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- 10008 discussions
10 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/93dda9c3ded3
changeset: 2541:93dda9c3ded3
user: rc
date: Thu Aug 06 10:48:14 2009 -0400
description:
Merge with f4f915fa16605ebbcf16ab9969c10e9380e402c6
0 file(s) affected in this change:
diffs (60 lines):
diff -r c819c7c0c1a6 -r 93dda9c3ded3 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py Thu Aug 06 10:34:01 2009 -0400
+++ b/lib/galaxy/datatypes/sequence.py Thu Aug 06 10:48:14 2009 -0400
@@ -334,28 +334,37 @@
"""
#these metadata values are not accessable by users, always overwrite
+ try:
+ maf_reader = bx.align.maf.Reader( open( dataset.file_name ) )
+ except:
+ return #not a maf file
species = []
species_chromosomes = {}
indexes = bx.interval_index_file.Indexes()
- try:
- maf_reader = bx.align.maf.Reader( open( dataset.file_name ) )
- while True:
- pos = maf_reader.file.tell()
- block = maf_reader.next()
- if block is None: break
- for c in block.components:
- spec = c.src
- chrom = None
- if "." in spec:
- spec, chrom = spec.split( ".", 1 )
- if spec not in species:
- species.append(spec)
- species_chromosomes[spec] = []
- if chrom and chrom not in species_chromosomes[spec]:
- species_chromosomes[spec].append( chrom )
- indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos, max=c.src_size )
- except: #bad MAF file
- pass
+ while True:
+ pos = maf_reader.file.tell()
+ block = maf_reader.next()
+ if block is None: break
+ for c in block.components:
+ spec = c.src
+ chrom = None
+ if "." in spec:
+ spec, chrom = spec.split( ".", 1 )
+ if spec not in species:
+ species.append(spec)
+ species_chromosomes[spec] = []
+ if chrom and chrom not in species_chromosomes[spec]:
+ species_chromosomes[spec].append( chrom )
+ forward_strand_start = c.forward_strand_start
+ forward_strand_end = c.forward_strand_end
+ try:
+ forward_strand_start = int( forward_strand_start )
+ forward_strand_end = int( forward_strand_end )
+ except ValueError:
+ continue #start and end are not integers, can't add component to index, goto next component
+ if forward_strand_end > forward_strand_start:
+ #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed
+ indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size )
dataset.metadata.species = species
#only overwrite the contents if our newly determined chromosomes don't match stored
chrom_file = dataset.metadata.species_chromosomes
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/c819c7c0c1a6
changeset: 2540:c819c7c0c1a6
user: rc
date: Thu Aug 06 10:34:01 2009 -0400
description:
Cleaned up unwanted code
2 file(s) affected in this change:
lib/galaxy/model/mapping.py
lib/galaxy/model/migrate/versions/0012_user_address.py
diffs (72 lines):
diff -r 24ccfa887fcd -r c819c7c0c1a6 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Thu Aug 06 09:52:59 2009 -0400
+++ b/lib/galaxy/model/mapping.py Thu Aug 06 10:34:01 2009 -0400
@@ -598,13 +598,6 @@
Column( "state", TrimmedString( 255 ), index=True ),
Column( "deleted", Boolean, index=True, default=False ) )
-RequestState_table = Table('request_state', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ))
-
Sample.table = Table('sample', metadata,
Column( "id", Integer, primary_key=True),
Column( "create_time", DateTime, default=now ),
diff -r 24ccfa887fcd -r c819c7c0c1a6 lib/galaxy/model/migrate/versions/0012_user_address.py
--- a/lib/galaxy/model/migrate/versions/0012_user_address.py Thu Aug 06 09:52:59 2009 -0400
+++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Thu Aug 06 10:34:01 2009 -0400
@@ -40,13 +40,6 @@
Column( "deleted", Boolean, index=True, default=False ),
Column( "purged", Boolean, index=True, default=False ) )
-#RequestState_table = Table('request_state', metadata,
-# Column( "id", Integer, primary_key=True),
-# Column( "create_time", DateTime, default=now ),
-# Column( "update_time", DateTime, default=now, onupdate=now ),
-# Column( "name", TrimmedString( 255 ), nullable=False ),
-# Column( "desc", TEXT ))
-
def upgrade():
# Load existing tables
metadata.reflect()
@@ -56,10 +49,6 @@
UserAddress_table.create()
except Exception, e:
log.debug( "Creating user_address table failed: %s" % str( e ) )
-# try:
-# RequestState_table.create()
-# except Exception, e:
-# log.debug( "Creating request_state table failed: %s" % str( e ) )
# Add 1 column to the request_type table
try:
@@ -92,25 +81,7 @@
assert col is Request_table.c.state
except Exception, e:
log.debug( "Adding column 'state' to request table failed: %s" % ( str( e ) ) )
-#
-# # new column which points to the current state in the request_state table
-# try:
-# col = Column( "request_state_id", Integer, index=True )
-# col.create( Request_table )
-# assert col is Request_table.c.request_state_id
-# except Exception, e:
-# log.debug( "Adding column 'request_state_id' to request table failed: %s" % ( str( e ) ) )
-# # Add 1 foreign key constraint to the form_definition_current table
-# if RequestState_table and Request_table:
-# try:
-# cons = ForeignKeyConstraint( [Request_table.c.request_state_id],
-# [RequestState_table.c.id],
-# name='request_request_state_id_fk' )
-# # Create the constraint
-# cons.create()
-# except Exception, e:
-# log.debug( "Adding foreign key constraint 'request_request_state_id_fk' to table 'request' failed: %s" % ( str( e ) ) )
-
+
def downgrade():
pass
1
0
10 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/f4f915fa1660
changeset: 2539:f4f915fa1660
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Aug 06 10:43:28 2009 -0400
description:
Fix for Maf.set_meta() when a component is provided that has a length of zero.
1 file(s) affected in this change:
lib/galaxy/datatypes/sequence.py
diffs (60 lines):
diff -r 24ccfa887fcd -r f4f915fa1660 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py Thu Aug 06 09:52:59 2009 -0400
+++ b/lib/galaxy/datatypes/sequence.py Thu Aug 06 10:43:28 2009 -0400
@@ -334,28 +334,37 @@
"""
#these metadata values are not accessable by users, always overwrite
+ try:
+ maf_reader = bx.align.maf.Reader( open( dataset.file_name ) )
+ except:
+ return #not a maf file
species = []
species_chromosomes = {}
indexes = bx.interval_index_file.Indexes()
- try:
- maf_reader = bx.align.maf.Reader( open( dataset.file_name ) )
- while True:
- pos = maf_reader.file.tell()
- block = maf_reader.next()
- if block is None: break
- for c in block.components:
- spec = c.src
- chrom = None
- if "." in spec:
- spec, chrom = spec.split( ".", 1 )
- if spec not in species:
- species.append(spec)
- species_chromosomes[spec] = []
- if chrom and chrom not in species_chromosomes[spec]:
- species_chromosomes[spec].append( chrom )
- indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos, max=c.src_size )
- except: #bad MAF file
- pass
+ while True:
+ pos = maf_reader.file.tell()
+ block = maf_reader.next()
+ if block is None: break
+ for c in block.components:
+ spec = c.src
+ chrom = None
+ if "." in spec:
+ spec, chrom = spec.split( ".", 1 )
+ if spec not in species:
+ species.append(spec)
+ species_chromosomes[spec] = []
+ if chrom and chrom not in species_chromosomes[spec]:
+ species_chromosomes[spec].append( chrom )
+ forward_strand_start = c.forward_strand_start
+ forward_strand_end = c.forward_strand_end
+ try:
+ forward_strand_start = int( forward_strand_start )
+ forward_strand_end = int( forward_strand_end )
+ except ValueError:
+ continue #start and end are not integers, can't add component to index, goto next component
+ if forward_strand_end > forward_strand_start:
+ #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed
+ indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size )
dataset.metadata.species = species
#only overwrite the contents if our newly determined chromosomes don't match stored
chrom_file = dataset.metadata.species_chromosomes
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/24ccfa887fcd
changeset: 2538:24ccfa887fcd
user: rc
date: Thu Aug 06 09:52:59 2009 -0400
description:
LIMS enhancements
- Requests page now displays all samples in grid layout
- New samples UI
- Requests states added
- CSV import for samples
- User address management
- New AddressField in form_builder
- Deletion added for forms, request types, requests & samples
- Editing added for requests and samples
- Grid filtering added for requests, forms, request types
24 file(s) affected in this change:
lib/galaxy/model/__init__.py
lib/galaxy/model/mapping.py
lib/galaxy/model/migrate/versions/0009_request_table.py
lib/galaxy/model/migrate/versions/0012_user_address.py
lib/galaxy/web/controllers/admin.py
lib/galaxy/web/controllers/forms.py
lib/galaxy/web/controllers/requests.py
lib/galaxy/web/controllers/requests_admin.py
lib/galaxy/web/controllers/user.py
lib/galaxy/web/form_builder.py
lib/galaxy/web/framework/helpers/grids.py
templates/admin/forms/create_form.mako
templates/admin/forms/edit_form.mako
templates/admin/forms/manage_forms.mako
templates/admin/requests/grid.mako
templates/admin/requests/manage_request_types.mako
templates/admin/samples/bar_codes.mako
templates/requests/edit_request.mako
templates/requests/grid.mako
templates/requests/new_request.mako
templates/requests/select_request_type.mako
templates/requests/show_request.mako
templates/user/address.mako
templates/user/index.mako
diffs (2925 lines):
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/model/__init__.py Thu Aug 06 09:52:59 2009 -0400
@@ -1121,15 +1121,18 @@
self.content = content
class Request( object ):
+ states = Bunch( UNSUBMITTED = 'Unsubmitted',
+ SUBMITTED = 'Submitted',
+ COMPLETE = 'Complete')
def __init__(self, name=None, desc=None, request_type=None, user=None,
- form_values=None, library=None, submitted=False):
+ form_values=None, library=None, state=False):
self.name = name
self.desc = desc
self.type = request_type
self.values = form_values
self.user = user
self.library = library
- self.submitted = submitted
+ self.state = state
self.samples_list = []
def add_sample(self, sample_name=None, sample_desc=None, sample_values=None):
# create a form_values row
@@ -1151,6 +1154,18 @@
if s.name == sample_name:
return s
return False
+ def submitted(self):
+ if self.state == self.states.SUBMITTED:
+ return True
+ return False
+ def unsubmitted(self):
+ if self.state == self.states.UNSUBMITTED:
+ return True
+ return False
+ def complete(self):
+ if self.state == self.states.COMPLETE:
+ return True
+ return False
class RequestType( object ):
def __init__(self, name=None, desc=None, request_form=None, sample_form=None):
@@ -1160,12 +1175,12 @@
self.sample_form = sample_form
class Sample( object ):
- def __init__(self, name=None, desc=None, request=None, form_values=None):
+ def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None):
self.name = name
self.desc = desc
self.request = request
self.values = form_values
-
+ self.bar_code = bar_code
def current_state(self):
return self.events[0].state
@@ -1180,6 +1195,37 @@
self.sample = sample
self.state = sample_state
self.comment = comment
+
+class UserAddress( object ):
+ 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
+ self.name = name
+ self.institution = institution
+ self.address = address
+ self.city = city
+ self.state = state
+ self.postal_code = postal_code
+ self.country = country
+ self.phone = phone
+ def display(self):
+ return self.name+'<br/>'+ \
+ self.institution+'<br/>'+ \
+ self.address+'<br/>'+ \
+ self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
+ self.country+'<br/>'+ \
+ 'Phone: '+self.phone
+ def get_html(self):
+ return self.name+'<br/>'+ \
+ self.institution+'<br/>'+ \
+ self.address+'<br/>'+ \
+ self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
+ self.country+'<br/>'+ \
+ 'Phone: '+self.phone
+
+
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/model/mapping.py Thu Aug 06 09:52:59 2009 -0400
@@ -46,7 +46,24 @@
Column( "external", Boolean, default=False ),
Column( "deleted", Boolean, index=True, default=False ),
Column( "purged", Boolean, index=True, default=False ) )
-
+
+UserAddress.table = Table( "user_address", metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "desc", TrimmedString( 255 )),
+ Column( "name", TrimmedString( 255 ), nullable=False),
+ Column( "institution", TrimmedString( 255 )),
+ Column( "address", TrimmedString( 255 ), nullable=False),
+ Column( "city", TrimmedString( 255 ), nullable=False),
+ Column( "state", TrimmedString( 255 ), nullable=False),
+ Column( "postal_code", TrimmedString( 255 ), nullable=False),
+ Column( "country", TrimmedString( 255 ), nullable=False),
+ Column( "phone", TrimmedString( 255 )),
+ Column( "deleted", Boolean, index=True, default=False ),
+ Column( "purged", Boolean, index=True, default=False ) )
+
History.table = Table( "history", metadata,
Column( "id", Integer, primary_key=True),
Column( "create_time", DateTime, default=now ),
@@ -558,7 +575,8 @@
Column( "name", TrimmedString( 255 ), nullable=False ),
Column( "desc", TEXT ),
Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) )
+ Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "deleted", Boolean, index=True, default=False ) )
FormValues.table = Table('form_values', metadata,
Column( "id", Integer, primary_key=True),
@@ -577,8 +595,15 @@
Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
- Column( "submitted", Boolean, index=True, default=False ),
+ Column( "state", TrimmedString( 255 ), index=True ),
Column( "deleted", Boolean, index=True, default=False ) )
+
+RequestState_table = Table('request_state', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "name", TrimmedString( 255 ), nullable=False ),
+ Column( "desc", TEXT ))
