def remove_table_from_database(config_file, table_name, alias, silent,
integrity_cancel):
""" Function removes a given table from a database
:param silent:
:param config_file:
:param table_name:
:param alias:
:return:
"""
_cfg, _tbl, _sil, _al = config_file, table_name, silent, alias
config, config_file = ConfigManager.confirm_config_set(config_file)
if alias != "None":
table_name = ConfigManager.get_name_by_alias(alias, config)
assert table_name is not None, TableNameAssertString.TABLE_NOT_FOUND
if not silent:
_remove_table_display_message_prelude(
config[ConfigKeys.DATABASES][ConfigKeys.db_name],
config[ConfigKeys.DATABASES][ConfigKeys.rel_work_dir], table_name,
alias)
cfg = ConfigManager(config, table_name)
engine = BaseData.get_engine(cfg.db_dir, cfg.db_name + ".db")
sess = BaseData.get_session_from_engine(engine)
TableClass = ClassManager.get_class_orm(table_name, engine)
UserClass = type(table_name, (Record, ), {})
mapper(UserClass, TableClass)
all_records = sess.query(UserClass).all()
for record in all_records:
if record:
print_if_not_silent(silent, " ..Removing record %s" % record._id)
try:
os.remove(record.full_path())
except OSError:
continue
TableClass.drop(engine)
cfg.remove_table_from_config_file(table_name)
os.remove(cfg.classes_file)
shutil.rmtree(cfg.table_dir)
if not silent:
_remove_columns_display_message_epilogue()
if not integrity_cancel:
integrity_check(_cfg, _tbl, _al, _sil)
def get_table(config_path, table_name=None, alias=None):
""" Primary method for users importing
:param config_path:
:param table_name:
:param alias:
:return:
"""
# Load config data from file
cfg, config_path = ConfigManager.confirm_config_set(config_path)
if alias:
table_name = ConfigManager.get_name_by_alias(alias, cfg)
config = ConfigManager(cfg, table_name)
# Get session to return
engine = BaseData.get_engine(config.db_dir, config.db_name + ".db")
sess = BaseData.get_session_from_engine(engine)
# Generate table class and name based on presence of alias
TableClass = ClassManager.get_class_orm(table_name, engine)
UserClass = type(table_name, (Record, ), {})
# Map to SQL orm
mapper(UserClass, TableClass)
return RecordList(sess, UserClass, config)
def summarize_database(config_file, view, query, table_name, alias, write,
write_tsv, unique):
""" Function will query all tables listed in the config file, outputting simple
metrics to the screen
:param config_file:
:param view:
:param query:
:param table_name:
:param alias:
:param write:
:param write_tsv:
:return:
"""
if not view:
if query != "None":
assert (query != "None"
and (table_name != "None" or alias != "None")
), SummarizeDBAssertString.QUERY_AND_TABLE_SET
assert not (table_name != "None" and alias != "None"
), SummarizeDBAssertString.ALIAS_OR_TABLE_ONLY
config, config_file = ConfigManager.confirm_config_set(config_file)
if not view.lower()[0] == "t":
_summarize_display_message_prelude(
config[ConfigKeys.DATABASES][ConfigKeys.db_name])
if alias != "None":
table_name = ConfigManager.get_name_by_alias(alias, config)
if table_name != "None" or alias != "None":
tables_in_database = (table_name, )
else:
tables_in_database = config[ConfigKeys.TABLES_TO_DB].keys()
if ("~>" in query) and ("->" in query):
assert table_name == 'None', "Query cannot contain '~>/->' statement with a table name"
matching_records = []
eval_sess, EvalClass, eval_cfg = load_table_metadata(
config, "evaluation")
eval_rl = RecordList(eval_sess,
EvalClass,
eval_cfg,
compute_metadata=False)
fxn_sess, FxnClass, fxn_cfg = load_table_metadata(config, "functions")
fxn_rl = RecordList(fxn_sess,
FxnClass,
fxn_cfg,
compute_metadata=False)
evaluation_query, block_1 = query.split("~>")
function_query, annotation_query = block_1.split("->")
if evaluation_query.replace(" ", "") != '':
eval_rl.query(evaluation_query)
else:
eval_rl.query()
if function_query.replace(" ", "") != '':
fxn_rl.query(function_query)
else:
fxn_rl.query()
for record in eval_rl:
if record in fxn_rl:
record_id = record._id.split(".")[0]
sess, UserClass, cfg = load_table_metadata(config, record_id)
annot_rl = RecordList(sess,
UserClass,
cfg,
compute_metadata=False)
_handle_query(annot_rl, annotation_query)
if write_tsv != 'None':
annot_rl.write_tsv(record_id + "." +
write_tsv.replace(".tsv", "") + ".tsv")
for record_2 in annot_rl:
matching_records.append(record_2)
if write_tsv == 'None' and write == 'None':
print(annot_rl.summarize())
if matching_records and write != "None":
rl = RecordList(compute_metadata=False,
records_list=matching_records)
rl.write_records(write)
return
