diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 52f722a248c..64477073c0a 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -15,6 +15,7 @@ import galaxy.datatypes.registry
from galaxy.datatypes.metadata import MetadataCollection
from galaxy.security import RBACAgent, get_permitted_actions
+
import logging
log = logging.getLogger( __name__ )
@@ -1095,6 +1096,58 @@ class MetadataFile( object ):
raise
# Return filename inside hashed directory
return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
+
+
+class FormDefinition( object ):
+ def __init__(self, name=None, desc=None, fields=[], current_form_id=None):
+ self.name = name
+ self.desc = desc
+ self.fields = fields
+ self.form_definition_current_id = current_form_id
+
+class FormDefinitionCurrent( object ):
+ def __init__(self, form_definition_id=None):
+ self.latest_form_id = form_definition_id
+
+class FormValues( object ):
+ def __init__(self, form_def_id=None, content=None):
+ self.form_definition_id = form_def_id
+ self.content = content
+
+class Request( object ):
+ def __init__(self, name=None, desc=None, request_type_id=None, user_id=None, form_values_id=None, library_id=None):
+ self.name = name
+ self.desc = desc
+ self.request_type_id = request_type_id
+ self.form_values_id = form_values_id
+ self.user_id = user_id
+ self.library_id = library_id
+
+class RequestType( object ):
+ def __init__(self, request_form_id=None, sample_form_id=None):
+ self.request_form_id = request_form_id
+ self.sample_form_id = sample_form_id
+
+class Sample( object ):
+ def __init__(self, name=None, desc=None, request_id=None, form_values_id=None):
+ self.name = name
+ self.desc = desc
+ self.request_id = request_id
+ self.form_values_id = form_values_id
+
+class SampleState( object ):
+ def __init__(self, name=None, desc=None, request_type_id=None):
+ self.name = name
+ self.desc = desc
+ self.request_type_id = request_type_id
+
+class SampleEvent( object ):
+ def __init__(self, sample_id=None, sample_state_id=None, comment=''):
+ self.sample_id = sample_id
+ self.sample_state_id = sample_state_id
+ self.comment = comment
+
+
## ---- Utility methods -------------------------------------------------------
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 5ccf0233a7c..6d4ed4144eb 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -520,9 +520,115 @@ MetadataFile.table = Table( "metadata_file", metadata,
Column( "deleted", Boolean, index=True, default=False ),
Column( "purged", Boolean, index=True, default=False ) )
+
+FormDefinitionCurrent.table = Table('form_definition_current', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "deleted", Boolean, index=True, default=False ))
+
+# new table to store all the forms which is created by the admin
+FormDefinition.table = Table('form_definition', 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 ),
+ Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True ),
+ Column( "fields", JSONType()))
+
+RequestType.table = Table('request_type', 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 ),
+ Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) )
+
+FormValues.table = Table('form_values', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "content", JSONType()) )
+
+Request.table = Table('request', 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 ),
+ Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+ 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( "deleted", Boolean, index=True, default=False ) )
+
+Sample.table = Table('sample', 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 ),
+ Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+ Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
+ Column( "deleted", Boolean, index=True, default=False ) )
+
+# new table to store all the possible sample states and the sample type it
+# belongs to
+SampleState.table = Table('sample_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 ),
+ Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) )
+
+SampleEvent.table = Table('sample_event', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ),
+ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ),
+ Column( "comment", TEXT ) )
+
+
+
# With the tables defined we can define the mappers and setup the
# 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) ),
+ ) )
+
+assign_mapper( context, FormValues, FormValues.table, properties=None)
+
+assign_mapper( context, Request, Request.table, properties=None)
+
+assign_mapper( context, RequestType, RequestType.table,
+ properties=dict( states=relation( SampleState, backref="request_type",
+ order_by=desc(SampleState.table.c.update_time) ),
+ ) )
+
+assign_mapper( context, FormDefinition, FormDefinition.table, properties=None)
+
+assign_mapper( context, FormDefinitionCurrent, FormDefinitionCurrent.table,
+ properties=dict( forms=relation( FormDefinition, backref='form_definition_current',
+ cascade="all, delete-orphan",
+ primaryjoin=( FormDefinitionCurrent.table.c.id == FormDefinition.table.c.form_definition_current_id ) ),
+ latest_form=relation( FormDefinition, post_update=True,
+ primaryjoin=( FormDefinitionCurrent.table.c.latest_form_id == FormDefinition.table.c.id ) )
+ ) )
+
+assign_mapper( context, SampleEvent, SampleEvent.table, properties=None)
+
+assign_mapper( context, SampleState, SampleState.table,
+ properties=None #dict( sample=relation( Sample, backref="sample" ),
+ )# )
+
assign_mapper( context, ValidationError, ValidationError.table )
assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.table,
@@ -590,6 +696,8 @@ assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation
assign_mapper( context, User, User.table,
properties=dict( histories=relation( History, backref="user",
order_by=desc(History.table.c.update_time) ),
+ requests=relation( Request, backref="user",
+ order_by=desc(Request.table.c.update_time) ),
active_histories=relation( History, primaryjoin=( ( History.table.c.user_id == User.table.c.id ) & ( not_( History.table.c.deleted ) ) ), order_by=desc( History.table.c.update_time ) ),
galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ),
stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user",
diff --git a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
new file mode 100644
index 00000000000..81b1558b432
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
@@ -0,0 +1,189 @@
+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 ) )
+
+
+FormDefinitionCurrent_table = Table('form_definition_current', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "latest_form_id", Integer,
+ #ForeignKey( "form_definition.id", use_alter=True, name='form_definition_current_latest_form_id_fk'),
+ index=True ),
+ Column( "deleted", Boolean, index=True, default=False ))
+FormDefinition_table = Table('form_definition', 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 ),
+ Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True, nullable=False ),
+ Column( "fields", JSONType()) )
+
+FormValues_table = Table('form_values', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "content", JSONType()) )
+
+RequestType_table = Table('request_type', 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 ),
+ Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+ Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) )
+# request table
