3127589facd0998822593cc31527a70233c67164 lrnassar Wed Jul 14 16:10:04 2021 -0700 Moving all qateam crons to the kent src tree qa utils. They are now all called from the bin. No RM. diff --git src/utils/qa/assemblyStatsCronSaveStats.py src/utils/qa/assemblyStatsCronSaveStats.py new file mode 100755 index 0000000..f66d601 --- /dev/null +++ src/utils/qa/assemblyStatsCronSaveStats.py @@ -0,0 +1,214 @@ + +# coding: utf-8 + +# In[2]: + + +#Made by Lou - 07/20/19 + +import datetime +from collections import OrderedDict +import getpass + +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 = get_ipython().getoutput(u'ls /hive/users/chmalee/logs/trimmedLogs/result/hgw1') +######################## 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 + get_ipython().system(u" cp /hive/users/chmalee/logs/trimmedLogs/result/'$machine'/'$log' /hive/users/'$user'/ErrorLogs/'$node''$machine''$log'") + else: + latestLogs = get_ipython().getoutput(u"ls /hive/users/chmalee/logs/trimmedLogs/result/'$node'") + latestLogs = latestLogs[len(latestLogs)-5:] + for log in latestLogs: #Copy the 5 latest error logs for each of the other nodes + get_ipython().system(u" cp /hive/users/chmalee/logs/trimmedLogs/result/'$node'/'$log' /hive/users/'$user'/ErrorLogs/'$node''$log'") + +# Run generateUsageStats.py with -d (directory), -t (default track stats), -o (output) +get_ipython().system(u" /cluster/home/'$user'/kent/src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py -d /hive/users/'$user'/ErrorLogs --allOutput -t -o /hive/users/'$user'/ErrorLogsOutput > /dev/null") + +#The following section pulls out a list of default track for the top X assemblies for filtering +file = open("/hive/users/"+user+"/ErrorLogsOutput/defaults.txt", "a") + +#The head command can be expanded to be more inclusive if additional assembly defaults are finding their way onto the list +get_ipython().system(u" sort /hive/users/'$user'/ErrorLogsOutput/dbCounts.tsv -rnk2 > /hive/users/'$user'/ErrorLogsOutput/dbCountsTopSorted.tsv") +dbs = get_ipython().getoutput(u'head -n 4 /hive/users/\'$user\'/ErrorLogsOutput/dbCountsTopSorted.tsv | cut -f1 -d "\t"') + +for db in dbs[0:4]: + #The following part queries hgTracks for each of the assemblies and extracts the list of defaults + get_ipython().system(u" echo '$db' > /hive/users/'$user'/ErrorLogsOutput/temp.txt") + defaults = get_ipython().getoutput(u'HGDB_CONF=$HOME/.hg.conf.beta /usr/local/apache/cgi-bin/hgTracks db=$(cat /hive/users/"$USER"/ErrorLogsOutput/temp.txt) > /dev/null') + for trackLogs in range(len(defaults)): + if trackLogs >= (len(defaults)-1): + pass + else: + defaultsLine = defaults[trackLogs].split(" ")[4] + defaultsLine = defaultsLine.split(',') + for track in range(len(defaultsLine)): + defaultsLine[track] = defaultsLine[track][0:(len(defaultsLine[track])-2)] + file.write(db+"\t"+defaultsLine[track]+"\n") + file.write(db+"\t"+"cytoBand"+"\n") +file.close() + +get_ipython().system(u' echo This cronjob pulls out GB stats over the last month, across all RR machines and Asia/Euro mirrors using the generateUsageStats.py script. It only counts each hgsid occurrence once, filtering our any hgsid that only showed up one time. > /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo List of db usage: >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'dbUse >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' sort /hive/users/"$USER"/ErrorLogsOutput/dbCounts.tsv -rnk2 > /hive/users/"$USER"/ErrorLogsOutput/dbCounts.tsv.sorted') +get_ipython().system(u' head -n 15 /hive/users/"$USER"/ErrorLogsOutput/dbCounts.tsv.sorted | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo "List of default track usage for hg38, sorted by how many users are turning off the track:" >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'trackUse$'\\t'% using$'\\t'% turning off$'\\t'trackName >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' grep ^hg38 /hive/users/"$USER"/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15 | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo "List of default track usage for hg19, sorted by how many users are turning off the track:" >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'trackUse$'\\t'% using$'\\t'% turning off$'\\t'trackName >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' grep ^hg19 /hive/users/"$USER"/ErrorLogsOutput/defaultCounts.tsv | grep -v "MarkH3k27ac" | sort -nrk 5 | awk -v OFS="\\t" \'{ print $1,$3,$4,$5,$2 }\' | head -n 15 | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo List of non-default track usage: >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'trackUse$'\\t'trackName >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' sort /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv -rnk3 > /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv.sorted') +get_ipython().system(u' cat /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv.sorted | grep -v -f /hive/users/"$USER"/ErrorLogsOutput/defaults.txt > /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv.sorted.noDefaults') +get_ipython().system(u' head -n 15 /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv.sorted.noDefaults | awk -v OFS="\\t" \'{ print $1,$3,$2 }\' | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo "List of public hub usage (only most used track represented):" >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'trackUse$'\\t'track$'\\t'pubHub >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/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 +get_ipython().system(u' sort /hive/users/"$USER"/ErrorLogsOutput/trackCountsHubs.tsv -rnk4 -t $\'\\t\' > /hive/users/"$USER"/ErrorLogsOutput/trackCountsHubs.tsv.sorted') +topHubs = get_ipython().getoutput(u'head -n 5000 /hive/users/"$USER"/ErrorLogsOutput/trackCountsHubs.tsv.sorted ') +#This section pulls out only a single occurence of each public hub, picking the first track (most uses) to represent it +results = OrderedDict() +for each in topHubs: + if len(results.keys()) < 15: + each = each.split('\t') + if each[0] not in results.keys(): + results[each[0]] = each[0:] + else: + pass +for key, value in results.items(): + file2.write(value[0]+"\t"+value[1]+"\t"+value[2]+"\t"+value[3]+"\n") +file2.close() + +get_ipython().system(u' cat /hive/users/"$USER"/ErrorLogsOutput/filteredHubs.txt | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo List of public hub track usage overall: >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'trackUse$'\\t'track$'\\t'pubHub >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' head /hive/users/"$USER"/ErrorLogsOutput/trackCountsHubs.tsv.sorted | awk -F "\\t" -v OFS="\\t" \'{ print $2,$4,$3,$1 }\' | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +#Query hubPublic and hubStats in order to filter out public hubs then sort out the IDs +get_ipython().system(u' /cluster/bin/x86_64/hgsql -h genome-centdb -e "select hubUrl from hubPublic" hgcentral > /hive/users/"$USER"/ErrorLogsOutput/hubPublicHubUrl.txt') +get_ipython().system(u' /cluster/bin/x86_64/hgsql -h genome-centdb -e "select hubUrl,id from hubStatus" hgcentral> /hive/users/"$USER"/ErrorLogsOutput/hubStatusHubUrl.txt') +get_ipython().system(u' grep -f /hive/users/"$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 +get_ipython().system(u' cat /hive/users/"$USER"/ErrorLogsOutput/publicIDs.txt | sed s/^/hub_/g > /hive/users/"$USER"/ErrorLogsOutput/hubPublicIDs.txt') +get_ipython().system(u' grep "hub_" /hive/users/"$USER"/ErrorLogsOutput/trackCounts.tsv | grep -vf /hive/users/"$USER"/ErrorLogsOutput/hubPublicIDs.txt | sort -rnk3 > /hive/users/"$USER"/ErrorLogsOutput/nonPublicHubTracksPopularity.txt') + +#Pull out top 100 hubs track (some are repeated) in order to ultimately filter out just 5 +get_ipython().system(u' head -n 100 /hive/users/"$USER"/ErrorLogsOutput/nonPublicHubTracksPopularity.txt > /hive/users/"$USER"/ErrorLogsOutput/nonPublicHubTracksPopularityTop1000.txt') + +#Pull out whole fields from euro and RR hubStatus in order to collect the info for matching IDs +get_ipython().system(u' ssh qateam@genome-euro "hgsql -e \'select id,hubUrl,shortLabel,lastOkTime from hubStatus\' hgcentral" > /hive/users/"$USER"/ErrorLogsOutput/genomeEuroHubStatus.txt') +get_ipython().system(u' /cluster/bin/x86_64/hgsql -h genome-centdb -e "select id,hubUrl,shortLabel,lastOkTime from hubStatus where lastOkTime !