def refreshJobs(self, button_refresh=None, data=None, update_job_info=None):
"""
2009-11-10
split out of on_button_refresh_clicked()
"""
if self.backend_ins is None:
sys.stderr.write("Backend is not selected yet! Select one.\n")
return False # 2009-11-10 to stop the timeout
update_node_info = self.checkbutton_update_node_info.get_active()
if update_job_info is None: #if it's none, get it from the checkbutton
update_job_info = self.checkbutton_update_job_info.get_active()
username = self.entry_username.get_text()
jobs_since = self.entry_jobs_since.get_text()
jobs_since = datetime.strptime(jobs_since, '%Y-%m-%d %H:%M')
only_running = self.checkbutton_running.get_active()
"""
real_node_range = self.parse_node_range(self.entry_node_range.get_text())
node2ps = self.node_process_instance.get_processes(real_node_range, self.ps_command, username, self.tmp_fname)
if node2ps=={}:
sys.stderr.write("No process data fetched.\n")
return
if self.no_of_refreshes == 0:
#extra work is needed in the first refresh
self.create_columns(node2ps.values()[0].label_list)
self.liststore = gtk.ListStore(str, str, str, str, str, str, str, str, str) #nine columns
for node in node2ps:
for ps_output in node2ps[node].ps_output_list:
if len(ps_output)==8: #cmd is not null
self.liststore.append([node]+ps_output)
"""
yh_gnome.create_columns(self.treeview1, self.backend_ins.display_job_label_ls)
self.liststore = gtk.ListStore(*self.backend_ins.display_job_label_type_ls)
list_2d = self.backend_ins.refresh(username, update_node_info, jobs_since, only_running, \
update_job_info=update_job_info)
yh_gnome.fill_treeview(self.treeview1, self.liststore, list_2d, reorderable=True, multi_selection=True)
"""
# set the TreeView mode to be liststore
self.treeview1.set_model(self.liststore)
for i in range(len(ps_output)+1):
# make it searchable
self.treeview1.set_search_column(i)
# Allow drag and drop reordering of rows
self.treeview1.set_reorderable(True)
#setting the selection mode
self.treeselection.set_mode(gtk.SELECTION_MULTIPLE)
"""
self.no_of_refreshes += 1
return True #2009-11-10 return True in order for the timeout to continue
def canvas_diff_matrix_item_event(self, widget, event=None):
"""
2009-5-19
when an entry in the canvas of diff matrix is selected, fill up the treeview_diff_details with details (which accession, which SNP etc.)
"""
if event.type == gtk.gdk.BUTTON_PRESS:
if event.button == 1:
previous_selected_item = self.canvas_diff_matrix.get_data(
'item_selected')
if previous_selected_item != None:
previous_selected_item.set(
fill_color='black'
) #change the previous selected widget color back to black
widget.set(fill_color='red'
) #change the current selected widget color to red
self.canvas_diff_matrix.set_data(
'item_selected',
widget) #remember the current selected widget
widget_name = widget.get_data('name')
self.app1_appbar1.push(widget_name)
yh_gnome.create_columns(
self.treeview_diff_details,
["row-id1", "col-id1", "nt1", "row-id2", "col-id2", "nt2"])
liststore_diff_details = gtk.ListStore(str, str, str, str, str,
str)
diff_code_pair = widget.get_data('diff_code_pair')
diff_details_ls = self.diff_code_pair2diff_details_ls.get(
diff_code_pair)
if diff_details_ls is None:
diff_details_ls = []
list_2d = []
for row in diff_details_ls:
list_2d.append(row)
yh_gnome.fill_treeview(self.treeview_diff_details,
liststore_diff_details,
list_2d,
reorderable=True)
return True
elif event.type == gtk.gdk.ENTER_NOTIFY:
# Make the outline heavy
widget.set_data('original_weight', widget.get_property('weight'))
widget.set(weight=1200)
return True
elif event.type == gtk.gdk.LEAVE_NOTIFY:
# Make the outline light
original_weight = widget.get_data('original_weight')
widget.set(weight=original_weight)
return True
return False
def displayQueueWindow(self):
"""
2010-5-25
display the node_queue_app
split out of on_menuitem_show_node_q_window_activate() to avoid looping.