+Request_table = Table('request', 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 ),
+ Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+ 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( "deleted", Boolean, index=True, default=False ) )
+
+Sample_table = Table('sample', 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 ),
+ Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+ Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
+ Column( "deleted", Boolean, index=True, default=False ) )
+
+SampleState_table = Table('sample_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 ),
+ Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) )
+
+SampleEvent_table = Table('sample_event', metadata,
+ Column( "id", Integer, primary_key=True),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ),
+ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ),
+ Column( "comment", TEXT ) )
+
+
+
+
+def upgrade():
+ # Load existing tables
+ metadata.reflect()
+
+ # Add all of the new tables above
+# metadata.create_all()
+ try:
+ FormDefinitionCurrent_table.create()
+ except Exception, e:
+ log.debug( "Creating form_definition_current table failed: %s" % str( e ) )
+ try:
+ FormDefinition_table.create()
+ except Exception, e:
+ log.debug( "Creating form_definition table failed: %s" % str( e ) )
+ # Add 1 foreign key constraint to the form_definition_current table
+ if FormDefinitionCurrent_table and FormDefinition_table:
+ try:
+ cons = ForeignKeyConstraint( [FormDefinitionCurrent_table.c.latest_form_id],
+ [FormDefinition_table.c.id],
+ name='form_definition_current_latest_form_id_fk' )
+ # Create the constraint
+ cons.create()
+ except Exception, e:
+ log.debug( "Adding foreign key constraint 'form_definition_current_latest_form_id_fk' to table 'form_definition_current' failed: %s" % ( str( e ) ) )
+ try:
+ FormValues_table.create()
+ except Exception, e:
+ log.debug( "Creating form_values table failed: %s" % str( e ) )
+ try:
+ RequestType_table.create()
+ except Exception, e:
+ log.debug( "Creating request_type table failed: %s" % str( e ) )
+ try:
+ Request_table.create()
+ except Exception, e:
+ log.debug( "Creating request table failed: %s" % str( e ) )
+ try:
+ Sample_table.create()
+ except Exception, e:
+ log.debug( "Creating sample table failed: %s" % str( e ) )
+ try:
+ SampleState_table.create()
+ except Exception, e:
+ log.debug( "Creating sample_state table failed: %s" % str( e ) )
+ try:
+ SampleEvent_table.create()
+ except Exception, e:
+ log.debug( "Creating sample_event table failed: %s" % str( e ) )
+
+
+
+def downgrade():
+ # Load existing tables
+ metadata.reflect()
+ try:
+ FormDefinition_table.drop()
+ except Exception, e:
+ log.debug( "Dropping form_definition table failed: %s" % str( e ) )
+ try:
+ FormDefinitionCurrent_table.drop()
+ except Exception, e:
+ log.debug( "Dropping form_definition_current table failed: %s" % str( e ) )
+ try:
+ FormValues_table.drop()
+ except Exception, e:
+ log.debug( "Dropping form_values table failed: %s" % str( e ) )
+ try:
+ Request_table.drop()
+ except Exception, e:
+ log.debug( "Dropping request table failed: %s" % str( e ) )
+ try:
+ RequestType_table.drop()
+ except Exception, e:
+ log.debug( "Dropping request_type table failed: %s" % str( e ) )
+ try:
+ Sample_table.drop()
+ except Exception, e:
+ log.debug( "Dropping sample table failed: %s" % str( e ) )
+ try:
+ SampleState_table.drop()
+ except Exception, e:
+ log.debug( "Dropping sample_state table failed: %s" % str( e ) )
+ try:
+ SampleEvent_table.drop()
+ except Exception, e:
+ log.debug( "Dropping sample_event table failed: %s" % str( e ) )
+
+
+
+
diff --git a/lib/galaxy/web/controllers/admin.py b/lib/galaxy/web/controllers/admin.py
index 75b60fe3ea5..b2dde3b99e3 100644
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -3,6 +3,7 @@ from datetime import datetime, timedelta
from galaxy import util, datatypes
from galaxy.web.base.controller import *
from galaxy.model.orm import *
+import sys
import logging
log = logging.getLogger( __name__ )
@@ -2097,4 +2098,123 @@ class Admin( BaseController ):
else:
last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 )
return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype )
-
+
+ def _get_all_forms(self, trans, all_versions=False):
+ '''
+ This method returns all the latest forms from the
+ form_definition_current table if all_versions is set to True. Otherwise
+ this method return all the versions of all the forms from form_definition
+ table
+ '''
+ if all_versions:
+ return trans.app.model.FormDefinition.query().all()
+ else:
+ fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+ return [fdc.latest_form for fdc in fdc_list]
+ @web.expose
+ @web.require_admin
+ def manage_request_types( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ forms = self._get_all_forms(trans, all_versions=True)
+ return trans.fill_template( '/admin/requests/manage_request_types.mako',
+ request_types=trans.app.model.RequestType.query().all(),
+ forms=forms,
+ deleted=False,
+ show_deleted=False,
+ msg=msg,
+ messagetype=messagetype )
+ @web.expose
+ @web.require_admin
+ def request_type( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ if params.get('create', False) == 'True':
+ return trans.fill_template( '/admin/requests/create_request_type.mako',
+ forms=self._get_all_forms(trans, all_versions=False),
+ msg=msg,
+ messagetype=messagetype)
+ elif params.get('add_states', False) == 'True':
+ return trans.fill_template( '/admin/requests/add_states.mako',
+ sample_type_name=util.restore_text( params.name ),
+ desc=util.restore_text( params.description ),
+ num_states=int(util.restore_text( params.num_states )),
+ request_form_id=int(util.restore_text( params.request_form_id )),
+ sample_form_id=int(util.restore_text( params.sample_form_id )),
+ msg=msg,
+ messagetype=messagetype)
+ elif params.get('save_new', False) == 'True':
+ st, msg = self._save_request_type(trans, params, None)
+ if not st:
+ return trans.fill_template( '/admin/requests/create_request_type.mako',
+ 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 )
+ 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()
+ return trans.fill_template( '/admin/requests/edit_request_type.mako',
+ request_type=rt,
+ forms=self._get_all_forms(trans, all_versions=False),
+ states_list=ss_list,
+ deleted=False,
+ show_deleted=False,
+ msg=msg,
+ messagetype=messagetype )
+ elif params.get('save_changes', False) == 'True':
+ st = trans.app.model.SampleType.get(int(util.restore_text( params.id )))
+ st, msg = self._save_sample_type(trans, params, st.id)
+ if st:
+ msg = "The sample type '%s' has been updated with the changes." % st.name
+ messagetype = 'done'
+ else:
+ messagetype = 'error'
+ ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.sample_type_id == st.id).all()
+ return trans.fill_template( '/admin/samples/edit_sample_type.mako',
+ sample_type=st,
+ forms=self._get_all_forms(trans, all_versions=False),
+ states_list=ss_list,
+ deleted=False,
+ show_deleted=False,
+ msg=msg,
+ messagetype=messagetype )
+ def _save_request_type(self, trans, params, request_type_id):
+ num_states = int( params.get( 'num_states', 0 ) )
+ proceed = True
+ for i in range( num_states ):
+ if not params.get( 'new_element_name_%i' % i, None ):
+ proceed = False
+ break
+ if not proceed:
+ msg = "All the state name(s) must be completed."
