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v1.7.6.1
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@Kinggerm
Kinggerm committed May 7, 2022
1 parent d105938 commit 0c17288
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Showing 4 changed files with 26 additions and 29 deletions.
26 changes: 20 additions & 6 deletions GetOrganelleLib/pipe_control_func.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,20 @@ def timed_log(log, output_base, prefix, log_level="NOTSET"):
return log_timed


def final_error_summary_log(log_handler, out_base, prefix, time0, graph_file="assembly_graph.fastg.*.fastg"):
log_handler = simple_log(log_handler, out_base, prefix=prefix + "get_org.")
log_handler.info("\nTotal cost " + "%.2f" % (time.time() - time0) + " s\n")
log_handler.info("#" * 30)
log_handler.info("For trouble-shooting, please ")
log_handler.info("Firstly, check https://github.com/Kinggerm/GetOrganelle/wiki/FAQ")
log_handler.info("Secondly, check if there are open/closed issues related at "
"https://github.com/Kinggerm/GetOrganelle/issues")
log_handler.info("If your problem was still not solved, "
"\n please open an issue at https://github.com/Kinggerm/GetOrganelle/issues"
"\n please provide the get_org.log.txt and the "
+ graph_file + " file(s) (can be visualized as *.png to protect your data privacy) if possible!")


if MAJOR_VERSION == 2:
class TimeoutError(Exception):
def __init__(self, value=""):
Expand Down Expand Up @@ -1117,10 +1131,10 @@ def get_current_db_versions(db_type, seq_db_path, lbl_db_path, clean_mode=True,
seed_f_hash != SEED_DB_HASH[db_version][og_type]["sha256"] or \
seed_f_hash != db_hash:
if log_handler:
log_handler.error(seed_f + " not damaged! "
log_handler.error(seed_f + " damaged! "
"Please run `get_organelle_config.py --clean` to reset!")
else:
sys.stdout.write(seed_f + " not damaged! "
sys.stdout.write(seed_f + " damaged! "
"Please run `get_organelle_config.py --clean` to reset!\n")
sys.exit()
if not clean_mode:
Expand Down Expand Up @@ -1162,10 +1176,10 @@ def get_current_db_versions(db_type, seq_db_path, lbl_db_path, clean_mode=True,
label_f_hash != LABEL_DB_HASH[db_version][og_type]["sha256"] or \
label_f_hash != db_hash:
if log_handler:
log_handler.error(label_f + " not damaged! "
log_handler.error(label_f + " damaged! "
"Please run `get_organelle_config.py --clean` to reset!")
else:
sys.stdout.write(label_f + " not damaged! "
sys.stdout.write(label_f + " damaged! "
"Please run `get_organelle_config.py --clean` to reset!\n")
sys.exit()
if not clean_mode:
Expand Down Expand Up @@ -1228,15 +1242,15 @@ def single_line_db_versions(existing_db, check_types, default_value="customized"
"0.0.1.minima":
{
"embplant_nr":
{"sha256": "603033541683b7c53fb63970c188eb2891844f6419eca342fa648f6ff5e29d71", "size": 16500},
{"sha256": "bf36ab074c3b020561e7211c0ae698290dc89276a96cf6ae42c093430d55e100", "size": 5435},
"embplant_pt":
{"sha256": "a38f3d65009c75aa00a13c8a737fb8390843409671d0e061d56d26b6b9c7ed14", "size": 88006},
"animal_mt":
{"sha256": "2d4e8f441a531cbee64d1514542edf3d158b2e1fcedccc15d32b7a3e9fa0a5a3", "size": 14483},
"fungus_mt":
{"sha256": "903e3a3c82aaedece3033218e0623caccabce3d58866d1577ecbfdf0d7115cca", "size": 20281},
"embplant_mt":
{"sha256": "f3621444441fbf4fa98835999b20e7ac1673a8866cb119707200412c46263570", "size": 148338},
{"sha256": "a8d78dfa5b8235af8038a3a292733e0799e9d67d146f05dc4d869fef5b0e6c15", "size": 40710},
"other_pt":
{"sha256": "62fb528edcd956ce605c9292063d3d7a0f168d36b6f4f114bb1050236622cc41", "size": 141269},
"fungus_nr":
Expand Down
3 changes: 2 additions & 1 deletion GetOrganelleLib/versions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,9 @@ def get_versions():
"features": [
"1. update the hash values of GetOrganelleDB v0.0.1.minima",
"2. get_organelle_config.py: fix a bug for malfunctioning --verbose",
"3. get_organelle_*.py: better log and fix typo"
],
"time": "2022-05-06 18:50 UTC-5"
"time": "2022-05-06 21:20 UTC-5"
},
{
"number": "1.7.6.0",
Expand Down
11 changes: 1 addition & 10 deletions get_organelle_from_assembly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1063,16 +1063,7 @@ def main():
log_handler.info("Thank you!")
except:
log_handler.exception("")
log_handler = simple_log(log_handler, options.output_base, prefix=options.prefix + "get_org.")
log_handler.info("\nTotal cost " + "%.2f" % (time.time() - time0) + " s")
log_handler.info("For trouble-shooting, please ")
log_handler.info("Firstly, check https://github.com/Kinggerm/GetOrganelle/wiki/FAQ")
log_handler.info("Secondly, check if there are open/closed issues related at "
"https://github.com/Kinggerm/GetOrganelle/issues")
log_handler.info("If your problem is still not solved, "
"\n please open an issue at https://github.com/Kinggerm/GetOrganelle/issues."
"\n please provide the get_org.log.txt "
"and the assembly graph (can be *.png to protect your data privacy) if possible!")
final_error_summary_log(log_handler, options.out_base, options.prefix, time0, "the slimmed_assembly_graph.*")
logging.shutdown()


Expand Down
15 changes: 3 additions & 12 deletions get_organelle_from_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4177,20 +4177,11 @@ def main():
log_handler = simple_log(log_handler, out_base, prefix=options.prefix + "get_org.")
log_handler.info("\nTotal cost " + "%.2f" % (time.time() - time0) + " s")
log_handler.info("Thank you!")
# except SystemExit:
# pass
except SystemExit:
final_error_summary_log(log_handler, out_base, options.prefix, time0)
except:
log_handler.exception("")
log_handler = simple_log(log_handler, out_base, prefix=options.prefix + "get_org.")
log_handler.info("\nTotal cost " + "%.2f" % (time.time() - time0) + " s")
log_handler.info("For trouble-shooting, please ")
log_handler.info("Firstly, check https://github.com/Kinggerm/GetOrganelle/wiki/FAQ")
log_handler.info("Secondly, check if there are open/closed issues related at "
"https://github.com/Kinggerm/GetOrganelle/issues")
log_handler.info("If your problem was still not solved, "
"\n please open an issue at https://github.com/Kinggerm/GetOrganelle/issues"
"\n please provide the get_org.log.txt "
"and the assembly graph (can be *.png to protect your data privacy) if possible!")
final_error_summary_log(log_handler, out_base, options.prefix, time0)
logging.shutdown()


Expand Down

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