- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2487: Bugfix for history refresh in IE
by Greg Von Kuster 16 Jul '09

16 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/46bd94b12a0c changeset: 2487:46bd94b12a0c user: James Taylor <james(a)jamestaylor.org> date: Thu Jul 16 15:35:58 2009 -0400 description: Bugfix for history refresh in IE 1 file(s) affected in this change: templates/root/history.mako diffs (18 lines): diff -r 079bf1a8422b -r 46bd94b12a0c templates/root/history.mako --- a/templates/root/history.mako Thu Jul 16 09:45:43 2009 -0400 +++ b/templates/root/history.mako Thu Jul 16 15:35:58 2009 -0400 @@ -73,9 +73,12 @@ }); // Updater updater({ - %for data in reversed( datasets ): + %for i, data in enumerate( reversed( datasets ) ): %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: - "${data.id}": "${data.state}"; + %if i > 0: + , + %endif + "${data.id}": "${data.state}" %endif %endfor });

1 0

[hg] galaxy 2484: Fix for deleted datasets in history pane
by Greg Von Kuster 16 Jul '09

16 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dacc94994979 changeset: 2484:dacc94994979 user: James Taylor <james(a)jamestaylor.org> date: Wed Jul 15 12:18:43 2009 -0400 description: Fix for deleted datasets in history pane 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (12 lines): diff -r 5707f033e31a -r dacc94994979 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Jul 15 12:00:02 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Jul 15 12:18:43 2009 -0400 @@ -68,7 +68,7 @@ .join( "dataset" ).filter( model.Dataset.purged == False ) \ .options( eagerload_all( "dataset.actions" ) ) if not show_deleted: - query.filter_by( deleted=False ) + query = query.filter( model.HistoryDatasetAssociation.deleted == False ) return trans.stream_template_mako( "root/history.mako", history = history, datasets = query.all(),

1 0

[hg] galaxy 2486: Replaced id's with objects as parameters to al...
by Greg Von Kuster 16 Jul '09

16 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/079bf1a8422b changeset: 2486:079bf1a8422b user: rc date: Thu Jul 16 09:45:43 2009 -0400 description: Replaced id's with objects as parameters to all the form & requests table classes 6 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/admin/requests/manage_request_types.mako diffs (296 lines): diff -r dd5f1fe8f5e9 -r 079bf1a8422b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Jul 15 14:11:35 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Jul 16 09:45:43 2009 -0400 @@ -1099,53 +1099,55 @@ class FormDefinition( object ): - def __init__(self, name=None, desc=None, fields=[], current_form_id=None): + def __init__(self, name=None, desc=None, fields=[], current_form=None): self.name = name self.desc = desc self.fields = fields - self.form_definition_current_id = current_form_id + self.form_definition_current = current_form class FormDefinitionCurrent( object ): - def __init__(self, form_definition_id=None): - self.latest_form_id = form_definition_id + def __init__(self, form_definition=None): + self.latest_form = form_definition class FormValues( object ): - def __init__(self, form_def_id=None, content=None): - self.form_definition_id = form_def_id + def __init__(self, form_def=None, content=None): + self.form_definition = form_def 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): + def __init__(self, name=None, desc=None, request_type=None, user=None, + form_values=None, library=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 + self.type = request_type + self.values = form_values + self.user = user + self.library = library 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 + def __init__(self, request_form=None, sample_form=None): + self.request_form = request_form + self.sample_form = sample_form class Sample( object ): - def __init__(self, name=None, desc=None, request_id=None, form_values_id=None): + def __init__(self, name=None, desc=None, request=None, form_values=None): self.name = name self.desc = desc - self.request_id = request_id - self.form_values_id = form_values_id + self.request = request + self.values = form_values + + class SampleState( object ): - def __init__(self, name=None, desc=None, request_type_id=None): + def __init__(self, name=None, desc=None, request_type=None): self.name = name self.desc = desc - self.request_type_id = request_type_id + self.request_type = request_type 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 + def __init__(self, sample=None, sample_state=None, comment=''): + self.sample = sample + self.state = sample_state self.comment = comment diff -r dd5f1fe8f5e9 -r 079bf1a8422b lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Jul 15 14:11:35 2009 -0400 +++ b/lib/galaxy/model/mapping.py Thu Jul 16 09:45:43 2009 -0400 @@ -613,7 +613,10 @@ primaryjoin=( Sample.table.c.request_id == Request.table.c.id ) ), ) ) -assign_mapper( context, FormValues, FormValues.table, properties=None) +assign_mapper( context, FormValues, FormValues.table, + properties=dict( form_definition=relation( FormDefinition, + primaryjoin=( FormValues.table.c.form_definition_id == FormDefinition.table.c.id ) ) + ) ) assign_mapper( context, Request, Request.table, properties=dict( values=relation( FormValues, @@ -723,9 +726,7 @@ 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) ), + order_by=desc(History.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 -r dd5f1fe8f5e9 -r 079bf1a8422b lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Wed Jul 15 14:11:35 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Thu Jul 16 09:45:43 2009 -0400 @@ -2185,8 +2185,8 @@ rt = trans.app.model.RequestType() 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.request_form = trans.app.model.FormDefinition.get(int( params.request_form_id )) + rt.sample_form = trans.app.model.FormDefinition.get(int( 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() @@ -2196,7 +2196,7 @@ 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 )) - ss = trans.app.model.SampleState(name, desc, rt.id) + ss = trans.app.model.SampleState(name, desc, rt) ss.flush() msg = "The new sample type named '%s' with %s state(s) has been created" % (rt.name, num_states) return rt, msg diff -r dd5f1fe8f5e9 -r 079bf1a8422b lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Wed Jul 15 14:11:35 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Thu Jul 16 09:45:43 2009 -0400 @@ -236,11 +236,11 @@ 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.id, values) + form_values = trans.app.model.FormValues(request_type.request_form, values) form_values.flush() - request = trans.app.model.Request(name, desc, request_type.id, - trans.user.id, form_values.id, - library_id) + request = trans.app.model.Request(name, desc, request_type, + trans.user, form_values, + trans.app.model.Library.get(library_id)) request.flush() else: # TODO editing @@ -252,7 +252,7 @@ messagetype = params.get( 'messagetype', 'done' ) request_type = trans.app.model.RequestType.get(int(params.request_type_id)) if request: - form_values = trans.app.model.FormValues.get(request.form_values_id) + form_values = request.values else: form_values = None # list of widgets to be rendered on the request form @@ -278,7 +278,8 @@ widget=lib_list, helptext='Associated library where the resultant \ dataset will be stored')) - widgets = self.__create_form(trans, request_type.request_form_id, widgets, form_values, **kwd) + 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, @@ -336,7 +337,7 @@ messagetype = params.get( 'messagetype', 'done' ) request = trans.app.model.Request.get(int( params.request_id )) if sample: - form_values = trans.app.model.FormValues.get(sample.form_values_id) + form_values = sample.values else: form_values = None # list of widgets to be rendered on the request form @@ -349,7 +350,8 @@ widget=TextField('desc', 40, util.restore_text( params.get( 'desc', '' ) )), helptext='(Optional)')) - widgets = self.__create_form(trans, request.type.sample_form_id, widgets, form_values, **kwd) + widgets = self.__create_form(trans, request.type.sample_form_id, widgets, + form_values, **kwd) 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=request.type.sample_form_id, @@ -393,13 +395,13 @@ for index, field in enumerate(request.type.sample_form.fields): values.append(util.restore_text(params.get('field_%i' % index, ''))) if not sample_id: - form_values = trans.app.model.FormValues(request.type.sample_form.id, values) + form_values = trans.app.model.FormValues(request.type.sample_form, values) form_values.flush() - sample = trans.app.model.Sample(name, desc, request.id, form_values.id) + sample = trans.app.model.Sample(name, desc, request, form_values) 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 = trans.app.model.SampleEvent(sample, state) event.flush() else: form_data.content = values diff -r dd5f1fe8f5e9 -r 079bf1a8422b lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Jul 15 14:11:35 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Jul 16 09:45:43 2009 -0400 @@ -242,15 +242,13 @@ 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) + curr_state = all_states[len(all_states)-1].state + states_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == sample.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) + curr_state = all_states[len(all_states)-1].state return curr_state def change_state(self, trans, sample_id_list): sample = trans.app.model.Sample.get(sample_id_list[0]) @@ -280,35 +278,33 @@ 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 + new_state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == sample.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) + for id in sample_id_list: + s = trans.app.model.Sample.get(id) + event = trans.app.model.SampleEvent(s, new_state, 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)) ) + id=trans.security.encode_id(sample.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 = [] all_events = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all() all_events.reverse() for event in all_events: - 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)) + events_list.append((event.state.name, event.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) + sample_name=sample.name, user=sample.request.user, + request=sample.request.name) \ No newline at end of file diff -r dd5f1fe8f5e9 -r 079bf1a8422b templates/admin/requests/manage_request_types.mako --- a/templates/admin/requests/manage_request_types.mako Wed Jul 15 14:11:35 2009 -0400 +++ b/templates/admin/requests/manage_request_types.mako Thu Jul 16 09:45:43 2009 -0400 @@ -41,18 +41,8 @@ <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><i>${request_type.desc}</i></td> - <% for form in forms: - if form.id == request_type.request_form_id: - form_name = form.name - break - %> - <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.request_form_id, read_only=True)}">${form_name}</a></td> - <% for form in forms: - if form.id == request_type.sample_form_id: - form_name = form.name - break - %> - <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.sample_form_id, read_only=True)}">${form_name}</a></td> + <td><a href="${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> </tr> %endfor </tbody>

