def __initialize_finish(self):
# Finalize the the widget's initialization (preferably after
# ensuring all required databases have been downloaded.
sets = geneset.list_all()
taxids = set(taxonomy.common_taxids() +
list(filter(None, [tid for _, tid, _ in sets])))
organisms = [(tid, name_or_none(tid)) for tid in taxids]
organisms = [(tid, name) for tid, name in organisms
if name is not None]
organisms = [(None, "None")] + sorted(organisms)
taxids = [tid for tid, _ in organisms]
names = [name for _, name in organisms]
self.taxid_list = taxids
self.speciesComboBox.clear()
self.speciesComboBox.addItems(names)
self.genesets = sets
if self.taxid in self.taxid_list:
taxid = self.taxid
else:
taxid = self.taxid_list[0]
self.taxid = None
self.setCurrentOrganism(taxid)
self.setBlocking(False)
self.__state = OWSetEnrichment.Ready
self.setStatusMessage("")
def __initialize_finish(self):
# Finalize the the widget's initialization (preferably after
# ensuring all required databases have been downloaded.
sets = geneset.list_all()
taxids = set(taxonomy.common_taxids() +
list(filter(None, [tid for _, tid, _ in sets])))
organisms = [(tid, name_or_none(tid)) for tid in taxids]
organisms = [(tid, name) for tid, name in organisms
if name is not None]
organisms = [(None, "None")] + sorted(organisms)
taxids = [tid for tid, _ in organisms]
names = [name for _, name in organisms]
self.taxid_list = taxids
self.speciesComboBox.clear()
self.speciesComboBox.addItems(names)
self.genesets = sets
if self.taxid in self.taxid_list:
taxid = self.taxid
else:
taxid = self.taxid_list[0]
self.taxid = None
self.setCurrentOrganism(taxid)
self.setBlocking(False)
self.__state = OWSetEnrichment.Ready
self.setStatusMessage("")
# read the information from the local file
with open(localfile, 'rb') as f:
gds_info, excluded = pickle.load(f, encoding='latin1')
f.close()
except FileNotFoundError as e:
print('{} file on the server not found!'.format(GDS_INFO))
force_update = True
# if needed to refresh the data base
if force_update:
gds_info, excluded = ({}, {})
# list of common organisms may have changed, rescan excluded list
excluded = dict([(id, taxid) for id, taxid in excluded.items()
if taxid not in taxonomy.common_taxids()])
excluded.update([(id, info["taxid"]) for id, info in gds_info.items()
if info["taxid"] not in taxonomy.common_taxids()])
gds_info = dict([(id, info) for id, info in gds_info.items()
if info["taxid"] in taxonomy.common_taxids()])
# get the list of GDS files from NCBI directory
print("Retrieving ftp directory ...")
ftp = ftplib.FTP(FTP_NCBI)
ftp.login()
ftp.cwd(NCBI_DIR)
dirlist = []
ftp.dir(dirlist.append)
m = re.compile("GDS[0-9]*")
gds_names = [m.search(d).group(0) for d in dirlist if m.search(d)]
with open(localfile, 'rb') as f:
gds_info, excluded = pickle.load(f, encoding='latin1')
f.close()
except FileNotFoundError as e:
print('{} file on the server not found!'.format(GDS_INFO))
force_update = True
# if needed to refresh the data base
if force_update:
gds_info, excluded = ({}, {})
# list of common organisms may have changed, rescan excluded list
excluded = dict([(id, taxid) for id, taxid in excluded.items()
if taxid not in taxonomy.common_taxids()])
excluded.update([(id, info["taxid"]) for id, info in gds_info.items()
if info["taxid"] not in taxonomy.common_taxids()])
gds_info = dict([(id, info) for id, info in gds_info.items()
if info["taxid"] in taxonomy.common_taxids()])
# get the list of GDS files from NCBI directory
print("Retrieving ftp directory ...")
ftp = ftplib.FTP(FTP_NCBI)
ftp.login()
ftp.cwd(NCBI_DIR)
dirlist = []
ftp.dir(dirlist.append)
m = re.compile("GDS[0-9]*")
gds_names = [m.search(d).group(0) for d in dirlist if m.search(d)]
def setUp(self):
self.common_ids = taxonomy.common_taxids()
self.organisms = [(taxonomy.name(tax_id), tax_id) for tax_id in self.common_ids]
self.taxon = taxonomy.Taxonomy()