Sample.table = Table('sample', metadata,
Column( "id", Integer, primary_key=True),
@@ -615,13 +640,14 @@
# relationships between the model objects.
assign_mapper( context, Sample, Sample.table,
- properties=dict( events=relation( SampleEvent, backref="sample",
- order_by=desc(SampleEvent.table.c.update_time) ),
- values=relation( FormValues,
- primaryjoin=( Sample.table.c.form_values_id == FormValues.table.c.id ) ),
- request=relation( Request,
- primaryjoin=( Sample.table.c.request_id == Request.table.c.id ) ),
- ) )
+ properties=dict(
+ events=relation( SampleEvent, backref="sample",
+ order_by=desc(SampleEvent.table.c.update_time) ),
+ values=relation( FormValues,
+ primaryjoin=( Sample.table.c.form_values_id == FormValues.table.c.id ) ),
+ request=relation( Request,
+ primaryjoin=( Sample.table.c.request_id == Request.table.c.id ) ),
+ ) )
assign_mapper( context, FormValues, FormValues.table,
properties=dict( form_definition=relation( FormDefinition,
@@ -673,6 +699,15 @@
assign_mapper( context, SampleState, SampleState.table,
properties=None )
+
+assign_mapper( context, UserAddress, UserAddress.table,
+ properties=dict(
+ user=relation( User,
+ primaryjoin=( UserAddress.table.c.user_id == User.table.c.id ),
+ backref='addresses',
+ order_by=desc(UserAddress.table.c.update_time)),
+ ) )
+
assign_mapper( context, ValidationError, ValidationError.table )
@@ -749,7 +784,9 @@
galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ),
stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user",
cascade="all, delete-orphan",
- collection_class=ordering_list( 'order_index' ) )
+ collection_class=ordering_list( 'order_index' ) ),
+# addresses=relation( UserAddress,
+# primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) )
) )
assign_mapper( context, Group, Group.table,
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/model/migrate/versions/0009_request_table.py
--- a/lib/galaxy/model/migrate/versions/0009_request_table.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Thu Aug 06 09:52:59 2009 -0400
@@ -32,7 +32,7 @@
col.create( Request_table )
assert col is Request_table.c.submitted
except Exception, e:
- log.debug( "Adding column 'submitted' to submitted table failed: %s" % ( str( e ) ) )
+ log.debug( "Adding column 'submitted' to request table failed: %s" % ( str( e ) ) )
# Add 1 column to the sample table
try:
@@ -46,7 +46,7 @@
col.create( Sample_table )
assert col is Sample_table.c.bar_code
except Exception, e:
- log.debug( "Adding column 'bar_code' to submitted table failed: %s" % ( str( e ) ) )
+ log.debug( "Adding column 'bar_code' to sample table failed: %s" % ( str( e ) ) )
def downgrade():
pass
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/model/migrate/versions/0012_user_address.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Thu Aug 06 09:52:59 2009 -0400
@@ -0,0 +1,118 @@
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exceptions import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+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 )
+
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+
+
+UserAddress_table = Table( "user_address", metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+ Column( "desc", TEXT),
+ Column( "name", TrimmedString( 255 ), nullable=False),
+ Column( "institution", TrimmedString( 255 )),
+ Column( "address", TrimmedString( 255 ), nullable=False),
+ Column( "city", TrimmedString( 255 ), nullable=False),
+ Column( "state", TrimmedString( 255 ), nullable=False),
+ Column( "postal_code", TrimmedString( 255 ), nullable=False),
+ Column( "country", TrimmedString( 255 ), nullable=False),
+ Column( "phone", TrimmedString( 255 )),
+ Column( "deleted", Boolean, index=True, default=False ),
+ Column( "purged", Boolean, index=True, default=False ) )
+
+#RequestState_table = Table('request_state', metadata,
+# Column( "id", Integer, primary_key=True),
+# Column( "create_time", DateTime, default=now ),
+# Column( "update_time", DateTime, default=now, onupdate=now ),
+# Column( "name", TrimmedString( 255 ), nullable=False ),
+# Column( "desc", TEXT ))
+
+def upgrade():
+ # Load existing tables
+ metadata.reflect()
+
+ # Add all of the new tables above
+ try:
+ UserAddress_table.create()
+ except Exception, e:
+ log.debug( "Creating user_address table failed: %s" % str( e ) )
+# try:
+# RequestState_table.create()
+# except Exception, e:
+# log.debug( "Creating request_state table failed: %s" % str( e ) )
+
+ # Add 1 column to the request_type table
+ try:
+ RequestType_table = Table( "request_type", metadata, autoload=True )
+ except NoSuchTableError:
+ RequestType_table = None
+ log.debug( "Failed loading table request_type" )
+ if RequestType_table:
+ try:
+ col = Column( "deleted", Boolean, index=True, default=False )
+ col.create( RequestType_table )
+ assert col is RequestType_table.c.deleted
+ except Exception, e:
+ log.debug( "Adding column 'deleted' to request_type table failed: %s" % ( str( e ) ) )
+
+ # Delete the submitted column
+ try:
+ Request_table = Table( "request", metadata, autoload=True )
+ except NoSuchTableError:
+ Request_table = None
+ log.debug( "Failed loading table request" )
+ if Request_table:
+ try:
+ Request_table.c.submitted.drop()
+ except Exception, e:
+ log.debug( "Deleting column 'submitted' to request table failed: %s" % ( str( e ) ) )
+ try:
+ col = Column( "state", TrimmedString( 255 ), index=True )
+ col.create( Request_table )
+ assert col is Request_table.c.state
+ except Exception, e:
+ log.debug( "Adding column 'state' to request table failed: %s" % ( str( e ) ) )
+#
+# # new column which points to the current state in the request_state table
+# try:
+# col = Column( "request_state_id", Integer, index=True )
+# col.create( Request_table )
+# assert col is Request_table.c.request_state_id
+# except Exception, e:
+# log.debug( "Adding column 'request_state_id' to request table failed: %s" % ( str( e ) ) )
+# # Add 1 foreign key constraint to the form_definition_current table
+# if RequestState_table and Request_table:
+# try:
+# cons = ForeignKeyConstraint( [Request_table.c.request_state_id],
+# [RequestState_table.c.id],
+# name='request_request_state_id_fk' )
+# # Create the constraint
+# cons.create()
+# except Exception, e:
+# log.debug( "Adding foreign key constraint 'request_request_state_id_fk' to table 'request' failed: %s" % ( str( e ) ) )
+
+
+def downgrade():
+ pass
+
+
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py Thu Aug 06 09:52:59 2009 -0400
@@ -2120,12 +2120,19 @@
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
+ show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) )
forms = self._get_all_forms(trans, all_versions=True)
+ request_types_list = trans.app.model.RequestType.query().all()
+ if show_filter == 'All':
+ request_types = request_types_list
+ elif show_filter == 'Deleted':
+ request_types = [rt for rt in request_types_list if rt.deleted]
+ else:
+ request_types = [rt for rt in request_types_list if not rt.deleted]
return trans.fill_template( '/admin/requests/manage_request_types.mako',
- request_types=trans.app.model.RequestType.query().all(),
+ request_types=request_types,
forms=forms,
- deleted=False,
- show_deleted=False,
+ show_filter=show_filter,
msg=msg,
messagetype=messagetype )
@web.expose
@@ -2155,13 +2162,10 @@
forms=self._get_all_forms(trans, all_versions=False),
msg=msg,
messagetype='error')
- return trans.fill_template( '/admin/requests/manage_request_types.mako',
- request_types=trans.app.model.RequestType.query().all(),
- forms=self._get_all_forms(trans, all_versions=True),
- deleted=False,
- show_deleted=False,
- msg=msg,
- messagetype=messagetype )
+ return trans.response.send_redirect( web.url_for( controller='admin',
+ action='manage_request_types',
+ msg='Request type <b>%s</b> has been created' % st.name,
+ messagetype='done') )
elif params.get('edit', False) == 'True':
rt = trans.app.model.RequestType.get(int(util.restore_text( params.id )))
ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
@@ -2197,8 +2201,8 @@
ss.delete()
ss.flush()
# unsubmitted state
- ss = trans.app.model.SampleState('Unsubmitted', 'Sample not yet submitted', rt)
- ss.flush()
+ #ss = trans.app.model.SampleState('Unsubmitted', 'Sample not yet submitted', rt)
+ ##ss.flush()
for i in range( num_states ):
name = util.restore_text( params.get( 'new_element_name_%i' % i, None ))
desc = util.restore_text( params.get( 'new_element_description_%i' % i, None ))
@@ -2206,3 +2210,31 @@
ss.flush()
msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states)
return rt, msg
+
+ @web.expose
+ @web.require_admin
+ def delete_request_type( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id )))
+ rt.deleted = True
+ rt.flush()
+ return trans.response.send_redirect( web.url_for( controller='admin',
+ action='manage_request_types',
+ msg='Request type <b>%s</b> has been deleted' % rt.name,
+ messagetype='done') )
+
+ @web.expose
+ @web.require_admin
+ def undelete_request_type( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id )))
+ rt.deleted = False
+ rt.flush()
+ return trans.response.send_redirect( web.url_for( controller='admin',
+ action='manage_request_types',
+ msg='Request type <b>%s</b> has been deleted' % rt.name,
+ messagetype='done') )
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/controllers/forms.py
--- a/lib/galaxy/web/controllers/forms.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/controllers/forms.py Thu Aug 06 09:52:59 2009 -0400
@@ -29,13 +29,19 @@
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
- return self._show_forms_list(trans, msg, messagetype)
- def _show_forms_list(self, trans, msg, messagetype):
+ show_filter = params.get( 'show_filter', 'Active' )
+ return self._show_forms_list(trans, msg, messagetype, show_filter)
+ def _show_forms_list(self, trans, msg, messagetype, show_filter='Active'):
fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+ if show_filter == 'All':
+ forms_list = fdc_list
+ elif show_filter == 'Deleted':
+ forms_list = [form for form in fdc_list if form.deleted]
+ else:
+ forms_list = [form for form in fdc_list if not form.deleted]
return trans.fill_template( '/admin/forms/manage_forms.mako',
- fdc_list=fdc_list,
- deleted=False,
- show_deleted=False,
+ fdc_list=forms_list,
+ show_filter=show_filter,
msg=msg,
messagetype=messagetype )
def _get_all_forms(self, trans, all_versions=False):
@@ -73,7 +79,34 @@
self.num_add_fields = 0
fd, msg = self.__save_form(trans, fdc_id=None, **kwd)
self.__get_saved_form(fd)
- return self._show_forms_list(trans, msg, messagetype)
+ return trans.response.send_redirect( web.url_for( controller='forms',
+ action='edit',
+ form_id=fd.id,
+ show_form=True) )
+ @web.expose
+ @web.require_admin
+ def delete( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id )))
+ fd.form_definition_current.deleted = True
+ fd.form_definition_current.flush()
+ return self._show_forms_list(trans,
+ msg='The form definition named %s is deleted.' % fd.name,
+ messagetype='done')
+ @web.expose
+ @web.require_admin
+ def undelete( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id )))
+ fd.form_definition_current.deleted = False
+ fd.form_definition_current.flush()
+ return self._show_forms_list(trans,
+ msg='The form definition named %s is undeleted.' % fd.name,
+ messagetype='done')
@web.expose
@web.require_admin
def edit( self, trans, **kwd ):
@@ -241,15 +274,22 @@
'''
import csv
fields = []
- reader = csv.reader(open(csv_file))
- for row in reader:
- options = row[5].split(',')
- fields.append({'label': row[0],
- 'helptext': row[1],
- 'visible': row[2],
- 'required': row[3],
- 'type': row[4],
- 'selectlist': options})
+ try:
+ reader = csv.reader(open(csv_file))
+ for row in reader:
+ options = row[5].split(',')
+ fields.append({'label': row[0],
+ 'helptext': row[1],
+ 'visible': row[2],
+ 'required': row[3],
+ 'type': row[4],
+ 'selectlist': options})
+ except:
+ return trans.response.send_redirect( web.url_for( controller='forms',
+ action='new',
+ status='error',
+ message='Error in importing <b>%s</b> file' % csv_file,
+ **kwd))
return fields
def __save_form(self, trans, fdc_id=None, **kwd):
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/controllers/requests.py Thu Aug 06 09:52:59 2009 -0400
@@ -14,6 +14,7 @@
title = "Sequencing Requests"
model_class = model.Request
default_sort_key = "-create_time"
+ show_filter = model.Request.states.UNSUBMITTED
columns = [
grids.GridColumn( "Name", key="name",
link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
@@ -23,18 +24,23 @@
link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
grids.GridColumn( "Type", key="request_type_id", method='get_request_type'),
grids.GridColumn( "Last update", key="update_time", format=time_ago ),
- grids.GridColumn( "Submitted", method='submitted'),
+ grids.GridColumn( "State", key='state'),
]
operations = [
-# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
- grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.submitted ) )
-# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
-# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
+ grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ),
+ grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ),
+ grids.GridOperation( "Delete", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ),
+ grids.GridOperation( "Undelete", allow_multiple=False, condition=( lambda item: item.deleted ) )
+
]
standard_filters = [
- grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+ grids.GridColumnFilter( model.Request.states.UNSUBMITTED,
+ args=dict( state=model.Request.states.UNSUBMITTED, deleted=False ) ),
+ grids.GridColumnFilter( model.Request.states.SUBMITTED,
+ args=dict( state=model.Request.states.SUBMITTED, deleted=False ) ),
+ grids.GridColumnFilter( model.Request.states.COMPLETE, args=dict( state=model.Request.states.COMPLETE, deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
- grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+ grids.GridColumnFilter( "All", args={} )
]
#default_filter = dict( deleted=False )
def get_current_item( self, trans ):
@@ -45,10 +51,8 @@
return query.filter_by( user=trans.user )
def number_of_samples(self, trans, request):
return str(len(request.samples))
- def submitted(self, trans, request):
- if request.submitted:
- return 'Yes'
- return 'No'
+ def get_state(self, trans, request):
+ return request.state
@@ -73,6 +77,8 @@
List all request made by the current user
'''
status = message = None
+ self.request_grid.default_filter = dict(state=trans.app.model.Request.states.UNSUBMITTED,