1 0

[hg] galaxy 2485: Initial pass at allowing the setting of certai...
by Greg Von Kuster 16 Jul '09

16 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dd5f1fe8f5e9 changeset: 2485:dd5f1fe8f5e9 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Jul 15 14:11:35 2009 -0400 description: Initial pass at allowing the setting of certain metadata parameters on upload (controlled via a flag). This allows the user to specify the 'base_name' to be used for Rgenetics datatypes, etc. Bunch of cleanup needed in upload. 9 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/registry.py lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/tools/parameters/grouping.py templates/tool_form.mako tools/data_source/upload.xml diffs (418 lines): diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Wed Jul 15 14:11:35 2009 -0400 @@ -49,6 +49,8 @@ """If False, the peek is regenerated whenever a dataset of this type is copied""" copy_safe_peek = True + + is_binary = True #The dataset contains binary data --> do not space_to_tab or convert newlines, etc. Allow binary file uploads of this type when True. #Composite datatypes composite_type = None @@ -250,7 +252,8 @@ def after_edit( self, dataset ): """This function is called on the dataset after metadata is edited.""" dataset.clear_associated_files( metadata_safe = True ) - def __new_composite_file( self, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, **kwds ): + def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, **kwds ): + kwds[ 'name' ] = name kwds[ 'optional' ] = optional kwds[ 'mimetype' ] = mimetype kwds[ 'description' ] = description @@ -258,7 +261,7 @@ return Bunch( **kwds ) def add_composite_file( self, name, **kwds ): #self.composite_files = self.composite_files.copy() - self.composite_files[ name ] = self.__new_composite_file( **kwds ) + self.composite_files[ name ] = self.__new_composite_file( name, **kwds ) def __substitute_composite_key( self, key, composite_file, dataset = None ): @@ -273,7 +276,7 @@ def writable_files( self, dataset = None ): files = odict() if self.composite_type != 'auto_primary_file': - files[ self.primary_file_name ] = self.__new_composite_file() + files[ self.primary_file_name ] = self.__new_composite_file( self.primary_file_name ) for key, value in self.get_composite_files( dataset = dataset ).iteritems(): files[ key ] = value return files diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Wed Jul 15 14:11:35 2009 -0400 @@ -117,7 +117,7 @@ class Rgenetics(Html): """class to use for rgenetics""" """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True) + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True, set_in_upload=True) file_ext="html" composite_type = 'auto_primary_file' @@ -151,10 +151,7 @@ else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' - #def sniff( self, filename ): - # """ - # """ - # return True + class Lped(Rgenetics): """fake class to distinguish different species of Rgenetics data collections @@ -245,7 +242,10 @@ MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_names", default=[], desc="Column names", readonly=True,visible=True ) MetadataElement( name="base_name", - desc="base name for all transformed versions of this genetic dataset", readonly=True) + desc="base name for all transformed versions of this genetic dataset", readonly=True, default='galaxy', set_in_upload=True) + ### Do we really need these below? can we rely on dataset.extra_files_path: os.path.join( dataset.extra_files_path, '%s.phenodata' % dataset.metadata.base_name ) ? + ### Do these have a different purpose? Ross will need to clarify + ### Uploading these datatypes will not work until this is sorted out (set_peek fails)... MetadataElement( name="pheno_path", desc="Path to phenotype data for this experiment", readonly=True) MetadataElement( name="pheno", @@ -253,11 +253,19 @@ file_ext = None + is_binary = True + + composite_type = 'basic' + + def __init__( self, **kwd ): + Html.__init__( self, **kwd ) + self.add_composite_file( '%s.phenodata', substitute_name_with_metadata = 'base_name' ) + def set_peek( self, dataset ): """expects a .pheno file in the extra_files_dir - ugh note that R is wierd and does not include the row.name in the header. why?""" - p = file(dataset.metadata.pheno_path,'r').readlines() + p = file(dataset.metadata.pheno_path,'r').readlines() #this fails head = p[0].strip().split('\t') head.insert(0,'ChipFileName') # fix R write.table b0rken-ness p[0] = '\t'.join(head) @@ -295,6 +303,7 @@ if not dataset.peek: dataset.set_peek() pk = dataset.peek # use the peek which is the pheno data insead of dataset (!) + ###this is probably not the best source, can we just access the raw data directly? if pk: p = pk.split('\n') h = p[0].strip().split('\t') # hope is header @@ -339,10 +348,6 @@ """Returns the mime type of the datatype""" return 'application/gzip' - def sniff(self): - """ can we be bothered looking for the signature or loading via rpy? - """ - return true class AffyBatch( RexpBase ): """derived class for BioC data structures in Galaxy """ diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/datatypes/metadata.py Wed Jul 15 14:11:35 2009 -0400 @@ -212,12 +212,13 @@ is a MetadataSpecCollection) of datatype. """ - def __init__( self, datatype, name=None, desc=None, param=MetadataParameter, default=None, no_value = None, visible=True, **kwargs ): + def __init__( self, datatype, name=None, desc=None, param=MetadataParameter, default=None, no_value = None, visible=True, set_in_upload = False, **kwargs ): self.name = name self.desc = desc or name self.default = default self.no_value = no_value self.visible = visible + self.set_in_upload = set_in_upload # Catch-all, allows for extra attributes to be set self.__dict__.update(kwargs) #set up param last, as it uses values set above diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Wed Jul 15 14:11:35 2009 -0400 @@ -308,3 +308,19 @@ def get_composite_extensions( self ): return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ] + def get_upload_metadata_params( self, context, group, tool ): + """Returns dict of case value:inputs for metadata conditional for upload tool""" + rval = {} + for ext, d_type in self.datatypes_by_extension.iteritems(): + inputs = [] + for meta_name, meta_spec in d_type.metadata_spec.iteritems(): + if meta_spec.set_in_upload: + help_txt = meta_spec.desc + if not help_txt or help_txt == meta_name: + help_txt = "" + inputs.append( '<param type="text" name="%s" label="Set metadata value for "%s"" value="%s" help="%s"/>' % ( meta_name, meta_name, meta_spec.default, help_txt ) ) + rval[ ext ] = "\n".join( inputs ) + if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype + rval[ 'auto' ] = rval[ 'txt' ] + return rval + diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jul 15 14:11:35 2009 -0400 @@ -596,18 +596,40 @@ elif elem.tag == "conditional": group = Conditional() group.name = elem.get( "name" ) - # Should have one child "input" which determines the case - input_elem = elem.find( "param" ) - assert input_elem is not None, "<conditional> must have a child <param>" - group.test_param = self.parse_param_elem( input_elem, enctypes, context ) - # Must refresh when test_param changes - group.test_param.refresh_on_change = True - # And a set of possible cases - for case_elem in elem.findall( "when" ): - case = ConditionalWhen() - case.value = case_elem.get( "value" ) - case.inputs = self.parse_input_elem( case_elem, enctypes, context ) - group.cases.append( case ) + + group.name = elem.get( "name" ) + + group.value_ref = elem.get( 'value_ref', None ) + group.value_ref_in_group = util.string_as_bool( elem.get( 'value_ref_in_group', 'True' ) ) + value_from = elem.get( "value_from" ) + if value_from: + value_from = value_from.split( ':' ) + group.value_from = locals().get( value_from[0] ) + group.test_param = rval[ group.value_ref ] + group.test_param.refresh_on_change = True + for attr in value_from[1].split( '.' ): + group.value_from = getattr( group.value_from, attr ) + for case_value, case_inputs in group.value_from( context, group, self ).iteritems(): + case = ConditionalWhen() + case.value = case_value + if case_inputs: + case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) + else: + case.inputs = {} + group.cases.append( case ) + else: + # Should have one child "input" which determines the case + input_elem = elem.find( "param" ) + assert input_elem is not None, "<conditional> must have a child <param>" + group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + # Must refresh when test_param changes + group.test_param.refresh_on_change = True + # And a set of possible cases + for case_elem in elem.findall( "when" ): + case = ConditionalWhen() + case.value = case_elem.get( "value" ) + case.inputs = self.parse_input_elem( case_elem, enctypes, context ) + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() @@ -615,6 +637,7 @@ group.title = elem.get( "title" ) group.file_type_name = elem.get( 'file_type_name', group.file_type_name ) group.default_file_type = elem.get( 'default_file_type', group.default_file_type ) + group.metadata_ref = elem.get( 