"""
if self.backend_ins is None:
sys.stderr.write("Backend is not selected yet! Select one.\n")
return False # 2009-11-10 to stop the timeout
yh_gnome.create_columns(self.treeview_node_queue, self.backend_ins.display_node_label_ls)
self.liststore_node_queue = gtk.ListStore(*self.backend_ins.display_node_label_type_ls)
list_2d = self.backend_ins.returnQueueNodeInfo()
yh_gnome.fill_treeview(self.treeview_node_queue, self.liststore_node_queue, list_2d, reorderable=True, multi_selection=True)
self.node_queue_app.show_all()
def show_nodes_of_this_job(self, widget, event=None, data=None):
"""
2008-11-06
fill in the treeview_nodes
execute upon clicking the 'show nodes' in the popup menu
"""
if self.backend_ins is None:
sys.stderr.write("Backend is not selected yet! Select one.\n")
return
yh_gnome.create_columns(self.treeview_nodes, self.backend_ins.display_node_label_ls)
self.liststore_nodes = gtk.ListStore(*self.backend_ins.display_node_label_type_ls)
job_id_ls = self.get_selected_job_id_ls()
list_2d = self.backend_ins.returnNodeInfoGivenJobs(job_id_ls)
yh_gnome.fill_treeview(self.treeview_nodes, self.liststore_nodes, list_2d, reorderable=True, multi_selection=True)
def canvas_diff_matrix_item_event(self, widget, event=None):
"""
2009-5-19
when an entry in the canvas of diff matrix is selected, fill up the treeview_diff_details with details (which accession, which SNP etc.)
"""
if event.type == gtk.gdk.BUTTON_PRESS:
if event.button == 1:
previous_selected_item = self.canvas_diff_matrix.get_data('item_selected')
if previous_selected_item != None:
previous_selected_item.set(fill_color='black') #change the previous selected widget color back to black
widget.set(fill_color='red') #change the current selected widget color to red
self.canvas_diff_matrix.set_data('item_selected', widget) #remember the current selected widget
widget_name = widget.get_data('name')
self.app1_appbar1.push(widget_name)
yh_gnome.create_columns(self.treeview_diff_details, ["row-id1", "col-id1", "nt1", "row-id2", "col-id2", "nt2"])
liststore_diff_details = gtk.ListStore(str, str, str, str, str, str)
diff_code_pair = widget.get_data('diff_code_pair')
diff_details_ls = self.diff_code_pair2diff_details_ls.get(diff_code_pair)
if diff_details_ls is None:
diff_details_ls = []
list_2d = []
for row in diff_details_ls:
list_2d.append(row)
yh_gnome.fill_treeview(self.treeview_diff_details, liststore_diff_details, list_2d, reorderable=True)
return True
elif event.type == gtk.gdk.ENTER_NOTIFY:
# Make the outline heavy
widget.set_data('original_weight', widget.get_property('weight'))
widget.set(weight=1200)
return True
elif event.type == gtk.gdk.LEAVE_NOTIFY:
# Make the outline light
original_weight = widget.get_data('original_weight')
widget.set(weight=original_weight)
return True
return False
def on_button_input_run_clicked(self, widget, event=None, data=None):
"""
2009-5-18
add one more column: row category from dataset1
2008-02-06
fix a bug. self.class_chosen could be 0
"""
if self.class_chosen!=None:
self.hostname = self.entry_hostname.get_text()
self.dbname = self.entry_dbname.get_text()
self.schema = self.entry_schema.get_text()
import MySQLdb
self.conn = MySQLdb.connect(db=self.dbname,host=self.hostname)
self.curs = self.conn.cursor()
self.input_fname1 = os.path.expanduser(self.entry_1st_input_fname.get_text())
self.input_fname2 = os.path.expanduser(self.entry_2nd_input_fname.get_text())
self.ecotype_table = self.entry_ecotype_table.get_text()
