def _exec_many(self, sql_query, values):
"""Execute many sql statements
Notes
=====
- This is a private method, and so it is presumed whoever uses it knows what they are doing.
For this reason, it is not decorated with _not_if_read_only. It is therefore possible to write
to the DB using this method, even with self.read_only = True
"""
chunk_counter = 0
for chunk in get_list_in_chunks(values):
if anvio.DISPLAY_DB_CALLS:
header = f"MULTI SQL // {chunk_counter} of {len(values)} with {len(chunk)} {len(chunk)} entries"
self.run.warning(None, header=header, progress=self.progress, lc='yellow')
self.run.info_single(f"{sql_query}", nl_after=1, cut_after=None, level=0, mc='yellow')
sql_exec_timer = terminal.Timer()
self.cursor.executemany(sql_query, chunk)
if anvio.DISPLAY_DB_CALLS:
self.run.info("exec", f"{sql_exec_timer.time_elapsed()}", mc='yellow')
chunk_counter += 1
return True
def _fetchall(self, response, table_name):
"""Wrapper for fetchall"""
DISPLAY_DB_CALLS = False if table_name in self.tables_to_exclude_from_db_call_reports else anvio.DISPLAY_DB_CALLS
if DISPLAY_DB_CALLS:
sql_exec_timer = terminal.Timer()
results = response.fetchall()
if DISPLAY_DB_CALLS:
self.run.info("fetchall", f"{sql_exec_timer.time_elapsed()}", mc='yellow', nl_after=1)
return results
def process(self):
timer = terminal.Timer()
try:
self.load_pdb_db()
timer.make_checkpoint('PDB DB loaded')
self.run_fasta_to_pir()
timer.make_checkpoint('Converted gene FASTA to PIR')
self.check_database()
timer.make_checkpoint('Checked databases')
self.run_search_and_parse_results()
timer.make_checkpoint('Ran DIAMOND search and parsed hits')
self.get_structures()
timer.make_checkpoint('Obtained template structures')
self.run_align_to_templates(
self.list_of_template_code_and_chain_ids)
timer.make_checkpoint('Sequence aligned to templates')
self.run_get_model(self.num_models, self.deviation, self.very_fast)
timer.make_checkpoint('Ran structure predictions')
self.tidyup()
self.pick_best_model()
self.run_add_chain_identifiers_to_best_model()
timer.make_checkpoint('Picked best model and tidied up')
self.out["structure_exists"] = True
except self.EndModeller as e:
pass
except ModellerScriptError as e:
print(e)
finally:
timer.gen_report(title='ID %s Time Report' %
str(self.corresponding_gene_call),
run=self.run)
self.abort()
return self.out
def _exec(self, sql_query, value=None):
"""Execute an arbitrary sql statement
Notes
=====
- This is a private method, and so it is presumed whoever uses it knows what they are doing.
For this reason, it is not decorated with _not_if_read_only. It is therefore possible to write
to the DB using this method, even with self.read_only = True
"""
# this is an ugly workaround to not display DB calls if they involve talbes
# such as `self` or `sqlite_master` (comlete list in self.tables_to_exclude_from_db_call_reports).
# Otherwise when the user sets the `--display-db-calls` flag, the output is heavily
# dominated by queries to `self`. Even though Meren is implementing this sadness,
# Iva agreed to it as well. Just saying:
if any(table_name for table_name in self.tables_to_exclude_from_db_call_reports if f' {table_name} ' in sql_query):
DISPLAY_DB_CALLS = False
else:
DISPLAY_DB_CALLS = anvio.DISPLAY_DB_CALLS
if DISPLAY_DB_CALLS:
self.progress.reset()
self.run.warning(None, header='EXECUTING SQL', lc='yellow', nl_before=1)
self.run.info_single(f"{os.path.abspath(self.db_path)}", cut_after=None, level=0, mc='yellow', nl_after=1)
self.run.info_single(f"{sql_query}", cut_after=None, level=0, mc='yellow', nl_after=1)
sql_exec_timer = terminal.Timer()
if value:
ret_val = self.cursor.execute(sql_query, value)
else:
ret_val = self.cursor.execute(sql_query)
if DISPLAY_DB_CALLS:
self.run.info("exec", f"{sql_exec_timer.time_elapsed()}", mc='yellow')
self.commit()
return ret_val