+ deleted=False)
if 'operation' in kwargs:
operation = kwargs['operation'].lower()
if operation == "show_request":
@@ -81,6 +87,23 @@
elif operation == "submit":
id = trans.security.decode_id(kwargs['id'])
return self.__submit(trans, id)
+ elif operation == "delete":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.__delete_request(trans, id)
+ elif operation == "undelete":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.__undelete_request(trans, id)
+ elif operation == "edit":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.__edit_request(trans, id)
+ if 'show_filter' in kwargs.keys():
+ if kwargs['show_filter'] == 'All':
+ self.request_grid.default_filter = {}
+ elif kwargs['show_filter'] == 'Deleted':
+ self.request_grid.default_filter = dict(deleted=True)
+ else:
+ self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False)
+ self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.UNSUBMITTED)
# Render the list view
return self.request_grid( trans, template='/requests/grid.mako', **kwargs )
@@ -94,21 +117,19 @@
message="Invalid request ID",
**kwd) )
self.current_samples = []
+ self.edit_mode = False
for s in request.samples:
self.current_samples.append([s.name, s.values.content])
if add_sample:
self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
- # selectfield of all samples
- copy_list = SelectField('copy_sample')
- copy_list.add_option('None', -1, selected=True)
- for i, s in enumerate(self.current_samples):
- copy_list.add_option(i+1, i)
self.details_state = 'Show request details'
return trans.fill_template( '/requests/show_request.mako',
request=request,
request_details=self.request_details(trans, id),
current_samples = self.current_samples,
- sample_copy=copy_list, details_state=self.details_state)
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
def request_details(self, trans, id):
'''
Shows the request details
@@ -128,19 +149,37 @@
value=request.create_time,
helptext=''))
# library associated
- request_details.append(dict(label='Library',
- value=request.library.name,
- helptext='Associated library where the resultant \
- dataset will be stored'))
+ if request.library:
+ request_details.append(dict(label='Library',
+ value=request.library.name,
+ helptext='Associated library where the resultant \
+ dataset will be stored'))
+ else:
+ request_details.append(dict(label='Library',
+ value=None,
+ helptext='Associated library where the resultant \
+ dataset will be stored'))
+
# form fields
for index, field in enumerate(request.type.request_form.fields):
if field['required']:
req = 'Required'
else:
req = 'Optional'
- request_details.append(dict(label=field['label'],
- value=request.values.content[index],
- helptext=field['helptext']+' ('+req+')'))
+ if field['type'] == 'AddressField':
+ if request.values.content[index]:
+ request_details.append(dict(label=field['label'],
+ value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
+ helptext=field['helptext']+' ('+req+')'))
+ else:
+ request_details.append(dict(label=field['label'],
+ value=None,
+ helptext=field['helptext']+' ('+req+')'))
+
+ else:
+ request_details.append(dict(label=field['label'],
+ value=request.values.content[index],
+ helptext=field['helptext']+' ('+req+')'))
return request_details
def __update_samples(self, request, **kwd):
@@ -156,6 +195,13 @@
for field_index in range(len(request.type.sample_form.fields)):
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
self.current_samples.append([sample_name, sample_values])
+
+ def __copy_sample(self):
+ copy_list = SelectField('copy_sample')
+ copy_list.add_option('None', -1, selected=True)
+ for i, s in enumerate(self.current_samples):
+ copy_list.add_option(s[0], i)
+ return copy_list
@web.expose
def show_request(self, trans, **kwd):
params = util.Params( kwd )
@@ -169,7 +215,28 @@
status='error',
message="Invalid request ID",
**kwd) )
- if params.get('add_sample_button', False) == 'Add New':
+ if params.get('import_samples_button', False) == 'Import samples':
+ import traceback
+ try:
+ fname = params.get('import_samples', '')
+ import csv
+ reader = csv.reader(open(fname))
+ for row in reader:
+ self.current_samples.append([row[0], row[1:]])
+ return trans.fill_template( '/requests/show_request.mako',
+ request=request,
+ request_details=self.request_details(trans, request.id),
+ current_samples=self.current_samples,
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
+ except:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message='Error in importing <b>%s</b> samples file' % fname,
+ **kwd))
+ elif params.get('add_sample_button', False) == 'Add New':
# save the all (saved+unsaved) sample info in 'current_samples'
self.__update_samples(request, **kwd)
# add an empty or filled sample
@@ -182,17 +249,14 @@
else:
self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1),
[val for val in self.current_samples[src_sample_index][1]]])
- # selectfield of all samples
- copy_list = SelectField('copy_sample')
- copy_list.add_option('None', -1, selected=True)
- for i, s in enumerate(self.current_samples):
- copy_list.add_option(i+1, i)
return trans.fill_template( '/requests/show_request.mako',
request=request,
request_details=self.request_details(trans, request.id),
- current_samples = self.current_samples,
- sample_copy=copy_list, details_state=self.details_state)
- if params.get('save_samples_button', False) == 'Save':
+ current_samples=self.current_samples,
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
+ elif params.get('save_samples_button', False) == 'Save':
# update current_samples
self.__update_samples(request, **kwd)
# check for duplicate sample names
@@ -211,35 +275,59 @@
msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
break
if msg:
- copy_list = SelectField('copy_sample')
- copy_list.add_option('None', -1, selected=True)
- for i, s in enumerate(self.current_samples):
- copy_list.add_option(i+1, i)
return trans.fill_template( '/requests/show_request.mako',
request=request,
request_details=self.request_details(trans, request.id),
current_samples = self.current_samples,
- sample_copy=copy_list, details_state=self.details_state,
+ sample_copy=self.__copy_sample(), details_state=self.details_state,
messagetype='error', msg=msg)
# save all the new/unsaved samples entered by the user
- for index in range(len(self.current_samples)-len(request.samples)):
- sample_index = index + len(request.samples)
- sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
- sample_values = []
- for field_index in range(len(request.type.sample_form.fields)):
- sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
- form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
- form_values.flush()
- s = trans.app.model.Sample(sample_name, '', request, form_values)
- s.flush()
- # set the initial state
- state = s.request.type.states[0]
- event = trans.app.model.SampleEvent(s, state)
- event.flush()
+ if not self.edit_mode:
+ for index in range(len(self.current_samples)-len(request.samples)):
+ sample_index = index + len(request.samples)
+ sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
+ sample_values = []
+ for field_index in range(len(request.type.sample_form.fields)):
+ sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
+ form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
+ form_values.flush()
+ s = trans.app.model.Sample(sample_name, '', request, form_values)
+ s.flush()
+ else:
+ for index in range(len(self.current_samples)):
+ sample_index = index
+ sample_name = self.current_samples[sample_index][0]
+ new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
+ sample_values = []
+ for field_index in range(len(request.type.sample_form.fields)):
+ sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
+ sample = request.has_sample(sample_name)
+ if sample:
+ form_values = trans.app.model.FormValues.get(sample.values.id)
+ form_values.content = sample_values
+ form_values.flush()
+ sample.name = new_sample_name
+ sample.flush()
return trans.response.send_redirect( web.url_for( controller='requests',
action='list',
operation='show_request',
id=trans.security.encode_id(request.id)) )
+ elif params.get('edit_samples_button', False) == 'Edit samples':
+ self.edit_mode = True
+ return trans.fill_template( '/requests/show_request.mako',
+ request=request,
+ request_details=self.request_details(trans, request.id),
+ current_samples=self.current_samples,
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
+ elif params.get('cancel_changes_button', False) == 'Cancel':
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ operation='show_request',
+ id=trans.security.encode_id(request.id)) )
+
+
@web.expose
def delete_sample(self, trans, **kwd):
params = util.Params( kwd )
@@ -253,16 +341,15 @@
s.delete()
s.flush()
request.flush()
- del self.current_samples[sample_index]
- copy_list = SelectField('copy_sample')
- copy_list.add_option('None', -1, selected=True)
- for i, s in enumerate(self.current_samples):
- copy_list.add_option(i+1, i)
+ del self.current_samples[sample_index]
return trans.fill_template( '/requests/show_request.mako',
request=request,
request_details=self.request_details(trans, request.id),
current_samples = self.current_samples,
- sample_copy=copy_list, details_state=self.details_state)
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
+
@web.expose
def toggle_request_details(self, trans, **kwd):
params = util.Params( kwd )
@@ -272,121 +359,95 @@
if self.details_state == 'Show request details':
self.details_state = 'Hide request details'
elif self.details_state == 'Hide request details':
- self.details_state = 'Show request details'
- copy_list = SelectField('copy_sample')
- copy_list.add_option('None', -1, selected=True)
- for i, s in enumerate(self.current_samples):
- copy_list.add_option(i+1, i)
+ self.details_state = 'Show request details'
return trans.fill_template( '/requests/show_request.mako',
request=request,
request_details=self.request_details(trans, request.id),
current_samples = self.current_samples,
- sample_copy=copy_list, details_state=self.details_state)
+ sample_copy=self.__copy_sample(),
+ details_state=self.details_state,
+ edit_mode=self.edit_mode)
+ def __select_request_type(self, trans, rtid):
+ rt_ids = ['none']
+ for rt in trans.app.model.RequestType.query().all():
+ if not rt.deleted:
+ rt_ids.append(str(rt.id))
+ select_reqtype = SelectField('select_request_type',
+ refresh_on_change=True,
+ refresh_on_change_values=rt_ids[1:])
+ if rtid == 'none':
+ select_reqtype.add_option('Select one', 'none', selected=True)
+ else:
+ select_reqtype.add_option('Select one', 'none')
+ for rt in trans.app.model.RequestType.query().all():
+ if not rt.deleted:
+ if rtid == rt.id:
+ select_reqtype.add_option(rt.name, rt.id, selected=True)
+ else:
+ select_reqtype.add_option(rt.name, rt.id)
+ return select_reqtype
@web.expose
def new(self, trans, **kwd):
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
if params.get('select_request_type', False) == 'True':
- return trans.fill_template( '/requests/select_request_type.mako',
- request_types=trans.app.model.RequestType.query().all(),
- libraries=self.get_authorized_libs(trans),
+ return trans.fill_template( '/requests/new_request.mako',
+ select_request_type=self.__select_request_type(trans, 'none'),
+ widgets=[],
msg=msg,
- messagetype=messagetype )
+ messagetype=messagetype)
elif params.get('create', False) == 'True':
- return self.__show_request_form(trans=trans,
- request=None, **kwd)
- elif params.get('save', False) == 'True':
- request_type = trans.app.model.RequestType.get(int(params.request_type_id))
- msg = self.__validate(trans,
- [('name','Name')],
- request_type.request_form.fields,
- **kwd)
- if msg:
- kwd['create'] = 'True'
- return trans.response.send_redirect( web.url_for( controller='requests',
- action='new',
- msg=msg,
- messagetype='error',
- **kwd) )
- request = self.__save_request(trans, None, **kwd)
- msg = 'The new request named %s has been created' % request.name
- request_type_id = int(util.restore_text( params.request_type_id ))
- if params.get('create_request_button', False) == 'Save':
- return trans.response.send_redirect( web.url_for( controller='requests',
- action='list',
- msg=msg ,
- messagetype='done') )
- elif params.get('create_request_samples_button', False) == 'Add samples':
- new_kwd = {}
- new_kwd['id'] = trans.security.encode_id(request.id)
- new_kwd['operation'] = 'show_request'
- new_kwd['add_sample'] = True
- return trans.response.send_redirect( web.url_for( controller='requests',
- action='list',
- msg=msg ,
- messagetype='done',
- **new_kwd) )
+ if params.get('create_request_button', False) == 'Save' \
+ or params.get('create_request_samples_button', False) == 'Add samples':
+ request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+ if not util.restore_text(params.get('name', '')):
+ msg = 'Please enter the <b>Name</b> of the request'
+ kwd['create'] = 'True'
+ kwd['messagetype'] = 'error'
+ kwd['msg'] = msg
+ kwd['create_request_button'] = None
+ kwd['create_request_samples_button'] = None
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='new',
+ **kwd) )
+ request = self.__save_request(trans, None, **kwd)
+ msg = 'The new request named %s has been created' % request.name
+ if params.get('create_request_button', False) == 'Save':
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ msg=msg ,
+ messagetype='done') )
+ elif params.get('create_request_samples_button', False) == 'Add samples':
+ new_kwd = {}
+ new_kwd['id'] = trans.security.encode_id(request.id)
+ new_kwd['operation'] = 'show_request'
+ new_kwd['add_sample'] = True
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ msg=msg ,
+ messagetype='done',
+ **new_kwd) )
+ else:
+ return self.__show_request_form(trans, **kwd)
+ elif params.get('refresh', False) == 'true':
+ return self.__show_request_form(trans, **kwd)
- def __validate(self, trans, main_fields=[], form_fields=[], **kwd):
- '''
- Validates the request entered by the user
- '''
- params = util.Params( kwd )
- for field, field_name in main_fields:
- if not util.restore_text(params.get(field, '')):
- return 'Please enter the <b>%s</b> of the request' % field_name
- # check rest of the fields of the form
- for index, field in enumerate(form_fields):
- if not util.restore_text(params.get('field_%i' % index, None)) \
- and field['required'] == 'required':
- return 'Please enter the <b>%s</b> field of the request' % field['label']
- return None
- def __save_request(self, trans, request_id=None, **kwd):
- '''
- This method saves a new request if request_id is None.
