans.sa_session.query( trans.app.model.HistoryDatasetAssociationSubset ) \
.filter_by( hda=input_dataset, location=regions_str ) \
.first()
if subset_dataset_association:
# Data subset exists.
subset_dataset = subset_dataset_association.subset
else:
# Need to create subset.
data_source = input_dataset.datatype.data_sources[ 'data' ]
converted_dataset = input_dataset.get_converted_dataset( trans, data_source )
deps = input_dataset.get_converted_dataset_deps( trans, data_source )
# Create new HDA for input dataset's subset.
new_dataset = trans.app.model.HistoryDatasetAssociation( extension=input_dataset.ext, \
dbkey=input_dataset.dbkey, \
create_dataset=True, \
sa_session=trans.sa_session,
name="Subset [%s] of data %i" % \
( regions_str, input_dataset.hid ),
visible=False )
target_history.add_dataset( new_dataset )
trans.sa_session.add( new_dataset )
trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions )
# Write subset of data to new dataset
data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' )
trans.app.object_store.create( new_dataset.dataset )
data_provider.write_data_to_file( regions, new_dataset.file_name )
# TODO: (a) size not working; (b) need to set peek.
new_dataset.set_size()
new_dataset.info = "Data subset for trackster"
new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK )
# Set metadata.
# TODO: set meta internally if dataset is small enough?
trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool,
trans, incoming={ 'input1': new_dataset },
overwrite=False, job_params={ "source" : "trackster" } )
# Add HDA subset association.
subset_association = trans.app.model.HistoryDatasetAssociationSubset( hda=input_dataset, subset=new_dataset, location=regions_str )
trans.sa_session.add( subset_association )
subset_dataset = new_dataset
trans.sa_session.flush()
# Add dataset to tool's parameters.
if not set_param_value( tool_params, jida.name, subset_dataset ):
return { "error" : True, "message" : "error setting parameter %s" % jida.name }
#
# Execute tool and handle outputs.
#
try:
subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params,
history=target_history,
job_params={ "source" : "trackster" } )
except Exception, e:
# Lots of things can go wrong when trying to execute tool.
return { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) }