=\'\'" hgcentral > /hive/users/"$USER"/ErrorLogsOutput/RRHubStatus.txt') + +hubs = get_ipython().getoutput(u'cat /hive/users/"$USER"/ErrorLogsOutput/nonPublicHubTracksPopularityTop1000.txt') +lastMonth = today - datetime.timedelta(days=30) +lastMonthFormat = lastMonth.strftime('%Y-%m') +hubsDic = OrderedDict() + +for hub in hubs: #Start iterating through top 100 hub track lines + #Pull out the use number, associated db, and hubkey + hub = hub.split("\t") + hubKey = hub[1].split("_")[1] + 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 + rrHub = get_ipython().getoutput(u"grep ^'$hubKey'$'\\t' /hive/users/'$user'/ErrorLogsOutput/RRHubStatus.txt") + if rrHub != []: + #Pull out matching hubURL, ShortLabel, lastOKtime (used to see compare against) + #recurring hubIDs between RR and euro + rrHub = rrHub[0].split("\t") + rrHubURL = rrHub[1] + rrHubShortLabel = rrHub[2] + rrHubLastOk = rrHub[3] + rrHubLastOk = datetime.datetime.strptime(rrHubLastOk.split(" ")[0], '%Y-%m-%d') + if rrHubLastOk > lastMonth: #If hub has been OK in last month, assume it's correct + #Pull out all relevant info and save to dictionary + hubsDic[hubKey] = {} + hubsDic[hubKey]['shortLabel'] = rrHubShortLabel + hubsDic[hubKey]['hubURL'] = rrHubURL + hubsDic[hubKey]['hubCount'] = hubCount + hubsDic[hubKey]['hubDb'] = hubDb + hubsDic[hubKey]['machine'] = "RR" + entryMade = True #Set true so that the hubID isn't searched for in Euro + if entryMade is False: #This assumes that the hubID was either not present in the RR hubStatus, or it pointed to a hub not used in last month + euroHub = get_ipython().getoutput(u"grep ^'$hubKey'$'\\t' /hive/users/'$user'/ErrorLogsOutput/genomeEuroHubStatus.txt") + if euroHub != []: + euroHub = euroHub[0].split("\t") + euroHubURL = euroHub[1] + euroHubShortLabel = euroHub[2] + euroHubLastOk = euroHub[3] + euroHubLastOk = datetime.datetime.strptime(euroHubLastOk.split(" ")[0], '%Y-%m-%d') + if euroHubLastOk > lastMonth: + hubsDic[hubKey] = {} + hubsDic[hubKey]['shortLabel'] = euroHubShortLabel + hubsDic[hubKey]['hubURL'] = euroHubURL + hubsDic[hubKey]['hubCount'] = hubCount + hubsDic[hubKey]['hubDb'] = hubDb + hubsDic[hubKey]['machine'] = "Euro" + entryMade = True + +#Create new file to write out the top 10 most used hubs +hubsNotPublic = open("/hive/users/"+user+"/ErrorLogsOutput/hubsNotPublic.txt", "a") +n=-1 +for key in hubsDic.keys(): + n+=1 + if n < 15: + 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() + +get_ipython().system(u' echo >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u' echo "List of hub uses that are Not public hubs. Some public hubs sneak in due to alternative mirror or hubUrl:" >> /hive/users/qateam/ErrorLogsOutput/results.txt') +get_ipython().system(u" echo db$'\\t'machine$'\\t'trackUse$'\\t'shortLabel$'\\t'hubUrl >> /hive/users/qateam/ErrorLogsOutput/results.txt") +get_ipython().system(u' echo -------------------------------------------------------------------------------------- >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u' cat /hive/users/"$USER"/ErrorLogsOutput/hubsNotPublic.txt | ~markd/bin/tabFmt >> /hive/users/qateam/ErrorLogsOutput/results.txt') + +get_ipython().system(u" cat /hive/users/qateam/ErrorLogsOutput/results.txt > /usr/local/apache/htdocs-genecats/qa/test-results/usageStats/'$lastMonthFormat'") + +get_ipython().system(u" rm /hive/users/'$user'/ErrorLogs/*") +get_ipython().system(u" rm /hive/users/'$user'/ErrorLogsOutput/*") +