+ return None, msg
+ if not request_type_id: # create a new sample type to save
+ rt = trans.app.model.RequestType()
+ else: # use the existing sample type to save changes
+ rt = trans.app.model.RequestType.get(request_type_id)
+ rt.name = util.restore_text( params.name )
+ rt.desc = util.restore_text( params.description ) or ""
+ rt.request_form_id = int(util.restore_text( params.request_form_id ))
+ rt.sample_form_id = int(util.restore_text( params.sample_form_id ))
+ rt.flush()
+ # set sample states
+ ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
+ for ss in ss_list:
+ ss.delete()
+ ss.flush()
+ for i in range( num_states ):
+ name = params.get( 'new_element_name_%i' % i, None )
+ desc = params.get( 'new_element_description_%i' % i, None )
+ ss = trans.app.model.SampleState(name, desc, rt.id)
+ ss.flush()
+ msg = "The new sample type named '%s' with %s state(s) has been created" % (rt.name, num_states)
+ return rt, msg
diff --git a/lib/galaxy/web/controllers/forms.py b/lib/galaxy/web/controllers/forms.py
new file mode 100644
index 00000000000..bde94a2a4cf
--- /dev/null
+++ b/lib/galaxy/web/controllers/forms.py
@@ -0,0 +1,323 @@
+from galaxy.web.base.controller import *
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+import logging, os, sys
+from galaxy.web.form_builder import *
+from galaxy.tools.parameters.basic import parameter_types
+from elementtree.ElementTree import XML, Element
+from galaxy.util.odict import odict
+import copy
+
+log = logging.getLogger( __name__ )
+
+
+class Forms( BaseController ):
+ @web.expose
+ @web.require_admin
+ def index( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ return trans.fill_template( "/sample/index.mako",
+ default_action=params.get( 'default_action', None ),
+ msg=msg,
+ messagetype=messagetype )
+ @web.expose
+ @web.require_admin
+ def manage( self, trans, **kwd ):
+ 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):
+ fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+ return trans.fill_template( '/admin/forms/manage_forms.mako',
+ fdc_list=fdc_list,
+ deleted=False,
+ show_deleted=False,
+ msg=msg,
+ messagetype=messagetype )
+ def _get_all_forms(self, trans, all_versions=False):
+ '''
+ This method returns all the latest forms from the
+ form_definition_current table if all_versions is set to True. Otherwise
+ this method return all the versions of all the forms from form_definition
+ table
+ '''
+ if all_versions:
+ return trans.app.model.FormDefinition.query().all()
+ else:
+ fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+ return [fdc.latest_form for fdc in fdc_list]
+ @web.expose
+ @web.require_admin
+ def new( self, trans, **kwd ):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ if params.get('new', False) and not params.get('create_form', False):
+ self.current_form = {}
+ self.current_form['name'] = 'New Form'
+ self.current_form['desc'] = ''
+ self.current_form['fields'] = []
+ inputs = [ ( 'Name', TextField('name', 40,self.current_form['name'] ) ),
+ ( 'Description', TextField('description', 40, self.current_form['desc']) ) ]
+ return trans.fill_template( '/admin/forms/create_form.mako',
+ inputs=inputs,
+ msg=msg,
+ messagetype=messagetype )
+ elif params.get('create_form', False) == 'True':
+ if 'submitted' in params.new:
+ self.num_add_fields = 0
+ fd, msg = self.__save_form(trans, params)
+ self.__get_saved_form(fd)
+ return self._show_forms_list(trans, msg, messagetype)
+ @web.expose
+ @web.require_admin
+ def edit( self, trans, **kwd ):
+ '''
+ This callback method is for handling all the editing functions like:
+ remaning fields, adding/deleting fields, changing fields attributes
+ '''
+ 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 )))
+ # SHOW THE FORM FOR EDITING.
+ if params.get('show_form', False) == 'True':
+ self.__get_saved_form(fd)
+ # the following two dicts store the unsaved select box options
+ self.del_options = {}
+ self.add_options = {}
+ return self.__show(trans, params, fd)
+ # DELETE FIELD
+ elif params.get('remove_button', False):
+ self.__update_current_form(params)
+ index = int(params.get('remove_button', None).split(' ')[2])-1
+ self.__remove_field(index)
+ return self.__show(trans, params, fd)
+ # SAVE CHANGES
+ elif params.get('save_changes_button', False) == 'Save':
+ self.__update_current_form(params)
+ fd_new, msg = self.__save_form(trans, params, fd.form_definition_current.id)
+ if not fd_new:
+ return self.__show(trans, params, fd, msg, 'error')
+ else:
+ fd = fd_new
+ msg = "The form '%s' has been updated with the changes." % fd.name
+ return self.__show(trans, params, fd, msg)
+ #ADD A FIELD
+ elif params.get('add_field_button', False) == 'Add field':
+ self.__update_current_form(params)
+ self.__add_field()
+ # show the form again with one empty field
+ return self.__show(trans, params, fd)
+ # SHOW FORM READ ONLY
+ elif params.get('read_only', False):
+ return trans.fill_template( '/admin/forms/show_form_read_only.mako',
+ form=fd,
+ msg=msg,
+ messagetype=messagetype )
+ # REFRESH PAGE, SelectField is selected/deselected as the type of a field
+ elif params.get('refresh', False) == 'true':
+ self.__update_current_form(params)
+ return self.__show(trans, params, fd)
+ # REMOVE SelectField OPTION
+ elif params.get('select_box_options', False) == 'remove':
+ #self.__update_current_form(params)
+ index = int(params.get( 'field_index', None ))
+ option = int(params.get( 'option_index', None ))
+ del self.current_form['fields'][index]['selectlist'][option]
+ return self.__show(trans, params, fd)
+ # ADD SelectField OPTION
+ elif params.get('select_box_options', False) == 'add':
+ #self.__update_current_form(params)
+ index = int(params.get( 'field_index', None ))
+ self.current_form['fields'][index]['selectlist'].append('')
+ return self.__show(trans, params, fd)
+ def __remove_field(self, index):
+ del self.current_form['fields'][index]
+ def __add_field(self):
+ '''
+ add an empty field to the fields list
+ '''
+ empty_field = { 'label': '',
+ 'helptext': '',
+ 'visible': True,
+ 'required': False,
+ 'type': BaseField.form_field_types()[0],
+ 'selectlist': '' }
+ self.current_form['fields'].append(empty_field)
+ def __get_field(self, params, index):
+ name = params.get( 'field_name_%i' % index, None )
+ helptext = params.get( 'field_helptext_%i' % index, None )
+ required = params.get( 'field_required_%i' % index, False )
+ field_type = params.get( 'field_type_%i' % index, None )
+ if field_type == 'SelectField':
+ selectlist = self.__get_selectbox_options(params, index)
+ else:
+ selectlist = None
+ return {'label': name,
+ 'helptext': helptext,
+ 'visible': True,
+ 'required': required,
+ 'type': field_type,
+ 'selectlist': selectlist }
+ def __get_selectbox_options(self, params, index):
+ '''
+ This method gets all the options entered by the user for field when
+ the fieldtype is SelectField
+ '''
+ ctr=0
+ sb_options = []
+ while True:
+ option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None )
+ ctr = ctr+1
+ if option:
+ sb_options.append(option)
+ else:
+ return sb_options
+ def __get_saved_form(self, fd):
+ self.current_form = {}
+ self.current_form['name'] = fd.name
+ self.current_form['desc'] = fd.desc
+ self.current_form['fields'] = list(copy.deepcopy(fd.fields))
+ def __validate_form(self, params):
+ '''
+ This method checks the following text inputs are filled out by the user
+ - the name of form
+ - name of all the fields
+ '''
+ # form name
+ if not util.restore_text( params.name ):
+ return None, 'Form name must be filled.'
+ # fields
+ for i in range( len(self.current_form['fields']) ):
+ if not params.get( 'field_name_%i' % i, None ):
+ return None, "All the field label(s) must be completed."
+ return True, ''
+ def __get_form(self, params):
+ name = util.restore_text( params.name )
+ desc = util.restore_text( params.description ) or ""
+ # set form fields
+ fields = []
+ for i in range( len(self.current_form['fields']) ):
+ fields.append(self.__get_field(params, i))
+ fields = fields
+ return name, desc, fields
+ def __update_current_form(self, params):
+ name, desc, fields = self.__get_form(params)
+ self.current_form = {}
+ self.current_form['name'] = name
+ self.current_form['desc'] = desc
+ self.current_form['fields'] = fields
+
+ def __save_form(self, trans, params, fdc_id=None):
+ '''
+ This method saves the current form
+ '''
+ # check the form for invalid inputs
+ flag, msg = self.__validate_form(params)
+ if not flag:
+ return None, msg
+ fd = trans.app.model.FormDefinition()
+ fd.name, fd.desc, fd.fields = self.__get_form(params)
+ if fdc_id: # save changes to the existing form
+ # change the pointer in the form_definition_current table to point
+ # to this new record
+ fdc = trans.app.model.FormDefinitionCurrent.get(fdc_id)
+ else: # create a new form
+ fdc = trans.app.model.FormDefinitionCurrent()
+ # create corresponding row in the form_definition_current table
+ fd.form_definition_current = fdc
+ fdc.latest_form = fd
+ trans.sa_session.save_or_update( fdc )
+ trans.sa_session.flush()
+ msg = "The new form named '%s' has been created. " % (fd.name)
+ request_types = trans.app.model.RequestType.query().all()
+ if not request_types:
+ msg = msg + "Now you can create requests to associate with this form."
