def test_common_taxonomy(self):
self.assertGreater(len(taxonomy.common_taxids()), 0)
self.assertEqual(taxonomy.name(self.human), 'H**o sapiens')
self.assertEqual(taxonomy.name(self.dicty), 'Dictyostelium discoideum')
self.assertEqual(taxonomy.species_name_to_taxid('H**o sapiens'),
self.human)
self.assertEqual(
taxonomy.species_name_to_taxid('Dictyostelium discoideum'),
self.dicty)
self.assertGreater(len(taxonomy.shortname(self.human)), 0)
self.assertGreater(len(taxonomy.shortname(self.dicty)), 0)
def test_uncommon_taxonomy(self):
self.assertTrue(self.dog not in taxonomy.common_taxids())
self.assertEqual(taxonomy.name(self.dog), 'Canis lupus familiaris')
# not supported yet.
self.assertIsNone(
taxonomy.species_name_to_taxid('Canis lupus familiaris'))
self.assertFalse(len(taxonomy.shortname(self.dog)))
def create_model(self):
allkeys = set(self.allinfo_local)
if self.allinfo_remote is not None:
allkeys = allkeys | set(self.allinfo_remote)
allkeys = sorted(allkeys)
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(self._header_labels)
current_index = -1
for i, file_path in enumerate(allkeys):
data_info = self._parse_info(file_path)
row = []
for info_tag, header_setting in self.HEADER_SCHEMA:
item = QStandardItem()
try:
data = data_info.__getattribute__(info_tag)
except AttributeError:
# unknown tag in JSON
data = ''
# first column indicating cached data sets
if info_tag == 'islocal':
item.setData(' ' if data else '', Qt.DisplayRole)
item.setData(data_info, Qt.UserRole)
else:
# parse taxid to common name
if info_tag == 'taxid' and data in common_taxids():
data = shortname(data)[0].title()
if info_tag == 'tags':
data = ', '.join(data) if data else ''
item.setData(data, Qt.DisplayRole)
# set icon to Target column
if info_tag == 'target' and data:
item.setIcon(
Orange.widgets.data.owdatasets.variable_icon(data))
row.append(item)
model.appendRow(row)
if os.path.join(*file_path) == self.selected_id:
current_index = i
return model, current_index
def register_serverfiles(genesets):
""" Registers using the common hierarchy and organism. """
org = genesets.common_org()
hierarchy = genesets.common_hierarchy()
fn = filename(hierarchy, org)
file_path = os.path.join(DOMAIN_PATH, fn)
if org is not None:
taxname = taxonomy.name(org)
title = "Gene sets: " + ", ".join(hierarchy) + (
(" (" + taxname + ")") if org is not None else "")
tags = list(hierarchy) + ["gene sets"] + (
[taxname] if org is not None else []) + taxonomy.shortname(org)
genesets.to_gmt_file_format(file_path)
create_info_file(file_path, title=title, tags=tags)
def prepare_gene_sets_serverfiles():
Path('serverfiles/gene_sets/').mkdir(parents=True, exist_ok=True)
for file in list_files('data/gene_sets/'):
source_path = str(file.absolute())
dest_path = f'serverfiles/gene_sets/{file.name}'
shutil.copy2(source_path, dest_path)
hierarchy, tax_id = filename_parse(file.name)
title = f"Gene sets: {', '.join(hierarchy)} ({common_taxid_to_name(tax_id)})"
tags = list(hierarchy) + ['gene sets',
common_taxid_to_name(tax_id)
] + shortname(tax_id)
server_file = ServerFile(domain='gene_sets',
file_path=dest_path,
title=title,
description='',
tags=tags)
server_file.to_server_format()