details: http://www.bx.psu.edu/hg/galaxy/rev/20591fa0d05d changeset: 1542:20591fa0d05d user: Greg Von Kuster greg@bx.psu.edu date: Thu Oct 02 15:51:17 2008 -0400 description: Reverting to rev 1459.
1 file(s) affected in this change:
lib/galaxy/web/controllers/root.py
diffs (458 lines):
diff -r 993bed7b5e26 -r 20591fa0d05d lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 02 13:18:50 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 15:51:17 2008 -0400 @@ -21,7 +21,9 @@
@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 -----------------------------------------------------
@@ -66,10 +68,10 @@ @web.expose def dataset_state ( self, trans, id=None, stamp=None ): if id is not None: - try: - data = self.app.model.Dataset.get( id ) + try: + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return trans.show_error_message( "Unable to check dataset id %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) trans.response.headers['X-Dataset-State'] = data.state trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -80,13 +82,13 @@ @web.expose def dataset_code( self, trans, id=None, hid=None, stamp=None ): if id is not None: - try: - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + try: + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return trans.show_error_message( "Unable to check dataset id %s." % str( id ) ) + return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return trans.fill_template( "root/history_item.mako", data=hda.dataset, hid=hid ) + return trans.fill_template("root/history_item.mako", data=data, hid=hid) else: return trans.show_error_message( "Must specify a dataset id.")
@@ -101,11 +103,11 @@ ids = map( int, ids.split( "," ) ) states = states.split( "," ) for id, state in zip( ids, states ): - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda.dataset.state != state: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data.state != state: rval[id] = { - "state": hda.dataset.state, - "html": trans.fill_template( "root/history_item.mako", data=hda, hid=hda.hid ) + "state": data.state, + "html": trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ) } return rval
@@ -123,36 +125,36 @@ except: return "hid '%s' is invalid" %str( hid ) history = trans.get_history() - for hda in history.datasets: - if hda.hid == hid: - history_dataset_assoc = hda + for dataset in history.datasets: + if dataset.hid == hid: + data = dataset break else: - raise Exception( "History_dataset_association with hid '%s' does not exist." % str( hid ) ) + raise Exception( "No dataset with hid '%d'" % hid ) else: try: - history_dataset_assoc = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + data = self.app.model.HistoryDatasetAssociation.get( id ) except: - return "Dataset id '%s' is invalid." %str( id ) - if history_dataset_assoc: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( history_dataset_assoc.extension.lower() ) + return "Dataset id '%s' is invalid" %str( id ) + if data: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) if tofile: - fStat = os.stat(history_dataset_assoc.file_name) + fStat = os.stat(data.file_name) trans.response.headers['Content-Length'] = int(fStat.st_size) if toext[0:1] != ".": toext = "." + toext valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = history_dataset_assoc.name + fname = data.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (history_dataset_assoc.hid, fname, toext) - trans.log_event( "Display dataset id: '%s'." % str(id) ) + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) + trans.log_event( "Display dataset id: %s" % str(id) ) try: - return open( history_dataset_assoc.file_name ) + return open( data.file_name ) except: - return "Dataset id '%s' contains no content." % str( id ) + return "This dataset contains no content" else: - return "Dataset id '%s' does not exist." % str( id ) + return "No dataset with id '%s'" % str( id )
@web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"): @@ -160,36 +162,36 @@ Returns child data directly into the browser, based upon parent_id and designation. """ try: - hda = self.app.model.HistoryDatasetAssociation.get( parent_id ) - if hda: - child = hda.get_child_by_designation( designation ) + data = self.app.model.HistoryDatasetAssociation.get( parent_id ) + if data: + child = data.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 history_dataset_association id '%s'" % ( designation, str( parent_id ) ) + return "A child named %s could not be found for data %s" % ( designation, 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""" - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: - trans.response.set_content_type( hda.get_mime() ) + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: + trans.response.set_content_type(data.get_mime()) trans.log_event( "Formatted dataset id %s for display at %s" % ( str(id), display_app ) ) - return hda.as_display_type( display_app, **kwd ) + return data.as_display_type(display_app, **kwd) else: - return "Dataset 'id' %s does not exist." % str( id ) + return "No data with id=%d" % id
@web.expose def peek(self, trans, id=None): """Returns a 'peek' at the data""" - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: yield "<html><body><pre>" - yield hda.peek + yield data.peek yield "</pre></body></html>" else: - yield "Dataset 'id' %s does not exist." % str( id ) + yield "No data with id=%d" % id
@web.expose def edit(self, trans, id=None, hid=None, **kwd): @@ -197,75 +199,76 @@ if hid is not None: history = trans.get_history() # TODO: hid handling - hda = history.datasets[ int( hid ) - 1 ] + data = 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: - 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 ) ) ) + 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 ) ) )
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( hda, p.datatype ) + trans.app.datatypes_registry.change_datatype( data, p.datatype ) trans.app.model.flush() elif p.save: # The user clicked the Save button on the 'Edit Attributes' form - hda.name = p.name - hda.info = p.info + data.name = p.name + data.info = p.info
