From 40d89888538e569715ff3315bdc972237e392e1a Mon Sep 17 00:00:00 2001 From: Brandon King Date: Tue, 4 Dec 2007 19:59:33 +0000 Subject: [PATCH] [project @ Config Step: Detect missing cycles patch] * Now detects error case of missing cycles and reports a more meaningful error message in the error log. It also records a copy of the original error message and then suppresses the remaining error message of this type. --- gaworkflow/pipeline/configure_run.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gaworkflow/pipeline/configure_run.py b/gaworkflow/pipeline/configure_run.py index 8bcf6a9..a0d8c33 100644 --- a/gaworkflow/pipeline/configure_run.py +++ b/gaworkflow/pipeline/configure_run.py @@ -126,6 +126,9 @@ s_stderr_taskcomplete = re.compile('^Task complete, exiting') s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py') s_species_dir_err = re.compile('Error: Lane [1-8]:') s_goat_traceb = re.compile("^Traceback \(most recent call last\):") +s_missing_cycles = re.compile('^Error: Tile s_[1-8]_[0-9]+: Different number of cycles: [0-9]+ instead of [0-9]+') + +SUPPRESS_MISSING_CYCLES = False ##Ignore - Example of out above each ignore regex. @@ -260,6 +263,7 @@ def config_stderr_handler(line, conf_info): False if neutral message (i.e. doesn't signify failure or success) """ + global SUPPRESS_MISSING_CYCLES # Detect invalid species directory error if s_species_dir_err.search(line): @@ -273,6 +277,16 @@ def config_stderr_handler(line, conf_info): elif s_stderr_taskcomplete.search(line): logging.info('Configure step successful (from: stderr)') return True + # Detect missing cycles + elif s_missing_cycles.search(line): + + # Only display error once + if not SUPPRESS_MISSING_CYCLES: + logging.error("Missing cycles detected; Not all cycles copied?") + logging.debug("CONF:STDERR:MISSING_CYCLES: %s" % (line)) + SUPPRESS_MISSING_CYCLES = True + return RUN_ABORT + # Log all other output as debug output else: logging.debug('CONF:STDERR:?: %s' % (line)) -- 2.30.2