a9b9871b59c77090d2df3c6fbcc26e90eff3fc53 wong Mon Oct 24 17:27:06 2011 -0700 changes name of variable that I already used, but not in scope or the same context, this fix is onyl for aesthetics diff --git python/lib/ucscgenomics/mkChangeNotes.py python/lib/ucscgenomics/mkChangeNotes.py index 1f3f8bb..56d3568 100755 --- python/lib/ucscgenomics/mkChangeNotes.py +++ python/lib/ucscgenomics/mkChangeNotes.py @@ -1,700 +1,700 @@ #!/hive/groups/encode/dcc/bin/python import sys, os, re, argparse, subprocess, math from ucscgenomics import ra, track, qa class makeNotes(object): def checkMetaDbForFiles(self, status, state): if state == 'new': (mdb, files, loose) = (self.newMdb, self.newReleaseFiles, self.loose) elif state == 'old': (mdb, files, loose) = (self.oldMdb, self.oldReleaseFiles, self.loose) errors = [] revokedset = set() revokedfiles = set() atticset = set() supplementalset = set() filtermdb = ra.RaFile() for i in files: if re.match('supplemental', i): supplementalset.add(i) if not re.match('wgEncode.*', i): continue filestanza = mdb.filter(lambda s: re.match(".*%s.*" % i,s['fileName']), lambda s: s) #should only return 1, just in case if filestanza: for j in filestanza: filtermdb[j.name] = j if 'objStatus' in j and re.search('revoked|replaced|renamed', j['objStatus']): revokedfiles.add(i) revokedset.add(j.name) if 'attic' in j: atticset.add(j.name) else: #pass if loose and re.match('.*bai', i): pass else: errors.append("metaDb: %s is not mentioned in %s" % (i, status)) return (filtermdb, revokedset, revokedfiles, atticset, supplementalset, errors) def __checkAlphaForDropped(self, status, type): (new, old) = (self.newMdb, self.oldMdb) errors=[] diff = set(old) -set(new) for i in diff: errors.append("%s: %s missing from %s" % (type, i, status)) return errors def __checkFilesForDropped(self): (new, old) = (self.newReleaseFiles, self.oldReleaseFiles) diff = set(old) - set(new) return diff def checkTableStatus(self, status, state): errors=[] revokedset = set() (database, composite, loose) = (self.database, self.composite, self.loose) if state == 'new': (mdb, files, revokedset) = (self.newMdb, self.newReleaseFiles, self.revokedSet) elif state == 'old': (mdb, files) = (self.oldMdb, self.oldReleaseFiles) #home = os.environ['HOME'] #dbhost = '' #dbuser = '' #dbpassword = '' #p = re.compile('db.(\S+)=(\S+)') #with open("%s/.hg.conf" % home) as f: # for line in f: # line.rstrip("\n\r") # if p.match(line): # m = p.match(line) # if m.groups(1)[0] == 'host': # dbhost = m.groups(1)[1] # if m.groups(1)[0] == 'user': # dbuser = m.groups(1)[1] # if m.groups(1)[0] == 'password': # dbpassword = m.groups(1)[1] #db = MySQLdb.connect (host = dbhost, # user = dbuser, # passwd = dbpassword, # db = database) #cursor = db.cursor () #cursor.execute ("show tables like '%s%s'" % (composite, "%")) #tableset = set(cursor.fetchall()) mdbtableset = set(mdb.filter(lambda s: s['objType'] == 'table' and 'tableName' in s and 'attic' not in s, lambda s: s['metaObject'])) mdbtableset = mdbtableset - revokedset mdbtableset = set(mdb.filter(lambda s: s['metaObject'] in mdbtableset, lambda s: s['tableName'])) revokedtableset = set(mdb.filter(lambda s: s['metaObject'] in revokedset, lambda s: s['tableName'])) sep = "','" tablestr = sep.join(mdbtableset) tablestr = "'" + tablestr + "'" #this should really be using python's database module, but I'd need admin access to install it #at this point, I am just parsing the output form hgsql cmd = "hgsql %s -e \"select table_name from information_schema.TABLES where table_name in (%s)\"" % (database, tablestr) p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True) - output = p.stdout.read() + cmdoutput = p.stdout.read() - sqltableset = set(output.split("\n")[1:-1]) + sqltableset = set(cmdoutput.split("\n")[1:-1]) missingTableNames = set(mdb.filter(lambda s: s['objType'] == 