+ return fd, msg
+
+ class FieldUI(object):
+ def __init__(self, index, field=None, field_type=None):
+ '''
+ This method returns a list of widgets which describes a field. This
+ includes label, helptext, type, & required/optional
+ '''
+ self.index = index
+ self.label = TextField('field_name_'+str(index), 40, '')
+ self.helptext = TextField('field_helptext_'+str(index), 40, '')
+ self.fieldtype = SelectField('field_type_'+str(index),
+ refresh_on_change=True,
+ refresh_on_change_values=['SelectField'])
+ self.selectbox_options = []
+ for ft in BaseField.form_field_types():
+ self.fieldtype.add_option(ft, ft)
+ self.required = SelectField('field_required_'+str(index), display='radio')
+ self.required.add_option('Required', 'true')
+ self.required.add_option('Optional', 'true', selected=True)
+ if field:
+ self.fill(field, field_type)
+ def fill(self, field, field_type=None):
+ # label
+ self.label.value = field['label']
+ # helptext
+ self.helptext.value = field['helptext']
+ # type
+ self.fieldtype = SelectField('field_type_'+str(self.index),
+ refresh_on_change=True,
+ refresh_on_change_values=['SelectField'])
+ if field_type:
+ field['type'] = unicode(field_type)
+ if field_type == 'SelectField' and not field['selectlist']:
+ field['selectlist'] = ['', '']
+ for ft in BaseField.form_field_types():
+ if ft == field['type']:
+ self.fieldtype.add_option(ft, ft, selected=True)
+ if ft == 'SelectField':
+ self.selectbox_ui(field)
+ else:
+ self.fieldtype.add_option(ft, ft)
+ # required/optional
+ if field['required']:
+ self.required = SelectField('required_'+str(self.index), display='radio')
+ self.required.add_option('Required', 'true', selected=True)
+ self.required.add_option('Optional', 'true')
+ def selectbox_ui(self, field):
+ self.selectbox_options = []
+ if field['selectlist']:
+ for ctr, option in enumerate(field['selectlist']):
+ self.selectbox_options.append(('Option '+str(ctr+1),
+ TextField('field_'+str(self.index)+'_option_'+str(ctr),
+ 40, option)))
+ def get(self):
+ return [( 'Label', self.label ),
+ ( 'Help text', self.helptext ),
+ ( 'Type', self.fieldtype, self.selectbox_options),
+ ( '', self.required)]
+ def __repr__(self):
+ return str(self.index)+'.'+self.label
+ def label(self):
+ return str(self.index)+'.'+self.label
+
+ def __show(self, trans, params, form, msg=None, messagetype='done'):
+ '''
+ This method displays the form and any of the changes made to it
+ '''
+ # name & description
+ form_details = [ ( 'Name', TextField('name', 40, self.current_form['name']) ),
+ ( 'Description', TextField('description', 40, self.current_form['desc']) ) ]
+ # fields
+ field_details = []
+ for index, field in enumerate(self.current_form['fields']):
+ field_ui = self.FieldUI(index, field)
+ field_details.append( field_ui.get() )
+ return trans.fill_template( '/admin/forms/edit_form.mako',
+ form_details=form_details,
+ field_details=field_details,
+ form=form,
+ field_types=BaseField.form_field_types(),
+ msg=msg,
+ messagetype=messagetype )
diff --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py
new file mode 100644
index 00000000000..73f39573703
--- /dev/null
+++ b/lib/galaxy/web/controllers/requests.py
@@ -0,0 +1,429 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys
+from galaxy.web.form_builder import *
+
+log = logging.getLogger( __name__ )
+
+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
+class RequestsListGrid( grids.Grid ):
+ title = "Requests"
+ model_class = model.Request
+ default_sort_key = "-create_time"
+ columns = [
+ grids.GridColumn( "Name", key="name",
+ link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+ attach_popup=True ),
+ grids.GridColumn( "Description", key='desc'),
+ grids.GridColumn( "Sample(s)", method='number_of_samples',
+ link=( lambda item: iff( item.deleted, None, dict( operation="samples", id=item.id ) ) ), ),
+ grids.GridColumn( "Type", key="request_type_id", method='get_request_type'),
+ grids.GridColumn( "Last update", key="update_time", format=time_ago )
+ ]
+ operations = [
+# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+ grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+# 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' ) )
+ ]
+ #default_filter = dict( deleted=False )
+ def get_current_item( self, trans ):
+ return None
+ def get_request_type(self, trans, request):
+ 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( user=trans.user )
+ def number_of_samples(self, trans, request):
+ return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all()))
+
+class SamplesListGrid( grids.Grid ):
+ model_class = model.Sample
+ default_sort_key = "-create_time"
+ columns = [
+ grids.GridColumn( "Name", key="name",
+ link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ),
+ attach_popup=True ),
+ grids.GridColumn( "Description", key='desc' ),
+ grids.GridColumn( "Status", method="get_status",
+ link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )),
+
+ grids.GridColumn( "Last update", key="update_time", format=time_ago )
+
+ # Valid for filtering but invisible
+ #grids.GridColumn( "Deleted", key="deleted", visible=False )
+ ]
+ operations = [
+# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+# 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' ) )
+ ]
+ def __init__(self, request):
+ self.request = request
+ def get_current_item( self, trans ):
+ return None
+ def apply_default_filter( self, trans, query ):
+ return query.filter_by( request_id=self.request.id )
+ def get_status(self, trans, sample):
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ return curr_state.name
+
+class Requests( BaseController ):
+ request_grid = RequestsListGrid()
+
+ @web.expose
+ def index( self, trans ):
+ return trans.fill_template( "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
+ def list( self, trans, **kwargs ):
+ '''
+ List all request made by the current user
+ '''
+ status = message = None
+ if 'operation' in kwargs:
+ operation = kwargs['operation'].lower()
+ if operation == "show_request":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_read_only(trans, id)
+ elif operation == "samples":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_samples(trans, id, kwargs)
+ elif operation == "show_sample":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_sample_read_only(trans, id)
+ elif operation == "events":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_events(trans, id)
+ # Render the list view
+ return self.request_grid( trans, status=status, message=message, template='/requests/grid.mako', **kwargs )
+ def show_samples(self, trans, id, kwargs):
+ '''
+ Shows all the samples associated with this request
+ '''
+ status = message = None
+ request = trans.app.model.Request.get(id)
+ self.samples_grid = SamplesListGrid(request)
+ return self.samples_grid( trans, status=status, message=message, template='/sample/grid.mako', **kwargs )
+ def show_read_only(self, trans, id):
+ '''
+ Shows the request details
+ '''
+ request = trans.app.model.Request.get(id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ request_form = trans.app.model.FormDefinition.get(request_type.request_form_id)
+ request_values = trans.app.model.FormValues.get(request.form_values_id)
+ libraries = self.get_authorized_libs(trans)
+ # list of widgets to be rendered on the request form
+ request_details = []
+ # main details
+ request_details.append(dict(label='Name',
+ value=request.name,
+ helptext=''))
+ request_details.append(dict(label='Description',
+ value=request.desc,
+ helptext=''))
+ request_details.append(dict(label='Type',
+ value=request_type.name,
+ helptext=''))
+ request_details.append(dict(label='Date created',
+ value=request.create_time,
+ helptext=''))
+ request_details.append(dict(label='Date updated',
+ value=request.create_time,
+ helptext=''))
+ request_details.append(dict(label='User',
+ value=str(trans.user.email),
+ helptext=''))
+ # library associated
+ request_details.append(dict(label='Library',
+ value=trans.app.model.Library.get(request.library_id).name,
+ helptext='Associated library where the resultant \
+ dataset will be stored'))
+ # form fields