- '''
- params = util.Params( kwd )
- if not request_id:
- request_type = trans.app.model.RequestType.get(int(params.request_type_id ))
- else:
- # TODO editing
- pass
- name = util.restore_text(params.get('name', ''))
- desc = util.restore_text(params.get('desc', ''))
- try:
- library_id = int(util.restore_text(params.get('library_id', None)))
- except:
- msg = "Sequencing request could not be saved. Invalid library"
- return trans.response.send_redirect( web.url_for( controller='requests',
- action='list',
- status='error',
- message=msg,
- **kwd) )
- values = []
- for index, field in enumerate(request_type.request_form.fields):
- values.append(util.restore_text(params.get('field_%i' % index, '')))
- if not request_id:
- form_values = trans.app.model.FormValues(request_type.request_form, values)
- form_values.flush()
- request = trans.app.model.Request(name, desc, request_type,
- trans.user, form_values,
- trans.app.model.Library.get(library_id),
- submitted=False)
- request.flush()
- else:
- # TODO editing
- pass
- return request
- def __show_request_form(self, trans, request=None, **kwd):
+
+ def __show_request_form(self, trans, **kwd):
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
- request_type = trans.app.model.RequestType.get(int(params.request_type_id))
- if request:
- form_values = request.values
- else:
- form_values = None
+ try:
+ request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+ except:
+ return trans.fill_template( '/requests/new_request.mako',
+ select_request_type=self.__select_request_type(trans, 'none'),
+ widgets=[],
+ msg=msg,
+ messagetype=messagetype)
+ form_values = None
+ select_request_type = self.__select_request_type(trans, request_type.id)
# list of widgets to be rendered on the request form
widgets = []
widgets.append(dict(label='Name',
@@ -397,53 +458,305 @@
widget=TextField('desc', 40,
util.restore_text( params.get( 'desc', '' ) )),
helptext='(Optional)'))
+
# libraries selectbox
libraries = self.get_authorized_libs(trans)
- if libraries:
- libui = self.__library_ui(libraries, **kwd)
- widgets.append(libui)
+ libui = self.__library_ui(libraries, **kwd)
+ widgets = widgets + libui
widgets = self.__create_form(trans, request_type.request_form_id, widgets,
form_values, **kwd)
title = 'Add a new request of type: %s' % request_type.name
return trans.fill_template( '/requests/new_request.mako',
- request_form_id=request_type.request_form_id,
- request_type=request_type,
- widgets=widgets,
- title=title,
- msg=msg,
- messagetype=messagetype)
+ select_request_type=select_request_type,
+ request_type=request_type,
+ widgets=widgets,
+ msg=msg,
+ messagetype=messagetype)
- def __library_ui(self, libraries, **kwd):
+ def __library_ui(self, libraries, request=None, **kwd):
params = util.Params( kwd )
- create_lib_str = 'Create a new library'
- value = int(params.get( 'library_id', 0 ))
- if not value: # if no library previously selected
- # show the selectbox with 'create a new library' option selected
- lib_list = SelectField('library_id', refresh_on_change=True,
- refresh_on_change_values=[create_lib_str])
- #lib_list.add_option(create_lib_str, 0, selected=True)
- for lib in libraries:
+ lib_id = params.get( 'library_id', 'none' )
+ lib_list = SelectField('library_id', refresh_on_change=True,
+ refresh_on_change_values=['new'])
+ if request and lib_id == 'none':
+ if request.library:
+ lib_id = str(request.library.id)
+ if lib_id == 'none':
+ lib_list.add_option('Select one', 'none', selected=True)
+ else:
+ lib_list.add_option('Select one', 'none')
+ for lib in libraries:
+ if str(lib.id) == lib_id:
+ lib_list.add_option(lib.name, lib.id, selected=True)
+ else:
lib_list.add_option(lib.name, lib.id)
- widget = dict(label='Library',
- widget=lib_list,
- helptext='Associated library where the resultant \
- dataset will be stored.')
- else: # if some library previously selected
- # show the selectbox with some library selected
- lib_list = SelectField('library_id', refresh_on_change=True,
- refresh_on_change_values=[create_lib_str])
- #lib_list.add_option(create_lib_str, 0)
- for lib in libraries:
- if value == lib.id:
- lib_list.add_option(lib.name, lib.id, selected=True)
+ if lib_id == 'new':
+ lib_list.add_option('Create a new library', 'new', selected=True)
+ else:
+ lib_list.add_option('Create a new library', 'new')
+ widget = dict(label='Library',
+ widget=lib_list,
+ helptext='Associated library where the resultant \
+ dataset will be stored.')
+ if lib_id == 'new':
+ new_lib = dict(label='Create a new Library',
+ widget=TextField('new_library_name', 40,
+ util.restore_text( params.get( 'new_library_name', '' ) )),
+ helptext='Enter a library name here to request a new library')
+ return [widget, new_lib]
+ else:
+ return [widget]
+
+ def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd):
+ params = util.Params( kwd )
+ form = trans.app.model.FormDefinition.get(form_id)
+ # form fields
+ for index, field in enumerate(form.fields):
+ # value of the field
+ if field['type'] == 'CheckboxField':
+ value = util.restore_text( params.get( 'field_%i' % index, False ) )
+ else:
+ value = util.restore_text( params.get( 'field_%i' % index, '' ) )
+ if not value:
+ if form_values:
+ value = str(form_values.content[index])
+ # create the field
+ fw = eval(field['type'])('field_%i' % index)
+ if field['type'] == 'TextField':
+ fw.set_size(40)
+ fw.value = value
+ elif field['type'] == 'TextArea':
+ fw.set_size(3, 40)
+ fw.value = value
+ elif field['type'] == 'AddressField':
+ fw.user = trans.user
+ fw.value = value
+ fw.params = params
+ elif field['type'] == 'SelectField':
+ for option in field['selectlist']:
+ if option == value:
+ fw.add_option(option, option, selected=True)
+ else:
+ fw.add_option(option, option)
+ elif field['type'] == 'CheckboxField':
+ fw.checked = value
+ # require/optional
+ if field['required'] == 'required':
+ req = 'Required'
+ else:
+ req = 'Optional'
+ widgets.append(dict(label=field['label'],
+ widget=fw,
+ helptext=field['helptext']+' ('+req+')'))
+ return widgets
+ def __validate(self, trans, request):
+ '''
+ Validates the request entered by the user
+ '''
+ empty_fields = []
+ if not request.library:
+ empty_fields.append('Library')
+ # check rest of the fields of the form
+ for index, field in enumerate(request.type.request_form.fields):
+ if field['required'] == 'required' and request.values.content[index] in ['', None]:
+ empty_fields.append(field['label'])
+ if empty_fields:
+ msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
+ for ef in empty_fields:
+ msg = msg + '<b>' +ef + '</b><br/>'
+ return msg
+ return None
+ def __save_request(self, trans, request=None, **kwd):
+ '''
+ This method saves a new request if request_id is None.
+ '''
+ params = util.Params( kwd )
+ request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+ name = util.restore_text(params.get('name', ''))
+ desc = util.restore_text(params.get('desc', ''))
+ # library
+ try:
+ library = trans.app.model.Library.get(int(params.get('library_id', None)))
+ except:
+ library = None
+ # fields
+ values = []
+ for index, field in enumerate(request_type.request_form.fields):
+ if field['type'] == 'AddressField':
+ value = util.restore_text(params.get('field_%i' % index, ''))
+ if value == 'new':
+ # save this new address in the list of this user's addresses
+ user_address = trans.app.model.UserAddress( user=trans.user )
+ user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
+ user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
+ user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
+ user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
+ user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
+ user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
+ user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
+ user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
+ user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
+ user_address.flush()
+ trans.user.refresh()
+ values.append(int(user_address.id))
+ elif value == unicode('none'):
+ values.append('')
else:
- lib_list.add_option(lib.name, lib.id)
- widget = dict(label='Library',
- widget=lib_list,
- helptext='Associated library where the resultant \
- dataset will be stored.')
- return widget
-
+ values.append(int(value))
+ else:
+ values.append(util.restore_text(params.get('field_%i' % index, '')))
+ form_values = trans.app.model.FormValues(request_type.request_form, values)
+ form_values.flush()
+ if not request:
+ request = trans.app.model.Request(name, desc, request_type,
+ trans.user, form_values,
+ library=library,
+ state=trans.app.model.Request.states.UNSUBMITTED)
+ request.flush()
+ else:
+ request.name = name
+ request.desc = desc
+ request.type = request_type
+ request.user = trans.user
+ request.values = form_values
+ request.library = library
+ request.state = trans.app.model.Request.states.UNSUBMITTED
+ request.flush()
+ return request
+ @web.expose
+ def edit(self, trans, **kwd):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ try:
+ request = trans.app.model.Request.get(int(params.get('request_id', None)))
+ except:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message="Invalid request ID",
+ **kwd) )
+ if params.get('show', False) == 'True':
+ return self.__edit_request(trans, request.id, **kwd)
+ elif params.get('save_changes_request_button', False) == 'Save changes' \
+ or params.get('edit_samples_button', False) == 'Edit samples':
+ request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+ if not util.restore_text(params.get('name', '')):
+ msg = 'Please enter the <b>Name</b> of the request'
+ kwd['messagetype'] = 'error'
+ kwd['msg'] = msg
+ kwd['show'] = 'True'
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='edit',
+ **kwd) )
+ request = self.__save_request(trans, request, **kwd)
+ msg = 'The changes made to the request named %s has been saved' % request.name
+ if params.get('save_changes_request_button', False) == 'Save changes':
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ message=msg ,
+ status='done') )
+ elif params.get('edit_samples_button', False) == 'Edit samples':
+ new_kwd = {}
+ new_kwd['request_id'] = request.id
+ new_kwd['edit_samples_button'] = 'Edit samples'
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='show_request',
+ msg=msg ,
+ messagetype='done',
+ **new_kwd) )
+ elif params.get('refresh', False) == 'true':
+ return self.__edit_request(trans, request.id, **kwd)
+
+ def __edit_request(self, trans, id, **kwd):
+ try:
+ request = trans.app.model.Request.get(id)
+ except:
+ msg = "Invalid request ID"
+ log.warn( msg )
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message=msg) )
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ select_request_type = self.__select_request_type(trans, request.type.id)
+ # list of widgets to be rendered on the request form
+ widgets = []
+ if util.restore_text( params.get( 'name', '' ) ):
+ name = util.restore_text( params.get( 'name', '' ) )
+ else:
+ name = request.name
+ widgets.append(dict(label='Name',
+ widget=TextField('name', 40, name),
+ helptext='(Required)'))
+ if util.restore_text( params.get( 'desc', '' ) ):
+ desc = util.restore_text( params.get( 'desc', '' ) )
+ else:
+ desc = request.desc
+ widgets.append(dict(label='Description',
+ widget=TextField('desc', 40, desc),
+ helptext='(Optional)'))
+
+ # libraries selectbox
+ libraries = self.get_authorized_libs(trans)
+ libui = self.__library_ui(libraries, request, **kwd)
+ widgets = widgets + libui
+ widgets = self.__create_form(trans, request.type.request_form_id, widgets,
+ request.values, **kwd)
+ return trans.fill_template( '/requests/edit_request.mako',
+ select_request_type=select_request_type,
+ request_type=request.type,
+ request=request,
+ widgets=widgets,
+ msg=msg,
+ messagetype=messagetype)
+ return self.__show_request_form(trans)
+ def __delete_request(self, trans, id):
+ try:
+ request = trans.app.model.Request.get(id)
+ except:
+ msg = "Invalid request ID"
+ log.warn( msg )
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message=msg,
+ **kwd) )
+ # change request's submitted field
+ if not request.unsubmitted():
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message='This request cannot be deleted as it is already been submitted',
+ **kwd) )
+ request.deleted = True
+ request.flush()
+ kwd = {}
+ kwd['id'] = trans.security.encode_id(request.id)
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ **kwd) )
+ def __undelete_request(self, trans, id):
+ try:
+ request = trans.app.model.Request.get(id)
+ except:
+ msg = "Invalid request ID"
+ log.warn( msg )
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message=msg,
+ **kwd) )
+ # change request's submitted field
+ request.deleted = False
+ request.flush()
+ kwd = {}
+ kwd['id'] = trans.security.encode_id(request.id)
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ **kwd) )
def __submit(self, trans, id):
try:
request = trans.app.model.Request.get(id)
@@ -455,13 +768,21 @@
status='error',
message=msg,
**kwd) )
+ msg = self.__validate(trans, request)
+ if msg:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='edit',
+ messagetype = 'error',
+ msg=msg,
+ request_id=request.id,
+ show='True') )
# get the new state
- new_state = request.type.states[1]
+ new_state = request.type.states[0]
for s in request.samples:
event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
event.flush()
# change request's submitted field
- request.submitted = True
+ request.state = request.states.SUBMITTED
request.flush()
kwd = {}
kwd['id'] = trans.security.encode_id(request.id)
@@ -482,54 +803,28 @@
status='error',
message=msg,
**kwd) )
+ msg = self.__validate(trans, request)
+ if msg:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='edit',
+ messagetype = 'error',
+ msg=msg,
+ request_id=request.id,
+ show='True') )
# get the new state
- new_state = request.type.states[1]
+ new_state = request.type.states[0]
for s in request.samples:
event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
event.flush()
# change request's submitted field
- request.submitted = True
+ request.state = request.states.SUBMITTED
request.flush()
## TODO
kwd['id'] = trans.security.encode_id(request.id)
return trans.response.send_redirect( web.url_for( controller='requests',
action='list',
**kwd) )
- def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd):
- params = util.Params( kwd )
- form = trans.app.model.FormDefinition.get(form_id)
- # form fields
- for index, field in enumerate(form.fields):
- # value of the field
- if field['type'] == 'CheckboxField':
- value = util.restore_text( params.get( 'field_%i' % index, False ) )
- else:
- value = util.restore_text( params.get( 'field_%i' % index, '' ) )
- # create the field
- fw = eval(field['type'])('field_%i' % index)
- if field['type'] == 'TextField':
- fw.set_size(40)
- fw.value = value
- elif field['type'] == 'TextArea':
- fw.set_size(3, 40)
- fw.value = value
- elif field['type'] == 'SelectField':
- for option in field['selectlist']:
