From 0c17288a1afe6e65cf745b47405d78759fe5a1b1 Mon Sep 17 00:00:00 2001 From: Kinggerm Date: Fri, 6 May 2022 21:18:31 -0400 Subject: [PATCH] v1.7.6.1 --- GetOrganelleLib/pipe_control_func.py | 26 ++++++++++++++++++++------ GetOrganelleLib/versions.py | 3 ++- get_organelle_from_assembly.py | 11 +---------- get_organelle_from_reads.py | 15 +++------------ 4 files changed, 26 insertions(+), 29 deletions(-) diff --git a/GetOrganelleLib/pipe_control_func.py b/GetOrganelleLib/pipe_control_func.py index 829fe1c..9e763dc 100755 --- a/GetOrganelleLib/pipe_control_func.py +++ b/GetOrganelleLib/pipe_control_func.py @@ -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=""): @@ -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: @@ -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: @@ -1228,7 +1242,7 @@ 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": @@ -1236,7 +1250,7 @@ def single_line_db_versions(existing_db, check_types, default_value="customized" "fungus_mt": {"sha256": "903e3a3c82aaedece3033218e0623caccabce3d58866d1577ecbfdf0d7115cca", "size": 20281}, "embplant_mt": - {"sha256": "f3621444441fbf4fa98835999b20e7ac1673a8866cb119707200412c46263570", "size": 148338}, + {"sha256": "a8d78dfa5b8235af8038a3a292733e0799e9d67d146f05dc4d869fef5b0e6c15", "size": 40710}, "other_pt": {"sha256": "62fb528edcd956ce605c9292063d3d7a0f168d36b6f4f114bb1050236622cc41", "size": 141269}, "fungus_nr": diff --git a/GetOrganelleLib/versions.py b/GetOrganelleLib/versions.py index dd8bd44..8d0f530 100644 --- a/GetOrganelleLib/versions.py +++ b/GetOrganelleLib/versions.py @@ -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", diff --git a/get_organelle_from_assembly.py b/get_organelle_from_assembly.py index 6d8f4c2..8949c2d 100755 --- a/get_organelle_from_assembly.py +++ b/get_organelle_from_assembly.py @@ -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() diff --git a/get_organelle_from_reads.py b/get_organelle_from_reads.py index 1e6b461..53775cc 100755 --- a/get_organelle_from_reads.py +++ b/get_organelle_from_reads.py @@ -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()