+ for field in request_form.fields:
+ if field['required']:
+ req = 'Required'
+ else:
+ req = 'Optional'
+ request_details.append(dict(label=field['label'],
+ value=request_values.content[field['label']],
+ helptext=field['helptext']+' ('+req+')'))
+ return trans.fill_template( '/requests/view_request.mako',
+ request_form_id=request_form.id,
+ request_details=request_details,
+ request_type=request_type)
+ @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),
+ msg=msg,
+ messagetype=messagetype )
+ elif params.get('create', False) == 'True':
+ request_type_id = int(util.restore_text( params.request_type_id ))
+ return self.__show_request_form(trans, params, request_type_id)
+ elif params.get('save', False) == 'True':
+ request = self.__save(trans, params)
+ msg = 'The new request named %s has been created' % request.name
+ request_type_id = int(util.restore_text( params.request_type_id ))
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ msg=msg ,
+ messagetype='done') )
+ return self.__show_request_form(trans, params, request_type_id, request=request)
+ def __save(self, trans, params, request_id=None):
+ '''
+ This method save a new request if request_id is None.
+ '''
+ if not request_id:
+ request_type_id = int(util.restore_text( params.request_type_id ))
+ request_form_id = trans.app.model.RequestType.get(request_type_id).request_form_id
+ request_form = trans.app.model.FormDefinition.get(request_form_id)
+ else:
+ request = trans.app.model.Request.get(request_id)
+ form_values = trans.app.model.FormValues.get(request.form_values_id)
+ request_form = trans.app.model.FormDefinition.get(form_values.request_form_id)
+ name = params.get('name', '')
+ desc = params.get('desc', '')
+ library_id = params.get('library', '')
+ values = {}
+ for field in request_form.fields:
+ values[field['label']] = params.get(field['label'], '')
+ if not request_id:
+ form_values = trans.app.model.FormValues(request_form_id, values)
+ form_values.flush()
+ request = trans.app.model.Request(name, desc, request_type_id,
+ trans.user.id, form_values.id,
+ library_id)
+ request.flush()
+ else:
+ form_values.content = values
+ form_values.flush()
+ return request
+ def __show_request_form(self, trans, params, request_type_id, request=None):
+ request_type = trans.app.model.RequestType.get(request_type_id)
+ request_form_id = request_type.request_form_id
+ if request:
+ form_values = trans.app.model.FormValues.get(request.form_values_id)
+ else:
+ form_values = None
+ # list of widgets to be rendered on the request form
+ widgets = []
+ widgets.append(dict(label='Name',
+ widget=TextField('name'),
+ helptext='(Required)'))
+ widgets.append(dict(label='Description',
+ widget=TextField('desc'),
+ helptext='(Optional)'))
+ widgets[0]['widget'].set_size(40)
+ widgets[1]['widget'].set_size(40)
+ # libraries selectbox
+ libraries = self.get_authorized_libs(trans)
+ lib_list = SelectField('library')
+ for lib in libraries:
+ lib_list.add_option(lib.name, lib.id)
+ widgets.append(dict(label='Library',
+ widget=lib_list,
+ helptext='Associated library where the resultant \
+ dataset will be stored'))
+ widgets = self.__create_form(trans, params, request_form_id, widgets, form_values)
+ title = 'Add a new request of type: %s' % request_type.name
+ return trans.fill_template( '/requests/new_request.mako',
+ request_form_id=request_form_id,
+ request_type=request_type,
+ widgets=widgets,
+ title=title)
+
+ def __create_form(self, trans, params, form_id, widgets=[], form_values=None):
+ form = trans.app.model.FormDefinition.get(form_id)
+ if not form_values:
+ values = {}
+ for field in form.fields:
+ if field['type'] in ['SelectField' or 'CheckBoxField']:
+ values[field['label']] = False
+ else:
+ values[field['label']] = ''
+ else:
+ values = form_values.content
+ # form fields
+ for field in form.fields:
+ fw = eval(field['type'])(field['label'])
+ if field['type'] == 'TextField':
+ fw.set_size(40)
+ fw.value = values[field['label']]
+ elif field['type'] == 'TextArea':
+ fw.set_size(3, 40)
+ fw.value = values[field['label']]
+ elif field['type'] == 'SelectField':
+ for option in field['selectlist']:
+ fw.add_option(option, option, values[field['label']])
+ elif field['type'] == 'CheckBoxField':
+ fw.checked = values[field['label']]
+
+ if field['required']:
+ req = 'Required'
+ else:
+ req = 'Optional'
+ widgets.append(dict(label=field['label'],
+ widget=fw,
+ helptext=field['helptext']+' ('+req+')'))
+ return widgets
+ @web.expose
+ def add_sample(self, trans, **kwd):
+ params = util.Params( kwd )
+ msg = util.restore_text( params.get( 'msg', '' ) )
+ messagetype = params.get( 'messagetype', 'done' )
+ request_id = int(util.restore_text( params.get( 'id', '' ) ))
+ return self.__show_sample_form(trans, params, request_id)
+
+ def __show_sample_form(self, trans, params, request_id, sample=None):
+ request = trans.app.model.Request.get(request_id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ sample_form_id = request_type.sample_form_id
+ if sample:
+ form_values = trans.app.model.FormValues.get(sample.form_values_id)
+ else:
+ form_values = None
+ # list of widgets to be rendered on the request form
+ widgets = []
+ widgets.append(dict(label='Name',
+ widget=TextField('name'),
+ helptext='(Required)'))
+ widgets.append(dict(label='Description',
+ widget=TextField('desc'),
+ helptext='(Optional)'))
+ widgets[0]['widget'].set_size(40)
+ widgets[1]['widget'].set_size(40)
+ widgets = self.__create_form(trans, params, sample_form_id, widgets, form_values)
+ title = 'Add a new sample to request: %s of type: %s' % (request.name, request_type.name)
+ return trans.fill_template( '/sample/new_sample.mako',
+ sample_form_id=sample_form_id,
+ request_id=request.id,
+ widgets=widgets,
+ title=title)
+ @web.expose
+ def samples(self, trans, **kwd):
+ params = util.Params( kwd )
+ if params.get('save', False) == 'True':
+ sample = self.__save_sample(trans, params)
+ return trans.response.send_redirect( web.url_for( controller='requests',
+ action='list',
+ operation='samples',
+ id=trans.security.encode_id(sample.request_id)) )
+ def __save_sample(self, trans, params, sample_id=None):
+ if not sample_id:
+ request = trans.app.model.Request.get(int(util.restore_text( params.request_id )))
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+ else:
+ sample = trans.app.model.Sample.get(sample_id)
+ form_data = trans.app.model.FormData.get(sample.form_data_id)
+ form = trans.app.model.FormDefinition.get(form_data.form_definition_id)
+ name = params.get('name', '')
+ desc = params.get('desc', '')
+ values = {}
+ for field in sample_form.fields:
+ values[field['label']] = params.get(field['label'], '')
+ if not sample_id:
+ form_values = trans.app.model.FormValues(sample_form.id, values)
+ form_values.flush()
+ sample = trans.app.model.Sample(name, desc, request.id, form_values.id)
+ sample.flush()
+ # set the initial state
+ state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id).first()
+ event = trans.app.model.SampleEvent(sample.id, state.id)
+ event.flush()
+ else:
+ form_data.content = values
+ form_data.flush()
+ return sample
+ def show_sample_read_only(self, trans, sample_id):
+ '''
+ Shows the sample details
+ '''
+ sample = trans.app.model.Sample.get(sample_id)
+ request = trans.app.model.Request.get(sample.request_id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+ sample_values = trans.app.model.FormValues.get(sample.form_values_id)
+ # list of widgets to be rendered on the request form
+ sample_details = []
+ # main details
+ sample_details.append(dict(label='Name',
+ value=sample.name,
+ helptext=''))
+ sample_details.append(dict(label='Description',
+ value=sample.desc,
+ helptext=''))
+ sample_details.append(dict(label='Date created',
+ value=sample.create_time,
+ helptext=''))
+ sample_details.append(dict(label='Date updated',
+ value=sample.create_time,
+ helptext=''))
+ sample_details.append(dict(label='User',
+ value=str(trans.user.email),
+ helptext=''))
+ sample_details.append(dict(label='Request',
+ value=request.name,
+ helptext='Name/ID of the request this sample belongs to.'))
