ba44900e4c5c8364c27120e499a7872711a3b4ef gperez2 Mon Jan 6 14:27:06 2025 -0800 Editing the script to have /usr/bin/curl instead of /cluster/software/bin/curl.bad due to an error regarding libssl.so.3, no RM diff --git src/utils/qa/hubPublicAutoUpdate src/utils/qa/hubPublicAutoUpdate index 848e4c1..d984237 100755 --- src/utils/qa/hubPublicAutoUpdate +++ src/utils/qa/hubPublicAutoUpdate @@ -74,31 +74,31 @@ hubPublicDic[hub[0]] = {'hubUrl':hub[0],'shortLabel':hub[1],'longLabel':hub[2],\ 'registrationTime':hub[3],'dbCount':hub[4],\ 'dbList':hub[5],'descriptionUrl':hub[6]} return(hubPublicDic) def escapeDoubleQuotesOnLabels(label): """Look for single and double quotes in labels""" if '"' in label: label = label.replace('"','\\"') if "'" in label: label = label.replace("'","\\'") return(label) def curl(url): """Run curl command on URL - for http + ftp support""" - rawCurlOutput = subprocess.run("/cluster/software/bin/curl.bad --user-agent \"genome.ucsc.edu/net.c\" -skL --fail --connect-timeout 10.0 "+url,\ + rawCurlOutput = subprocess.run("/usr/bin/curl --user-agent \"genome.ucsc.edu/net.c\" -skL --fail --connect-timeout 10 "+url,\ check=True, shell=True, stdout=subprocess.PIPE, universal_newlines=True) curlStdout = rawCurlOutput.stdout return(curlStdout) def buildCurrentHubTxtDic(hub): """Query hub.txt file and build dic of values""" currentHub = {} response = curl(hub) for line in response.splitlines(): if "\t" in line.rstrip(): line = line.split("\t") currentHub[line[0]] = line[1] else: line = line.split(" ") currentHub[line[0]] = " ".join(line[1:])