- if option == value:
- fw.add_option(option, option, selected=True)
- else:
- fw.add_option(option, option)
- elif field['type'] == 'CheckboxField':
- fw.checked = value
- # require/optional
- if field['required'] == 'required':
- req = 'Required'
- else:
- req = 'Optional'
- widgets.append(dict(label=field['label'],
- widget=fw,
- helptext=field['helptext']+' ('+req+')'))
- return widgets
+
@web.expose
def show_events(self, trans, **kwd):
params = util.Params( kwd )
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/controllers/requests_admin.py Thu Aug 06 09:52:59 2009 -0400
@@ -26,6 +26,7 @@
link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
grids.GridColumn( "Type", key="request_type_id", method='get_request_type'),
grids.GridColumn( "Last update", key="update_time", format=time_ago ),
+ grids.GridColumn( "State", key='state'),
grids.GridColumn( "User", key="user_id", method='get_user')
]
@@ -36,9 +37,10 @@
# grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
]
standard_filters = [
- grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
- grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
- grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+ grids.GridColumnFilter( model.Request.states.SUBMITTED,
+ args=dict( state=model.Request.states.SUBMITTED, deleted=False ) ),
+ grids.GridColumnFilter( model.Request.states.COMPLETE, args=dict( state=model.Request.states.COMPLETE, deleted=False ) ),
+ grids.GridColumnFilter( "All", args=dict( deleted=False ) )
]
def get_user(self, trans, request):
return trans.app.model.User.get(request.user_id).email
@@ -48,7 +50,8 @@
request_type = trans.app.model.RequestType.get(request.request_type_id)
return request_type.name
def apply_default_filter( self, trans, query ):
- return query.filter_by(submitted=True)
+ return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED,
+ self.model_class.state==self.model_class.states.COMPLETE))
def number_of_samples(self, trans, request):
return str(len(request.samples))
@@ -59,13 +62,6 @@
@web.require_admin
def index( self, trans ):
return trans.fill_template( "/admin/requests/index.mako" )
- def get_authorized_libs(self, trans):
- all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
- authorized_libraries = []
- for library in all_libraries:
- if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library) or trans.app.security_agent.check_folder_contents(trans.user, library) or trans.app.security_agent.show_library_item(trans.user, library):
- authorized_libraries.append(library)
- return authorized_libraries
@web.expose
@web.require_admin
def list( self, trans, **kwargs ):
@@ -73,11 +69,19 @@
List all request made by the current user
'''
status = message = None
+ self.request_grid.default_filter = dict(state=trans.app.model.Request.states.SUBMITTED,
+ deleted=False)
if 'operation' in kwargs:
operation = kwargs['operation'].lower()
if operation == "show_request":
id = trans.security.decode_id(kwargs['id'])
return self.__show_request(trans, id)
+
+ if 'show_filter' in kwargs.keys():
+ if kwargs['show_filter'] == 'All':
+ self.request_grid.default_filter = dict(deleted=False)
+ else:
+ self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False)
# Render the list view
return self.request_grid( trans, template='/admin/requests/grid.mako', **kwargs )
def __show_request(self, trans, id):
@@ -122,7 +126,6 @@
Shows the request details
'''
request = trans.app.model.Request.get(id)
- libraries = self.get_authorized_libs(trans)
# list of widgets to be rendered on the request form
request_details = []
# main details
@@ -152,55 +155,124 @@
req = 'Required'
else:
req = 'Optional'
- request_details.append(dict(label=field['label'],
- value=request.values.content[index],
- helptext=field['helptext']+' ('+req+')'))
+ if field['type'] == 'AddressField':
+ if request.values.content[index]:
+ request_details.append(dict(label=field['label'],
+ value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
+ helptext=field['helptext']+' ('+req+')'))
+ else:
+ request_details.append(dict(label=field['label'],
+ value=None,
+ helptext=field['helptext']+' ('+req+')'))
+ else:
+ request_details.append(dict(label=field['label'],
+ value=request.values.content[index],
+ helptext=field['helptext']+' ('+req+')'))
return request_details
@web.expose
@web.require_admin
def bar_codes(self, trans, **kwd):
params = util.Params( kwd )
- request_id = params.get('request_id', None)
- if request_id:
- request_id = int(request_id)
- request = trans.app.model.Request.get(request_id)
- return trans.fill_template( '/admin/samples/bar_codes.mako',
- samples_list=[s for s in request.samples],
- user=request.user,
- request=request)
+ try:
+ request = trans.app.model.Request.get(int(params.get('request_id', None)))
+ except:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message="Invalid request ID",
+ **kwd) )
+ widgets = []
+ for index, sample in enumerate(request.samples):
+ if sample.bar_code:
+ bc = sample.bar_code
+ else:
+ bc = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
+ widgets.append(TextField('sample_%i_bar_code' % index,
+ 40,
+ bc))
+ return trans.fill_template( '/admin/samples/bar_codes.mako',
+ samples_list=[s for s in request.samples],
+ user=request.user, request=request, widgets=widgets)
@web.expose
@web.require_admin
def save_bar_codes(self, trans, **kwd):
params = util.Params( kwd )
- request_id = params.get('request_id', None)
- if request_id:
- request_id = int(request_id)
- request = trans.app.model.Request.get(request_id)
- # validate
- # bar codes need to be globally unique
- unique = True
- for index in range(len(request.samples)):
- bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
- all_samples = trans.app.model.Sample.query.all()
- for sample in all_samples:
- if bar_code == sample.bar_code:
- unique = False
- if not unique:
- return trans.fill_template( '/admin/samples/bar_codes.mako',
- samples_list=[s for s in request.samples],
- user=request.user,
- request=request,
- messagetype='error',
- msg='Samples cannot have same bar code.')
+ try:
+ request = trans.app.model.Request.get(int(params.get('request_id', None)))
+ except:
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ status='error',
+ message="Invalid request ID",
+ **kwd) )
+ # validate
+ # bar codes need to be globally unique
+ msg = ''
+ for index in range(len(request.samples)):
+ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
+ # check for empty bar code
+ if not bar_code.strip():
+ msg = 'Please fill the bar code for sample <b>%s</b>.' % request.samples[index].name
+ break
+ # check all the unsaved bar codes
+ count = 0
+ for i in range(len(request.samples)):
+ if bar_code == util.restore_text(params.get('sample_%i_bar_code' % i, '')):
+ count = count + 1
+ if count > 1:
+ msg = '''The bar code <b>%s</b> of sample <b>%s</b> already belongs
+ another sample in this request. The sample bar codes must
+ be unique throughout the system''' % \
+ (bar_code, request.samples[index].name)
+ break
+ # check all the saved bar codes
+ all_samples = trans.app.model.Sample.query.all()
+ for sample in all_samples:
+ if bar_code == sample.bar_code:
+ msg = '''The bar code <b>%s</b> of sample <b>%s</b> already
+ belongs another sample. The sample bar codes must be
+ unique throughout the system''' % \
+ (bar_code, request.samples[index].name)
+ break
+ if msg:
+ break
+ if msg:
+ widgets = []
for index, sample in enumerate(request.samples):
- bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
- sample.bar_code = bar_code
- sample.flush()
+ if sample.bar_code:
+ bc = sample.bar_code
+ else:
+ bc = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
+ widgets.append(TextField('sample_%i_bar_code' % index,
+ 40,
+ util.restore_text(params.get('sample_%i_bar_code' % index, ''))))
+ return trans.fill_template( '/admin/samples/bar_codes.mako',
+ samples_list=[s for s in request.samples],
+ user=request.user, request=request, widgets=widgets, messagetype='error',
+ msg=msg)
+ # now save the bar codes
+ for index, sample in enumerate(request.samples):
+ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
+ sample.bar_code = bar_code
+ sample.flush()
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='list',
operation='show_request',
id=trans.security.encode_id(request.id)) )
+ def __set_request_state(self, request):
+ # check if all the samples of the current request are in the final state
+ complete = True
+ for s in request.samples:
+ if s.current_state().id != request.type.states[-1].id:
+ complete = False
+ if complete:
+ request.state = request.states.COMPLETE
+ else:
+ request.state = request.states.SUBMITTED
+ request.flush()
+
+
def change_state(self, trans, sample):
possible_states = sample.request.type.states
curr_state = sample.current_state()
@@ -236,6 +308,7 @@
and trans.app.model.SampleState.table.c.id == selected_state)[0]
event = trans.app.model.SampleEvent(sample, new_state, comments)
event.flush()
+ self.__set_request_state(sample.request)
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='show_events',
sample_id=sample.id))
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/controllers/user.py Thu Aug 06 09:52:59 2009 -0400
@@ -21,7 +21,7 @@
require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>."
class User( BaseController ):
-
+ edit_address_id = None
@web.expose
def index( self, trans, **kwd ):
return trans.fill_template( '/user/index.mako', user=trans.get_user() )
@@ -224,3 +224,186 @@
else:
# User not logged in, history group must be only public
return trans.show_error_message( "You must be logged in to change your default permitted actions." )
+
+ @web.expose
+ def manage_addresses(self, trans, **kwd):
+ if trans.user:
+ params = util.Params( kwd )
+ show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) )
+ if show_filter == 'All':
+ addresses = [address for address in trans.user.addresses]
+ elif show_filter == 'Deleted':
+ addresses = [address for address in trans.user.addresses if address.deleted]
+ else:
+ addresses = [address for address in trans.user.addresses if not address.deleted]
+ return trans.fill_template( 'user/address.mako',
+ addresses=addresses,
+ show_filter=show_filter)
+ else:
+ # User not logged in, history group must be only public
+ return trans.show_error_message( "You must be logged in to change your default permitted actions." )
+
+ @web.expose
+ def new_address( self, trans, short_desc='', name='', institution='', address1='',
+ address2='', city='', state='', postal_code='', country='', phone='' ):
+ if trans.app.config.require_login:
+ refresh_frames = [ 'masthead', 'history', 'tools' ]
+ else:
+ refresh_frames = [ 'masthead', 'history' ]
+ if not trans.app.config.allow_user_creation and not trans.user_is_admin():
+ return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' )
+ short_desc_error = name_error = institution_error = address1_error = city_error = None
+ address2_error = state_error = postal_code_error = country_error = phone_error = None
+ if short_desc:
+ if not len( short_desc ):
+ short_desc_error = 'Enter a short description for this address'
+ elif not len( name ):
+ name_error = 'Enter the full name'
+ elif not len( institution ):
+ institution_error = 'Enter the institution associated with the user'
+ elif not len ( address1 ):
+ address1_error = 'Enter the address'
+ elif not len( city ):
+ city_error = 'Enter the city'
+ elif not len( state ):
+ state_error = 'Enter the state/province/region'
+ elif not len( postal_code ):
+ postal_code_error = 'Enter the postal code'
+ elif not len( country ):
+ country_error = 'Enter the country'
+ else:
+ user_address = trans.app.model.UserAddress( user=trans.user, desc=short_desc,
+ name=name, institution=institution,
+ address=address1+' '+address2, city=city,
+ state=state, postal_code=postal_code,
+ country=country, phone=phone)
+ user_address.flush()
+ return trans.response.send_redirect( web.url_for( controller='user',
+ action='manage_addresses',
+ msg='Address <b>%s</b> has been added' % user_address.desc,
+ messagetype='done') )
+
+ return trans.show_form(
+ web.FormBuilder( web.url_for(), "New address", submit_text="Save" )
+ .add_text( "short_desc", "Short address description", value=short_desc, error=short_desc_error )
+ .add_text( "name", "Name", value=name, error=name_error )
+ .add_text( "institution", "Institution", value=institution, error=institution_error )
+ .add_text( "address1", "Address Line 1", value=address1, error=address1_error )
+ .add_text( "address2", "Address Line 2", value=address2, error=address2_error )
+ .add_text( "city", "City", value=city, error=city_error )
+ .add_text( "state", "State/Province/Region", value=state, error=state_error )
+ .add_text( "postal_code", "Postal Code", value=postal_code, error=postal_code_error )
+ .add_text( "country", "Country", value=country, error=country_error )
+ .add_text( "phone", "Phone", value=phone, error=phone_error ) )
+
+
+ @web.expose
+ def edit_address( self, trans, address_id=None, short_desc='', name='', institution='', address1='',
+ address2='', city='', state='', postal_code='', country='', phone='' ):
+ import sys
+
+ if trans.app.config.require_login:
+ refresh_frames = [ 'masthead', 'history', 'tools' ]
+ else:
+ refresh_frames = [ 'masthead', 'history' ]
+ if not trans.app.config.allow_user_creation and not trans.user_is_admin():
+ return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' )
+ short_desc_error = name_error = institution_error = address1_error = city_error = None
+ address2_error = state_error = postal_code_error = country_error = phone_error = None
+ if short_desc:
+ if not len( short_desc ):
+ short_desc_error = 'Enter a short description for this address'
+ elif not len( name ):
+ name_error = 'Enter the full name'
+ elif not len( institution ):
+ institution_error = 'Enter the institution associated with the user'
+ elif not len ( address1 ):
+ address1_error = 'Enter the address'
+ elif not len( city ):
+ city_error = 'Enter the city'
+ elif not len( state ):
+ state_error = 'Enter the state/province/region'
+ elif not len( postal_code ):
+ postal_code_error = 'Enter the postal code'
+ elif not len( country ):
+ country_error = 'Enter the country'
+ else:
+ if self.edit_address_id:
+ try:
+ user_address = trans.app.model.UserAddress.get(int(self.edit_address_id))
+ except:
+ return trans.response.send_redirect( web.url_for( controller='user',
+ action='manage_addresses',
+ msg='Invalid address ID',
+ messagetype='error') )
+ user_address.desc = short_desc
+ user_address.name = name
+ user_address.institution = institution
+ user_address.address = address1+' '+address2
+ user_address.city = city
+ user_address.state = state
+ user_address.postal_code = postal_code
+ user_address.country = country
+ user_address.phone = phone
+ user_address.flush()
+ self.edit_address_id = None
+ return trans.response.send_redirect( web.url_for( controller='user',
+ action='manage_addresses',