+ # get the current state of the sample
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ sample_details.append(dict(label='State',
+ value=curr_state.name,
+ helptext=curr_state.desc))
+ # form fields
+ for field in sample_form.fields:
+ if field['required']:
+ req = 'Required'
+ else:
+ req = 'Optional'
+ sample_details.append(dict(label=field['label'],
+ value=sample_values.content[field['label']],
+ helptext=field['helptext']+' ('+req+')'))
+ return trans.fill_template( '/sample/view_sample.mako',
+ sample_details=sample_details)
+ def show_events(self, trans, sample_id):
+ sample = trans.app.model.Sample.get(sample_id)
+ events_list = []
+ for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all():
+ state = trans.app.model.SampleState.get(event.sample_state_id)
+ events_list.append((state.name, event.update_time, state.desc, event.comment))
+ return trans.fill_template( '/sample/sample_events.mako',
+ events_list=events_list,
+ sample_name=sample.name,
+ request=trans.app.model.Request.get(sample.request_id).name)
+
+
+
+
diff --git a/lib/galaxy/web/controllers/requests_admin.py b/lib/galaxy/web/controllers/requests_admin.py
new file mode 100644
index 00000000000..e5af7438d4f
--- /dev/null
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -0,0 +1,315 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys
+from galaxy.web.form_builder import *
+from datetime import datetime, timedelta
+
+log = logging.getLogger( __name__ )
+
+
+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
+class RequestsListGrid( grids.Grid ):
+ title = "Requests"
+ model_class = model.Request
+ default_sort_key = "-create_time"
+ columns = [
+ grids.GridColumn( "Name", key="name",
+ link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+ attach_popup=True ),
+ grids.GridColumn( "Description", key="desc"),
+ grids.GridColumn( "Sample(s)", method='number_of_samples',
+ link=( lambda item: iff( item.deleted, None, dict( operation="samples", 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( "User", key="user_id", method='get_user')
+
+ ]
+ operations = [
+# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+ grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+# 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' ) )
+ ]
+ def get_user(self, trans, request):
+ return trans.app.model.User.get(request.user_id).email
+ def get_current_item( self, trans ):
+ return None
+ def get_request_type(self, trans, request):
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ return request_type.name
+ def apply_default_filter( self, trans, query ):
+ return query
+ def number_of_samples(self, trans, request):
+ return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all()))
+
+class SamplesListGrid( grids.Grid ):
+ model_class = model.Sample
+ default_sort_key = "-create_time"
+ columns = [
+ grids.GridColumn( "Name", key="name",
+ link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ),
+ attach_popup=True ),
+ grids.GridColumn( "Description", key='desc' ),
+ grids.GridColumn( "Status", method="get_status",
+ link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )),
+
+ grids.GridColumn( "Last update", key="update_time", format=time_ago )
+
+ # Valid for filtering but invisible
+ #grids.GridColumn( "Deleted", key="deleted", visible=False )
+ ]
+ operations = [
+# grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
+ grids.GridOperation( "Change state", condition=( lambda item: not item.deleted ) ),
+# grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+# 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' ) )
+ ]
+ def __init__(self, request, user):
+ self.request = request
+ self.user = user
+ def get_current_item( self, trans ):
+ return None
+ def apply_default_filter( self, trans, query ):
+ return query.filter_by( request_id=self.request.id )
+ def get_status(self, trans, sample):
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ return curr_state.name
+
+class Requests( BaseController ):
+ request_grid = RequestsListGrid()
+
+ @web.expose
+ @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 ):
+ '''
+ List all request made by the current user
+ '''
+ status = message = None
+ if 'operation' in kwargs:
+ operation = kwargs['operation'].lower()
+ if operation == "show_request":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_read_only(trans, id)
+ elif operation == "samples":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_samples(trans, id, kwargs)
+ elif operation == "show_sample":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_sample_read_only(trans, id)
+ elif operation == "change state":
+ id_list = [trans.security.decode_id(id) for id in util.listify(kwargs['id'])]
+ return self.change_state(trans, id_list)
+ elif operation == "events":
+ id = trans.security.decode_id(kwargs['id'])
+ return self.show_events(trans, id)
+ # Render the list view
+ return self.request_grid( trans, status=status, message=message, template='/admin/requests/grid.mako', **kwargs )
+ def show_samples(self, trans, id, kwargs):
+ '''
+ Shows all the samples associated with this request
+ '''
+ status = message = None
+ request = trans.app.model.Request.get(id)
+ self.samples_grid = SamplesListGrid(request, trans.app.model.User.get(request.user_id))
+ return self.samples_grid( trans, status=status, message=message, template='/admin/samples/grid.mako', **kwargs )
+ def show_read_only(self, trans, id):
+ '''
+ Shows the request details
+ '''
+ request = trans.app.model.Request.get(id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ request_form = trans.app.model.FormDefinition.get(request_type.request_form_id)
+ request_values = trans.app.model.FormValues.get(request.form_values_id)
+ libraries = self.get_authorized_libs(trans)
+ # list of widgets to be rendered on the request form
+ request_details = []
+ # main details
+ request_details.append(dict(label='Name',
+ value=request.name,
+ helptext=''))
+ request_details.append(dict(label='Description',
+ value=request.desc,
+ helptext=''))
+ request_details.append(dict(label='Type',
+ value=request_type.name,
+ helptext=''))
+ request_details.append(dict(label='Date created',
+ value=request.create_time,
+ helptext=''))
+ request_details.append(dict(label='Date updated',
+ value=request.create_time,
+ helptext=''))
+ request_details.append(dict(label='User',
+ value=str(trans.user.email),
+ helptext=''))
+ # library associated
+ request_details.append(dict(label='Library',
+ value=trans.app.model.Library.get(request.library_id).name,
+ helptext='Associated library where the resultant \
+ dataset will be stored'))
+ # form fields
+ for field in request_form.fields:
+ if field['required']:
+ req = 'Required'
+ else:
+ req = 'Optional'
+ request_details.append(dict(label=field['label'],
+ value=request_values.content[field['label']],
+ helptext=field['helptext']+' ('+req+')'))
+ return trans.fill_template( '/admin/requests/view_request.mako',
+ request_form_id=request_form.id,
+ request_details=request_details,
+ request_type=request_type)
+
+ @web.expose
+ @web.require_admin
+ def samples(self, trans, **kwd):
+ params = util.Params( kwd )
+ if params.get('save', False) == 'True':
+ sample = self.__save_sample(trans, params)
+ return self.show_samples(trans, sample.request_id, {})
+ def show_sample_read_only(self, trans, sample_id):
+ '''
+ Shows the sample details
+ '''
+ sample = trans.app.model.Sample.get(sample_id)
