def projects(project):
log = task.logger
conf = task.conf
projects_out_port = task.ports("projects_out")
log.info("--- [{0}] --------------------------------------------".format(project["id"]))
projdb = ProjectDb(project["db"])
total_samples = projdb.get_total_affected_samples()
if total_samples == 0:
log.warn("There are no samples, recurrences cannot be calculated.")
projdb.close()
return
log.info("Calculating project recurrences for variant genes ...")
projdb.compute_affected_genes_recurrences(total_samples)
if not conf.get("variants_only", False):
log.info("Calculating project recurrences for genes ...")
projdb.compute_gene_recurrences(total_samples)
log.info("Calculating project recurrences for pathways ...")
projdb.compute_pathway_recurrences(total_samples)
projdb.commit()
projdb.close()
projects_out_port.send(project)
