details: http://www.bx.psu.edu/hg/galaxy/rev/0041f2ba49ed changeset: 1540:0041f2ba49ed user: Greg Von Kuster greg@bx.psu.edu date: Thu Oct 02 12:45:03 2008 -0400 description: Fix all root controller methods so that history_dataset_association.id is not confused with history_dataset_association.dataset_id.

1 file(s) affected in this change:

lib/galaxy/web/controllers/root.py

diffs (415 lines):

diff -r dd58d5aeb274 -r 0041f2ba49ed lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Oct 01 12:43:59 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 12:45:03 2008 -0400 @@ -21,9 +21,7 @@

@web.expose def index(self, trans, id=None, tool_id=None, mode=None, m_c=None, m_a=None, **kwd): - return trans.fill_template( "root/index.mako", - tool_id=tool_id, - m_c=m_c, m_a=m_a ) + return trans.fill_template( "root/index.mako", tool_id=tool_id, m_c=m_c, m_a=m_a )

## ---- Tool related -----------------------------------------------------

@@ -68,10 +66,10 @@ @web.expose def dataset_state ( self, trans, id=None, stamp=None ): if id is not None: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) + try: + data = self.app.model.Dataset.get( id ) except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset id %s." %str( id ) ) trans.response.headers['X-Dataset-State'] = data.state trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -82,13 +80,13 @@ @web.expose def dataset_code( self, trans, id=None, hid=None, stamp=None ): if id is not None: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) + try: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset id %s." % str( id ) ) trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return trans.fill_template("root/history_item.mako", data=data, hid=hid) + return trans.fill_template( "root/history_item.mako", data=hda.dataset, hid=hid ) else: return trans.show_error_message( "Must specify a dataset id.")

@@ -103,11 +101,11 @@ ids = map( int, ids.split( "," ) ) states = states.split( "," ) for id, state in zip( ids, states ): - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data.state != state: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda.dataset.state != state: rval[id] = { - "state": data.state, - "html": trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ) + "state": hda.dataset.state, + "html": trans.fill_template( "root/history_item.mako", data=hda, hid=hda.hid ) } return rval

@@ -133,7 +131,6 @@ raise Exception( "History_dataset_association with hid '%s' does not exist." % str( hid ) ) else: try: - id = int( id ) history_dataset_assoc = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() except: return "Dataset id '%s' is invalid." %str( id ) @@ -163,36 +160,36 @@ Returns child data directly into the browser, based upon parent_id and designation. """ try: - data = self.app.model.HistoryDatasetAssociation.get( parent_id ) - if data: - child = data.get_child_by_designation(designation) + hda = self.app.model.HistoryDatasetAssociation.get( parent_id ) + if hda: + child = hda.get_child_by_designation( designation ) if child: return self.display(trans, id=child.id, tofile=tofile, toext=toext) except Exception: pass - return "A child named %s could not be found for data %s" % ( designation, parent_id ) + return "A child named '%s' could not be found for history_dataset_association id '%s'" % ( designation, str( parent_id ) )

@web.expose def display_as( self, trans, id=None, display_app=None, **kwd ): """Returns a file in a format that can successfully be displayed in display_app""" - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: - trans.response.set_content_type(data.get_mime()) + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: + trans.response.set_content_type( hda.get_mime() ) trans.log_event( "Formatted dataset id %s for display at %s" % ( str(id), display_app ) ) - return data.as_display_type(display_app, **kwd) + return hda.as_display_type( display_app, **kwd ) else: - return "No data with id=%d" % id + return "Dataset 'id' %s does not exist." % str( id )

@web.expose def peek(self, trans, id=None): """Returns a 'peek' at the data""" - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: yield "<html><body><pre>" - yield data.peek + yield hda.peek yield "</pre></body></html>" else: - yield "No data with id=%d" % id + yield "Dataset 'id' %s does not exist." % str( id )

@web.expose def edit(self, trans, id=None, hid=None, **kwd): @@ -200,76 +197,75 @@ if hid is not None: history = trans.get_history() # TODO: hid handling - data = history.datasets[ int( hid ) - 1 ] + hda = history.datasets[ int( hid ) - 1 ] elif id is None: - return trans.show_error_message( "Problem loading dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) + return trans.show_error_message( "Problem loading dataset id '%s' with history id '%s'." % ( str( id ), str( hid ) ) ) else: - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data is None: - return trans.show_error_message( "Problem retrieving dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda is None: + return trans.show_error_message( "Problem retrieving dataset 'id' %s with history id '%s'." % ( str( id ), str( hid ) ) )

p = util.Params(kwd, safe=False)

if p.change: # The user clicked the Save button on the 'Change data type' form - trans.app.datatypes_registry.change_datatype( data, p.datatype ) + trans.app.datatypes_registry.change_datatype( hda, p.datatype ) trans.app.model.flush() elif p.save: # The user clicked the Save button on the 'Edit Attributes' form - data.name = p.name - data.info = p.info + hda.name = p.name + hda.info = p.info