+ request = trans.app.model.Request.get(sample.request_id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+ sample_values = trans.app.model.FormValues.get(sample.form_values_id)
+ # list of widgets to be rendered on the request form
+ sample_details = []
+ # main details
+ sample_details.append(dict(label='Name',
+ value=request.name,
+ helptext=''))
+ sample_details.append(dict(label='Description',
+ value=request.desc,
+ helptext=''))
+ sample_details.append(dict(label='Date created',
+ value=sample.create_time,
+ helptext=''))
+ sample_details.append(dict(label='Date updated',
+ value=sample.create_time,
+ helptext=''))
+ sample_details.append(dict(label='User',
+ value=str(trans.user.email),
+ helptext=''))
+ sample_details.append(dict(label='Request',
+ value=request.name,
+ helptext='Name/ID of the request this sample belongs to.'))
+ # get the current state of the sample
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ sample_details.append(dict(label='State',
+ value=curr_state.name,
+ helptext=curr_state.desc))
+ # form fields
+ for field in sample_form.fields:
+ if field['required']:
+ req = 'Required'
+ else:
+ req = 'Optional'
+ sample_details.append(dict(label=field['label'],
+ value=sample_values.content[field['label']],
+ helptext=field['helptext']+' ('+req+')'))
+ return trans.fill_template( '/admin/samples/view_sample.mako',
+ sample_details=sample_details)
+ def __get_all_states(self, trans, sample):
+ request = trans.app.model.Request.get(sample.request_id)
+ request_type = trans.app.model.RequestType.get(request.request_type_id)
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ states_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id)
+ return states_list
+ def __get_curr_state(self, trans, sample):
+ all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+ curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+ return curr_state
+ def change_state(self, trans, sample_id_list):
+ sample = trans.app.model.Sample.get(sample_id_list[0])
+ states_list = self.__get_all_states(trans, sample)
+ curr_state = self.__get_curr_state(trans, sample)
+ states_input = SelectField('select_state')
+ for state in states_list:
+ if len(sample_id_list) == 1:
+ if curr_state.name == state.name:
+ states_input.add_option(state.name+' (Current)', state.name, selected=True)
+ else:
+ states_input.add_option(state.name, state.name)
+ else:
+ states_input.add_option(state.name, state.name)
+ widgets = []
+ widgets.append(('Select the new state of the sample(s) from the list of possible state(s)',
+ states_input))
+ widgets.append(('Comments', TextArea('comment')))
+ title = 'Change current state of sample: ' + sample.name
+ return trans.fill_template( '/admin/samples/change_state.mako',
+ widgets=widgets, title=title,
+ sample_id_list=util.object_to_string(sample_id_list))
+ @web.expose
+ @web.require_admin
+ def save_state(self, trans, **kwd):
+ params = util.Params( kwd )
+ sample_id_list = util.string_to_object(util.restore_text( params.sample_id_list ))
+ comments = util.restore_text( params.comment )
+ sample = trans.app.model.Sample.get(sample_id_list[0])
+ request = trans.app.model.Request.get(sample.request_id)
+ selected_state = util.restore_text( params.select_state )
+ new_state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request.request_type_id
+ and trans.app.model.SampleState.table.c.name == selected_state)[0]
+ for sample_id in sample_id_list:
+ event = trans.app.model.SampleEvent(sample_id, new_state.id, comments)
+ event.flush()
+ return trans.response.send_redirect( web.url_for( controller='requests_admin',
+ action='list',
+ operation='samples',
+ id=trans.security.encode_id(request.id)) )
+ @web.expose
+ @web.require_admin
+ def show_events(self, trans, sample_id):
+ sample = trans.app.model.Sample.get(sample_id)
+ request = trans.app.model.Request.get(sample.request_id)
+ events_list = []
+ for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).order_by(trans.app.model.SampleEvent.c.update_time.desc()).all():
+ state = trans.app.model.SampleState.get(event.sample_state_id)
+ delta = datetime.utcnow() - event.update_time
+ if delta > timedelta( minutes=60 ):
+ last_update = '%s hours' % int( delta.seconds / 60 / 60 )
+ else:
+ last_update = '%s minutes' % int( delta.seconds / 60 )
+ events_list.append((state.name, state.desc, last_update, event.comment))
+ return trans.fill_template( '/admin/samples/events.mako',
+ events_list=events_list,
+ sample_name=sample.name, user=trans.app.model.User.get(request.user_id),
+ request=request.name)
+
\ No newline at end of file
diff --git a/lib/galaxy/web/form_builder.py b/lib/galaxy/web/form_builder.py
index f250af01e34..c550f88905b 100644
--- a/lib/galaxy/web/form_builder.py
+++ b/lib/galaxy/web/form_builder.py
@@ -9,6 +9,11 @@ class BaseField(object):
def get_html( self, prefix="" ):
"""Returns the html widget corresponding to the parameter"""
raise TypeError( "Abstract Method" )
+ @staticmethod
+ def form_field_types():
+ return ['TextField', 'TextArea', 'SelectField', 'CheckboxField']
+
+
class TextField(BaseField):
"""
@@ -26,6 +31,8 @@ class TextField(BaseField):
def get_html( self, prefix="" ):
return '' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) )
rval.append( ' ' )
return "\n".join( rval )
+ def get_selected(self):
+ '''
+ This method returns the currently selected option's text and value
+ '''
+ for text, value, selected in self.options:
+ if selected:
+ return text, value
+ if self.options:
+ return self.options[0]
+ return None
+
class DrillDownField( BaseField ):
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index b4c2b5c82c2..f51a11bf5d9 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -607,6 +607,11 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
if dbkey == ds.dbkey:
return ds
return None
+
+ def request_types(self):
+ if self.app.model.RequestType.query().all():
+ return True
+ return False
class FormBuilder( object ):
"""
diff --git a/run_functional_tests.sh b/run_functional_tests.sh
old mode 100644
new mode 100755
diff --git a/templates/admin/forms/create_form.mako b/templates/admin/forms/create_form.mako
new file mode 100644
index 00000000000..1a647668750
--- /dev/null
+++ b/templates/admin/forms/create_form.mako
@@ -0,0 +1,31 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
diff --git a/templates/admin/forms/edit_form.mako b/templates/admin/forms/edit_form.mako
new file mode 100644
index 00000000000..ee9a3e64f03
--- /dev/null
+++ b/templates/admin/forms/edit_form.mako
@@ -0,0 +1,105 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
+<%def name="render_selectbox_options( index, field_attr )">
+ %if field_attr[0] == 'Type':
+ %if field_attr[1].get_selected()[0] == 'SelectField':
+ <% options = field_attr[2] %>
+
+
Options
+ %for i, option in enumerate(options):
+
${i+1}
+ ${option[1].get_html()}
+ ##
+
Remove
+ %endfor
+
+ ##
+ %endif
+ %endif
+
+
+
+<%def name="render_field( index, field )">
+
+
+ Field ${1+index}
+
+ %for field_attr in field:
+
+ ${field_attr[0]}
+ ${field_attr[1].get_html()}
+ ${render_selectbox_options( index, field_attr )}
+
+ %endfor
+
+
+
+ %else:
+
+ %endif
+
+ ${form.name}
+ ${form.desc}
+
+
+
+
+ %if deleted:
+ Deleted
+ %endif
+ Forms
+
+
+
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if not fdc_list:
+ %if deleted:
+ There are no deleted forms
+ %else:
+ There are no forms.