'metadata_ref', group.metadata_ref ) rval[ group.file_type_name ].refresh_on_change = True rval[ group.file_type_name ].refresh_on_change_values = self.app.datatypes_registry.get_composite_extensions() group.inputs = self.parse_input_elem( elem, enctypes, context ) @@ -917,7 +940,10 @@ old_current_case = group_state['__current_case__'] group_prefix = "%s|" % ( key ) # Deal with the 'test' element and see if it's value changed - test_param_key = group_prefix + input.test_param.name + if input.value_ref and not input.value_ref_in_group: #we are referencing an existant parameter, which is not part of this group + test_param_key = prefix + input.test_param.name + else: + test_param_key = group_prefix + input.test_param.name test_param_error = None test_incoming = get_incoming_value( incoming, test_param_key, None ) if test_param_key not in incoming \ diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Wed Jul 15 14:11:35 2009 -0400 @@ -46,21 +46,26 @@ uploaded_datasets = dataset_upload_input.get_uploaded_datasets( trans, incoming ) for uploaded_dataset in uploaded_datasets: precreated_dataset = self.get_precreated_dataset( uploaded_dataset.precreated_name ) - dataset = self.add_file( trans, uploaded_dataset.primary_file, uploaded_dataset.name, uploaded_dataset.file_type, uploaded_dataset.is_multi_byte, uploaded_dataset.dbkey, space_to_tab = uploaded_dataset.space_to_tab, info = uploaded_dataset.info, precreated_dataset = precreated_dataset ) - if uploaded_dataset.composite_files: + dataset = self.add_file( trans, uploaded_dataset.primary_file, uploaded_dataset.name, uploaded_dataset.file_type, uploaded_dataset.is_multi_byte, uploaded_dataset.dbkey, space_to_tab = uploaded_dataset.space_to_tab, info = uploaded_dataset.info, precreated_dataset = precreated_dataset, metadata = uploaded_dataset.metadata ) + composite_files = dataset.datatype.get_composite_files( dataset ) + if composite_files: os.mkdir( dataset.extra_files_path ) #make extra files path - for name, value in uploaded_dataset.composite_files.iteritems(): + for name, value in composite_files.iteritems(): #what about binary files here, need to skip converting newlines - if value is None and not dataset.datatype.writable_files[ name ].optional: + if uploaded_dataset.composite_files[ value.name ] is None and not value.optional: dataset.info = "A required composite data file was not provided (%s)" % name dataset.state = dataset.states.ERROR break - elif value is not None: - if value.space_to_tab: - sniff.convert_newlines_sep2tabs( value.filename ) + elif uploaded_dataset.composite_files[ value.name] is not None: + if uploaded_dataset.composite_files[ value.name ].space_to_tab: + sniff.convert_newlines_sep2tabs( uploaded_dataset.composite_files[ value.name ].filename ) else: - sniff.convert_newlines( value.filename ) - shutil.move( value.filename, os.path.join( dataset.extra_files_path, name ) ) + sniff.convert_newlines( uploaded_dataset.composite_files[ value.name ].filename ) + shutil.move( uploaded_dataset.composite_files[ value.name ].filename, os.path.join( dataset.extra_files_path, name ) ) + if dataset.datatype.composite_type == 'auto_primary_file': + #now that metadata is set, we should create the primary file as required + open( dataset.file_name, 'wb+' ).write( dataset.datatype.generate_primary_file( dataset = dataset ) ) + data_list.append( dataset ) #clean up extra temp names uploaded_dataset.clean_up_temp_files() @@ -125,7 +130,7 @@ trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) return dict( output=data ) - def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None ): + def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None, metadata = {} ): def dataset_no_data_error( data, message = 'there was an error uploading your file' ): data.info = "No data: %s." % message data.state = data.states.ERROR @@ -217,6 +222,7 @@ if trans.app.datatypes_registry.get_datatype_by_extension( file_type ).composite_type != 'auto_primary_file' and self.check_html( temp_name ): return dataset_no_data_error( data, message = "you attempted to upload an inappropriate file" ) #raise BadFileException( "you attempted to upload an inappropriate file." ) + #if data_type != 'binary' and data_type != 'zip' and not trans.app.datatypes_registry.get_datatype_by_extension( ext ).is_binary: if data_type != 'binary' and data_type != 'zip': if space_to_tab: self.line_count = sniff.convert_newlines_sep2tabs( temp_name ) @@ -235,9 +241,14 @@ data.info = info data.flush() shutil.move( temp_name, data.file_name ) - data.state = data.states.OK + ## FIXME + data.state = data.states.OK ##THIS SHOULD BE THE LAST THING DONE + #### its bad to set other things after this point, i.e. metadata and composite files...this creates a race condition where a dataset could be pushed into a job before its metadata, etc is set data.set_size() data.init_meta() + #need to set metadata, has to be done after extention is set + for meta_name, meta_value in metadata.iteritems(): + setattr( data.metadata, meta_name, meta_value ) if self.line_count is not None: try: if is_multi_byte: diff -r dacc94994979 -r dd5f1fe8f5e9 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Wed Jul 15 12:18:43 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jul 15 14:11:35 2009 -0400 @@ -92,6 +92,7 @@ self.file_type_name = 'file_type' self.default_file_type = 'txt' self.file_type_to_ext = { 'auto':self.default_file_type } + self.metadata_ref = 'files_metadata' def get_file_type( self, context ): return context.get( self.file_type_name, self.default_file_type ) def get_datatype_ext( self, trans, context ): @@ -297,6 +298,7 @@ self.composite_files = odict() self.dbkey = None self.warnings = [] + self.metadata = {} self._temp_filenames = [] #store all created filenames here, delete on cleanup def register_temp_file( self, filename ): @@ -333,6 +335,13 @@ dataset.datatype = d_type dataset.dbkey = dbkey + #load metadata + files_metadata = context.get( self.metadata_ref, {} ) + for meta_name, meta_spec in d_type.metadata_spec.iteritems(): + if meta_spec.set_in_upload: + if meta_name in files_metadata: + dataset.metadata[ meta_name ] = files_metadata[ meta_name ] + temp_name = None precreated_name = None is_multi_byte = False @@ -359,10 +368,10 @@ dataset.warnings.extend( warnings ) dataset.register_temp_file( temp_name ) - keys = writable_files.keys() + keys = [ value.name for value in writable_files.values() ] for i, group_incoming in enumerate( groups_incoming[ writable_files_offset : ] ): key = keys[ i + writable_files_offset ] - if group_incoming is None and not writable_files[ key ].optional: + if group_incoming is None and not writable_files[ writable_files.keys()[ keys.index( key ) ] ].optional: dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) dataset.composite_files[ key ] = None else: @@ -372,7 +381,7 @@ dataset.register_temp_file( temp_name ) else: dataset.composite_files[ key ] = None - if not writable_files[ key ].optional: + if not writable_files[ writable_files.keys()[ keys.index( key ) ] ].optional: dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) return [ dataset ] else: @@ -404,6 +413,8 @@ Group.__init__( self ) self.test_param = None self.cases = [] + self.value_ref = None + self.value_ref_in_group = True #When our test_param is not part of the conditional Group, this is False def get_current_case( self, value, trans ): # Convert value to user representation str_value = self.test_param.filter_value( value, trans ) @@ -460,4 +471,4 @@ class ConditionalWhen( object ): def __init__( self ): self.value = None - self.inputs = None \ No newline at end of file + self.inputs = None diff -r dacc94994979 -r dd5f1fe8f5e9 templates/tool_form.mako --- a/templates/tool_form.mako Wed Jul 15 12:18:43 2009 -0400 +++ b/templates/tool_form.mako Wed Jul 15 14:11:35 2009 -0400 @@ -102,7 +102,9 @@ current_case = group_state['__current_case__'] group_prefix = prefix + input.name + "|" %> - ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %if input.value_ref_in_group: + ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %endif ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} %elif input.type == "upload_dataset": %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before diff -r dacc94994979 -r dd5f1fe8f5e9 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Wed Jul 15 12:18:43 2009 -0400 +++ b/tools/data_source/upload.xml Wed Jul 15 14:11:35 2009 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.0.1"> +<tool name="Upload File" id="upload1" version="1.0.2"> <description> from your computer </description> @@ -15,7 +15,7 @@ </options> </param> <param name="async_datasets" type="hidden" value="None"/> - <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type"> + <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> <param name="file_data" type="file" size="30" label="File" ajax-upload="true"> <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  </param> @@ -25,6 +25,7 @@ </param> </upload_dataset> <param name="dbkey" type="genomebuild" label="Genome" /> + <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />  </inputs> <help>