# The following for loop will save all metadata_spec items - for name, spec in hda.datatype.metadata_spec.items(): + for name, spec in data.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( hda.metadata, name, None ) + setattr(data.metadata,name,None) else: - setattr( hda.metadata, name, spec.unwrap( p.get( name, None ), p ) ) + setattr(data.metadata,name,spec.unwrap(p.get(name, None), p))
- hda.datatype.after_edit( hda ) + data.datatype.after_edit( data ) 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 hda.datatype.metadata_spec.items(): + for name, spec in data.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( hda.metadata, name, spec.unwrap( spec.get( 'default' ), spec ) ) - hda.datatype.set_meta( hda ) - hda.datatype.after_edit( hda ) + setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec )) + data.datatype.set_meta( data ) + data.datatype.after_edit( data ) 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 = hda.datatype.convert_dataset(trans, hda, target_type) + msg = data.datatype.convert_dataset(trans, data, target_type) return trans.show_ok_message( msg, refresh_frames=['history'] ) - hda.datatype.before_edit( hda ) + data.datatype.before_edit( data )
- if "dbkey" in hda.datatype.metadata_spec and not hda.metadata.dbkey: + if "dbkey" in data.datatype.metadata_spec and not data.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 - hda.metadata.dbkey = hda.dbkey + data.metadata.dbkey = data.dbkey metadata = list() # a list of MetadataParemeters - for name, spec in hda.datatype.metadata_spec.items(): + for name, spec in data.datatype.metadata_spec.items(): if spec.visible: - metadata.append( spec.wrap( hda.metadata.get( name ), hda ) ) + metadata.append( spec.wrap( data.metadata.get(name), data ) ) # 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 id '%s'" % str( id ) ) - return trans.fill_template( "/dataset/edit_attributes.mako", data=hda, metadata=metadata, datatypes=ldatatypes, err=None ) + 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 )
@web.expose def delete( self, trans, id = None, **kwd): @@ -280,21 +283,21 @@ int( id ) except: continue - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: - # Walk up parent hdas to find the containing history - topmost_parent = hda + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: + # Walk up parent datasets to find the containing history + topmost_parent = data 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 - hda.mark_deleted() - hda.clear_associated_files() + data.mark_deleted() + data.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id '%s' marked as deleted" % str( id ) ) - if hda.parent_id is None: + trans.log_event( "Dataset id %s marked as deleted" % str(id) ) + if data.parent_id is None: try: - self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) + self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return self.history( trans ) @@ -307,21 +310,21 @@ except: return "Dataset id '%s' is invalid" %str( id ) history = trans.get_history() - hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - if hda: + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data: # Walk up parent datasets to find the containing history - topmost_parent = hda + topmost_parent = data 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 - hda.mark_deleted() - hda.clear_associated_files() + data.mark_deleted() + data.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id '%s' marked as deleted async" % str( id ) ) - if hda.parent_id is None: + trans.log_event( "Dataset id %s marked as deleted async" % str(id) ) + if data.parent_id is None: try: - self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) + self.app.job_stop_queue.put( data.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return "OK" @@ -331,7 +334,8 @@ @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): @@ -363,16 +367,16 @@ 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 hda in history.datasets: - hda.deleted = True - hda.dataset.deleted = True - hda.clear_associated_files() + for dataset in history.datasets: + dataset.deleted = True + dataset.clear_associated_files() self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @@ -420,7 +424,9 @@ 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 ): @@ -546,23 +552,23 @@ """Adds a POSTed file to a History""" try: history = trans.app.model.History.get( history_id ) - 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" ) + 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" ) file_data.file.seek( 0 ) data_file.write( file_data.file.read() ) data_file.close() - hda.dataset.state = hda.dataset.states.OK - hda.init_meta() - hda.set_meta() - hda.flush() - history.add_dataset( hda ) + data.state = data.states.OK + data.init_meta() + data.set_meta() + data.flush() + history.add_dataset( data ) history.flush() - 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 ) + "." ) + 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)+".") except: return trans.show_error_message("Adding File to History has Failed")
@@ -570,11 +576,13 @@ def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" try: - old_hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() - new_hda = old_hda.copy() + 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 ) history = trans.get_history() - history.add_dataset( new_hda ) - new_hda.flush() + history.add_dataset(new_data) + new_data.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>" ) @@ -594,7 +602,7 @@ @web.expose def dataset_errors( self, trans, id=None, **kwd ): """View/fix errors associated with dataset""" - hda = trans.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + data = trans.app.model.HistoryDatasetAssociation.get( id ) p = kwd if p.get("fix_errors", None): # launch tool to create new, (hopefully) error free dataset @@ -602,19 +610,18 @@ tool_params["tool_id"] = 'fix_errors' tool_params["runtool_btn"] = 'T' tool_params["input"] = id - tool_params["ext"] = hda.ext + tool_params["ext"] = data.ext # send methods selected - repair_methods = hda.datatype.repair_methods( hda ) + repair_methods = data.datatype.repair_methods( data ) 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( hda.history_id ) - return trans.fill_template('dataset/validation.tmpl', data=hda, history=history) + history = trans.app.model.History.get( data.history_id ) + return trans.fill_template('dataset/validation.tmpl', data=data, history=history)
# ---- Debug methods ----------------------------------------------------