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Merge pull request #54 from bwlang - parent tag copying for multiple workflow run output histories.

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This commit is contained in:
Dannon Baker
2012-07-22 18:02:43 -04:00
parent 97c4be251d 331d218056
commit 6442df74db
2 changed files with 124 additions and 109 deletions
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lib/galaxy/model/__init__.py
+117 -94
View File
@@ -102,7 +102,7 @@ class User( object, APIItem ):
class Job( object ):
"""
A job represents a request to run a tool given input datasets, tool
A job represents a request to run a tool given input datasets, tool
parameters, and output datasets.
"""
states = Bunch( NEW = 'new',
@@ -216,7 +216,7 @@ class Task( object ):
self.stdout = None
self.stderr = None
self.prepare_input_files_cmd = prepare_files_cmd
def set_state( self, state ):
self.state = state
@@ -285,7 +285,7 @@ class JobExternalOutputMetadata( object ):
class JobExportHistoryArchive( object ):
def __init__( self, job=None, history=None, dataset=None, compressed=False, \
history_attrs_filename=None, datasets_attrs_filename=None,
history_attrs_filename=None, datasets_attrs_filename=None,
jobs_attrs_filename=None ):
self.job = job
self.history = history
@@ -378,7 +378,7 @@ class History( object, UsesAnnotations ):
self.datasets = []
self.galaxy_sessions = []
def _next_hid( self ):
# TODO: override this with something in the database that ensures
# TODO: override this with something in the database that ensures
# better integrity
if len( self.datasets ) == 0:
return 1
@@ -435,6 +435,9 @@ class History( object, UsesAnnotations ):
# Copy annotation.
self.copy_item_annotation( db_session, self.user, self, target_user, new_history )
#Copy Tags
new_history.copy_tags_from(target_user=target_user, source_history=self)
# Copy HDAs.
if activatable:
hdas = self.activatable_datasets
@@ -495,6 +498,12 @@ class History( object, UsesAnnotations ):
rval = galaxy.datatypes.data.nice_size( rval )
return rval
def copy_tags_from(self,target_user,source_history):
for src_shta in source_history.tags:
new_shta = src_shta.copy()
new_shta.user = target_user
self.tags.append(new_shta)
class HistoryUserShareAssociation( object ):
def __init__( self ):
self.history = None
@@ -514,7 +523,7 @@ class Role( object, APIItem ):
api_collection_visible_keys = ( 'id', 'name' )
api_element_visible_keys = ( 'id', 'name', 'description', 'type' )
private_id = None
types = Bunch(
types = Bunch(
PRIVATE = 'private',
SYSTEM = 'system',
USER = 'user',
@@ -657,7 +666,7 @@ class Dataset( object ):
self.external_filename = external_filename
self._extra_files_path = extra_files_path
self.file_size = file_size
def get_file_name( self ):
if not self.external_filename:
assert self.id is not None, "ID must be set before filename used (commit the object)"
@@ -961,17 +970,17 @@ class DatasetInstance( object ):
session.flush()
return None
def get_metadata_dataset( self, trans, dataset_ext ):
"""
Returns an HDA that points to a metadata file which contains a
"""
Returns an HDA that points to a metadata file which contains a
converted data with the requested extension.
"""
for name, value in self.metadata.items():
# HACK: MetadataFile objects do not have a type/ext, so need to use metadata name
# to determine type.
if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, trans.app.model.MetadataFile ):
# HACK: MetadataFile objects cannot be used by tools, so return
# HACK: MetadataFile objects cannot be used by tools, so return
# a fake HDA that points to metadata file.
fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK,
fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK,
external_filename=value.file_name )
fake_hda = trans.app.model.HistoryDatasetAssociation( dataset=fake_dataset )
return fake_hda
@@ -1039,14 +1048,14 @@ class DatasetInstance( object ):
return self.datatype.get_display_applications_by_dataset( self, trans )
class HistoryDatasetAssociation( DatasetInstance ):