if "~>" in query:
assert table_name == 'None', "Query cannot contain a '~>' statement with a table name"
matching_records = []
eval_sess, EvalClass, eval_cfg = load_table_metadata(
config, "evaluation")
eval_rl = RecordList(eval_sess,
EvalClass,
eval_cfg,
compute_metadata=False)
evaluation_query, annotation_query = query.split("~>")
if evaluation_query.replace(" ", "") != '':
eval_rl.query(evaluation_query)
else:
eval_rl.query()
for record in eval_rl:
record_id = record._id.split(".")[0]
sess, UserClass, cfg = load_table_metadata(config, record_id)
annot_rl = RecordList(sess, UserClass, cfg, compute_metadata=False)
_handle_query(annot_rl, annotation_query)
if write_tsv != 'None':
annot_rl.write_tsv(record_id + "." +
write_tsv.replace(".tsv", "") + ".tsv")
for record_2 in annot_rl:
matching_records.append(record_2)
if write_tsv == 'None' and write == 'None':
print(annot_rl.summarize())
if matching_records and write != "None":
rl = RecordList(compute_metadata=False,
records_list=matching_records)
rl.write_records(write)
return
if "->" in query:
assert table_name == 'None', "Query cannot contain a '->' statement with a table name"
matching_records = []
eval_sess, EvalClass, eval_cfg = load_table_metadata(
config, "functions")
eval_rl = RecordList(eval_sess,
EvalClass,
eval_cfg,
compute_metadata=False)
evaluation_query, annotation_query = query.split("->")
if evaluation_query.replace(" ", "") != '':
eval_rl.query(evaluation_query)
else:
eval_rl.query()
for record in eval_rl:
record_id = record._id.split(".")[0]
sess, UserClass, cfg = load_table_metadata(config, record_id)
annot_rl = RecordList(sess, UserClass, cfg, compute_metadata=False)
_handle_query(annot_rl, annotation_query)
if write_tsv != 'None':
annot_rl.write_tsv(record_id + "." +
write_tsv.replace(".tsv", "") + ".tsv")
for record_2 in annot_rl:
matching_records.append(record_2)
if write_tsv == 'None' and write == 'None':
print(annot_rl.summarize())
if matching_records and write != "None":
rl = RecordList(compute_metadata=False,
records_list=matching_records)
rl.write_records(write)
return
if ">>" in query:
assert table_name == 'None', "Query cannot contain a '>>' statement with a table name"
eval_sess, EvalClass, eval_cfg = load_table_metadata(
config, "evaluation")
eval_rl = RecordList(eval_sess,
EvalClass,
eval_cfg,
compute_metadata=False)
evaluation_query, annotation_query = query.split(">>")
if evaluation_query.replace(" ", "") != '':
eval_rl.query(evaluation_query)
else:
eval_rl.query()
sess, UserClass, cfg = load_table_metadata(config, "functions")
if len(eval_rl) > 0:
in_query = ""
for record in eval_rl:
in_query += "_id == '%s' OR " % record._id
annot_rl = RecordList(sess, UserClass, cfg, compute_metadata=False)
if annotation_query.replace(" ", "") != '':
annot_rl.query(annotation_query + " AND " + in_query[:-4])
else:
annot_rl.query(in_query[:-4])
if annot_rl is not None:
if write != "None":
annot_rl.write_records(write)
if write_tsv != "None":
annot_rl.write_tsv(write_tsv.replace(".tsv", "") + ".tsv")
if write_tsv == 'None' and write == 'None':
print(annot_rl.summarize())
else:
print(eval_rl.summarize())
return
if view == "None" and unique == 'None':
for tbl_name in tables_in_database:
# Display queried info for single table and break
if table_name == 'None' or table_name == tbl_name:
sess, UserClass, cfg = load_table_metadata(config, tbl_name)
annot_rl = RecordList(sess,
UserClass,
cfg,
compute_metadata=True)
_handle_query(annot_rl, query)
if len(annot_rl) > 1:
print(annot_rl.summarize())
elif len(annot_rl) == 1:
print(annot_rl[0])
for tbl_name in tables_in_database:
sess, UserClass, cfg = load_table_metadata(config, tbl_name)
annot_rl = RecordList(sess, UserClass, cfg)
# Display column info for table
if view.lower()[0] == "c":
# Display queried info for single table and break
# Do not need to query since only displaying columns
print(annot_rl.columns_summary())
elif view.lower()[0] == "t":
# Display queried info for single table and break
# Do not need to query since only displaying columns
print(annot_rl.table_name_summary())
if write != "None" and table_name == tbl_name:
_handle_query(annot_rl, query)
annot_rl.write_records(write)
if write_tsv != "None" and table_name == tbl_name:
_handle_query(annot_rl, query)
annot_rl.write_tsv(write_tsv)
if unique != 'None' and table_name == tbl_name:
_handle_query(annot_rl)
col_vals = set()
for record in annot_rl:
val = getattr(record, unique, "None")
if val:
col_vals.add(val)
col_vals = sorted(col_vals)
for val in col_vals:
print(val)