#! /usr/bin/env python3.6 import re, argparse, os, gzip, sys, datetime from collections import Counter, defaultdict from urllib import parse ##### # Define dictionaries for recording usage information ##### # General search term dictionaries searchTermUsers = defaultdict(Counter) # HGVS search term dictionaries hgvsTermUsers = defaultdict(Counter) ##### ##### ##### # Define set of Brian Lee's HGVS test search terms ##### hgvsTestTerms = {"NM_000310.3(PPT1):c.271_287del17insTT", "NM_007262.4(PARK7):c.-24+75_-24+92dup", "NM_006172.3(NPPA):c.456_*1delAA", "MYH11:c.503-14_503-12del", "NM_198576.3(AGRN):c.1057C>T", "NM_198056.2:c.1654G>T", "NP_002993.1:p.Asp92Glu", "NP_002993.1:p.D92E", "BRCA1 Ala744Cys", "NM_000828.4:c.-2G>A"} def findSearchTerms(line): """Find and record usage information about search terms found in log lines""" splitLine = line.rstrip().split(" ") ip = splitLine[0] line = parse.unquote(line) output = re.findall("hgt\.positionInput\=[^&]+&?", line) # If we find search terms in line, process them if output != []: # Stringify search terms and remove extra characters output = str(output).replace("&", "").replace("[", "").replace("]", "").replace("'", "") # Split on "=" sign and keep only part after this sign outputList = output.split("=") searchTerm = outputList[1] # Count up search term use per user/IP address searchTermUsers[searchTerm][ip] += 1 # Find search terms like NM_000310.3(PPT1):c.271_287del17insTT hgvs = re.findall("^[N][M|R|P]_[0-9]*\.[\(\)A-Z0-9]*:[a-z]\..*", searchTerm) if hgvs == []: # Find search terms like MYH11:c.503-14_503-12del hgvs = re.findall("^[A-Z0-9]*\:[a-z]\..*", searchTerm) if hgvs == []: # Find search terms like RCA1 Ala744Cys hgvs = re.findall("^[A-Z0-9]*\s[A-Z][a-z][a-z][0-9].*[A-Z][a-z][a-z]", searchTerm) # If we have HGVS results, stringify them and remove extra characters if hgvs != []: hgvs = str(hgvs).replace("&", "").replace("[", "").replace("]", "").replace("'", "") if hgvs in hgvsTestTerms: hgvs = "** " + hgvs hgvsTermUsers[hgvs][ip] += 1 def processFile(fileName, outputDir): """Process hgTracks lines in a file""" # Need to process gzipped files differently if fileName.endswith(".gz"): ifh = gzip.open(fileName, "r") else: ifh = open(fileName, "r") for line in ifh: if "str" not in str(type(line)): line = line.decode("utf-8") if "positionInput" in line: findSearchTerms(line) # Output results to file outputToFile(searchTermUsers, os.path.join(outputDir, "searchTermsUsers.tsv"), os.path.join(outputDir, "searchTermCounts.tsv")) outputToFile(hgvsTermUsers, os.path.join(outputDir, "hgvsTermsUsers.tsv"), os.path.join(outputDir, "hgvsTermCounts.tsv")) def processDir(dirName, outputDir): """Process files in a directory one-by-one using processFile function""" fileNames = os.listdir(dirName) for log in fileNames: fileName = os.path.join(dirName, log) processFile(fileName, outputDir) def outputToFile(usersDict, usersOutName, countsOutName): """Output supplied dictionary to a tab-separated file""" usersOut = open(usersOutName, "w", encoding="utf-8") countsOut = open(countsOutName, "w", encoding="utf-8") usersOut.write("# User/IP\tSearch term\tUse count\n") countsOut.write("# Search term\t# of users\t# of times searched\n") for term in usersDict: users = 0 totalUse = 0 for user in usersDict[term]: count = usersDict[term][user] if count!= 1: users += 1 totalUse += count usersOut.write(str(user) + "\t" + term + "\t" + str(count) + "\n") if users != 0 or totalUse != 0: countsOut.write(term + "\t" + str(users) + "\t" + str(totalUse) + "\n") def dumpToJson(data, outJsonName, outputDir): """Dump supplied dictionary to a JSON format file""" jsonOut = open(os.path.join(outputDir, outJsonName), "w") json.dump(data, jsonOut) jsonOut.close() def main(): # Parse command-line arguments parser = argparse.ArgumentParser() parser.add_argument("-f","--fileName", type=str, help='input file name, must be\ space-separated Apache access_log file') parser.add_argument("-d","--dirName", type=str , help='input directory name, files must\ be space-separated Apache access_log files. No other files should be present in this directory.') parser.add_argument("-j","--jsonOut", action='store_true', help='output json files\ for summary dictionaries') parser.add_argument("-o","--outDir", type=str, help='directory in which to place output files') args = parser.parse_args() # Print help message if no arguments are supplied if len(sys.argv) == 1: parser.print_help(sys.stderr) sys.exit(1) # File and directory options can't be used together. Catch this and exit. if args.fileName != None and args.dirName != None: print("-f/--fileName and -d/--dirName cannot be used together. Choose one and re-run.") sys.exit(1) # Catch it early if input file/directory doesn't exist and exit. if args.fileName: if not os.path.exists(args.fileName): print(args.fileName, "doesn't exist. Please run on a valid file.") exit(1) elif args.dirName: if not os.path.exists(args.dirName): print(args.dirName, "doesn't exist. Please run on a valid directory.") exit(1) # Setup output directory if args.outDir == None: # If an output directory is unspecified, then a new one with the current date/time is made currDateTime = datetime.datetime.now().strftime("%Y%m%d-%H%M%S") os.makedirs(currDateTime) outDir = currDateTime else: # Otherwise, user supplied a output directory name outDir = args.outDir if not os.path.exists(outDir): # If specied output directory doesn't exist, create it os.makedirs(outDir) # Process input to create dictionaries containing info about users per db/track/hub track if args.fileName: processFile(args.fileName, outDir) elif args.dirName: processDir(args.dirName, outDir) if args.jsonOut == True: dumpToJson(searchTermUsers, "searchTermUsers.json", outDir) dumpToJson(hgvsTermUsers, "hgvsTermUsers.json", outDir) if __name__ == "__main__": main()