def __init__( self,
hid = None,
history = None,
copied_from_history_dataset_association = None,
copied_from_library_dataset_dataset_association = None,
def __init__( self,
hid = None,
history = None,
copied_from_history_dataset_association = None,
copied_from_library_dataset_dataset_association = None,
sa_session = None,
**kwd ):
# FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
# FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
# parameter is True so that the new object can be flushed. Is there a better way?
DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
self.hid = hid
@@ -1055,18 +1064,18 @@ class HistoryDatasetAssociation( DatasetInstance ):
self.copied_from_history_dataset_association = copied_from_history_dataset_association
self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association
def copy( self, copy_children = False, parent_id = None ):
hda = HistoryDatasetAssociation( hid=self.hid,
name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset = self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
hda = HistoryDatasetAssociation( hid=self.hid,
name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset = self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
copied_from_history_dataset_association=self )
object_session( self ).add( hda )
object_session( self ).flush()
@@ -1086,7 +1095,7 @@ class HistoryDatasetAssociation( DatasetInstance ):
# The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version.
library_dataset = replace_dataset
else:
# If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new
# If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new
# LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset.
library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info )
object_session( self ).add( library_dataset )
@@ -1094,17 +1103,17 @@ class HistoryDatasetAssociation( DatasetInstance ):
if not user:
# This should never happen since users must be authenticated to upload to a data library
user = self.history.user
ldda = LibraryDatasetDatasetAssociation( name=self.name,
ldda = LibraryDatasetDatasetAssociation( name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
library_dataset=library_dataset,
visible=self.visible,
deleted=self.deleted,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
copied_from_history_dataset_association=self,
user=user )
@@ -1202,7 +1211,7 @@ class HistoryDatasetAssociationDisplayAtAuthorization( object ):
self.history_dataset_association = hda
self.user = user
self.site = site
class HistoryDatasetAssociationSubset( object ):
def __init__(self, hda, subset, location):
self.hda = hda
@@ -1252,7 +1261,7 @@ class Library( object, APIItem ):
# inherited is not applicable at the library level. The get_contents
# param is passed by callers that are inheriting a template - these
# are usually new library datsets for which we want to include template
# fields on the upload form, but not necessarily the contents of the
# fields on the upload form, but not necessarily the contents of the
# inherited template saved for the parent.
info_association, inherited = self.get_info_association()
if info_association:
@@ -1271,7 +1280,7 @@ class Library( object, APIItem ):
roles.append( lp.role )
return roles
def get_display_name( self ):
# Library name can be either a string or a unicode object. If string,
# Library name can be either a string or a unicode object. If string,
# convert to unicode object assuming 'utf-8' format.
name = self.name
if isinstance( name, str ):
@@ -1329,7 +1338,7 @@ class LibraryFolder( object, APIItem ):
# not inherited ( we do not want to display the inherited contents ).
# (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
# contents. We'll use this behavior until we hear from the community that
# contents should not be inherited. If we don't hear anything for a while,
# contents should not be inherited. If we don't hear anything for a while,
# eliminate the old commented out behavior.
#if not inherited and get_contents:
if get_contents:
@@ -1344,7 +1353,7 @@ class LibraryFolder( object, APIItem ):
# This needs to be a list
return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ]
def get_display_name( self ):
# Library folder name can be either a string or a unicode object. If string,
# Library folder name can be either a string or a unicode object. If string,
# convert to unicode object assuming 'utf-8' format.
name = self.name
if isinstance( name, str ):
