]) # get useful logs artifacts = f"{workdir}/artifacts/" logs_list = [ "/var/log/daemon.log", "/var/log/debug", "/var/log/middlewared.log", "/var/log/messages", "/var/log/syslog", ] if not os.path.exists(artifacts): os.makedirs(artifacts) for log in logs_list: get_file(log, artifacts, 'root', 'testing', ip) # get dmesg and put it in artifacts dmesg_option = '' if scale else ' -a' results = SSH_TEST(f'dmesg{dmesg_option}', 'root', 'testing', ip) dmsg = open(f'{artifacts}/dmesg', 'w') dmsg.writelines(results['output']) dmsg.close() # get core.get_jobs and put it in artifacts results = SSH_TEST('midclt call core.get_jobs | jq .', 'root', 'testing', ip) dmsg = open(f'{artifacts}/core.get_jobs', 'w') dmsg.writelines(results['output']) dmsg.close()
def home(): if request.method == "POST": url = request.form['url'] type_ = request.form['type'] get_file(url, type_) return render_template("home.html")
call(["py.test-3.6", "-v", "--junitxml", f"{results_xml}{i}_tests_result.xml"] + ( ["-k", testexpr] if testexpr else [] ) + [f"api2/{i}.py"]) # get useful logs artifacts = f"{workdir}/artifacts/{api}" logs_list = [ "/var/log/middlewared.log", "/var/log/messages", "/var/log/debug.log", "/var/log/console.log" ] if not path.exists(artifacts): makedirs(artifacts) for log in logs_list: get_file(log, artifacts, 'root', 'testing', ip) # get dmesg and put it in artifacs results = SSH_TEST('dmesg -a', 'root', 'testing', ip) dmsg = open(f'{artifacts}/dmesg', 'w') dmsg.writelines(results['output']) dmsg.close() # get core.get_jobs and put it in artifacs results = SSH_TEST('midclt call core.get_jobs | jq .', 'root', 'testing', ip) dmsg = open(f'{artifacts}/core_get_job', 'w') dmsg.writelines(results['output']) dmsg.close()
#---------------- elif x == 'help': logging.debug("print 'help_list'\n") print(help_list) #---------------- elif x == 'clear': logging.debug("refresh window\n") os.system('cls') print('=' * 64 + f"\n{title}\n" + '=' * 64) #---------------- elif 'load' in x: if 'from' in x: status_file = functions.get_file(x) else: status_file = 'status file.CSV' if change == True: print( "The function 'load' is block, because in this session status was changed!" ) else: if os.path.isfile(status_file) == True: if change == True: print("Warehouse status is changed!") if functions.confirm_choice() == True: logging.debug(f"loading data form {status_file}")
# write the integrated file integrated_coverage_file = "%s/genes_and_regions_coverage.tab"%cnv_outdir; integrated_coverage_file_tmp = "%s.tmp"%integrated_coverage_file if fun.file_is_empty(integrated_coverage_file) or opt.replace_cnv is True or opt.replace is True: # integrate in one df_genes = pd.read_csv(gene_to_coverage_file, sep="\t") df_regions = pd.read_csv(gene_to_coverage_file_regions, sep="\t") df_integrated = df_genes.merge(df_regions, on="ID", validate="one_to_one", suffixes=("", "_+-10kb_region")) # write df_integrated.to_csv(integrated_coverage_file_tmp, sep="\t", header=True, index=False) os.rename(integrated_coverage_file_tmp, integrated_coverage_file) # remove everyhing that is not the coverage file for f in os.listdir(cnv_outdir): if f not in {fun.get_file(gene_to_coverage_file), fun.get_file(gene_to_coverage_file_regions), fun.get_file(integrated_coverage_file)}: fun.delete_file_or_folder("%s/%s"%(cnv_outdir, f)) # In Laia's script, she calculates coverage as the median reads per gene (cov per gene) / mean of the cov per gene across all genes print("CNV analysis finished") ##################################### ##### STRUCTURAL VARIATION ########## ##################################### if opt.run_gridss: print("Starting structural variation analysis with GRIDSS. This will call and annotate genomic rearrangements. This is not prepared for real work") # create the directories