1 0

[hg] galaxy 2483: Updates to egg configs for Python 2.6 support....
by Greg Von Kuster 16 Jul '09

16 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5707f033e31a changeset: 2483:5707f033e31a user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Jul 15 12:00:02 2009 -0400 description: Updates to egg configs for Python 2.6 support. 2.6 is not yet supported, this commit is preliminary work for such support. 2 file(s) affected in this change: dist-eggs.ini eggs.ini diffs (80 lines): diff -r b0fb9200afe0 -r 5707f033e31a dist-eggs.ini --- a/dist-eggs.ini Tue Jul 14 16:55:18 2009 -0400 +++ b/dist-eggs.ini Wed Jul 15 12:00:02 2009 -0400 @@ -11,36 +11,49 @@ py2.4-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.4 py2.5-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.5 py2.5-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.5 +py2.6-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.6 +py2.6-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.6 py2.4-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.4 py2.4-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.4 py2.5-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.5 py2.5-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.5 +py2.6-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.6 +py2.6-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.6 py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5 +py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6 py2.5-macosx-10.5-i386-ucs2 = lion.bx.psu.edu /usr/bin/python2.5 py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4 py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5 +py2.6-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.6 py2.4-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 +py2.6-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.6 [groups] py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64 = py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 +py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 +py2.6-linux-x86_64 = py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 -linux-i686 = py2.4-linux-i686 py2.5-linux-i686 -linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 +py2.6-linux = py2.6-linux-i686 py2.6-linux-x86_64 +linux-i686 = py2.4-linux-i686 py2.5-linux-i686 py2.6-linux-i686 +linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 py2.6-linux-x86_64 linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 -macosx = py2.4-macosx py2.5-macosx +py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 +macosx = py2.4-macosx py2.5-macosx py2.6-macosx py2.4-solaris = py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 py2.5-solaris = py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2 -solaris = py2.4-solaris py2.5-solaris +py2.6-solaris = py2.6-solaris-2.11-i86pc-ucs2 py2.6-solaris-2.10-sun4u-ucs2 +solaris = py2.4-solaris py2.5-solaris py2.6-solaris py2.4-all = py2.4-linux py2.4-macosx py2.4-solaris py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris -all = py2.4-all py2.5-all +py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris +all = py2.4-all py2.5-all py2.6-all ; default hosts for platform-inspecific eggs -noplatform = py2.4-linux-i686-ucs4 py2.5-linux-i686-ucs4 +noplatform = py2.4-linux-i686-ucs4 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs4 diff -r b0fb9200afe0 -r 5707f033e31a eggs.ini --- a/eggs.ini Tue Jul 14 16:55:18 2009 -0400 +++ b/eggs.ini Wed Jul 15 12:00:02 2009 -0400 @@ -68,7 +68,7 @@ bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz -MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz +MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz @@ -79,7 +79,7 @@ Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-0.5.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz -flup = http://www.saddi.com/software/flup/dist/flup-r2311.tar.gz +flup = http://www.saddi.com/software/flup/dist/archive/flup-r2311.tar.gz lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz Mako = http://www.makotemplates.org/downloads/Mako-0.1.10.tar.gz MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52…

1 0

[hg] galaxy 2482: Removed a debug statement
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b0fb9200afe0 changeset: 2482:b0fb9200afe0 user: rc date: Tue Jul 14 16:55:18 2009 -0400 description: Removed a debug statement 1 file(s) affected in this change: lib/galaxy/web/controllers/requests.py diffs (11 lines): diff -r c60fc2075dd5 -r b0fb9200afe0 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Jul 14 15:49:53 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Tue Jul 14 16:55:18 2009 -0400 @@ -184,7 +184,6 @@ msg=msg, messagetype=messagetype ) elif params.get('create', False) == 'True': - print >> sys.stderr, '###KWD', kwd return self.__show_request_form(trans=trans, request=None, **kwd) elif params.get('save', False) == 'True':