@@ -1451,7 +1460,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
user=None,
sa_session=None,
**kwd ):
# FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
# FIXME: sa_session is must be passed to DataSetInstance if the create_dataset
# parameter in kwd is True so that the new object can be flushed. Is there a better way?
DatasetInstance.__init__( self, sa_session=sa_session, **kwd )
if copied_from_history_dataset_association:
@@ -1461,17 +1470,17 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
self.library_dataset = library_dataset
self.user = user
def to_history_dataset_association( self, target_history, parent_id = None, add_to_history = False ):
hda = HistoryDatasetAssociation( name=self.name,
hda = HistoryDatasetAssociation( name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
copied_from_library_dataset_dataset_association=self,
history=target_history )
object_session( self ).add( hda )
@@ -1486,17 +1495,17 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
object_session( self ).flush()
return hda
def copy( self, copy_children = False, parent_id = None, target_folder = None ):
ldda = LibraryDatasetDatasetAssociation( name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
ldda = LibraryDatasetDatasetAssociation( name=self.name,
info=self.info,
blurb=self.blurb,
peek=self.peek,
tool_version=self.tool_version,
extension=self.extension,
dbkey=self.dbkey,
dataset=self.dataset,
visible=self.visible,
deleted=self.deleted,
parent_id=parent_id,
copied_from_library_dataset_dataset_association=self,
folder=target_folder )
object_session( self ).add( ldda )
@@ -1534,7 +1543,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
# See if we have any associated templatesThe get_contents
# param is passed by callers that are inheriting a template - these
# are usually new library datsets for which we want to include template
# fields on the upload form, but not necessarily the contents of the
# fields on the upload form, but not necessarily the contents of the
# inherited template saved for the parent.
info_association, inherited = self.get_info_association()
if info_association:
@@ -1546,7 +1555,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
# not inherited ( we do not want to display the inherited contents ).
# (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit
# contents. We'll use this behavior until we hear from the community that
# contents should not be inherited. If we don't hear anything for a while,
# contents should not be inherited. If we don't hear anything for a while,
# eliminate the old commented out behavior.
#if not inherited and get_contents:
if get_contents:
@@ -1663,15 +1672,15 @@ class Event( object ):
self.message = message
class GalaxySession( object ):
def __init__( self,
id=None,
user=None,
remote_host=None,
remote_addr=None,
referer=None,
current_history=None,
session_key=None,
is_valid=False,
def __init__( self,
id=None,
user=None,
remote_host=None,
remote_addr=None,
referer=None,
current_history=None,
session_key=None,
is_valid=False,
prev_session_id=None ):
self.id = id
self.user = user
@@ -1718,6 +1727,12 @@ class StoredWorkflow( object, APIItem):
self.latest_workflow_id = None
self.workflows = []
def copy_tags_from(self,target_user,source_workflow):
for src_swta in source_workflow.owner_tags:
new_swta = src_swta.copy()
new_swta.user = target_user
self.tags.append(new_swta)
class Workflow( object ):
def __init__( self ):
self.user = None
@@ -1797,7 +1812,7 @@ class MetadataFile( object ):
raise
# Return filename inside hashed directory
return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
class FormDefinition( object, APIItem ):
# The following form_builder classes are supported by the FormDefinition class.
@@ -1813,7 +1828,7 @@ class FormDefinition( object, APIItem ):
def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ):
self.name = name
self.desc = desc
self.fields = fields
self.fields = fields
self.form_definition_current = form_definition_current
self.type = form_type
self.layout = layout
@@ -2012,7 +2027,7 @@ class Request( object, APIItem ):
samples.append( sample )
return samples
def send_email_notification( self, trans, common_state, final_state=False ):
# Check if an email notification is configured to be sent when the samples
# Check if an email notification is configured to be sent when the samples
# are in this state
if self.notification and common_state.id not in self.notification[ 'sample_states' ]:
return
@@ -2036,13 +2051,13 @@ Number of samples: %(num_samples)s
All samples in state: %(sample_state)s
"""
values = dict( user=self.user.email,
request_name=self.name,
request_type=self.type.name,
request_state=self.state,
num_samples=str( len( self.samples ) ),
sample_state=common_state.name,
create_time=self.create_time,
values = dict( user=self.user.email,
request_name=self.name,
request_type=self.type.name,
request_state=self.state,
num_samples=str( len( self.samples ) ),
sample_state=common_state.name,
create_time=self.create_time,
submit_time=self.create_time )
body = body % values
# check if this is the final state of the samples
@@ -2207,7 +2222,7 @@ class RequestTypePermissions( object ):
class Sample( object, APIItem ):