# The following for loop will save all metadata_spec items - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): if spec.get("readonly"): continue optional = p.get("is_"+name, None) if optional and optional == 'true': # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr(data.metadata,name,None) + setattr( hda.metadata, name, None ) else: - setattr(data.metadata,name,spec.unwrap(p.get(name, None), p)) + setattr( hda.metadata, name, spec.unwrap( p.get( name, None ), p ) )

- data.datatype.after_edit( data ) + hda.datatype.after_edit( hda ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): # We need to be careful about the attributes we are resetting if name != 'name' and name != 'info' and name != 'dbkey': if spec.get( 'default' ): - setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec )) - data.datatype.set_meta( data ) - data.datatype.after_edit( data ) + setattr( hda.metadata, name, spec.unwrap( spec.get( 'default' ), spec ) ) + hda.datatype.set_meta( hda ) + hda.datatype.after_edit( hda ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.convert_data: """The user clicked the Convert button on the 'Convert to new format' form""" target_type = kwd.get("target_type", None) if target_type: - msg = data.datatype.convert_dataset(trans, data, target_type) + msg = hda.datatype.convert_dataset(trans, hda, target_type) return trans.show_ok_message( msg, refresh_frames=['history'] ) - data.datatype.before_edit( data ) + hda.datatype.before_edit( hda )

- if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey: + if "dbkey" in hda.datatype.metadata_spec and not hda.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability # This looks like it does nothing, but getting the dbkey # returns the metadata dbkey unless it is None, in which # case it resorts to the old dbkey. Setting the dbkey # sets it properly in the metadata - data.metadata.dbkey = data.dbkey + hda.metadata.dbkey = hda.dbkey metadata = list() # a list of MetadataParemeters - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): if spec.visible: - metadata.append( spec.wrap( data.metadata.get(name), data ) ) + metadata.append( spec.wrap( hda.metadata.get( name ), hda ) ) # let's not overwrite the imported datatypes module with the variable datatypes? ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()] ldatatypes.sort() - trans.log_event( "Opened edit view on dataset %s" % str(id) ) - return trans.fill_template( "/dataset/edit_attributes.mako", data=data, metadata=metadata, - datatypes=ldatatypes, err=None ) + trans.log_event( "Opened edit view on dataset id '%s'" % str( id ) ) + return trans.fill_template( "/dataset/edit_attributes.mako", data=hda, metadata=metadata, datatypes=ldatatypes, err=None )

@web.expose def delete( self, trans, id = None, **kwd): @@ -284,21 +280,22 @@ int( id ) except: continue - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: - # Walk up parent datasets to find the containing history - topmost_parent = data + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + log.debug("***hda.dataset_id: %s" % str( hda.dataset_id)) + if hda: + # Walk up parent hdas to find the containing history + topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - data.mark_deleted() - data.clear_associated_files() + hda.mark_deleted() + hda.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if data.parent_id is None: + trans.log_event( "Dataset id '%s' marked as deleted" % str( id ) ) + if hda.parent_id is None: try: - self.app.job_stop_queue.put( data.creating_job_associations[0].job ) + self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return self.history( trans ) @@ -311,21 +308,21 @@ except: return "Dataset id '%s' is invalid" %str( id ) history = trans.get_history() - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: # Walk up parent datasets to find the containing history - topmost_parent = data + topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - data.mark_deleted() - data.clear_associated_files() + hda.mark_deleted() + hda.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id %s marked as deleted async" % str(id) ) - if data.parent_id is None: + trans.log_event( "Dataset id '%s' marked as deleted async" % str( id ) ) + if hda.parent_id is None: try: - self.app.job_stop_queue.put( data.creating_job_associations[0].job ) + self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return "OK" @@ -335,8 +332,7 @@ @web.expose def history_options( self, trans ): """Displays a list of history related actions""" - return trans.fill_template( "/history/options.mako", - user = trans.get_user(), history = trans.get_history() ) + return trans.fill_template( "/history/options.mako", user=trans.get_user(), history=trans.get_history() )