1 0

[hg] galaxy 2481: Updates to forms/requests:
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c60fc2075dd5 changeset: 2481:c60fc2075dd5 user: rc date: Tue Jul 14 15:49:53 2009 -0400 description: Updates to forms/requests: - Mappers added to form & requests tables - Required/optional fields in requests and samples are now enforced Bug fix: duplicate field names in a request is working now 9 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.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 templates/base.mako templates/sample/grid.mako templates/sample/sample_events.mako diffs (935 lines): diff -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/model/__init__.py Tue Jul 14 15:49:53 2009 -0400 @@ -1115,7 +1115,8 @@ 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): + 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 diff -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/model/mapping.py Tue Jul 14 15:49:53 2009 -0400 @@ -607,19 +607,39 @@ 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 ) ), ) ) assign_mapper( context, FormValues, FormValues.table, properties=None) -assign_mapper( context, Request, Request.table, properties=None) +assign_mapper( context, Request, Request.table, + properties=dict( values=relation( FormValues, + primaryjoin=( Request.table.c.form_values_id == FormValues.table.c.id ) ), + type=relation( RequestType, + primaryjoin=( Request.table.c.request_type_id == RequestType.table.c.id ) ), + user=relation( User, + primaryjoin=( Request.table.c.user_id == User.table.c.id ), + backref="requests" ), + library=relation( Library, + primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ), + ) ) assign_mapper( context, RequestType, RequestType.table, properties=dict( states=relation( SampleState, backref="request_type", order_by=desc(SampleState.table.c.update_time) ), + request_form=relation( FormDefinition, + primaryjoin=( RequestType.table.c.request_form_id == FormDefinition.table.c.id ) ), + sample_form=relation( FormDefinition, + primaryjoin=( RequestType.table.c.sample_form_id == FormDefinition.table.c.id ) ), ) ) -assign_mapper( context, FormDefinition, FormDefinition.table, properties=None) - +assign_mapper( context, FormDefinition, FormDefinition.table, + properties=dict( current=relation( FormDefinitionCurrent, + primaryjoin=( FormDefinition.table.c.form_definition_current_id == FormDefinitionCurrent.table.c.id ) ) + ) ) assign_mapper( context, FormDefinitionCurrent, FormDefinitionCurrent.table, properties=dict( forms=relation( FormDefinition, backref='form_definition_current', cascade="all, delete-orphan", @@ -628,11 +648,14 @@ primaryjoin=( FormDefinitionCurrent.table.c.latest_form_id == FormDefinition.table.c.id ) ) ) ) -assign_mapper( context, SampleEvent, SampleEvent.table, properties=None) +assign_mapper( context, SampleEvent, SampleEvent.table, + properties=dict( state=relation( SampleState, + primaryjoin=( SampleEvent.table.c.sample_state_id == SampleState.table.c.id ) ), + ) ) + assign_mapper( context, SampleState, SampleState.table, - properties=None #dict( sample=relation( Sample, backref="sample" ), - )# ) + properties=None ) assign_mapper( context, ValidationError, ValidationError.table ) @@ -701,8 +724,8 @@ 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) ), +# 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 -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Tue Jul 14 15:49:53 2009 -0400 @@ -2146,7 +2146,7 @@ msg=msg, messagetype=messagetype) elif params.get('save_new', False) == 'True': - st, msg = self._save_request_type(trans, params, None) + st, msg = self._save_request_type(trans, **kwd) if not st: return trans.fill_template( '/admin/requests/create_request_type.mako', forms=self._get_all_forms(trans, all_versions=False), @@ -2170,24 +2170,9 @@ 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): + + def _save_request_type(self, trans, **kwd): + params = util.Params( kwd ) num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) proceed = True for i in range( num_states ): @@ -2197,10 +2182,7 @@ 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 = trans.app.model.RequestType() 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 )) diff -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Tue Jul 14 15:49:53 2009 -0400 @@ -70,7 +70,7 @@ elif params.get('create_form', False) == 'True': if 'submitted' in params.new: self.num_add_fields = 0 - fd, msg = self.__save_form(trans, params) + fd, msg = self.__save_form(trans, fdc_id=None, **kwd) self.__get_saved_form(fd) return self._show_forms_list(trans, msg, messagetype) @web.expose @@ -90,29 +90,34 @@ # the following two dicts store the unsaved select box options self.del_options = {} self.add_options = {} - return self.__show(trans, params, fd) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) # DELETE FIELD elif params.get('remove_button', False): - self.__update_current_form(params) + self.__update_current_form(**kwd) index = int(params.get('remove_button', None).split(' ')[2])-1 self.__remove_field(index) - return self.__show(trans, params, fd) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) # 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) + self.__update_current_form(**kwd) + fd_new, msg = self.__save_form(trans, fd.form_definition_current.id, **kwd) if not fd_new: - return self.__show(trans, params, fd, msg, 'error') + return self.__show(trans=trans, form=fd, msg=msg, + messagetype='error', **kwd) else: fd = fd_new msg = "The form '%s' has been updated with the changes." % fd.name - return self.__show(trans, params, fd, msg) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) #ADD A FIELD elif params.get('add_field_button', False) == 'Add field': - self.__update_current_form(params) + self.__update_current_form(**kwd) self.__add_field() # show the form again with one empty field - return self.__show(trans, params, fd) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) # SHOW FORM READ ONLY elif params.get('read_only', False): return trans.fill_template( '/admin/forms/show_form_read_only.mako', @@ -121,21 +126,24 @@ 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) + self.__update_current_form(**kwd) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) # REMOVE SelectField OPTION elif params.get('select_box_options', False) == 'remove': - #self.__update_current_form(params) + #self.__update_current_form(**kwd) 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) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) # ADD SelectField OPTION elif params.get('select_box_options', False) == 'add': - #self.__update_current_form(params) + #self.__update_current_form(**kwd) index = int(params.get( 'field_index', None )) self.current_form['fields'][index]['selectlist'].append('') - return self.__show(trans, params, fd) + return self.__show(trans=trans, form=fd, msg=msg, + messagetype=messagetype, **kwd) def __remove_field(self, index): del self.current_form['fields'][index] def __add_field(self): @@ -149,26 +157,31 @@ 'type': BaseField.form_field_types()[0], 'selectlist': '' } self.current_form['fields'].append(empty_field) - def __get_field(self, params, index): + def __get_field(self, index, **kwd): + params = util.Params( kwd ) name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) required = params.get( 'field_required_%i' % index, False ) field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) ) if field_type == 'SelectField': - selectlist = self.__get_selectbox_options(params, index) - else: - selectlist = None + selectlist = self.__get_selectbox_options(index, **kwd) + return {'label': name, + 'helptext': helptext, + 'visible': True, + 'required': required, + 'type': field_type, + 'selectlist': selectlist } return {'label': name, 'helptext': helptext, 'visible': True, 'required': required, - 'type': field_type, - 'selectlist': selectlist } - def __get_selectbox_options(self, params, index): + 'type': field_type} + def __get_selectbox_options(self, index, **kwd): ''' This method gets all the options entered by the user for field when the fieldtype is SelectField ''' + params = util.Params( kwd ) ctr=0 sb_options = [] while True: @@ -183,12 +196,13 @@ 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): + def __validate_form(self, **kwd): ''' This method checks the following text inputs are filled out by the user - the name of form - name of all the fields ''' + params = util.Params( kwd ) # form name if not util.restore_text( params.name ): return None, 'Form name must be filled.' @@ -197,32 +211,33 @@ if not util.restore_text(params.get( 'field_name_%i' % i, None )): return None, "All the field label(s) must be completed." return True, '' - def __get_form(self, params): + def __get_form(self, **kwd): + params = util.Params( kwd ) 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.append(self.__get_field(i, **kwd)) fields = fields return name, desc, fields - def __update_current_form(self, params): - name, desc, fields = self.__get_form(params) + def __update_current_form(self, **kwd): + name, desc, fields = self.__get_form(**kwd) 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): + def __save_form(self, trans, fdc_id=None, **kwd): ''' This method saves the current form ''' # check the form for invalid inputs - flag, msg = self.__validate_form(params) + flag, msg = self.__validate_form(**kwd) if not flag: return None, msg fd = trans.app.model.FormDefinition() - fd.name, fd.desc, fd.fields = self.__get_form(params) + fd.name, fd.desc, fd.fields = self.__get_form(**kwd) if fdc_id: # save changes to the existing form # change the pointer in the form_definition_current table to point # to this new record @@ -302,10 +317,11 @@ def label(self): return str(self.index)+'.'+self.label - def __show(self, trans, params, form, msg=None, messagetype='done'): + def __show(self, trans, form, msg=None, messagetype='done', **kwd): ''' This method displays the form and any of the changes made to it ''' + params = util.Params( kwd ) # name & description form_details = [ ( 'Name', TextField('name', 40, self.current_form['name']) ), ( 'Description', TextField('description', 40, self.current_form['desc']) ) ] diff -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Tue Jul 14 15:49:53 2009 -0400 @@ -6,11 +6,9 @@ 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" @@ -41,8 +39,7 @@ 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 + 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): @@ -83,7 +80,7 @@ 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) + curr_state = all_states[len(all_states)-1].state return curr_state.name class Requests( BaseController ): @@ -92,6 +89,7 @@ @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 = [] @@ -134,9 +132,6 @@ 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 = [] @@ -148,7 +143,7 @@ value=request.desc, helptext='')) request_details.append(dict(label='Type', - value=request_type.name, + value=request.type.name, helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -157,26 +152,26 @@ value=request.create_time, helptext='')) request_details.append(dict(label='User', - value=str(trans.user.email), + value=str(request.user.email), helptext='')) # library associated request_details.append(dict(label='Library', - value=trans.app.model.Library.get(request.library_id).name, + value=request.library.name, helptext='Associated library where the resultant \ dataset will be stored')) # form fields - for field in request_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[field['label']], + value=request.values.content[index], helptext=field['helptext']+' ('+req+')')) return trans.fill_template( '/requests/view_request.mako', - request_form_id=request_form.id, + request_form_id=request.type.request_form.id, request_details=request_details, - request_type=request_type) + request_type=request.type) @web.expose def new(self, trans, **kwd): params = util.Params( kwd ) @@ -189,49 +184,74 @@ 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) + print >> sys.stderr, '###KWD', kwd + return self.