+ msg='Changes made to address <b>%s</b> are saved.' % user_address.desc,
+ messagetype='done') )
+ self.edit_address_id = address_id
+ return trans.show_form(
+ web.FormBuilder( web.url_for(), "Edit address", submit_text="Save changes" )
+ .add_text( "short_desc", "Short address description", value=short_desc, error=short_desc_error )
+ .add_text( "name", "Name", value=name, error=name_error )
+ .add_text( "institution", "Institution", value=institution, error=institution_error )
+ .add_text( "address1", "Address Line 1", value=address1, error=address1_error )
+ .add_text( "address2", "Address Line 2", value=address2, error=address2_error )
+ .add_text( "city", "City", value=city, error=city_error )
+ .add_text( "state", "State/Province/Region", value=state, error=state_error )
+ .add_text( "postal_code", "Postal Code", value=postal_code, error=postal_code_error )
+ .add_text( "country", "Country", value=country, error=country_error )
+ .add_text( "phone", "Phone", value=phone, error=phone_error ) )
+
+ @web.expose
+ def delete_address( self, trans, address_id=None):
+ if trans.app.config.require_login:
+ refresh_frames = [ 'masthead', 'history', 'tools' ]
+ else:
+ refresh_frames = [ 'masthead', 'history' ]
+ if not trans.app.config.allow_user_creation and not trans.user_is_admin():
+ return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' )
+ try:
+ user_address = trans.app.model.UserAddress.get(int(address_id))
+ except:
+ return trans.fill_template( 'user/address.mako',
+ msg='Invalid address ID',
+ messagetype='error' )
+ user_address.deleted = True
+ user_address.flush()
+ return trans.response.send_redirect( web.url_for( controller='user',
+ action='manage_addresses',
+ msg='Address <b>%s</b> deleted' % user_address.desc,
+ messagetype='done') )
+
+ @web.expose
+ def undelete_address( self, trans, address_id=None):
+ if trans.app.config.require_login:
+ refresh_frames = [ 'masthead', 'history', 'tools' ]
+ else:
+ refresh_frames = [ 'masthead', 'history' ]
+ if not trans.app.config.allow_user_creation and not trans.user_is_admin():
+ return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' )
+ try:
+ user_address = trans.app.model.UserAddress.get(int(address_id))
+ except:
+ return trans.fill_template( 'user/address.mako',
+ msg='Invalid address ID',
+ messagetype='error' )
+ user_address.deleted = False
+ user_address.flush()
+ return trans.response.send_redirect( web.url_for( controller='user',
+ action='manage_addresses',
+ msg='Address <b>%s</b> is restored' % user_address.desc,
+ messagetype='done') )
+
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/form_builder.py
--- a/lib/galaxy/web/form_builder.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/form_builder.py Thu Aug 06 09:52:59 2009 -0400
@@ -11,7 +11,7 @@
raise TypeError( "Abstract Method" )
@staticmethod
def form_field_types():
- return ['TextField', 'TextArea', 'SelectField', 'CheckboxField']
+ return ['TextField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField']
class TextField(BaseField):
"""
@@ -340,6 +340,64 @@
recurse_options( rval, self.options, expanded_options )
rval.append( '</ul></div>' )
return '\n'.join( rval )
+
+class AddressField(BaseField):
+ @staticmethod
+ def fields():
+ return [ ( "short_desc", "Short address description"),
+ ( "name", "Name" ),
+ ( "institution", "Institution" ),
+ ( "address1", "Address Line 1" ),
+ ( "address2", "Address Line 2" ),
+ ( "city", "City" ),
+ ( "state", "State/Province/Region" ),
+ ( "postal_code", "Postal Code" ),
+ ( "country", "Country" ),
+ ( "phone", "Phone" ) ]
+ def __init__(self, name, user=None, value=None, params=None):
+ self.name = name
+ self.user = user
+ self.value = value
+ self.select_address = None
+ self.params = params
+ def get_html(self):
+ from galaxy import util
+ address_html = ''
+ add_ids = ['none']
+ for a in self.user.addresses:
+ add_ids.append(str(a.id))
+ add_ids.append('new')
+ self.select_address = SelectField(self.name,
+ refresh_on_change=True,
+ refresh_on_change_values=add_ids)
+ if self.value == 'none':
+ self.select_address.add_option('Select one', 'none', selected=True)
+ else:
+ self.select_address.add_option('Select one', 'none')
+ for a in self.user.addresses:
+ if not a.deleted:
+ if self.value == str(a.id):
+ self.select_address.add_option(a.desc, str(a.id), selected=True)
+ # display this address
+ address_html = '''<div class="form-row">
+ %s
+ </div>''' % a.get_html()
+ else:
+ self.select_address.add_option(a.desc, str(a.id))
+ if self.value == 'new':
+ self.select_address.add_option('Add a new address', 'new', selected=True)
+ for field_name, label in self.fields():
+ add_field = TextField(self.name+'_'+field_name,
+ 40,
+ util.restore_text( self.params.get( self.name+'_'+field_name, '' ) ))
+ address_html += ''' <div class="form-row">
+ <label>%s</label>
+ %s
+ </div>
+ ''' % (label, add_field.get_html())
+ else:
+ self.select_address.add_option('Add a new address', 'new')
+ return self.select_address.get_html()+address_html
def get_suite():
diff -r 11a2d159e280 -r 24ccfa887fcd lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py Wed Aug 05 12:59:24 2009 -0400
+++ b/lib/galaxy/web/framework/helpers/grids.py Thu Aug 06 09:52:59 2009 -0400
@@ -43,6 +43,8 @@
query = column.filter( query, column_filter, filter_args )
# Carry filter along to newly generated urls
extra_url_args[ "f-" + column.key ] = column_filter
+ if filter_args:
+ query = query.filter_by( **filter_args )
# Process sort arguments
sort_key = sort_order = None
if 'sort' in kwargs:
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/forms/create_form.mako
--- a/templates/admin/forms/create_form.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/forms/create_form.mako Thu Aug 06 09:52:59 2009 -0400
@@ -26,7 +26,7 @@
<div style="clear: both"></div>
</div>
<div class="form-row">
- <input type="submit" name="save_form" value="Save"/>
+ <input type="submit" name="save_form" value="Add fields"/>
</div>
</form>
</div>
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/forms/edit_form.mako
--- a/templates/admin/forms/edit_form.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/forms/edit_form.mako Thu Aug 06 09:52:59 2009 -0400
@@ -84,7 +84,7 @@
<div style="clear: both"></div>
</div>
%endfor
- <div class="toolFormTitle">Sample fields (${len(form.fields)})</div>
+ <div class="toolFormTitle">Fields (${len(form.fields)})</div>
%for ctr, field in enumerate(field_details):
${render_field( ctr, field )}
%endfor
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/forms/manage_forms.mako
--- a/templates/admin/forms/manage_forms.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/forms/manage_forms.mako Thu Aug 06 09:52:59 2009 -0400
@@ -3,6 +3,10 @@
<%def name="title()">Manage Form Definitions</%def>
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
## Render a row
<%def name="render_row( form, ctr )">
@@ -12,11 +16,18 @@
<tr>
%endif
<td>
- <b><a href="${h.url_for( controller='forms', action='edit', form_id=form.id, read_only=True )}">${form.name}</a></b>
+ <a href="${h.url_for( controller='forms', action='edit', form_id=form.id, read_only=True )}">${form.name}</a>
<a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a>
- <div popupmenu="form-${form.id}-popup">
- <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit form definition</a>
- </div>
+ %if form.form_definition_current.deleted:
+ <div popupmenu="form-${form.id}-popup">
+ <a class="action-button" href="${h.url_for( action='undelete', form_id=form.id )}">Undelete</a>
+ </div>
+ %else:
+ <div popupmenu="form-${form.id}-popup">
+ <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit form definition</a>
+ <a class="action-button" confirm="Click OK to delete the form ${form.name}." href="${h.url_for( action='delete', form_id=form.id )}">Delete</a>
+ </div>
+ %endif
</td>
<td><i>${form.desc}</i></td>
</tr>
@@ -24,36 +35,33 @@
<h2>
- %if deleted:
- Deleted
- %endif
Forms
</h2>
-
-
<ul class="manage-table-actions">
- %if not deleted:
- <li>
- <a class="action-button" href="${h.url_for( controller='forms', action='new', new=True )}">
- <img src="${h.url_for('/static/images/silk/add.png')}" />
- <span>Define a new form</span></a>
- </li>
- %endif
+ <li>
+ <a class="action-button" href="${h.url_for( controller='forms', action='new', new=True )}">
+ <img src="${h.url_for('/static/images/silk/add.png')}" />
+ <span>Define a new form</span></a>
+ </li>
</ul>
-
-%if msg:
- ${render_msg( msg, messagetype )}
-%endif
-
+<div class="grid-header">
+ ##<span class="title">Filter:</span>
+ %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ):
+ %if i > 0:
+ <span>|</span>
+ %endif
+ %if show_filter == filter:
+ <span class="filter"><a href="${h.url_for( controller='forms', action='manage', show_filter=filter )}"><b>${filter}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='forms', action='manage', show_filter=filter )}">${filter}</a></span>
+ %endif
+ %endfor
+</div>
%if not fdc_list:
- %if deleted:
- There are no deleted forms
- %else:
- There are no forms.
- %endif
+ There are no forms.
%else:
<table class="grid">
<thead>
@@ -70,4 +78,4 @@
%endfor
</tbody>
</table>
-%endif
+%endif
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/requests/grid.mako
--- a/templates/admin/requests/grid.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/requests/grid.mako Thu Aug 06 09:52:59 2009 -0400
@@ -76,15 +76,27 @@
<div class="grid-header">
<h2>${grid.title}</h2>
-## %if len(query.all()):
-## <span class="title">Filter:</span>
-## %for i, filter in enumerate( grid.standard_filters ):
-## %if i > 0:
-## <span>|</span>
-## %endif
-## <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
-## %endfor
-## %endif
+ ##%if len(query.all()):
+ ##<span class="title">Filter:</span>
+ %for i, filter in enumerate( grid.standard_filters ):
+ %if i > 0:
+ <span>|</span>
+ %endif
+ %if 'state' in grid.default_filter:
+ %if grid.default_filter['state'] == filter.label:
+ <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span>
+ %endif
+ %else:
+ %if filter.label == 'All':
+ <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span>
+ %endif
+ %endif
+ %endfor
+ ##%endif
</div>
@@ -95,7 +107,7 @@
<table class="grid">
<thead>
<tr>
- <th></th>
+ ##<th></th>
%for column in grid.columns:
%if column.visible:
<%
@@ -137,9 +149,9 @@
%endif
>
## Item selection column
- <td style="width: 1.5em;">
- <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
- </td>
+ ##<td style="width: 1.5em;">
+ ## <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+ ##</td>
## Data columns
%for column in grid.columns:
%if column.visible:
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/requests/manage_request_types.mako
--- a/templates/admin/requests/manage_request_types.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/requests/manage_request_types.mako Thu Aug 06 09:52:59 2009 -0400
@@ -3,10 +3,11 @@
<%def name="title()">request Types</%def>
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
<h2>
- %if deleted:
- Deleted
- %endif
Request Types
</h2>
@@ -16,16 +17,21 @@
</li>
</ul>
-%if msg:
- ${render_msg( msg, messagetype )}
-%endif
-
+<div class="grid-header">
+ ##<span class="title">Filter:</span>
+ %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ):
+ %if i > 0:
+ <span>|</span>
+ %endif
+ %if show_filter == filter:
+ <span class="filter"><a href="${h.url_for( controller='admin', action='manage_request_types', show_filter=filter )}"><b>${filter}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='admin', action='manage_request_types', show_filter=filter )}">${filter}</a></span>
+ %endif
+ %endfor
+</div>
%if not request_types:
- %if deleted:
- There are no deleted request types
- %else:
- There are no request types.
- %endif
+ There are no request types.
%else:
<table class="grid">
<thead>
@@ -39,7 +45,19 @@
<tbody>
%for request_type in request_types:
<tr>
- <td><b><a href="${h.url_for( controller='admin', action='request_type', edit='True', id=request_type.id)}">${request_type.name}</a></b></td>
+ <td>
+ <a href="${h.url_for( controller='admin', action='request_type', edit='True', id=request_type.id)}">${request_type.name}</a>
+ <a id="request_type-${request_type.id}-popup" class="popup-arrow" style="display: none;">▼</a>
+ %if request_type.deleted:
+ <div popupmenu="request_type-${request_type.id}-popup">
+ <a class="action-button" href="${h.url_for( action='undelete_request_type', request_type_id=request_type.id )}">Undelete</a>
+ </div>
+ %else:
+ <div popupmenu="request_type-${request_type.id}-popup">
+ <a class="action-button" confirm="Click OK to delete the request type ${request_type.name}." href="${h.url_for( action='delete_request_type', request_type_id=request_type.id )}">Delete</a>
+ </div>
+ %endif
+ </td>
<td><i>${request_type.desc}</i></td>
<td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.request_form.id, read_only=True)}">${request_type.request_form.name}</a></td>
<td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.sample_form.id, read_only=True)}">${request_type.sample_form.name}</a></td>
diff -r 11a2d159e280 -r 24ccfa887fcd templates/admin/samples/bar_codes.mako
--- a/templates/admin/samples/bar_codes.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/admin/samples/bar_codes.mako Thu Aug 06 09:52:59 2009 -0400
@@ -1,12 +1,14 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
-<h2>Bar codes for Samples of Request "${request.name}"</h2>
-<h3>User: ${user.email}</h3>
%if msg:
${render_msg( msg, messagetype )}
%endif
+
+
+<h2>Bar codes for Samples of Request "${request.name}"</h2>
+<h3>User: ${user.email}</h3>
<ul class="manage-table-actions">
<li>
@@ -31,7 +33,7 @@
<td><b><a>${sample.name}</a></b></td>
<td><a>${sample.desc}</a></td>
<td>
- <input type="text" name="sample_${index}_bar_code" value=${sample.bar_code} size="40"/>
+ ${widgets[index].get_html()}
</td>
</tr>
%endfor
diff -r 11a2d159e280 -r 24ccfa887fcd templates/requests/edit_request.mako
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/requests/edit_request.mako Thu Aug 06 09:52:59 2009 -0400
@@ -0,0 +1,84 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+ $( "select[refresh_on_change='true']").change( function() {
+ var refresh = false;
+ var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+ if ( refresh_on_change_values ) {
+ refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+ var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+ for( i= 0; i < refresh_on_change_values.length; i++ ) {
+ if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+ refresh = true;
+ break;
+ }
+ }
+ }
+ else {
+ refresh = true;
+ }
+ if ( refresh ){
+ $( "#edit_request" ).submit();
+ }
+ });
+});
+</script>
+
+<br/>
+<br/>
+<ul class="manage-table-actions">
+ <li>
+ <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
+ <span>Browse requests</span></a>
+ </li>
+</ul>
+
+<div class="toolForm">
+ <div class="toolFormTitle">Edit request "${request.name}"</div>
+ %if len(select_request_type.options) == 1:
+ There are no request types created for a new request.
