From 661c967ada4dd5900dd926cb78c6e5d8b076a8f1 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 31 Mar 2009 01:33:27 +0000 Subject: [PATCH] Use the image directory name to detect what type of image dir we have, firecrest or ipar. Also remove the pesky return that was preventing --extract-results from actually generating the compressed eland files. And finally change some of the logging to logging.info instead of debug as there wasn't currently a way to generate logging.debug messages. --- htsworkflow/pipelines/runfolder.py | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index 5d663b3..097a617 100644 --- a/htsworkflow/pipelines/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -232,16 +232,27 @@ def get_specific_run(gerald_dir): runfolder_dir = os.path.abspath(os.path.join(image_dir, '..','..')) - logging.debug('--- use-run detected options ---') - logging.debug('runfolder: %s' % (runfolder_dir,)) - logging.debug('image_dir: %s' % (image_dir,)) - logging.debug('bustard_dir: %s' % (bustard_dir,)) - logging.debug('gerald_dir: %s' % (gerald_dir,)) + logging.info('--- use-run detected options ---') + logging.info('runfolder: %s' % (runfolder_dir,)) + logging.info('image_dir: %s' % (image_dir,)) + logging.info('bustard_dir: %s' % (bustard_dir,)) + logging.info('gerald_dir: %s' % (gerald_dir,)) # find our processed image dir - image_run = ipar.ipar(image_dir) - if image_run is None: + image_run = None + # split into parent, and leaf directory + # leaf directory should be an IPAR or firecrest directory + data_dir, short_image_dir = os.path.split(image_dir) + logging.info('data_dir: %s' % (data_dir,)) + logging.info('short_iamge_dir: %s' %(short_image_dir,)) + + # guess which type of image processing directory we have by looking + # in the leaf directory name + if re.search('Firecrest', short_image_dir, re.IGNORECASE) is not None: image_run = firecrest.firecrest(image_dir) + elif re.search('IPAR', short_image_dir, re.IGNORECASE) is not None: + image_run = ipar.ipar(image_dir) + # if we din't find a run, report the error and return if image_run is None: msg = '%s does not contain an image processing step' % (image_dir,) logging.error(msg) @@ -373,8 +384,6 @@ def extract_results(runs, output_base_dir=None): # save run file r.save(cycle_dir) - return - # Copy Summary.htm summary_path = os.path.join(r.gerald.pathname, 'Summary.htm') if os.path.exists(summary_path): -- 2.30.2