self.ecotype2accession_table = self.entry_ecotype2accession_table.get_text()
self.diff_details_table = self.entry_diff_details_table.get_text()
self.qc_cross_match_table = self.entry_qc_cross_match_table.get_text()
self.latex_output_fname = os.path.expanduser(self.entry_latex_output_fname.get_text())
if self.qc_class_ins!=None:
del self.qc_class_ins #release memory (maybe it works by 'del')
self.qc_class_ins = None
if self.class_chosen == 2:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](self.curs, self.input_fname1, self.input_fname2, \
self.latex_output_fname, self.ecotype2accession_table, \
self.diff_details_table, self.qc_cross_match_table)
elif self.class_chosen==0:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](curs=self.curs, input_fname1=self.input_fname1, input_fname2=self.input_fname2)
else:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](self.curs, self.input_fname1, self.input_fname2)
self.qc_class_ins.load_dstruc()
if self.qc_class_ins.header1[0]:
dataset1_row_id = self.qc_class_ins.header1[0]
else:
dataset1_row_id = 'dataset1 row id'
if self.qc_class_ins.header1[1]:
dataset1_row_category = self.qc_class_ins.header1[1]
else:
dataset1_row_category = 'dataset1 row category'
if self.qc_class_ins.header2[0]:
dataset2_row_id = self.qc_class_ins.header2[0]
else:
dataset2_row_id = 'dataset2 row id'
if self.qc_class_ins.header2[1]:
dataset2_row_category = self.qc_class_ins.header2[1]
else:
dataset2_row_category = 'dataset2 row category'
yh_gnome.create_columns(self.treeview_strains1, ['Index', dataset1_row_id, dataset1_row_category, dataset2_row_id, dataset2_row_category])
self.strain_index2row_id1 = {}
self.liststore_strains1 = gtk.ListStore(int, str, str, str, str)
strain_acc_list1_2d = [[0, 'ALL', '', '', '']]
self.strain_index2row_id1[0] = 'ALL'
row_id22category = {} #row_id2 's category offers some info on row_id2
for row_id2, row_index2 in self.qc_class_ins.row_id2row_index2.iteritems():
row_id22category[row_id2] = self.qc_class_ins.category_list2[row_index2]
row_id12category = {}
for row_id1, row_index1 in self.qc_class_ins.row_id2row_index1.iteritems():
row_id12category[row_id1] = self.qc_class_ins.category_list1[row_index1]
strain_index = len(self.strain_index2row_id1) #starting from 1
for row_id1, row_id2 in self.qc_class_ins.row_id12row_id2.iteritems():
if row_id2 in row_id22category:
row_id2_category = row_id22category[row_id2]
else:
row_id2_category = ''
if row_id1 in row_id12category:
row_id1_category = row_id12category[row_id1]
else:
row_id1_category = ''
strain_acc_list1_2d.append([strain_index, repr(row_id1), repr(row_id1_category), repr(row_id2), row_id2_category])
self.strain_index2row_id1[strain_index] = row_id1
strain_index += 1
yh_gnome.fill_treeview(self.treeview_strains1, self.liststore_strains1, strain_acc_list1_2d, reorderable=True)
"""
#2008-01-24
yh_gnome.create_columns(self.treeview_strains2, [self.qc_class_ins.header2[0], self.qc_class_ins.header2[1]])
self.liststore_strains2 = gtk.ListStore(str, str)
strain_acc_list2_2d = [['ALL', '']]
for i in range(len(self.qc_class_ins.strain_acc_list2)):
strain_acc_list2_2d.append([self.qc_class_ins.strain_acc_list2[i], self.qc_class_ins.category_list2[i]])
yh_gnome.fill_treeview(self.treeview_strains2, self.liststore_strains2, strain_acc_list2_2d, reorderable=True)
"""
self.app_input_appbar.push("Check the other window for available strains.")
self.app1.show_all()
else:
self.app_input_appbar.push("Error: Can't Run cuz No Class Chosen!")