+ %else:
+ <div class="toolFormBody">
+ <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests', action='edit', request_id=request.id)}" method="post" >
+ <div class="form-row">
+ <label>
+ Select Request Type:
+ </label>
+ ${select_request_type.get_html()}
+ </div>
+
+ %if select_request_type.get_selected() != ('Select one', 'none'):
+ %for i, field in enumerate(widgets):
+ <div class="form-row">
+ <label>${field['label']}</label>
+ ${field['widget'].get_html()}
+ %if field['label'] == 'Library' and new_library:
+ ${new_library.get_html()}
+ %endif
+ <div class="toolParamHelp" style="clear: both;">
+ ${field['helptext']}
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ %endfor
+ <div class="form-row">
+ <div style="float: left; width: 250px; margin-right: 10px;">
+ <input type="hidden" name="refresh" value="true" size="40"/>
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ <div class="form-row">
+ <input type="submit" name="save_changes_request_button" value="Save changes"/>
+ ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
+ </div>
+ %endif
+ </form>
+ </div>
+</div>
+%endif
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd templates/requests/grid.mako
--- a/templates/requests/grid.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/requests/grid.mako Thu Aug 06 09:52:59 2009 -0400
@@ -76,15 +76,19 @@
<div class="grid-header">
<h2>${grid.title}</h2>
-## %if len(query.all()):
-## <span class="title">Filter:</span>
-## %for i, filter in enumerate( grid.standard_filters ):
-## %if i > 0:
-## <span>|</span>
-## %endif
-## <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
-## %endfor
-## %endif
+ ##%if len(query.all()):
+ ##<span class="title">Filter:</span>
+ %for i, filter in enumerate( grid.standard_filters ):
+ %if i > 0:
+ <span>|</span>
+ %endif
+ %if grid.show_filter == filter.label:
+ <span class="filter"><a href="${h.url_for( controller='requests', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='requests', action='list', show_filter=filter.label )}">${filter.label}</a></span>
+ %endif
+ %endfor
+ ##%endif
</div>
<ul class="manage-table-actions">
@@ -103,7 +107,7 @@
<table class="grid">
<thead>
<tr>
- <th></th>
+ ##<th></th>
%for column in grid.columns:
%if column.visible:
<%
@@ -145,9 +149,9 @@
%endif
>
## Item selection column
- <td style="width: 1.5em;">
- <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
- </td>
+ ##<td style="width: 1.5em;">
+ ## <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+ ##</td>
## Data columns
%for column in grid.columns:
%if column.visible:
@@ -196,7 +200,7 @@
</tr>
%endfor
</tbody>
-## <tfoot>
+ <tfoot>
## <tr>
## <td></td>
## <td colspan="100">
@@ -208,7 +212,7 @@
## %endfor
## </td>
## </tr>
-## </tfoot>
+ </tfoot>
</table>
</form>
%endif
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd templates/requests/new_request.mako
--- a/templates/requests/new_request.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/requests/new_request.mako Thu Aug 06 09:52:59 2009 -0400
@@ -1,10 +1,35 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
-
%if msg:
${render_msg( msg, messagetype )}
%endif
+
+<script type="text/javascript">
+$( function() {
+ $( "select[refresh_on_change='true']").change( function() {
+ var refresh = false;
+ var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+ if ( refresh_on_change_values ) {
+ refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+ var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+ for( i= 0; i < refresh_on_change_values.length; i++ ) {
+ if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+ refresh = true;
+ break;
+ }
+ }
+ }
+ else {
+ refresh = true;
+ }
+ if ( refresh ){
+ $( "#new_request" ).submit();
+ }
+ });
+});
+</script>
+
<br/>
<br/>
<ul class="manage-table-actions">
@@ -15,32 +40,45 @@
</ul>
<div class="toolForm">
- <div class="toolFormTitle">${title}</div>
- <div class="toolFormBody">
- <form id="new_request" name="new_request" action="${h.url_for( controller='requests', action='new', save=True, request_form_id=request_form_id, request_type_id=request_type.id )}" method="post" >
- %for i, field in enumerate(widgets):
+ <div class="toolFormTitle">Add a new request</div>
+ %if len(select_request_type.options) == 1:
+ There are no request types created for a new request.
+ %else:
+ <div class="toolFormBody">
+ <form name="new_request" id="new_request" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
<div class="form-row">
- <label>${field['label']}</label>
- ${field['widget'].get_html()}
- %if field['label'] == 'Library' and new_library:
- ${new_library.get_html()}
- %endif
- <div class="toolParamHelp" style="clear: both;">
- ${field['helptext']}
+ <label>
+ Select Request Type:
+ </label>
+ ${select_request_type.get_html()}
+ </div>
+
+ %if select_request_type.get_selected() != ('Select one', 'none'):
+ %for i, field in enumerate(widgets):
+ <div class="form-row">
+ <label>${field['label']}</label>
+ ${field['widget'].get_html()}
+ %if field['label'] == 'Library' and new_library:
+ ${new_library.get_html()}
+ %endif
+ <div class="toolParamHelp" style="clear: both;">
+ ${field['helptext']}
+ </div>
+ <div style="clear: both"></div>
+ </div>
+ %endfor
+ <div class="form-row">
+ <div style="float: left; width: 250px; margin-right: 10px;">
+ <input type="hidden" name="refresh" value="true" size="40"/>
+ </div>
+ <div style="clear: both"></div>
</div>
- <div style="clear: both"></div>
- </div>
- %endfor
- <div class="form-row">
- <div style="float: left; width: 250px; margin-right: 10px;">
- <input type="hidden" name="new" value="submitted" size="40"/>
- </div>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="create_request_button" value="Save"/>
- <input type="submit" name="create_request_samples_button" value="Add samples"/>
- </div>
+ <div class="form-row">
+ <input type="submit" name="create_request_button" value="Save"/>
+ <input type="submit" name="create_request_samples_button" value="Add samples"/>
+ </div>
+ %endif
</form>
</div>
-</div>
\ No newline at end of file
+</div>
+%endif
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd templates/requests/select_request_type.mako
--- a/templates/requests/select_request_type.mako Wed Aug 05 12:59:24 2009 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-
-%if msg:
- ${render_msg( msg, messagetype )}
-%endif
-<br/>
-<br/>
-<ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests', action='list')}">
- <span>Browse requests</span></a>
- </li>
-</ul>
-
-<div class="toolForm">
- <div class="toolFormTitle">Add a new request</div>
- %if not request_types:
- There are no request types created for a new request.
- %else:
- <div class="toolFormBody">
- <form name="select_request_type" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
- <div class="form-row">
- <label>
- Select Request Type:
- </label>
- <select name="request_type_id">
- %for rt in request_types:
- <option value="${rt.id}">${rt.name}</option>
- %endfor
- </select>
- <input type="submit" name="create_request" value="Go"/>
- </div>
- </form>
- </div>
- %endif
-</div>
diff -r 11a2d159e280 -r 24ccfa887fcd templates/requests/show_request.mako
--- a/templates/requests/show_request.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/requests/show_request.mako Thu Aug 06 09:52:59 2009 -0400
@@ -13,7 +13,7 @@
<ul class="manage-table-actions">
- %if not request.submitted and request.samples:
+ %if request.unsubmitted() and request.samples:
<li>
<a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='submit_request', id=request.id)}">
<span>Submit request</span></a>
@@ -29,7 +29,7 @@
<%def name="render_sample_form( index, sample_name, sample_values )">
<td>
- <input type="text" name=sample_${index}_name value="${sample_name}" size="15"/>
+ <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/>
<div class="toolParamHelp" style="clear: both;">
<i>${' (required)' }</i>
</div>
@@ -38,7 +38,7 @@
</td>
%for field_index, field in enumerate(request.type.sample_form.fields):
<td>
- <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="15"/>
+ <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/>
<div class="toolParamHelp" style="clear: both;">
<i>${'('+field['required']+')' }</i>
</div>
@@ -51,7 +51,11 @@
${sample.name}
</td>
<td>
- <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+ %if sample.request.unsubmitted():
+ Unsubmitted
+ %else:
+ <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+ %endif
</td>
%for field_index, field in enumerate(request.type.sample_form.fields):
<td>
@@ -77,7 +81,11 @@
<i>None</i>
%else:
%if rd['label'] == 'Library':
- <a href="${h.url_for( controller='library', action='browse_library', id=request.library.id )}">${rd['value']}</a>
+ %if rd['value']:
+ <a href="${h.url_for( controller='library', action='browse_library', id=request.library.id )}">${rd['value']}</a>
+ %else:
+ <i>None</i>
+ %endif
%else:
${rd['value']}
%endif
@@ -85,13 +93,23 @@
</div>
<div style="clear: both"></div>
%endfor
+ %if request.unsubmitted():
+ <div class="form-row">
+ <ul class="manage-table-actions">
+ <li>
+ <a class="action-button" href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}">
+ <span>Edit request details</span></a>
+ </li>
+ </ul>
+ </div>
+ %endif
%endif
</div>
</div>
<div class="toolForm">
##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
- <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests', action='show_request', request_id=request.id )}" method="post" >
+ <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests', action='show_request' )}" method="post" >
<div class="form-row">
%if current_samples:
<table class="grid">
@@ -116,46 +134,77 @@
request.refresh()
%>
%for sample_index, sample in enumerate(current_samples):
- <tr>
- <td>${sample_index+1}</td>
- %if sample_index in range(len(request.samples)):
- ${render_sample( sample_index, request.samples[sample_index] )}
- %else:
+ %if edit_mode:
+ <tr>
+ <td>${sample_index+1}</td>
${render_sample_form( sample_index, sample[0], sample[1])}
- %endif
- <td>
- %if not request.submitted:
- <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
- <img src="${h.url_for('/static/images/delete_icon.png')}" />
- <span></span></a>
+ <td>
+ %if request.unsubmitted():
+ <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
+ <img src="${h.url_for('/static/images/delete_icon.png')}" />
+ <span></span></a>
+ %endif
+ </td>
+ </tr>
+ %else:
+ <tr>
+ <td>${sample_index+1}</td>
+ %if sample_index in range(len(request.samples)):
+ ${render_sample( sample_index, request.samples[sample_index] )}
+ %else:
+ ${render_sample_form( sample_index, sample[0], sample[1])}
%endif
- </td>
- </tr>
+ <td>
+ %if request.unsubmitted():
+ <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
+ <img src="${h.url_for('/static/images/delete_icon.png')}" />
+ <span></span></a>
+ %endif
+ </td>
+ </tr>
+ %endif
%endfor
</tbody>
</table>
%else:
- <label>There are no samples.</label>
+ <div class="form-row">
+ <label>There are no samples.</label>
+ </div>
%endif
</div>
- %if not request.submitted:
- <br/>
- <br/>
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- %if current_samples:
- <a>Copy from sample no. </a>
- ${sample_copy.get_html()}
- %endif
- <input type="submit" name="add_sample_button" value="Add New"/>
-
- </li>
- </ul>
- </div>
+ %if request.unsubmitted() and not edit_mode:
+ <table class="grid">
+ <tbody>
+ <tr>
+ <div class="form-row">
+ <td>
+ %if current_samples:
+ <input type="submit" name="edit_samples_button" value="Edit samples"/>
+ %endif
+ </td>
+ <td>
+ ##<div class="form-row">
+ <label>Import from csv file</label>
+ <input type="text" name="import_samples" value="" size="20"/>
+ <input type="submit" name="import_samples_button" value="Import samples"/>
+ ##</div>
+ </td>
+ <td>
+ ##<div class="form-row">
+ %if current_samples:
+ <label>Copy from sample</label>
+ ${sample_copy.get_html()}
+ %endif
+ <input type="submit" name="add_sample_button" value="Add New"/>
+ ##</div>
+ </td>
+ </div>
+ </tr>
+ </tbody>
+ </table>
%endif
- %if not request.submitted and (request.samples or current_samples):
+ %if request.unsubmitted() and (request.samples or current_samples):
<div class="form-row">
<div style="float: left; width: 250px; margin-right: 10px;">
<input type="hidden" name="refresh" value="true" size="40"/>
@@ -164,8 +213,12 @@
</div>
<div class="form-row">
<input type="submit" name="save_samples_button" value="Save"/>
+ %if edit_mode:
+ <input type="submit" name="cancel_changes_button" value="Cancel"/>
+ %endif
</div>
%endif
##</div>
+ <input type="hidden" name="request_id" value="${request.id}" />
</form>
</div>
diff -r 11a2d159e280 -r 24ccfa887fcd templates/user/address.mako
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/user/address.mako Thu Aug 06 09:52:59 2009 -0400
@@ -0,0 +1,83 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+<h2>Manage Addresses</h2>
+<ul class="manage-table-actions">
+ <li>
+ <a class="action-button" href="${h.url_for( controller='user', action='new_address')}">
+ <span>Add a new address</span></a>
+ <a class="action-button" href="${h.url_for( controller='user', action='index')}">
+ <span>User preferences</span></a>
+ </li>
+</ul>
+%if not trans.user.addresses:
+ There are no addresses
+%else:
+<div class="grid-header">
+ ##<span class="title">Filter:</span>
+ %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ):
+ %if i > 0:
+ <span>|</span>
+ %endif
+ %if show_filter == filter:
+ <span class="filter"><a href="${h.url_for( controller='user', action='manage_addresses', show_filter=filter )}"><b>${filter}</b></a></span>
+ %else:
+ <span class="filter"><a href="${h.url_for( controller='user', action='manage_addresses', show_filter=filter )}">${filter}</a></span>
+ %endif
+ %endfor
+</div>
+
+
+
+<div class="toolForm">
+ ##<div class="toolFormTitle">Addresses</div>
+ <div class="toolFormBody">
+ <% trans.user.refresh() %>
+ %if not trans.user.addresses:
+ <label>There are no addresses</label>
+ %else:
+ <table class="grid">
+ <tbody>
+ %for index, address in enumerate(addresses):
+ <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+
+ <td>
+ <div class="form-row">
+ <label>${address.desc}</label>
+ ${address.display()}
+ </div>
+ <div class="form-row">
+ <ul class="manage-table-actions">
+ <li>
+ %if not address.deleted:
+ <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id,
+ short_desc=address.desc,
+ name=address.name, institution=address.institution,
+ address1=address.address, city=address.city,
+ state=address.state, postal_code=address.postal_code,
+ country=address.country, phone=address.phone)}">
+ <span>Edit</span></a>
+ <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}">
+ <span>Delete address</span></a>
+ %else:
+ <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}">
+ <span>Undelete address</span></a>
+ %endif
+
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ %endfor
+ </tbody>
+ </table>
+ %endif
+ </div>
+</div>
+%endif
\ No newline at end of file
diff -r 11a2d159e280 -r 24ccfa887fcd templates/user/index.mako
--- a/templates/user/index.mako Wed Aug 05 12:59:24 2009 -0400
+++ b/templates/user/index.mako Thu Aug 06 09:52:59 2009 -0400
@@ -1,5 +1,6 @@
<%inherit file="/base.mako"/>
<%def name="title()">User preferences</%def>
+
<h2>${_('User preferences')}</h2>
@@ -9,6 +10,7 @@
<li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li>
<li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li>
<li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li>
+ <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li>
<li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li>
</ul>
%else:
1
0
Hi all,
I'm trying install some local tools, but only locally to the galaxy user
(e.g. ~/local_tools/bin). In order to avoid specifying the full path in
each and every tool's XML file how can I specify a PATH for galaxy to
find the binaries? It seems that Galaxy ignores the default $PATH
although SGE can.
