961e7d93ed7c65ec1bc2929c411c4e6256f6d3ca lrnassar Wed Nov 24 14:25:19 2021 -0800 Adding full path to curl, because apparently we have 2 different versions of curl in the bins. No RM. diff --git src/utils/qa/hubPublicAutoUpdate src/utils/qa/hubPublicAutoUpdate index da2847f..c8089e4 100755 --- src/utils/qa/hubPublicAutoUpdate +++ src/utils/qa/hubPublicAutoUpdate @@ -1,174 +1,174 @@ #!/usr/bin/env python3 #Lou Aug 2021 """ Given a server (dev/hgwbeta/rr) will query hubPublic table URLs and verify that the shortLabel, longLabel, dbCount and dbList matches what is in the hubPublic table. Any inconsistencies will be automatically updated. Will print out the commands as well as run them. Can optionally be run in test mode where it will only print commands without executing. Example run: hubPublicAutoUpdate dev hubPublicAutoUpdate hgwbeta -t hubPublicAutoUpdate rr """ import subprocess,sys,argparse def parseArgs(): """ Parse the command line arguments. """ parser = argparse.ArgumentParser(description = __doc__, formatter_class=argparse.RawDescriptionHelpFormatter) optional = parser._action_groups.pop() required = parser.add_argument_group('required arguments') required.add_argument ("server", help = "Server from which to query the hubPublic table. Can be dev, hgwbeta, or rr.") optional.add_argument ("-t", "--test", dest = "testMode", default = False, action = "store_true", help = "Optional: Run in test mode. Print out any discrepancies but do not run any " + \ "commands.") if (len(sys.argv) == 1): parser.print_usage() print("\nGiven a server (dev/hgwbeta/rr) will query hubPublic table URLs and verify that\n" + \ "the shortLabel, longLabel, dbCount and dbList matches what is in the hubPublic table.\n" + \ "Any inconsistencies will be automatically updated. Will print out the commands as\n" + \ "well as run them.\n\n" + \ "Can optionally be run in test mode where it will only print commands without executing.\n\n" + \ "Example run:\n" + \ " hubPublicAutoUpdate dev\n" + \ " hubPublicAutoUpdate hgwbeta -t\n" + \ " hubPublicAutoUpdate rr\n") exit(0) parser._action_groups.append(optional) options = parser.parse_args() return options def evaluateServer(serverToQuery): """Evaluate the input server, ensure it is valid and return corresponding hgsqlInputs""" if serverToQuery == 'dev': hgsqlInput = ['','hgcentraltest'] elif serverToQuery == 'hgwbeta': hgsqlInput = ['-h hgwbeta ','hgcentralbeta'] elif serverToQuery == 'rr': hgsqlInput = ['-h genome-centdb ','hgcentral'] else: sys.exit("Server called must be either 'dev', 'hgwbeta', or 'rr'") return(hgsqlInput) def buildPubHubDic(hgsqlInput): """Build a dictionary out of the requested server's hubPublic table""" hubPublicDic = {} hubPublic = subprocess.run("/cluster/bin/x86_64/hgsql "+hgsqlInput[0]+"-e 'select * from hubPublic' "+hgsqlInput[1],\ check=True, shell=True, stdout=subprocess.PIPE, universal_newlines=True) hubPublicOutput = hubPublic.stdout.split('\n')[1:-1] for hub in hubPublicOutput: hub = hub.split('\t') hubPublicDic[hub[0]] = {} hubPublicDic[hub[0]] = {'hubUrl':hub[0],'shortLabel':hub[1],'longLabel':hub[2],\ 'registrationTime':hub[3],'dbCount':hub[4],\ 'dbList':hub[5],'descriptionUrl':hub[5]} 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("curl --user-agent \"genome.ucsc.edu/net.c\" -skL --fail --connect-timeout 10.0 "+url,\ + rawCurlOutput = subprocess.run("/cluster/software/bin/curl --user-agent \"genome.ucsc.edu/net.c\" -skL --fail --connect-timeout 10.0 "+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:]) return(currentHub) def queryHubTxt(currentHub,hub): """Query genomes.txt file and fill out dbList and dbCount values""" currentHub['dbList'] = [] genomeFileLocation = currentHub['genomesFile'].rstrip().lstrip() if genomeFileLocation.startswith("http"): genomeUrl = genomeFileLocation else: genomeUrl = "/".join(hub.split('/')[:-1])+"/"+genomeFileLocation genomeInfo = curl(genomeUrl) for line in genomeInfo.splitlines(): if "\t" in line: line = line.split("\t") if line[0].rstrip().lstrip() == 'genome': while "" in line: line.remove("") currentHub['dbList'].append(line[1].rstrip().lstrip()) else: line = line.split(" ") if line[0].rstrip().lstrip() == 'genome': while "" in line: line.remove("") currentHub['dbList'].append(line[1].rstrip().lstrip()) currentHub['dbCount'] = len(currentHub['dbList']) return(currentHub) def printHgsql(hub,varToEdit,newVarValue,hgsqlInput,testMode): """hgsql command to fix the difference""" cmd = "/cluster/bin/x86_64/hgsql "+hgsqlInput[0]+"-e \"update hubPublic set "+varToEdit+" = '"+str(newVarValue)+ \ "' where hubUrl = '"+hub+"'\" "+hgsqlInput[1] if not testMode: subprocess.run(cmd, check=True, shell=True, stdout=subprocess.PIPE, universal_newlines=True) print(cmd) def compareResults(hubPublicDic,currentHub,hub,hgsqlInput,testMode): """Compare the hubPublic values to the queried currentHub values and report""" if hubPublicDic[hub]['shortLabel'] != currentHub['shortLabel'].rstrip().lstrip(): printHgsql(hub,'shortLabel',escapeDoubleQuotesOnLabels(currentHub['shortLabel'].rstrip().lstrip()),hgsqlInput,testMode) if hubPublicDic[hub]['longLabel'] != currentHub['longLabel'].rstrip().lstrip(): printHgsql(hub,'longLabel',escapeDoubleQuotesOnLabels(currentHub['longLabel'].rstrip().lstrip()),hgsqlInput,testMode) if int(hubPublicDic[hub]['dbCount']) != int(currentHub['dbCount']): printHgsql(hub,'dbCount',currentHub['dbCount'],hgsqlInput,testMode) if set(hubPublicDic[hub]['dbList'][:-1].split(',')) != set(currentHub['dbList']): printHgsql(hub,'dbList',",".join(currentHub['dbList'])+",",hgsqlInput,testMode) def hubPublicCompare(hubPublicDic,hgsqlInput,testMode): """Query hub.txt files and compare values to hubPublic values""" for hub in hubPublicDic.keys(): try: #Try for timeout connections currentHub = buildCurrentHubTxtDic(hub) currentHub = queryHubTxt(currentHub,hub) compareResults(hubPublicDic,currentHub,hub,hgsqlInput,testMode) except: print("The following hub has an error or is not responsive: "+str(hub)) def main(): """Initialize options and call other functions""" options = parseArgs() serverToQuery = options.server testMode = options.testMode hgsqlInput = evaluateServer(serverToQuery) hubPublicDic = buildPubHubDic(hgsqlInput) hubPublicCompare(hubPublicDic,hgsqlInput,testMode) main()