'table' and 'tableName' not in s and 'attic' not in s, lambda s: s['metaObject'])) missingFromDb = mdbtableset - sqltableset if missingTableNames: for i in missingTableNames: errors.append("table: %s is type obj, but missing tableName field called by %s" % (i, status)) if missingFromDb: for i in missingFromDb: errors.append("table: %s table not found in Db called by %s" % (i, status)) return (mdbtableset, revokedtableset, errors) def getGbdbFiles(self, state): database = self.database revokedset = set() if state == 'new': (tableset, revokedset, mdb) = (self.newTableSet, self.revokedSet, self.newMdb) elif state == 'old': (tableset, mdb) = (self.oldTableSet, self.oldMdb) errors = [] gbdbtableset = qa.getGbdbTables(self.database, tableset) revokedtableset = qa.getGbdbTables(self.database, revokedset) file1stanzalist = mdb.filter(lambda s: s['tableName'] in gbdbtableset, lambda s: s) revokedstanzalist = mdb.filter(lambda s: s['tableName'] in revokedtableset, lambda s: s) gbdbfileset = set() revokedfileset = set() for i in file1stanzalist: filelist = i['fileName'].split(',') for j in filelist: if os.path.isfile("/gbdb/%s/bbi/%s" % (database, j)): gbdbfileset.add(j) else: errors.append("gbdb: %s does not exist in /gbdb/%s/bbi" % (j, database)) for i in revokedstanzalist: filelist = i['fileName'].split(',') for j in filelist: if os.path.isfile("/gbdb/%s/bbi/%s" % (database, j)): revokedfileset.add(j) else: errors.append("gbdb: revoked gbdb %s does not exist in /gbdb/%s/bbi" % (j, database)) return (gbdbfileset, revokedfileset, errors) def __getTableSize(self): (mdbtableset, database) = (self.newTableSet, self.database) tablesize = float(0) tablelist = list() for i in mdbtableset: tablelist.append("table_name = '%s'" % i) orsep = " OR " orstr = orsep.join(tablelist) cmd = "hgsql %s -e \"SELECT ROUND(data_length/1024/1024,2) total_size_mb, ROUND(index_length/1024/1024,2) total_index_size_mb FROM information_schema.TABLES WHERE %s\"" % (database, orstr) p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True) - output = p.stdout.read() - for i in output.split("\n")[1:-1]: + cmdoutput = p.stdout.read() + for i in cmdoutput.split("\n")[1:-1]: fields = i.split() for j in fields: tablesize = tablesize + float(j) return math.ceil(tablesize) def __checkMd5sums(self): (newfiles, oldfiles, loose) = (self.newReleaseFiles, self.oldReleaseFiles, self.loose) errors = [] for i in oldfiles: if i not in newfiles: pass elif re.match('wgEncode.*', i): if oldfiles[i].md5sum != newfiles[i].md5sum: errors.append("file: %s have changed md5sums between releases. %s vs %s" % (i, oldfiles[i].md5sum, newfiles[i].md5sum)) if loose: return list() else: return errors def __makeFileSizes(self, c, args, inlist): checklist = list() for i in inlist: checklist.append("%s/%s" % (c.downloadsDirectory + 'release' + args['releaseNew'], i)) filesizes = 0 for i in checklist: realpath = os.path.realpath(i) filesizes = filesizes + int(os.path.getsize(realpath)) filesizes = math.ceil(float(filesizes) / (1024**2)) return int(filesizes) def __cleanSpecialFiles(self, inlist): specialRemoveList = ['md5sum.history'] for i in specialRemoveList: if i in inlist: inlist.remove(i) return(inlist) def __separateOutAdditional(self): (oldReleaseFiles, totalFiles, newSupplementalSet, oldSupplementalSet) = (self.oldTotalFiles, self.totalFiles, self.newSupplementalSet, self.oldSupplementalSet) additionalList = set() oldAdditionalList = set() newTotal = set() newOld = set() for i in totalFiles: if i in newSupplementalSet: continue elif not re.match('wgEncode.*', i): additionalList.add(i) else: newTotal.add(i) for i in oldReleaseFiles: if not re.match('wgEncode.