__show_request_form(trans=trans, + request=None, **kwd) elif params.get('save', False) == 'True': - request = self.__save(trans, params) + request_type = trans.app.model.RequestType.get(int(params.request_type_id)) + msg = self.__validate(trans, + [('name','Name'), ('library_id','Library')], + 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 )) 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): + def __validate(self, trans, main_fields=[], form_fields=[], **kwd): ''' - This method save a new request if request_id is None. + 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, None)): + 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']: + 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_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) + request_type = trans.app.model.RequestType.get(int(params.request_type_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) + # TODO editing + pass name = util.restore_text(params.get('name', '')) desc = util.restore_text(params.get('desc', '')) - library_id = util.restore_text(params.get('library', '')) - values = {} - for field in request_form.fields: - values[field['label']] = util.restore_text(params.get(field['label'], '')) + library_id = int(util.restore_text(params.get('library_id', 0))) + 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_form_id, values) + form_values = trans.app.model.FormValues(request_type.request_form.id, values) form_values.flush() - request = trans.app.model.Request(name, desc, request_type_id, + 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() + # TODO editing + pass 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 + def __show_request_form(self, trans, request=None, **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 = trans.app.model.FormValues.get(request.form_values_id) else: @@ -239,56 +259,63 @@ # list of widgets to be rendered on the request form widgets = [] widgets.append(dict(label='Name', - widget=TextField('name'), + widget=TextField('name', 40, + util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) widgets.append(dict(label='Description', - widget=TextField('desc'), + widget=TextField('desc', 40, + util.restore_text( params.get( 'desc', '' ) )), helptext='(Optional)')) - widgets[0]['widget'].set_size(40) - widgets[1]['widget'].set_size(40) # libraries selectbox + value = int(params.get( 'library_id', 0 )) libraries = self.get_authorized_libs(trans) - lib_list = SelectField('library') + lib_list = SelectField('library_id') for lib in libraries: - lib_list.add_option(lib.name, lib.id) + if lib.id == value: + lib_list.add_option(lib.name, lib.id, selected=True) + else: + 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) + 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_form_id, + request_form_id=request_type.request_form_id, request_type=request_type, widgets=widgets, - title=title) + title=title, + msg=msg, + messagetype=messagetype) - def __create_form(self, trans, params, form_id, widgets=[], form_values=None): + def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd): + params = util.Params( kwd ) 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']) + 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 = values[field['label']] + fw.value = value elif field['type'] == 'TextArea': fw.set_size(3, 40) - fw.value = values[field['label']] + fw.value = value 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 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']: req = 'Required' else: @@ -302,13 +329,13 @@ 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) + return self.__show_sample_form(trans, sample=None, **kwd) - 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 + def __show_sample_form(self, trans, sample=None, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + request = trans.app.model.Request.get(int( params.request_id )) if sample: form_values = trans.app.model.FormValues.get(sample.form_values_id) else: @@ -316,50 +343,63 @@ # list of widgets to be rendered on the request form widgets = [] widgets.append(dict(label='Name', - widget=TextField('name'), + widget=TextField('name', 40, + util.restore_text( params.get( 'name', '' ) )), helptext='(Required)')) widgets.append(dict(label='Description', - widget=TextField('desc'), + widget=TextField('desc', 40, + util.restore_text( params.get( '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) + widgets = self.__create_form(trans, request.type.sample_form_id, widgets, form_values, **kwd) + 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, + sample_form_id=request.type.sample_form_id, request_id=request.id, widgets=widgets, - title=title) + title=title, + msg=msg, + messagetype=messagetype) @web.expose def samples(self, trans, **kwd): params = util.Params( kwd ) if params.get('save', False) == 'True': - sample = self.__save_sample(trans, params) + request = trans.app.model.Request.get(int(params.request_id )) + msg = self.__validate(trans, + [('name','Name')], + request.type.sample_form.fields, + **kwd) + if msg: + return trans.response.send_redirect( web.url_for( controller='requests', + action='add_sample', + msg=msg, + messagetype='error', + **kwd) ) + sample = self.__save_sample(trans, sample_id=None, **kwd) + msg = 'The new sample named %s has been created' % sample.name 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): + id=trans.security.encode_id(sample.request_id), + **kwd) ) + def __save_sample(self, trans, sample_id=None, **kwd): + params = util.Params( kwd ) 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) + request = trans.app.model.Request.get(int(params.request_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) + #TODO editing + pass name = util.restore_text(params.get('name', '')) desc = util.restore_text(params.get('desc', '')) - values = {} - for field in sample_form.fields: - values[field['label']] = util.restore_text(params.get(field['label'], '')) + values = [] + for index, field in enumerate(request.type.sample_form.fields): + values.append(util.restore_text(params.get('field_%i' % index, ''))) if not sample_id: - form_values = trans.app.model.FormValues(sample_form.id, values) + form_values = trans.app.model.FormValues(request.type.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() + 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: @@ -371,10 +411,10 @@ 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) + request = sample.request + request_type = sample.request.type + sample_form = sample.request.type.sample_form + sample_values = sample.values # list of widgets to be rendered on the request form sample_details = [] # main details @@ -398,31 +438,37 @@ 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) + curr_state = all_states[len(all_states)-1].state sample_details.append(dict(label='State', value=curr_state.name, helptext=curr_state.desc)) # form fields - for field in sample_form.fields: + for index, field in enumerate(sample_form.fields): if field['required']: req = 'Required' else: req = 'Optional' sample_details.append(dict(label=field['label'], - value=sample_values.content[field['label']], + value=sample_values.content[index], 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)) + all_events = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all() + all_events.reverse() + for event in all_events: + 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((event.state.name, event.state.desc, last_update, 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) + request=sample.request.name) diff -r dc5068efc3e7 -r c60fc2075dd5 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Jul 14 11:33:42 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Jul 14 15:49:53 2009 -0400 @@ -146,9 +146,6 @@ 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 = [] @@ -160,7 +157,7 @@ value=request.desc, helptext='')) request_details.append(dict(label='Type', - value=request_type.name, + value=request.type.name, helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -169,7 +166,7 @@ value=request.create_time, helptext='')) request_details.append(dict(label='User', - value=str(trans.user.email), + value=str(request.user.email), helptext='')) # library associated request_details.append(dict(label='Library', @@ -177,18 +174,18 @@ helptext='Associated library where the resultant \ dataset will be stored')) # form fields - for field in request_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[field['label']], + value=request.values.content[index], helptext=field['helptext']+' ('+req+')')) return trans.fill_template( '/admin/requests/view_request.mako', - request_form_id=request_form.id, + request_form_id=request.type.request_form.id, request_details=request_details, - request_type=request_type) + request_type=request.type) @web.expose @web.require_admin @@ -202,10 +199,10 @@ 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) + request = sample.request + request_type = sample.request.type + sample_form = sample.request.type.sample_form + sample_values = sample.values # list of widgets to be rendered on the request form sample_details = [] # main details @@ -229,18 +226,18 @@ 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) + curr_state = all_states[len(all_states)-1].state sample_details.append(dict(label='State', value=curr_state.name, helptext=curr_state.desc)) # form fields - for field in sample_form.fields: + for index, field in enumerate(sample_form.fields): if field['required']: req = 'Required' else: req = 'Optional' sample_details.append(dict(label=field['label'], - value=sample_values.content[field['label']], + value=sample_values.content[index], helptext=field['helptext']+' ('+req+')')) return trans.fill_template( '/admin/samples/view_sample.mako', sample_details=sample_details) @@ -300,7 +297,9 @@ 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(): + all_events = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all() + all_events.reverse() + for event in all_events: state = trans.app.model.SampleState.get(event.sample_state_id) delta = datetime.utcnow() - event.update_time if delta > timedelta( minutes=60 ): diff -r dc5068efc3e7 -r c60fc2075dd5 templates/base.mako --- a/templates/base.mako Tue Jul 14 11:33:42 2009 -0400 +++ b/templates/base.mako Tue Jul 14 15:49:53 2009 -0400 @@ -58,4 +58,5 @@ $( "#edit_form" ).submit(); } }); -}); \ No newline at end of file +}); +</script> \ No newline at end of file diff -r dc5068efc3e7 -r c60fc2075dd5 templates/sample/grid.mako --- a/templates/sample/grid.mako Tue Jul 14 11:33:42 2009 -0400 +++ b/templates/sample/grid.mako Tue Jul 14 15:49:53 2009 -0400 @@ -89,7 +89,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='requests', action='add_sample', id=grid.request.id)}"> + <a class="action-button" href="${h.url_for( controller='requests', action='add_sample', request_id=grid.request.id)}"> <img src="${h.url_for('/static/images/silk/add.png')}" /> <span>Add sample</span></a> </li> diff -r dc5068efc3e7 -r c60fc2075dd5 templates/sample/sample_events.mako --- a/templates/sample/sample_events.mako Tue Jul 14 11:33:42 2009 -0400 +++ b/templates/sample/sample_events.mako Tue Jul 14 15:49:53 2009 -0400 @@ -14,17 +14,17 @@ <thead> <tr> <th>State</th> + <th>Description</th> <th>Updated</th> - <th>Description</th> <th>Comments</th> </tr> </thead> <tbody> - %for state, updated, desc, comments in events_list: + %for state, desc, updated, comments in events_list: <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> <td><b><a>${state}</a></b></td> + <td><a>${desc}</a></td> <td><a>${updated}</a></td> - <td><a>${desc}</a></td> <td><a>${comments}</a></td> </tr> %endfor

