1f929ead8ac83586b318b169e58509c181341276 lrnassar Fri Jul 5 13:38:34 2024 -0700 Changing location of tabFmt script which was moved. diff --git src/utils/qa/assemblyStatsCron.py src/utils/qa/assemblyStatsCron.py index 7cdc554..76c44b4 100755 --- src/utils/qa/assemblyStatsCron.py +++ src/utils/qa/assemblyStatsCron.py @@ -1,287 +1,287 @@ #07/20/19 #This was adapted from a jupyter notebook - hence lots of weird bash calls import datetime from collections import OrderedDict import getpass import subprocess def bash(cmd): """Run the cmd in bash subprocess""" try: rawBashOutput = subprocess.run(cmd, check=True, shell=True,\ stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.STDOUT) bashStdoutt = rawBashOutput.stdout except subprocess.CalledProcessError as e: raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) return(bashStdoutt) def bashNoErrorCatch(cmd): """Run the cmd in bash subprocess, don't catch error since grep returns exit code 1 when no match is found""" try: rawBashOutput = subprocess.run(cmd, check=True, shell=True,\ stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.STDOUT) bashStdoutt = rawBashOutput.stdout.rstrip().split("\n") except: bashStdoutt = [] return(bashStdoutt) user = getpass.getuser() # Get the year to query proper wwwstats directory today = datetime.datetime.today() year = str(today).split('-')[0] # Get the last 5 error logs from the RR latestLogs = bash('ls /hive/users/chmalee/logs/trimmedLogs/result/hgw1').rstrip().split("\n") ######################## FOR TESTING JUST ONE LOG # latestLogs = latestLogs[len(latestLogs)-1:] ######################### latestLogs = latestLogs[len(latestLogs)-5:] nodes = ['RR', 'asiaNode', 'euroNode'] #Add nodes with error logs, nodes can be added or removed machines = ['hgw1','hgw2'] #Add hgw machines to check for node in nodes: if node == 'RR': for machine in machines: for log in latestLogs: #Copy the 5 latest error logs for each of the rr machines bash("cp /hive/users/chmalee/logs/trimmedLogs/result/"+machine+'/'+log+' /hive/users/'+user+'/ErrorLogs/'+node+machine+log) else: latestLogs = bash("ls /hive/users/chmalee/logs/trimmedLogs/result/"+node).rstrip().split("\n") latestLogs = latestLogs[len(latestLogs)-5:] for log in latestLogs: #Copy the 5 latest error logs for each of the other nodes bash('cp /hive/users/chmalee/logs/trimmedLogs/result/'+node+'/'+log+' /hive/users/'+user+'/ErrorLogs/'+node+log) # Run generateUsageStats.py with -d (directory), -t (default track stats), -o (output) bash("/cluster/home/"+user+'/kent/src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py -d /hive/users/'+user+'/ErrorLogs --allOutput -t -o /hive/users/'+user+'/ErrorLogsOutput > /dev/null') #The following section pulls out a list of default track for the top X assemblies for filtering file = open("/hive/users/"+user+"/ErrorLogsOutput/defaults.txt", "a") #The head command can be expanded to be more inclusive if additional assembly defaults are finding their way onto the list bash("sort /hive/users/"+user+'/ErrorLogsOutput/dbCounts.tsv -rnk2 > /hive/users/'+user+'/ErrorLogsOutput/dbCountsTopSorted.tsv') dbs = bash('head -n 4 /hive/users/'+user+'/ErrorLogsOutput/dbCountsTopSorted.tsv | cut -f1 -d "\t"').rstrip().split("\n") for db in dbs[0:4]: #The following part queries hgTracks for each of the assemblies and extracts the list of defaults bash('echo '+db+' > /hive/users/'+user+'/ErrorLogsOutput/temp.txt') defaults = bash('HGDB_CONF=$HOME/.hg.conf.beta /usr/local/apache/cgi-bin/hgTracks db='+db+' hgt.trackImgOnly=1 > /dev/null').rstrip().split("\n") for trackLogs in range(len(defaults)): if trackLogs >= (len(defaults)-1): pass else: defaultsLine = defaults[trackLogs].split(" ")[4] defaultsLine = defaultsLine.split(',') for track in range(len(defaultsLine)): defaultsLine[track] = defaultsLine[track][0:(len(defaultsLine[track])-2)] file.write(db+"\t"+defaultsLine[track]+"\n") file.write(db+"\t"+"cytoBand"+"\n") file.close() bash('echo This cronjob pulls out GB stats