Cheers,
Chris
2
5
06 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/1ba58ed85a5f
changeset: 2536:1ba58ed85a5f
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Wed Aug 05 11:54:34 2009 -0400
description:
Testing framework will now click the add button for nested repeats when repeat content has been specfied.
3 file(s) affected in this change:
test-data/joiner_out4.bed
test/base/twilltestcase.py
tools/filters/joiner.xml
diffs (133 lines):
diff -r 93d502caec2a -r 1ba58ed85a5f test-data/joiner_out4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/joiner_out4.bed Wed Aug 05 11:54:34 2009 -0400
@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + NoChrom
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + NoChrom
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - NoChrom
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + NoChrom
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - NoChrom
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - NoChrom
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + NoChrom
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - NoChrom
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + NoChrom
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + NoChrom
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - NoChrom
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + NoChrom
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - NoChrom
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - NoChrom
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + NoChrom
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - NoChrom
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
diff -r 93d502caec2a -r 1ba58ed85a5f test/base/twilltestcase.py
--- a/test/base/twilltestcase.py Wed Aug 05 11:19:46 2009 -0400
+++ b/test/base/twilltestcase.py Wed Aug 05 11:54:34 2009 -0400
@@ -650,9 +650,17 @@
break
# To help with debugging a tool, print out the form controls when the test fails
print "form '%s' contains the following controls ( note the values )" % f.name
+ control_names = []
for i, control in enumerate( f.controls ):
print "control %d: %s" % ( i, str( control ) )
try:
+ #check if a repeat element needs to be added
+ if control.name not in kwd and control.name.endswith( '_add' ):
+ #control name doesn't exist, could be repeat
+ repeat_startswith = control.name[0:-4]
+ if repeat_startswith and not [ c_name for c_name in control_names if c_name.startswith( repeat_startswith ) ] and [ c_name for c_name in kwd.keys() if c_name.startswith( repeat_startswith ) ]:
+ tc.submit( control.name )
+ return self.submit_form( form_no=form_no, button=button, **kwd )
# Check for refresh_on_change attribute, submit a change if required
if 'refresh_on_change' in control.attrs.keys():
changed = False
@@ -677,6 +685,7 @@
except Exception, e:
log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) )
continue
+ control_names.append( control.name )
# No refresh_on_change attribute found in current form, so process as usual
for control_name, control_value in kwd.items():
if not isinstance( control_value, list ):
diff -r 93d502caec2a -r 1ba58ed85a5f tools/filters/joiner.xml
--- a/tools/filters/joiner.xml Wed Aug 05 11:19:46 2009 -0400
+++ b/tools/filters/joiner.xml Wed Aug 05 11:54:34 2009 -0400
@@ -98,7 +98,7 @@
<param name="fill_empty_columns_switch" value="no_fill"/>
<output name="out_file1" file="joiner_out2.bed"/>
</test>
-<test>
+ <test>
<param name="input1" value="1.bed"/>
<param name="input2" value="2.bed"/>
<param name="field1" value="2"/>
@@ -110,6 +110,22 @@
<param name="column_fill_type" value="single_fill_value"/>
<param name="fill_value" value="~"/>
<output name="out_file1" file="joiner_out3.bed"/>
+ </test>
+ <test>
+ <param name="input1" value="1.bed"/>
+ <param name="input2" value="2.bed"/>
+ <param name="field1" value="2"/>
+ <param name="field2" value="2"/>
+ <param name="unmatched" value="Yes"/>
+ <param name="partial" value="Yes"/>
+ <param name="fill_empty_columns_switch" value="fill_empty"/>
+ <param name="fill_columns_by" value="fill_all"/>
+ <param name="column_fill_type" value="fill_value_by_column"/>
+ <param name="column_number1" value="6"/>
+ <param name="fill_value1" value="+"/>
+ <param name="column_number2" value="1"/>
+ <param name="fill_value2" value="NoChrom"/>
+ <output name="out_file1" file="joiner_out4.bed"/>
</test>
</tests>
<help>
1
0
06 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/11a2d159e280
changeset: 2537:11a2d159e280
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Wed Aug 05 12:59:24 2009 -0400
description:
In tool tests, only add a file once if it is required.
1 file(s) affected in this change:
lib/galaxy/tools/test.py
diffs (29 lines):
diff -r 1ba58ed85a5f -r 11a2d159e280 lib/galaxy/tools/test.py
--- a/lib/galaxy/tools/test.py Wed Aug 05 11:54:34 2009 -0400
+++ b/lib/galaxy/tools/test.py Wed Aug 05 12:59:24 2009 -0400
@@ -25,7 +25,7 @@
for input_name, input_value in self.tool.inputs.items():
if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ):
self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value)
- elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ):
+ elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files:
self.required_files.append( ( value, extra ) )
except: pass
self.inputs.append( ( name, value, extra ) )
@@ -37,7 +37,7 @@
if name != grouping_value.test_param.name:
for case in grouping_value.cases:
for case_input_name, case_input_value in case.inputs.items():
- if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ):
+ if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files:
self.required_files.append( ( value, extra ) )
return True
elif isinstance( case_input_value, grouping.Conditional ):
@@ -49,6 +49,6 @@
# with the same name ( "input2" ) is not yet supported in our test code ( the lat one added is the only
# one used ).
for input_name, input_value in grouping_value.inputs.items():
- if input_name == name and isinstance( input_value, basic.DataToolParameter ):
+ if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files:
self.required_files.append( ( value, extra ) )
return True
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/ab5bf78270af
changeset: 2533:ab5bf78270af
user: James Taylor <james(a)jamestaylor.org>
date: Wed Aug 05 10:44:57 2009 -0400
description:
Bugfix in process_css.py
1 file(s) affected in this change:
static/june_2007_style/process_css.py
diffs (21 lines):
diff -r f0978599ba8d -r ab5bf78270af static/june_2007_style/process_css.py
--- a/static/june_2007_style/process_css.py Wed Aug 05 08:58:23 2009 -0400
+++ b/static/june_2007_style/process_css.py Wed Aug 05 10:44:57 2009 -0400
@@ -139,7 +139,7 @@
pad = 10
- class SpriteGroup():
+ class SpriteGroup( object ):
def __init__( self, name ):
self.name = name
self.offset = 0
@@ -152,7 +152,7 @@
self.offset += sprite.image.size[1] + pad
return sprite
- class Sprite():
+ class Sprite( object ):
def __init__( self, fname, offset ):
self.fname = fname
self.image = Image.open( os.path.join( image_dir, fname ) )
1
0
06 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/93d502caec2a
changeset: 2535:93d502caec2a
user: rc
date: Wed Aug 05 11:19:46 2009 -0400
description:
Fixed the issue which was causing the 'Lab' tab in the masthead to appear automatically. Now, this tab is visible only when request types have been created by the admin.
1 file(s) affected in this change:
templates/base_panels.mako
diffs (30 lines):
diff -r 80e1c1772ed5 -r 93d502caec2a templates/base_panels.mako
--- a/templates/base_panels.mako Wed Aug 05 11:02:53 2009 -0400
+++ b/templates/base_panels.mako Wed Aug 05 11:19:46 2009 -0400
@@ -149,15 +149,17 @@
${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))}
${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))}
-
- <td class="tab">
- <a>Lab</a>
- <div class="submenu">
- <ul>
- <li><a target="requests" href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li>
- </ul>
- </div>
- </td>
+
+ %if trans.request_types():
+ <td class="tab">
+ <a>Lab</a>
+ <div class="submenu">
+ <ul>
+ <li><a target="requests" href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li>
+ </ul>
+ </div>
+ </td>
+ %endif
%if app.config.get_bool( 'enable_tracks', False ):
<td class="tab">
1
0
06 Aug '09
details: http://www.bx.psu.edu/hg/galaxy/rev/f0978599ba8d
changeset: 2532:f0978599ba8d
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Wed Aug 05 08:58:23 2009 -0400
description:
Allow nested groupings in testing framework.
3 file(s) affected in this change:
test-data/joiner_out3.bed
test/functional/test_toolbox.py
tools/filters/joiner.xml
diffs (171 lines):
diff -r 0d5182c4870b -r f0978599ba8d test-data/joiner_out3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/joiner_out3.bed Wed Aug 05 08:58:23 2009 -0400
@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + X X X X X X
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + X X X X X X
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - X X X X X X
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + X X X X X X
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - X X X X X X
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - X X X X X X
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + X X X X X X
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - X X X X X X
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + X X X X X X
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + X X X X X X
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - X X X X X X
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + X X X X X X
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - X X X X X X
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - X X X X X X
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + X X X X X X
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - X X X X X X
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
diff -r 0d5182c4870b -r f0978599ba8d test/functional/test_toolbox.py
--- a/test/functional/test_toolbox.py Tue Aug 04 16:32:57 2009 -0400
+++ b/test/functional/test_toolbox.py Wed Aug 05 08:58:23 2009 -0400
@@ -65,52 +65,39 @@
def shortDescription( self ):
return self.name
- def __expand_grouping( self, tool_inputs, declared_inputs, repeat_index=0, repeat_sep='' ):
+ def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):
expanded_inputs = {}
for key, value in tool_inputs.items():
- if isinstance(value, grouping.Conditional):
- for i, case in enumerate(value.cases):
- if declared_inputs[value.test_param.name] == case.value:
+ if isinstance( value, grouping.Conditional ):
+ if prefix:
+ new_prefix = "%s|%s" % ( prefix, value.name )
+ else:
+ new_prefix = value.name
+ for i, case in enumerate( value.cases ):
+ if declared_inputs[ value.test_param.name ] == case.value:
if isinstance(case.value, str):
- if repeat_sep:
- cond_sep = "%s%s" % ( repeat_sep, value.test_param.name )
- else:
- cond_sep = "%s|%s" % ( value.name, value.test_param.name )
- expanded_inputs[ cond_sep ] = case.value.split( "," )
+ expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value.split( "," )
else:
- if repeat_sep:
- cond_sep = "%s%s" % ( repeat_sep, value.test_param.name )
- else:
- cond_sep = "%s|%s" % ( value.name, value.test_param.name )
- expanded_inputs[ cond_sep ] = case.value
+ expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value
for input_name, input_value in case.inputs.items():
- if isinstance(input_value, grouping.Conditional):
- expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=repeat_sep ) )
- elif isinstance(declared_inputs[input_name], str):
- if repeat_sep:
- cond_sep = "%s%s" % ( repeat_sep, input_name )
- else:
- cond_sep = "%s|%s" % ( value.name, input_name )
- expanded_inputs.update( { cond_sep : declared_inputs[ input_name ].split( "," ) } )
- else:
- if repeat_sep:
- cond_sep = "%s%s" % ( repeat_sep, input_name )
- else:
- cond_sep = "%s|%s" % ( value.name, input_name )
- expanded_inputs.update( { cond_sep : declared_inputs[ input_name ] } )
+ expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, prefix = new_prefix ) )
elif isinstance( value, grouping.Repeat ):
- for r_name, r_value in value.inputs.items():
- repeat_sep = "%s_%d|%s" % ( value.name, repeat_index, r_name )
- if isinstance( r_value, grouping.Conditional ):
- cond_sep = repeat_sep + "|"
- expanded_inputs.update( self.__expand_grouping( { r_name:r_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=cond_sep ) )
- else:
- expanded_inputs.update( { repeat_sep : [ declared_inputs[ r_name ] ] } )
- repeat_index += 1
+ for repeat_index in xrange( 0, 1 ): #need to allow for and figure out how many repeats we have
+ for r_name, r_value in value.inputs.iteritems():
+ new_prefix = "%s_%d" % ( value.name, repeat_index )
+ if prefix:
+ new_prefix = "%s|%s" % ( prefix, new_prefix )
+ expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value }, declared_inputs, prefix = new_prefix ) )
elif isinstance(declared_inputs[value.name], str):
- expanded_inputs[value.name] = declared_inputs[value.name].split(",")
+ if prefix:
+ expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name].split(",")
+ else:
+ expanded_inputs[value.name] = declared_inputs[value.name].split(",")
else:
- expanded_inputs[value.name] = declared_inputs[value.name]
+ if prefix:
+ expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name]
+ else:
+ expanded_inputs[value.name] = declared_inputs[value.name]
return expanded_inputs
def get_testcase( testdef, name ):
diff -r 0d5182c4870b -r f0978599ba8d tools/filters/joiner.xml
--- a/tools/filters/joiner.xml Tue Aug 04 16:32:57 2009 -0400
+++ b/tools/filters/joiner.xml Wed Aug 05 08:58:23 2009 -0400
@@ -98,7 +98,7 @@
<param name="fill_empty_columns_switch" value="no_fill"/>
<output name="out_file1" file="joiner_out2.bed"/>
</test>
-<!--this throws an exception in the test framework - we need tests for the fill empty columns enhancements <test>
+<test>
<param name="input1" value="1.bed"/>
<param name="input2" value="2.bed"/>
<param name="field1" value="2"/>
@@ -110,7 +110,7 @@
<param name="column_fill_type" value="single_fill_value"/>
<param name="fill_value" value="~"/>
<output name="out_file1" file="joiner_out3.bed"/>
- </test>-->
+ </test>
</tests>
<help>
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