*', i): if i in totalFiles: pass elif i in newSupplementalSet: continue else: oldAdditionalList.add(i) else: newOld.add(i) oldReleaseFiles = newOld return(newOld, additionalList, oldAdditionalList, newTotal) def __printWithPath(self, set, c, release): output = [] for i in sorted(set): output.append("%s/%s" % (c.httpDownloadsPath + 'release' + release, i)) return output def __printGbdbPath(self, set, database): output = [] for i in sorted(set): output.append("/gbdb/%s/bbi/%s" % (database, i)) return output def __printIter(self, inlist): output = [] for i in sorted(inlist): output.append(i) return output def printReport(self, args, c): (totalFiles, newGbdbSet, newTableSet, additionalList, oldAdditionalList, pushTables, pushFiles, pushGbdbs, oldTableSet, oldReleaseFiles, oldGbdbSet, atticSet, revokedFiles, revokedTableSet, revokedGbdbs, missingFiles, newSupplementalSet, oldSupplementalSet, tableSize) = (self.totalFiles, self.newGbdbSet, self.newTableSet, self.additionalList, self.oldAdditionalList, self.pushTables, self.pushFiles, self.pushGbdbs, self.oldTableSet, self.oldTotalFiles, self.oldGbdbSet, self.atticSet, self.revokedFiles, self.revokedTableSet, self.revokedGbdbs, self.missingFiles, self.newSupplementalSet, self.oldSupplementalSet, self.tableSize) #the groups here need to be predefined, I just copied and pasted after working out what they were sep = "\n" output = [] output.append("mkChangeNotes v2") output.append("%s %s Release %s vs Release %s" % (args['database'], args['composite'], args['releaseNew'], args['releaseOld'])) output.append("") output.append("QA Count Summaries for Release %s:" % args['releaseNew']) output.append("Tables: %d" % int(len(newTableSet))) output.append("Files: %d" % int(len(totalFiles - revokedFiles))) output.append("Gbdbs: %d" % int(len(newGbdbSet))) output.append("Supplemental: %d" % int(len(newSupplementalSet - oldSupplementalSet))) output.append("Other: %d" % int(len(additionalList))) output.append("\n") output.append("Sizes of New:") totalsize = 0 size = 0 tableGb = int(tableSize/1024) totalsize = totalsize + tableSize if tableGb > 1: output.append("Tables: %d MB (%d GB)" % (tableSize, tableGb)) elif tableSize: output.append("Tables: %d MB" % tableSize) size = int(self.__makeFileSizes(c, args, pushFiles)) totalsize = totalsize + size if int(size/1024) > 1: output.append("Files: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Files: %d MB" % size) size = int(self.__makeFileSizes(c, args, pushGbdbs)) totalsize = totalsize + size if int(size/1024) > 1: output.append("Gbdbs: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Gbdbs: %d MB" % size) size = int(self.__makeFileSizes(c, args, (newSupplementalSet - oldSupplementalSet))) totalsize = totalsize + size if int(size/1024) > 1: output.append("Supplemental: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Supplemental: %d MB" % size) size = int(self.__makeFileSizes(c, args, (additionalList))) totalsize = totalsize + size if int(size/1024) > 1: output.append("Other: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Other: %d MB" % size) if int(totalsize/1024) > 1: output.append("Total: %d MB (%d GB)" % (totalsize, int(totalsize/1024))) else: output.append("Total: %d MB" % totalsize) tableprint = len(newTableSet | oldTableSet | revokedTableSet) self.newTables = set(pushTables) if tableprint: output.append("\n") output.append("TABLES:") output.append("New: %s" % len(pushTables)) output.append("Untouched: %s" % len(oldTableSet & newTableSet)) output.append("Revoked/Replaced/Renamed: %s" % len(revokedTableSet)) output.append("New + Untouched: %s" % len(newTableSet)) output.append("Total (New + Untouched + Revoked/Replaced/Renamed): %s" % len(newTableSet | oldTableSet | revokedTableSet)) if tableprint and not args['summary']: output.append("") output.append("New Tables (%s):" % len(pushTables)) output.extend(self.__printIter(pushTables)) output.append("") output.append("Untouched (%s):" % len(oldTableSet & newTableSet)) output.extend(self.