def build_report(): '''build report from scratch. Any existing report will be overwritten. ''' E.info("starting report build process from scratch") P.run_report(clean=True)
def build_report(): '''build report from scratch. Any existing report will be overwritten. Currently report function is not active for this pipeline ''' E.info("starting report build process from scratch") P.run_report(clean=True)
def update_report(): '''update report.''' E.info("Updating Mapping Reported") statement = '''cd mapping.dir; python %(pipelinedir)s/pipeline_mapping.py -v5 -p1 make update_report ''' E.info("updating report") P.run_report(clean=False)
def update_report(): '''update report. This will update a report with any changes inside the report document or code. Note that updates to the data will not cause relevant sections to be updated. Use the cgatreport-clean utility first. ''' E.info("updating report") P.run_report(clean=False)
def build_report(): '''build report from scratch.''' try: os.symlink(os.path.abspath("conf.py"), os.path.join(os.path.abspath("mapping.dir"), "conf.py")) except OSError as e: E.warning(str(e)) E.info("Running mapping report build from scratch") # statement = '''cd mapping.dir; # python %(scripts_dir)s/CGATPipelines/pipeline_mapping.py # -v5 -p1 make build_report ''' # P.run() E.info("starting report build process from scratch") P.run_report(clean=True)
def build_report(): '''build report from scratch.''' try: os.symlink(os.path.abspath("conf.py"), os.path.join( os.path.abspath("mapping.dir"), "conf.py")) except OSError as e: E.warning(str(e)) E.info("Running mapping report build from scratch") # statement = '''cd mapping.dir; # python %(scripts_dir)s/CGATPipelines/pipeline_mapping.py # -v5 -p1 make build_report ''' # P.run() E.info("starting report build process from scratch") P.run_report(clean = True)
def update_report(): """update report.""" E.info("updating documentation") P.run_report(clean=False)
def update_report(): """update report.""" E.info("updating report") P.run_report(clean=False)
def update_report(): '''update report.''' E.info("updating documentation") P.run_report(clean=False)
def update_report(): '''update report.''' E.info("updating report") P.run_report(clean=False)
def build_report(): '''build report from scratch.''' E.info("starting report build process from scratch") P.run_report(clean=True)
def build_report(): """build report from scratch.""" E.info("starting documentation build process from scratch") P.run_report(clean=True)
# Generic pipeline tasks @follows(xxx) def full(): pass ################################################################## # --------------------------------------------------- # Generic pipeline tasks for CGATReport: @follows(mkdir("report")) def build_report(): '''build report from scratch. Any existing report will be overwritten.''' E.info("starting report build process from scratch") P.run_report(clean=True) @follows(mkdir("report")) def update_report(): '''update report. This will update a report with any changes inside the report document or code. Note that updates to the data will not cause relevant sections to be updated. Use the cgatreport-clean utility first. ''' E.info("updating report") P.run_report(clean=False) @follows(update_report)