def generate_report(model, scanned_par1, scanned_par2, outputdir, sim_plots_folder):
"""
The third pipeline step: report generation.
:param model: the model name
:param scanned_par1: the first scanned parameter
:param scanned_par2: the second scanned parameter
:param outputdir: the directory containing the report
:param sim_plots_folder: the folder containing the plots.
:return: no output
"""
if not os.path.exists(os.path.join(outputdir, sim_plots_folder)):
logger.error("input_dir " + os.path.join(outputdir, sim_plots_folder) +
" does not exist. Analyse the data first.")
return
logger.info("Generating a LaTeX report")
logger.info(model)
filename_prefix = "report__double_param_scan_"
latex_report_double_param_scan(outputdir, sim_plots_folder, filename_prefix,
model, scanned_par1, scanned_par2)
pdflatex = which("pdflatex")
if pdflatex is None:
logger.error("pdflatex not found! pdflatex must be installed for pdf reports.")
return
logger.info("Generating PDF report")
pdf_report(outputdir, filename_prefix + model + ".tex")
def main(argv=None):
# logging settings
home = os.path.expanduser("~")
if not os.path.exists(os.path.join(home, '.sb_pipe', 'logs')):
os.makedirs(os.path.join(home, '.sb_pipe', 'logs'))
# disable_existing_loggers=False to enable logging for Python third-party packages
fileConfig(os.path.join(SB_PIPE, 'logging_config.ini'),
defaults={'logfilename': os.path.join(home, '.sb_pipe', 'logs', 'sb_pipe_pydeps.log')},
disable_existing_loggers=False)
logger = logging.getLogger('sbpipe')
if which("CopasiSE") == None:
logger.error("CopasiSE not found. Please install Copasi as explained on the sb_pipe website.")
if which("R") == None:
logger.error("R not found. Skipping installation of R dependencies."
"sb_pipe will be severely affected due to this.")
python_deps(logger)
def python_deps(logger):
logger.info("Installing Python dependencies...")
if which("pip") == None:
logger.warn("pip not found. Skipping installation of Python dependencies."
"Please, install `python-dev` and `python-pip` packages.")
else:
out = install_python_deps(os.path.join(SB_PIPE, 'requirements.txt'))
logger.debug(out)
if (' ERROR:' in out or
' Error:' in out):
logger.error("Some error occurred when installing Python dependencies."
"Please check log files in logs/")
else:
logger.info("Python dependencies should have been installed correctly.")
def generate_report(model, outputdir, sim_plots_folder):
if not os.path.exists(os.path.join(outputdir, sim_plots_folder)):
logger.error("input_dir " + os.path.join(outputdir, sim_plots_folder) +
" does not exist. Analyse the data first.")
return
logger.info("Generating a LaTeX report")
filename_prefix="report__sensitivity_"
latex_report_simulate(outputdir, sim_plots_folder, model, filename_prefix)
pdflatex = which("pdflatex")
if pdflatex is None:
logger.error("pdflatex not found! pdflatex must be installed for pdf reports.")
return
logger.info("Generating PDF report")
pdf_report(outputdir, filename_prefix + model + ".tex")
def pdf_report(outputdir, filename):
"""
Generate a PDF report from LaTeX code
:param outputdir: the output directory
:param filename: the LaTeX file name
:return: no output
"""
pdflatex = which("pdflatex")
if pdflatex is None:
logger.error("pdflatex not found! pdflatex must be installed for pdf reports.")
return
currdir = os.getcwd()
os.chdir(outputdir)
logger.info(pdflatex + " -halt-on-error " + filename + " ... ")
p = subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=subprocess.PIPE)
p.communicate()[0]
p = subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=subprocess.PIPE)
p.communicate()[0]
os.chdir(currdir)