__printIter(oldTableSet & newTableSet)) output.append("") output.append("Revoked/Replaced/Renamed Tables (%s):" % len(revokedTableSet)) output.extend(self.__printIter(revokedTableSet)) dlprint = len(totalFiles | oldReleaseFiles | revokedFiles) self.newFiles = set(self.__printWithPath((pushFiles - revokedFiles), c, args['releaseNew'])) if dlprint: output.append("\n") #downlaodables = total - revoked output.append("DOWNLOAD FILES:") output.append("New: %s" % len(pushFiles - revokedFiles)) output.append("Untouched: %s" % len((totalFiles & oldReleaseFiles) - revokedFiles)) output.append("Revoked/Replaced/Renamed: %s" % len(revokedFiles)) output.append("New + Untouched: %s" % len((pushFiles - revokedFiles) | ((totalFiles & oldReleaseFiles) - revokedFiles))) output.append("Total (New + Untouched + Revoked/Replaced/Renamed): %s" % len(totalFiles | oldReleaseFiles | revokedFiles)) if dlprint and not args['summary']: output.append("") output.append("New Download Files (%s):" % len(pushFiles - revokedFiles)) output.extend(sorted(list(self.newFiles))) output.append("") output.append("Untouched Download Files (%s):" % len((totalFiles & oldReleaseFiles) - revokedFiles)) output.extend(self.__printWithPath(((totalFiles & oldReleaseFiles) - revokedFiles), c, args['releaseNew'])) output.append("") output.append("Revoked/Replaced/Renamed Download Files (%s):" % len(revokedFiles)) output.extend(self.__printWithPath(revokedFiles, c, args['releaseNew'])) gbdbprint = len(newGbdbSet | oldGbdbSet | revokedGbdbs) self.newGbdbs = set(self.__printGbdbPath(pushGbdbs, args['database'])) if gbdbprint: output.append("\n") output.append("GBDBS:") output.append("New: %s" % len(pushGbdbs)) output.append("Untouched: %s" % len((newGbdbSet & oldGbdbSet) - revokedGbdbs)) output.append("Revoked/Replaced/Renamed: %s" % len(revokedGbdbs)) output.append("New + Untouched: %s" % len(pushGbdbs | ((newGbdbSet & oldGbdbSet) - revokedGbdbs))) output.append("Total (New + Untouched + Revoked/Replaced/Renamed): %s" % len(newGbdbSet | oldGbdbSet | revokedGbdbs)) if gbdbprint and not args['summary']: output.append("") output.append("New Gbdb Files (%s):" % len(pushGbdbs)) output.extend(sorted(list(self.newGbdbs))) output.append("") output.append("Untouched Gbdb Files (%s):" % len((newGbdbSet & oldGbdbSet) - revokedGbdbs)) output.extend(self.__printGbdbPath((newGbdbSet & oldGbdbSet) - revokedGbdbs, args['database'])) output.append("") output.append("Revoked/Replaced/Renamed Gbdb Files (%s):" % len(revokedGbdbs)) output.extend(self.__printGbdbPath(revokedGbdbs, args['database'])) supplementalprint = len(newSupplementalSet | oldSupplementalSet) self.newSupplemental = set(self.__printWithPath(newSupplementalSet - oldSupplementalSet, c, args['releaseNew'])) if supplementalprint: output.append("\n") output.append("SUPPLEMENTAL FILES:") output.append("New: %s" % len(newSupplementalSet - oldSupplementalSet)) output.append("Untouched: %s" % len(oldSupplementalSet & newSupplementalSet)) output.append("Removed: %s" % len(oldSupplementalSet - newSupplementalSet)) output.append("New + Untouched: %s" % len((newSupplementalSet - oldSupplementalSet) | (oldSupplementalSet & newSupplementalSet))) output.append("Total: %s" % len(newSupplementalSet | oldSupplementalSet)) if supplementalprint and not args['summary']: output.append("") output.append("New Supplemental Files (%s):" % len(newSupplementalSet - oldSupplementalSet)) output.extend(sorted(list(self.newSupplemental))) output.append("") output.append("Untouched Supplemental Files (%s):" % len(oldSupplementalSet & newSupplementalSet)) output.extend(self.__printWithPath(oldSupplementalSet & newSupplementalSet, c, args['releaseNew'])) output.append("") output.append("Removed Supplemental Files (%s):" % len(oldSupplementalSet - newSupplementalSet)) output.extend(self.