# The following form_builder classes are supported by the Sample class.
supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ]
bulk_operations = Bunch( CHANGE_STATE = 'Change state',
bulk_operations = Bunch( CHANGE_STATE = 'Change state',
SELECT_LIBRARY = 'Select data library and folder' )
api_collection_visible_keys = ( 'id', 'name' )
def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None):
@@ -2290,8 +2305,8 @@ class Sample( object, APIItem ):
cmd = 'ssh %s "du -sh \'%s\'"' % ( login_str, filepath )
try:
output = pexpect.run( cmd,
events={ '.ssword:*': scp_configs['password']+'\r\n',
pexpect.TIMEOUT:print_ticks},
events={ '.ssword:*': scp_configs['password']+'\r\n',
pexpect.TIMEOUT:print_ticks},
timeout=10 )
except Exception, e:
return error_msg
@@ -2383,8 +2398,8 @@ class SampleRunAssociation( object ):
self.run = run
class UserAddress( object ):
def __init__( self, user=None, desc=None, name=None, institution=None,
address=None, city=None, state=None, postal_code=None,
def __init__( self, user=None, desc=None, name=None, institution=None,
address=None, city=None, state=None, postal_code=None,
country=None, phone=None ):
self.user = user
self.desc = desc
@@ -2493,8 +2508,8 @@ class VisualizationRevision( object ):
if not visualization:
visualization = self.visualization
return VisualizationRevision(
visualization=visualization,
return VisualizationRevision(
visualization=visualization,
title=self.title,
dbkey=self.dbkey,
config=self.config
@@ -2544,6 +2559,14 @@ class ItemTagAssociation ( object ):
self.value = None
self.user_value = None
def copy(self):
new_ta = type(self)()
new_ta.tag_id = self.tag_id
new_ta.user_tname = self.user_tname
new_ta.value = self.value
new_ta.user_value = self.user_value
return new_ta
class HistoryTagAssociation ( ItemTagAssociation ):
pass
@@ -2806,7 +2829,7 @@ class ToolVersion( object ):
if tva:
return sa_session.query( app.model.ToolVersion ) \
.filter( app.model.ToolVersion.table.c.id == tva.tool_id ) \
.first()
.first()
return None
def get_versions( self, app ):
sa_session = app.model.context.current
lib/galaxy/web/controllers/workflow.py
+7 -15
View File
@@ -508,7 +508,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
trans.response.set_content_type("image/svg+xml")
return self._workflow_to_svg_canvas( trans, stored ).standalone_xml()
@web.expose
@web.require_login( "use Galaxy workflows" )
def clone( self, trans, id ):
@@ -531,15 +530,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored )
if annotation_obj:
self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation )
# Clone tags.
for swta in stored.owner_tags:
new_swta = model.StoredWorkflowTagAssociation()
new_swta.tag = swta.tag
new_swta.user = trans.user
new_swta.user_tname = swta.user_tname
new_swta.user_value = swta.user_value
new_swta.value = swta.value
new_stored.tags.append( new_swta )
new_stored.copy_tags_from(trans.user,stored)
if not owner:
new_stored.name += " shared by '%s'" % stored.user.email
new_stored.user = user
@@ -918,11 +909,11 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
# TODO: handle the case where the imported workflow requires tools that are not available in
# the local Galaxy instance.
pass
# Provide user feedback.
workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( action='list' )
if response.status != 200:
return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) )
return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) )
if workflow.has_errors:
return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors. %s" % workflow_list_str )
if workflow.has_cycles:
@@ -1408,6 +1399,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
mx_ds_name = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( single_input ).name
nh_name = '%s on %s' % (nh_name, mx_ds_name)
new_history = trans.app.model.History( user=trans.user, name=nh_name )
new_history.copy_tags_from(trans.user, trans.get_history())
trans.sa_session.add( new_history )
target_history = new_history
else:
@@ -1834,9 +1826,9 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
trans.sa_session.flush()
return stored, missing_tool_tups
def _workflow_to_svg_canvas( self, trans, stored ):
def _workflow_to_svg_canvas( self, trans, stored ):
workflow = stored.latest_workflow
data = []