@web.expose def history_delete( self, trans, id=None, **kwd): @@ -368,16 +364,16 @@ trans.log_event( "History id %s marked as deleted" % str(hid) ) else: return trans.show_message( "You must select at least one history to delete." ) - return trans.show_message( "History deleted: %s" % ",".join(history_names), - refresh_frames=['history']) + return trans.show_message( "History deleted: %s" % ",".join(history_names), refresh_frames=['history'] )

@web.expose def clear_history( self, trans ): """Clears the history for a user""" history = trans.get_history() - for dataset in history.datasets: - dataset.deleted = True - dataset.clear_associated_files() + for hda in history.datasets: + hda.deleted = True + hda.dataset.deleted = True + hda.clear_associated_files() self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @@ -425,9 +421,7 @@ if not isinstance( id, list ): id = [ id ] trans.log_event( "History id %s available" % str( id ) ) - return trans.fill_template( "/history/list.mako", ids=id, - user=trans.get_user(), - current_history=trans.get_history() ) + return trans.fill_template( "/history/list.mako", ids=id, user=trans.get_user(), current_history=trans.get_history() )

@web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): @@ -553,23 +547,23 @@ """Adds a POSTed file to a History""" try: history = trans.app.model.History.get( history_id ) - data = trans.app.model.HistoryDatasetAssociation( name = name, info = info, extension = ext, dbkey = dbkey, create_dataset = True ) - data.flush() - data_file = open( data.file_name, "wb" ) + hda = trans.app.model.HistoryDatasetAssociation( name=name, info=info, extension=ext, dbkey=dbkey, create_dataset=True ) + hda.flush() + data_file = open( hda.file_name, "wb" ) file_data.file.seek( 0 ) data_file.write( file_data.file.read() ) data_file.close() - data.state = data.states.OK - data.init_meta() - data.set_meta() - data.flush() - history.add_dataset( data ) + hda.dataset.state = hda.dataset.states.OK + hda.init_meta() + hda.set_meta() + hda.flush() + history.add_dataset( hda ) history.flush() - data.set_peek() - data.set_size() - data.flush() - trans.log_event("Added dataset %d to history %d" %(data.id, trans.history.id)) - return trans.show_ok_message("Dataset "+str(data.hid)+" added to history "+str(history_id)+".") + hda.set_peek() + hda.set_size() + hda.flush() + trans.log_event( "Added dataset id '%s' to history id '%s'." % ( str( hda.dataset_id ), str( history_id ) ) ) + return trans.show_ok_message( "Dataset id " + str( hda.dataset_id ) + " added to history id " + str( history_id ) + "." ) except: return trans.show_error_message("Adding File to History has Failed")

@@ -577,13 +571,11 @@ def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" try: - old_data = self.app.model.HistoryDatasetAssociation.get( id ) - new_data = old_data.copy() - ## new_data.parent = None - ## history = trans.app.model.History.get( old_data.history_id ) + old_hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + new_hda = old_hda.copy() history = trans.get_history() - history.add_dataset(new_data) - new_data.flush() + history.add_dataset( new_hda ) + new_hda.flush() return trans.show_message( "<p>Secondary dataset has been made primary.</p>", refresh_frames=['history'] ) except: return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) @@ -603,7 +595,7 @@ @web.expose def dataset_errors( self, trans, id=None, **kwd ): """View/fix errors associated with dataset""" - data = trans.app.model.HistoryDatasetAssociation.get( id ) + hda = trans.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() p = kwd if p.get("fix_errors", None): # launch tool to create new, (hopefully) error free dataset @@ -611,18 +603,19 @@ tool_params["tool_id"] = 'fix_errors' tool_params["runtool_btn"] = 'T' tool_params["input"] = id - tool_params["ext"] = data.ext + tool_params["ext"] = hda.ext # send methods selected - repair_methods = data.datatype.repair_methods( data ) + repair_methods = hda.datatype.repair_methods( hda ) methods = [] for method, description in repair_methods: - if method in p: methods.append(method) + if method in p: + methods.append( method ) tool_params["methods"] = ",".join(methods) url = "/tool_runner/index?" + urllib.urlencode(tool_params) trans.response.send_redirect(url) else: - history = trans.app.model.History.get( data.history_id ) - return trans.fill_template('dataset/validation.tmpl', data=data, history=history) + history = trans.app.model.History.get( hda.history_id ) + return trans.fill_template('dataset/validation.tmpl', data=hda, history=history)

# ---- Debug methods ----------------------------------------------------