1 0

[hg] galaxy 2480: Fix job recovery when a tool has been removed ...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dc5068efc3e7 changeset: 2480:dc5068efc3e7 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jul 14 11:33:42 2009 -0400 description: Fix job recovery when a tool has been removed while the job is running 1 file(s) affected in this change: lib/galaxy/jobs/__init__.py diffs (24 lines): diff -r 3f407d489ade -r dc5068efc3e7 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri May 22 14:46:17 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Jul 14 11:33:42 2009 -0400 @@ -119,10 +119,17 @@ """ model = self.app.model for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all(): - log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) - self.queue.put( ( job.id, job.tool_id ) ) + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + else: + log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) + self.queue.put( ( job.id, job.tool_id ) ) for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all(): - if job.job_runner_name is None: + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + elif job.job_runner_name is None: log.debug( "no runner: %s is still in queued state, adding to the jobs queue" %job.id ) self.queue.put( ( job.id, job.tool_id ) ) else:

1 0

[hg] galaxy 2477: Fix some display problems with the tabs. Somet...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d202e2f4b910 changeset: 2477:d202e2f4b910 user: James Taylor <james(a)jamestaylor.org> date: Fri Jul 10 18:33:36 2009 -0400 description: Fix some display problems with the tabs. Sometimes you just have to use tables.... 5 file(s) affected in this change: static/june_2007_style/blue/panel_layout.css static/june_2007_style/panel_layout.css.tmpl static/scripts/galaxy.panels.js static/scripts/packed/galaxy.panels.js templates/base_panels.mako diffs (257 lines): diff -r 14fd033f08eb -r d202e2f4b910 static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Fri Jul 10 16:21:19 2009 -0400 +++ b/static/june_2007_style/blue/panel_layout.css Fri Jul 10 18:33:36 2009 -0400 @@ -35,7 +35,6 @@ border-bottom: solid #999 1px; font-size: 90%; } - #left, #left-border, #center, #right-border, #right { @@ -272,16 +271,22 @@ text-decoration: underline; } -div.tab-group + +.tab-group { margin: 0; padding: 0 10px; height: 100%; white-space: nowrap; + -moz-user-select: none; + -khtml-user-select: none; + user-select: none; + cursor: default; } -div.tab-group span.tab +.tab-group .tab { + background: #2C3143; position: relative; display: block; float: left; @@ -292,17 +297,17 @@ text-align: left; } -div.tab-group > span.tab:hover > a +.tab-group .tab:hover > a { color: gold !important; } -div.tab-group > span.active +.tab-group .active { background: rgb(1,1,1); } -div.tab-group span.tab div.submenu { +.tab-group .tab .submenu { display: none; position: absolute; z-index: 16000; @@ -318,7 +323,8 @@ -webkit-border-bottom-left-radius: 1em; } -div.tab-group span.tab div.submenu ul { +.tab-group .tab .submenu ul +{ display: block; margin: 0; padding: 0; @@ -326,7 +332,8 @@ background: #2C3143; } -div.tab-group span.tab div.submenu ul li { +.tab-group .tab .submenu ul li +{ display: block; padding: 0 1em; white-space: nowrap; diff -r 14fd033f08eb -r d202e2f4b910 static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jul 10 16:21:19 2009 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Jul 10 18:33:36 2009 -0400 @@ -35,7 +35,6 @@ border-bottom: solid #999 1px; font-size: 90%; } - #left, #left-border, #center, #right-border, #right { @@ -274,16 +273,23 @@ text-decoration: underline; } -div.tab-group +## Tabs + +.tab-group { margin: 0; padding: 0 10px; height: 100%; white-space: nowrap; + -moz-user-select: none; + -khtml-user-select: none; + user-select: none; + cursor: default; } -div.tab-group span.tab +.tab-group .tab { + background: ${masthead_bg}; position: relative; display: block; float: left; @@ -294,17 +300,17 @@ text-align: left; } -div.tab-group > span.tab:hover > a +.tab-group .tab:hover > a { color: gold !important; } -div.tab-group > span.active +.tab-group .active { background: rgb(1,1,1); } -div.tab-group span.tab div.submenu { +.tab-group .tab .submenu { display: none; position: absolute; z-index: 16000; @@ -320,7 +326,8 @@ -webkit-border-bottom-left-radius: 1em; } -div.tab-group span.tab div.submenu ul { +.tab-group .tab .submenu ul +{ display: block; margin: 0; padding: 0; @@ -328,7 +335,8 @@ background: ${masthead_bg}; } -div.tab-group span.tab div.submenu ul li { +.tab-group .tab .submenu ul li +{ display: block; padding: 0 1em; white-space: nowrap; diff -r 14fd033f08eb -r d202e2f4b910 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Fri Jul 10 16:21:19 2009 -0400 +++ b/static/scripts/galaxy.panels.js Fri Jul 10 18:33:36 2009 -0400 @@ -216,8 +216,8 @@ // Tab management $(function() { - $("span.tab").each( function() { - var submenu = $(this).children( "div.submenu" ); + $(".tab").each( function() { + var submenu = $(this).children( ".submenu" ); if ( submenu.length > 0 ) { if ( $.browser.msie ) { // Vile IE iframe hack -- even IE7 needs this diff -r 14fd033f08eb -r d202e2f4b910 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Fri Jul 10 16:21:19 2009 -0400 +++ b/static/scripts/packed/galaxy.panels.js Fri Jul 10 18:33:36 2009 -0400 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend ",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false} ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dia log-box").find(".buttons").html("");if(e){$.each(e,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"))}$(function(){$("span.tab").each(function(){var a=$(t his).children("div.submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file +function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragend ",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false} ;var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dia log-box").find(".buttons").html("");if(e){$.each(e,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"))}$(function(){$(".tab").each(function(){var a=$(this) .children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file diff -r 14fd033f08eb -r d202e2f4b910 templates/base_panels.mako --- a/templates/base_panels.mako Fri Jul 10 16:21:19 2009 -0400 +++ b/templates/base_panels.mako Fri Jul 10 18:33:36 2009 -0400 @@ -131,8 +131,10 @@ %endif </div> - <div style="position: absolute; left: 50%;"> - <div class="tab-group" style="position: relative; left: -50%;"> + <div style="position: absolute; left: 0; width: 100%; text-align: center;"> + + <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> + <tr> <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> <% @@ -145,31 +147,31 @@ if not visible: style = "display: none;" %> - <span class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></span> + <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></td> </%def> ${tab( "analysis", "Analyze Data", h.url_for( controller='root', action='index' ))} - + ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} - + ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} ${tab( "requests", "Requests", h.url_for( controller='requests', action='index' ), visible = (trans.user and trans.request_types)) } %if app.config.get_bool( 'enable_tracks', False ): - <span class="tab"> + <td class="tab"> Visualization <div class="submenu"> <ul> <li><a href="${h.url_for( controller='tracks', action='index' )}">Build track browser</a></li> </ul> </div> - </span> + </td> %endif ${tab( "admin", "Admin", h.url_for( controller='admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - <span class="tab"> + <td class="tab"> <a>Help</a> <div class="submenu"> <ul> @@ -178,9 +180,9 @@ <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> </ul> </div> - </span> + </td> - <span class="tab"> + <td class="tab"> <a>User</a> <% if trans.user: @@ -219,9 +221,11 @@ %endif </ul> </div> - </span> + </td> - </div> + </tr> + </table> + </div> </%def>

