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The constructed YAML value from the name of the enumerated value.
""""""
# mypy doesn't like indexing to construct the enumeration.
return cls[node.value]"
153,"def is_error(self):
"""""" Checks to see if the job errored out. """"""
try:
if self._task.is_alive():
if len(self._task.stderr.readlines()) > 0:
self._task.join()
self._write_log()
return True
except AttributeError:
pass
return False"
154,"def add_splash_ids(splash_mapping_file_pth, conn, db_type='sqlite'):
"""""" Add splash ids to database (in case stored in a different file to the msp files like for MoNA)
Example:
>>> from msp2db.db import get_connection
>>> from msp2db.parse import add_splash_ids
>>> conn = get_connection('sqlite', 'library.db')
>>> add_splash_ids('splash_mapping_file.csv', conn, db_type='sqlite')
Args:
splash_mapping_file_pth (str): Path to the splash mapping file (needs to be csv format and have no headers,
should contain two columns. The first the accession number the second the splash.
e.g. AU100601, splash10-0a4i-1900000000-d2bc1c887f6f99ed0f74 \n
""""""
# get dictionary of accession and library_spectra_meta_id
cursor = conn.cursor()
cursor.execute(""SELECT id, accession FROM library_spectra_meta"")
accession_d = {row[1]: row[0] for row in cursor}
if db_type == 'sqlite':
type_sign = '?'
else:
type_sign = '%s'
rows = []
c = 0
# loop through splash mapping file
with open(splash_mapping_file_pth, ""r"") as f:
for line in f:
c+=1
line = line.rstrip()
line_l = line.split(',')
accession = line_l[0]
splash = line_l[1]
try:
aid = accession_d[accession]
except KeyError as e:
print(""can't find accession {}"".format(accession))
continue
row = (splash, aid)
rows.append(row)
if c > 200:
print(row)
cursor.executemany(""UPDATE library_spectra_meta SET splash = {t} WHERE id = {t} "".format(t=type_sign), rows)
conn.commit()
rows = []
c = 0
cursor.executemany(""UPDATE library_spectra_meta SET splash = {t} WHERE id = {t} "".format(t=type_sign), rows)
conn.commit()"
155,"def _get_current_ids(self, source=True, meta=True, spectra=True, spectra_annotation=True):
""""""Get the current id for each table in the database
Args:
source (boolean): get the id for the table ""library_spectra_source"" will update self.current_id_origin
meta (boolean): get the id for the table ""library_spectra_meta"" will update self.current_id_meta
spectra (boolean): get the id for the table ""library_spectra"" will update self.current_id_spectra
spectra_annotation (boolean): get the id for the table ""library_spectra_annotation"" will update
self.current_id_spectra_annotation
""""""
# get the cursor for the database connection
c = self.c
# Get the last uid for the spectra_info table
if source:
c.execute('SELECT max(id) FROM library_spectra_source')
last_id_origin = c.fetchone()[0]
if last_id_origin:
self.current_id_origin = last_id_origin + 1
else:
self.current_id_origin = 1
if meta:
c.execute('SELECT max(id) FROM library_spectra_meta')
last_id_meta = c.fetchone()[0]
if last_id_meta:
self.current_id_meta = last_id_meta + 1