over the last month, across all RR machines and Asia/Euro mirrors using the generateUsageStats.py script. It only counts each hgsid occurrence once, filtering our any hgsid that only showed up one time. > /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo List of db usage: >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'dbUse >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('sort /hive/users/'+user+'/ErrorLogsOutput/dbCounts.tsv -rnk2 > /hive/users/'+user+'/ErrorLogsOutput/dbCounts.tsv.sorted') -bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/dbCounts.tsv.sorted | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/dbCounts.tsv.sorted | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo "List of default track usage for hg38, sorted by how many users are turning off the track:" >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'trackUse$'\\t'% using$'\\t'% turning off$'\\t'trackName >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') -bash('grep ^hg38 /hive/users/'+user+'/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15 | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('grep ^hg38 /hive/users/'+user+'/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15 | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo "List of default track usage for hg19, sorted by how many users are turning off the track:" >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'trackUse$'\\t'% using$'\\t'% turning off$'\\t'trackName >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') -bash('grep ^hg19 /hive/users/'+user+'/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15| ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('grep ^hg19 /hive/users/'+user+'/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15| /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo List of non-default track usage: >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'trackUse$'\\t'trackName >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('sort /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv -rnk3 > /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv.sorted') bash('cat /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv.sorted | grep -v -f /hive/users/'+user+'/ErrorLogsOutput/defaults.txt > /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv.sorted.noDefaults') -bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv.sorted.noDefaults | awk -v OFS="\\t" \'{ print $1,$3,$2 }\' | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv.sorted.noDefaults | awk -v OFS="\\t" \'{ print $1,$3,$2 }\' | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo "List of public hub usage (only most used track represented):" >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'trackUse$'\\t'track$'\\t'pubHub >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') file2 = open("/hive/users/"+user+"/ErrorLogsOutput/filteredHubs.txt", "a") #Using a file to be able to use the same ~markd/bin/tabFmt format bash("sort /hive/users/"+user+"/ErrorLogsOutput/trackCountsHubs.tsv -rnk4 -t $\'\\t\' > /hive/users/"+user+"/ErrorLogsOutput/trackCountsHubs.tsv.sorted") topHubs = bash('head -n 15000 /hive/users/'+user+'/ErrorLogsOutput/trackCountsHubs.tsv.sorted').rstrip().split("\n") #This section pulls out only a single occurence of each public hub, picking the first track (most uses) to represent it results = OrderedDict() for each in topHubs: if len(results.keys()) < 15: each = each.split('\t') if each[0] not in results.keys(): results[each[0]] = each[0:] else: pass for key, value in results.items(): file2.write(value[0]+"\t"+value[1]+"\t"+value[2]+"\t"+value[3]+"\n") file2.close() -bash('cat /hive/users/'+user+'/ErrorLogsOutput/filteredHubs.txt | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('cat /hive/users/'+user+'/ErrorLogsOutput/filteredHubs.txt | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo List of public hub track usage overall: >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'trackUse$'\\t'track$'\\t'pubHub >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') -bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/trackCountsHubs.tsv.sorted | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('head -n 15 /hive/users/'+user+'/ErrorLogsOutput/trackCountsHubs.tsv.sorted | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') #Query hubPublic and hubStats in order to filter out public hubs then sort out the IDs bash('/cluster/bin/x86_64/hgsql -h genome-centdb -e "select hubUrl from hubPublic" hgcentral > /hive/users/'+user+'/ErrorLogsOutput/hubPublicHubUrl.txt') bash('/cluster/bin/x86_64/hgsql -h genome-centdb -e "select hubUrl,id from hubStatus" hgcentral> /hive/users/'+user+'/ErrorLogsOutput/hubStatusHubUrl.txt') bash('grep -f /hive/users/'+user+'/ErrorLogsOutput/hubPublicHubUrl.txt /hive/users/'+user+'/ErrorLogsOutput/hubStatusHubUrl.txt | cut -f2 > /hive/users/'+user+'/ErrorLogsOutput/publicIDs.txt') #Add hub_ID format to match stats program output, then grep out the public hubs from the track list bash('cat /hive/users/'+user+'/ErrorLogsOutput/publicIDs.txt | sed s/^/hub_/g > /hive/users/'+user+'/ErrorLogsOutput/hubPublicIDs.txt') bash('grep "hub_" /hive/users/'+user+'/ErrorLogsOutput/trackCounts.tsv | sort -rnk3 > /hive/users/'+user+'/ErrorLogsOutput/allTracksOrderedUsage.txt') #Pull out whole fields from euro and RR hubStatus in order to collect the info for matching IDs bash('ssh qateam@genome-euro "hgsql -e \'select id,hubUrl,shortLabel,lastOkTime from hubStatus\' hgcentral" > /hive/users/'+user+'/ErrorLogsOutput/genomeEuroHubStatus.txt') bash('/cluster/bin/x86_64/hgsql -h genome-centdb -e "select id,hubUrl,shortLabel,lastOkTime from hubStatus where lastOkTime !=\'\'" hgcentral > /hive/users/'+user+'/ErrorLogsOutput/RRHubStatus.txt') #The genome-asia hubStatus is automatically generated via cron by qateam on asia and copied to dev. Use line below to create a new file from personal user if user != 'qateam': bash("ssh "+user+"@genome-asia \"hgsql -e 'select id,hubUrl,shortLabel,lastOkTime from hubStatus' hgcentral\" > /hive/users/"+user+"/ErrorLogsOutput/genomeAsiaHubStatus.txt") hubs = bash('cat /hive/users/'+user+'/ErrorLogsOutput/allTracksOrderedUsage.txt').rstrip().split("\n") pubHubUrls = bash('cat /hive/users/'+user+'/ErrorLogsOutput/hubPublicHubUrl.txt').rstrip().split("\n") lastMonth = today - datetime.timedelta(days=30) lastMonthFormat = lastMonth.strftime('%Y-%m') hubsDic = OrderedDict() for hub in hubs: #Start iterating through track lines, stop pulling items at 20 if len(hubsDic.keys()) < 20: #Pull out the use number, associated db, and hubkey hub = hub.split("\t") if 'hub' in hub[1]: hubKey = hub[1].split("_")[1] elif 'hub' in hub[0]: hubKey = hub[0].split("_")[1] else: print(hub) hubCount = hub[2] hubDb = hub[0] if hubKey not in hubsDic.keys(): #Check that this key has not yet been counted entryMade = False #Reset entryMade variable, made to check RR and then Euro if RR has no match # Grep out the proper hubstatus line, returns an empty list if no matches # ^1017$'\t' rrHub = bashNoErrorCatch("grep ^"+hubKey+"$'\\t' /hive/users/"+user+"/ErrorLogsOutput/RRHubStatus.txt") if rrHub != []: #Pull out matching hubURL, ShortLabel, lastOKtime (used to see compare against) #recurring hubIDs between RR and euro rrHub = rrHub[0].split("\t") if len(rrHub) > 2: rrHubURL = rrHub[1] rrHubShortLabel = rrHub[2] rrHubLastOk = rrHub[3] if rrHubLastOk != '': rrHubLastOk = datetime.datetime.strptime(rrHubLastOk.split(" ")[0], '%Y-%m-%d') if rrHubLastOk > lastMonth: #If hub has been OK in last month, assume it's correct if rrHubURL in pubHubUrls: entryMade = True else: #Pull out all relevant info and save to dictionary hubsDic[hubKey] = {} hubsDic[hubKey]['shortLabel'] = rrHubShortLabel hubsDic[hubKey]['hubURL'] = rrHubURL hubsDic[hubKey]['hubCount'] = hubCount hubsDic[hubKey]['hubDb'] = hubDb hubsDic[hubKey]['machine'] = "RR" entryMade = True #Set true so that the