1 0

[hg] galaxy 2479: Performance improvements for large histories (...
by Greg Von Kuster 15 Jul '09

15 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3f407d489ade changeset: 2479:3f407d489ade user: James Taylor <james(a)jamestaylor.org> date: Fri May 22 14:46:17 2009 -0400 description: Performance improvements for large histories (both on database query and javascript) 5 file(s) affected in this change: lib/galaxy/datatypes/registry.py lib/galaxy/model/mapping.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/__init__.py templates/root/history.mako diffs (243 lines): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri May 22 14:46:17 2009 -0400 @@ -211,7 +211,8 @@ builder = self.datatypes_by_extension[ext] except KeyError: builder = data.Text() - self.log.warning('unknown extension in data factory %s' % ext) + if ext is not None: + self.log.warning('unknown extension in data factory %s', ext) return builder def change_datatype(self, data, ext ): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/model/mapping.py Fri May 22 14:46:17 2009 -0400 @@ -690,7 +690,7 @@ assign_mapper( context, History, History.table, properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), - active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), lazy=False, viewonly=True ) + active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), viewonly=True ) ) ) assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation.table, diff -r feb7438276fb -r 3f407d489ade lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri May 22 14:46:17 2009 -0400 @@ -61,7 +61,18 @@ return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) else: template = "root/history.mako" - return trans.fill_template( "root/history.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) + show_deleted = util.string_as_bool( show_deleted ) + query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ + .filter( model.HistoryDatasetAssociation.history == history ) \ + .options( eagerload( "children" ) ) \ + .join( "dataset" ).filter( model.Dataset.purged == False ) \ + .options( eagerload_all( "dataset.actions" ) ) + if not show_deleted: + query.filter_by( deleted=False ) + return trans.stream_template_mako( "root/history.mako", + history = history, + datasets = query.all(), + show_deleted = show_deleted ) @web.expose def dataset_state ( self, trans, id=None, stamp=None ): diff -r feb7438276fb -r 3f407d489ade lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Jul 13 13:08:52 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri May 22 14:46:17 2009 -0400 @@ -23,6 +23,7 @@ pkg_resources.require( "Mako" ) import mako.template import mako.lookup +import mako.runtime pkg_resources.require( "Babel" ) from babel.support import Translations @@ -575,6 +576,23 @@ data.update( self.template_context ) data.update( kwargs ) return template.render( **data ) + def stream_template_mako( self, filename, **kwargs ): + template = self.webapp.mako_template_lookup.get_template( filename ) + template.output_encoding = 'utf-8' + data = dict( caller=self, t=self, trans=self, h=webhelpers, util=util, request=self.request, response=self.response, app=self.app ) + data.update( self.template_context ) + data.update( kwargs ) + ## return template.render( **data ) + def render( environ, start_response ): + response_write = start_response( self.response.wsgi_status(), + self.response.wsgi_headeritems() ) + class C: + def write( self, *args, **kwargs ): + response_write( *args, **kwargs ) + context = mako.runtime.Context( C(), **data ) + template.render_context( context ) + return [] + return render def fill_template_string(self, template_string, context=None, **kwargs): """ Fill in a template, putting any keyword arguments on the context. diff -r feb7438276fb -r 3f407d489ade templates/root/history.mako --- a/templates/root/history.mako Mon Jul 13 13:08:52 2009 -0400 +++ b/templates/root/history.mako Fri May 22 14:46:17 2009 -0400 @@ -70,7 +70,15 @@ $("#history-name-area").append( t ); t.focus(); return false; - }) + }); + // Updater + updater({ + %for data in reversed( datasets ): + %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: + "${data.id}": "${data.state}"; + %endif + %endfor + }); }) //' Functionized so AJAX'd datasets can call them // Get shown/hidden state from cookie @@ -80,7 +88,7 @@ var state = new CookieSet( "galaxy.history.expand_state" ); for ( id in state.store ) { if ( id ) { - $( "#" + id ).children( "div.historyItemBody" ).show(); + $( "#" + id + " div.historyItemBody" ).show(); } } // If Mozilla, hide scrollbars in hidden items since they cause animation bugs @@ -114,51 +122,51 @@ state.add( id ); state.save(); delete state; } - return false; + return false; }); // Delete link $(this).find( "a.historyItemDelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#progress-' + data_id ).show(); - $.ajax({ - url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Delete failed" ) }, - success: function() { - %if show_deleted: - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - %else: - $( "#historyItem-" + data_id ).fadeOut( "fast", function() { - $( "#historyItemContainer-" + data_id ).remove(); - if ( $( "div.historyItemContainer" ).length < 1 ) { - $( "#emptyHistoryMessage" ).show(); - } + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#progress-' + data_id ).show(); + $.ajax({ + url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Delete failed" ) }, + success: function() { + %if show_deleted: + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + %else: + $( "#historyItem-" + data_id ).fadeOut( "fast", function() { + $( "#historyItemContainer-" + data_id ).remove(); + if ( $( "div.historyItemContainer" ).length < 1 ) { + $( "#emptyHistoryMessage" ).show(); + } + }); + %endif + } + }); + return false; }); - %endif - } }); - return false; - }); - }); // Undelete link $(this).find( "a.historyItemUndelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#progress-' + data_id ).show(); - $.ajax({ - url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Undelete failed" ) }, - success: function() { - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - } + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#progress-' + data_id ).show(); + $.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } + }); + return false; + }); }); - return false; - }); - }); }); }; // Looks for changes in dataset state using an async request. Keeps @@ -261,36 +269,21 @@ <%namespace file="history_common.mako" import="render_dataset" /> -<% activatable_datasets = history.activatable_datasets %> +%if not datasets: -%if ( show_deleted and not activatable_datasets ) or ( not show_deleted and not history.active_datasets ): <div class="infomessagesmall" id="emptyHistoryMessage"> + %else: - <% - if show_deleted: - ## All datasets - datasets_to_show = activatable_datasets - else: - ## Active (not deleted) - datasets_to_show = history.active_datasets - %> + ## Render requested datasets, ordered from newest to oldest - %for data in reversed( datasets_to_show ): + %for data in reversed( datasets ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted )} </div> %endif %endfor - <script type="text/javascript"> - var tracked_datasets = {}; - %for data in reversed( history.active_datasets ): - %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: - tracked_datasets[ ${data.id} ] = "${data.state}"; - %endif - %endfor - updater( tracked_datasets ); - </script> + <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif ${_("Your history is empty. Click 'Get Data' on the left pane to start")}

1 0