def on_button_input_run_clicked(self, widget, event=None, data=None):
"""
2009-5-18
add one more column: row category from dataset1
2008-02-06
fix a bug. self.class_chosen could be 0
"""
if self.class_chosen != None:
self.hostname = self.entry_hostname.get_text()
self.dbname = self.entry_dbname.get_text()
self.schema = self.entry_schema.get_text()
import MySQLdb
self.conn = MySQLdb.connect(db=self.dbname, host=self.hostname)
self.curs = self.conn.cursor()
self.input_fname1 = os.path.expanduser(
self.entry_1st_input_fname.get_text())
self.input_fname2 = os.path.expanduser(
self.entry_2nd_input_fname.get_text())
self.ecotype_table = self.entry_ecotype_table.get_text()
self.ecotype2accession_table = self.entry_ecotype2accession_table.get_text(
)
self.diff_details_table = self.entry_diff_details_table.get_text()
self.qc_cross_match_table = self.entry_qc_cross_match_table.get_text(
)
self.latex_output_fname = os.path.expanduser(
self.entry_latex_output_fname.get_text())
if self.qc_class_ins != None:
del self.qc_class_ins #release memory (maybe it works by 'del')
self.qc_class_ins = None
if self.class_chosen == 2:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](self.curs, self.input_fname1, self.input_fname2, \
self.latex_output_fname, self.ecotype2accession_table, \
self.diff_details_table, self.qc_cross_match_table)
elif self.class_chosen == 0:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](
curs=self.curs,
input_fname1=self.input_fname1,
input_fname2=self.input_fname2)
else:
self.qc_class_ins = self.qc_class_dict[self.class_chosen](
self.curs, self.input_fname1, self.input_fname2)
self.qc_class_ins.load_dstruc()
if self.qc_class_ins.header1[0]:
dataset1_row_id = self.qc_class_ins.header1[0]
else:
dataset1_row_id = 'dataset1 row id'
if self.qc_class_ins.header1[1]:
dataset1_row_category = self.qc_class_ins.header1[1]
else:
dataset1_row_category = 'dataset1 row category'
if self.qc_class_ins.header2[0]:
dataset2_row_id = self.qc_class_ins.header2[0]
else:
dataset2_row_id = 'dataset2 row id'
if self.qc_class_ins.header2[1]:
dataset2_row_category = self.qc_class_ins.header2[1]
else:
dataset2_row_category = 'dataset2 row category'
yh_gnome.create_columns(self.treeview_strains1, [
'Index', dataset1_row_id, dataset1_row_category,
dataset2_row_id, dataset2_row_category
])
self.strain_index2row_id1 = {}
self.liststore_strains1 = gtk.ListStore(int, str, str, str, str)
strain_acc_list1_2d = [[0, 'ALL', '', '', '']]
self.strain_index2row_id1[0] = 'ALL'
row_id22category = {
} #row_id2 's category offers some info on row_id2
for row_id2, row_index2 in self.qc_class_ins.row_id2row_index2.iteritems(
):
row_id22category[row_id2] = self.qc_class_ins.category_list2[
row_index2]
row_id12category = {}
for row_id1, row_index1 in self.qc_class_ins.row_id2row_index1.iteritems(
):
row_id12category[row_id1] = self.qc_class_ins.category_list1[
row_index1]
strain_index = len(self.strain_index2row_id1) #starting from 1
for row_id1, row_id2 in self.qc_class_ins.row_id12row_id2.iteritems(
):
if row_id2 in row_id22category:
row_id2_category = row_id22category[row_id2]
else:
row_id2_category = ''
if row_id1 in row_id12category:
row_id1_category = row_id12category[row_id1]
else:
row_id1_category = ''
strain_acc_list1_2d.append([
strain_index,
repr(row_id1),
repr(row_id1_category),
repr(row_id2), row_id2_category
])
self.strain_index2row_id1[strain_index] = row_id1
strain_index += 1
yh_gnome.fill_treeview(self.treeview_strains1,
self.liststore_strains1,
strain_acc_list1_2d,
reorderable=True)
"""
#2008-01-24
yh_gnome.create_columns(self.treeview_strains2, [self.qc_class_ins.header2[0], self.qc_class_ins.header2[1]])
self.liststore_strains2 = gtk.ListStore(str, str)
strain_acc_list2_2d = [['ALL', '']]
for i in range(len(self.qc_class_ins.strain_acc_list2)):
strain_acc_list2_2d.append([self.qc_class_ins.strain_acc_list2[i], self.qc_class_ins.category_list2[i]])
yh_gnome.fill_treeview(self.treeview_strains2, self.liststore_strains2, strain_acc_list2_2d, reorderable=True)
"""
self.app_input_appbar.push(
"Check the other window for available strains.")
self.app1.show_all()
else:
self.app_input_appbar.push("Error: Can't Run cuz No Class Chosen!")