hubID isn't searched for in Euro if entryMade is False: #This assumes that the hubID was either not present in the RR hubStatus, or it pointed to a hub not used in last month euroHub = bashNoErrorCatch("grep ^"+hubKey+"$'\\t' /hive/users/"+user+"/ErrorLogsOutput/genomeEuroHubStatus.txt") if euroHub != []: euroHub = euroHub[0].split("\t") if len(euroHub) > 2: euroHubURL = euroHub[1] euroHubShortLabel = euroHub[2] euroHubLastOk = euroHub[3] if euroHubLastOk != '': euroHubLastOk = datetime.datetime.strptime(euroHubLastOk.split(" ")[0], '%Y-%m-%d') if euroHubLastOk > lastMonth: if euroHub[1] in pubHubUrls: entryMade = True else: hubsDic[hubKey] = {} hubsDic[hubKey]['shortLabel'] = euroHubShortLabel hubsDic[hubKey]['hubURL'] = euroHubURL hubsDic[hubKey]['hubCount'] = hubCount hubsDic[hubKey]['hubDb'] = hubDb hubsDic[hubKey]['machine'] = "Euro" entryMade = True if entryMade is False: #This assumes that the hubID was either not present in the RR hubStatus, or it pointed to a hub not used in last month asiaHub = bashNoErrorCatch("grep ^"+hubKey+"$'\\t' /hive/users/"+user+"/ErrorLogsOutput/genomeAsiaHubStatus.txt") if asiaHub != []: asiaHub = asiaHub[0].split("\t") if len(asiaHub) > 2: asiaHubURL = asiaHub[1] asiaHubShortLabel = asiaHub[2] asiaHubLastOk = asiaHub[3] if asiaHubLastOk != '': asiaHubLastOk = datetime.datetime.strptime(asiaHubLastOk.split(" ")[0], '%Y-%m-%d') if asiaHubLastOk > lastMonth: if asiaHub[1] in pubHubUrls: pass else: hubsDic[hubKey] = {} hubsDic[hubKey]['shortLabel'] = asiaHubShortLabel hubsDic[hubKey]['hubURL'] = asiaHubURL hubsDic[hubKey]['hubCount'] = hubCount hubsDic[hubKey]['hubDb'] = hubDb hubsDic[hubKey]['machine'] = "Asia" entryMade = True else: bash("echo The following hub: "+hub+" was not found in the RR/euro/asia hubStatus with a lastOkTime within the last month. This likely means an error has occurred. >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") #Create new file to write out the top 20 most used hubs hubsNotPublic = open("/hive/users/"+user+"/ErrorLogsOutput/hubsNotPublic.txt", "a") for key in hubsDic.keys(): hubsNotPublic.write(hubsDic[key]['hubDb']+"\t"+hubsDic[key]['machine']+"\t"+str(hubsDic[key]['hubCount'])+"\t"+hubsDic[key]['shortLabel']+"\t"+hubsDic[key]['hubURL']+"\n") hubsNotPublic.close() bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo "List of hub uses that are not public hubs. Some public hubs sneak in due to alternative hubUrl. This includes curated hubs:" >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("echo db$'\\t'machine$'\\t'trackUse$'\\t'shortLabel$'\\t'hubUrl >> /hive/users/"+user+"/ErrorLogsOutput/results.txt") bash('echo -------------------------------------------------------------------------------------- >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') -bash('cat /hive/users/'+user+'/ErrorLogsOutput/hubsNotPublic.txt | ~markd/bin/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') +bash('cat /hive/users/'+user+'/ErrorLogsOutput/hubsNotPublic.txt | /cluster/home/lrnassar/temp/tabFmt >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo Previous outputs of this cron can be found here: https://genecats.gi.ucsc.edu/qa/test-results/usageStats/ >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash('echo Archive of monthly raw data can be found here: /hive/users/qateam/assemblyStatsCronArchive/ >> /hive/users/'+user+'/ErrorLogsOutput/results.txt') bash("mkdir -p /hive/users/"+user+"/assemblyStatsCronArchive/"+lastMonthFormat) bash("cp /hive/users/"+user+"/ErrorLogsOutput/* /hive/users/"+user+"/assemblyStatsCronArchive/"+lastMonthFormat) if user == 'qateam': bash("cat /hive/users/"+user+"/ErrorLogsOutput/results.txt > /usr/local/apache/htdocs-genecats/qa/test-results/usageStats/"+lastMonthFormat) resultsFile = open('/hive/users/'+user+'/ErrorLogsOutput/results.txt','r') for line in resultsFile: print(line.rstrip()) resultsFile.close() bash("rm /hive/users/"+user+"/ErrorLogs/*") bash("rm /hive/users/"+user+"/ErrorLogsOutput/*")