+ %endif
+%else:
+
+
+
+ Name
+ Description
+
+
+
+ %for ctr, fdc in enumerate( fdc_list ):
+
+ ${render_row( fdc.latest_form, ctr )}
+
+ %endfor
+
+
+%endif
diff --git a/templates/admin/forms/show_form_read_only.mako b/templates/admin/forms/show_form_read_only.mako
new file mode 100644
index 00000000000..e295b67ad4c
--- /dev/null
+++ b/templates/admin/forms/show_form_read_only.mako
@@ -0,0 +1,67 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
\ No newline at end of file
diff --git a/templates/admin/index.mako b/templates/admin/index.mako
index 158489ac515..e78c0355a4c 100644
--- a/templates/admin/index.mako
+++ b/templates/admin/index.mako
@@ -103,13 +103,35 @@
+
+
+ Forms
+
+
+
+
+ Requests
+
+
+ ##
<%def name="center_panel()">
-
-
+ <%
+ center_url = h.url_for( action='center' )
+ %>
+
diff --git a/templates/admin/requests/add_states.mako b/templates/admin/requests/add_states.mako
new file mode 100644
index 00000000000..0c58bfdee00
--- /dev/null
+++ b/templates/admin/requests/add_states.mako
@@ -0,0 +1,26 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
\ No newline at end of file
diff --git a/templates/admin/requests/create_request_type.mako b/templates/admin/requests/create_request_type.mako
new file mode 100644
index 00000000000..6a336e0eadd
--- /dev/null
+++ b/templates/admin/requests/create_request_type.mako
@@ -0,0 +1,66 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
\ No newline at end of file
diff --git a/templates/admin/requests/edit_request_type.mako b/templates/admin/requests/edit_request_type.mako
new file mode 100644
index 00000000000..b67a0c8e96d
--- /dev/null
+++ b/templates/admin/requests/edit_request_type.mako
@@ -0,0 +1,78 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+<% num_states=len(states_list) %>
+
+
\ No newline at end of file
diff --git a/templates/admin/requests/grid.mako b/templates/admin/requests/grid.mako
new file mode 100644
index 00000000000..bb54a758589
--- /dev/null
+++ b/templates/admin/requests/grid.mako
@@ -0,0 +1,205 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Requests
+
+%if message:
+
+
${message}
+
+
+%endif
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+
+
+<%def name="stylesheets()">
+
+ %if deleted:
+ Deleted
+ %endif
+ Request Types
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if not request_types:
+ %if deleted:
+ There are no deleted request types
+ %else:
+ There are no request types.
+ %endif
+%else:
+
+
+
+ Name
+ Description
+ Request Form
+ Sample Form
+
+
+
+ %for request_type in request_types:
+
+ ${request_type.name} ${request_type.desc} ${form_name} ${form_name}
+ %endfor
+
+
+%endif
\ No newline at end of file
diff --git a/templates/admin/requests/view_request.mako b/templates/admin/requests/view_request.mako
new file mode 100644
index 00000000000..3671ca81a5f
--- /dev/null
+++ b/templates/admin/requests/view_request.mako
@@ -0,0 +1,20 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
\ No newline at end of file
diff --git a/templates/admin/samples/change_state.mako b/templates/admin/samples/change_state.mako
new file mode 100644
index 00000000000..48e110a1e61
--- /dev/null
+++ b/templates/admin/samples/change_state.mako
@@ -0,0 +1,30 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
\ No newline at end of file
diff --git a/templates/admin/samples/edit_sample.mako b/templates/admin/samples/edit_sample.mako
new file mode 100644
index 00000000000..d007cd7339f
--- /dev/null
+++ b/templates/admin/samples/edit_sample.mako
@@ -0,0 +1,83 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
\ No newline at end of file
diff --git a/templates/admin/samples/events.mako b/templates/admin/samples/events.mako
new file mode 100644
index 00000000000..fbe75f89144
--- /dev/null
+++ b/templates/admin/samples/events.mako
@@ -0,0 +1,33 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Events for Sample ${sample_name}
+
+Events for Sample "${sample_name}" of Request: ${request}
+User: ${user.email}
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
\ No newline at end of file
diff --git a/templates/admin/samples/grid.mako b/templates/admin/samples/grid.mako
new file mode 100644
index 00000000000..116e05ad64f
--- /dev/null
+++ b/templates/admin/samples/grid.mako
@@ -0,0 +1,203 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples
+
+%if message:
+
+
${message}
+
+
+%endif
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+
+
+<%def name="stylesheets()">
+ Samples
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if not samples_list:
+ You have no samples.
+%else:
+
+
+
+ Name
+ Description
+ Type
+ State
+
+
+
+ %for id, name, desc, st, state in samples_list:
+
+ ${name} ${desc} ${st} ${state}
+ %endfor
+
+
+%endif
\ No newline at end of file
diff --git a/templates/sample/edit_sample.mako b/templates/sample/edit_sample.mako
new file mode 100644
index 00000000000..402970fe248
--- /dev/null
+++ b/templates/sample/edit_sample.mako
@@ -0,0 +1,64 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
diff --git a/templates/sample/grid.mako b/templates/sample/grid.mako
new file mode 100644
index 00000000000..bbeeb080a50
--- /dev/null
+++ b/templates/sample/grid.mako
@@ -0,0 +1,210 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples
+
+%if message:
+
+
${message}
+
+
+%endif
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+
+
+<%def name="stylesheets()">
+ Events for Sample "${sample_name}" of Request: ${request}
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
\ No newline at end of file
diff --git a/templates/sample/view_sample.mako b/templates/sample/view_sample.mako
new file mode 100644
index 00000000000..b1a954f1c3f
--- /dev/null
+++ b/templates/sample/view_sample.mako
@@ -0,0 +1,19 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
})
+ Define a new form
+