__printWithPath(oldSupplementalSet - newSupplementalSet, c, args['releaseNew'])) otherprint = len(additionalList | oldAdditionalList) self.newOthers = set(self.__printWithPath(additionalList, c, args['releaseNew'])) if otherprint: output.append("\n") output.append("OTHER FILES:") output.append("New: %s" % len(additionalList)) output.append("Revoked/Replace: %s" % len(oldAdditionalList - additionalList)) output.append("Total: %s" % len(additionalList | oldAdditionalList)) if otherprint and not args['summary']: output.append("") output.append("New Other Files (%s):" % len(additionalList)) output.extend(sorted(list(self.newOthers))) output.append("") output.append("Revoked Other Files (%s):" % len(oldAdditionalList - additionalList)) output.extend(self.__printWithPath((oldAdditionalList - additionalList), c, args['releaseNew'])) output.append("\n") if len(missingFiles): output.append("Files that dropped between releases (%s):" % len(missingFiles)) output.extend(self.__printWithPath(missingFiles, c, args['releaseOld'])) output.append("\n") if not args['ignore']: output.append("No Errors") return output def printReportOne(self, args, c): (totalFiles, revokedFiles, newGbdbSet, revokedGbdbs, newTableSet, revokedTables, additionalList, atticSet, newSupplementalSet, tableSize) = (self.totalFiles, self.revokedFiles, self.newGbdbSet, self.revokedGbdbs, self.newTableSet, self.revokedTableSet, self.additionalList, self.atticSet, self.newSupplementalSet, self.tableSize) output = [] output.append("mkChangeNotes v2") output.append("%s %s Release %s" % (args['database'], args['composite'], args['releaseNew'])) output.append("") output.append("QA Count Summaries for Release %s:" % args['releaseNew']) output.append("Tables: %d" % int(len(newTableSet - revokedTables))) output.append("Files: %d" % int(len(totalFiles - revokedFiles))) output.append("Gbdbs: %d" % int(len(newGbdbSet - revokedGbdbs))) output.append("Supplemental: %d" % int(len(newSupplementalSet))) output.append("Other: %d" % int(len(additionalList))) output.append("") output.append("REVOKED:") output.append("Tables: %s" % len(revokedTables)) output.append("Files: %s" % len(revokedFiles)) output.append("Gbdbs: %s" % len(revokedGbdbs)) output.append("\n") totalsize = 0; output.append("Sizes of New:") tableGb = int(tableSize / 1024) if tableGb > 1: output.append("Tables: %d MB (%d GB)" % (tableSize, tableGb)) else: output.append("Tables: %d MB" % tableSize) totalsize = totalsize + tableSize size = int(self.__makeFileSizes(c, args, totalFiles - revokedFiles)) totalsize = totalsize + size if int(size/1024) > 1: output.append("Files: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Files: %d MB" % size) size = int(self.__makeFileSizes(c, args, newGbdbSet - revokedGbdbs)) totalsize = totalsize + size if int(size/1024) > 1: output.append("Gbdbs: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Gbdbs: %d MB" % size) size = int(self.__makeFileSizes(c, args, newSupplementalSet)) totalsize = totalsize + size if int(size/1024) > 1: output.append("Supplemental: %d MB (%d GB)" % (size, int(size/1024))) else: output.append("Supplemental: %d MB" % size) size = int(self.__makeFileSizes(c, args, (additionalList))) totalsize = totalsize + size if int(size/1024) > 1: output.append("Other: %d MB" % size) else: output.append("Other: %d MB" % size) if int(totalsize/1024) > 1: output.append("Total: %d MB (%d GB)" % (totalsize, int(totalsize/1024))) else: output.append("Total: %d MB" % totalsize) output.append("\n") self.newTables = set(self.__printIter(newTableSet - revokedTables)) self.newFiles = set(self.__printWithPath(totalFiles - revokedFiles, c, args['releaseNew'])) self.newGbdbs = set(self.__printGbdbPath(newGbdbSet - revokedGbdbs, args['database'])) self.newSupplemental = set(self.__printWithPath(newSupplementalSet, c, args['releaseNew'])) self.newOthers = set(self.__printWithPath(additionalList, c, args['releaseNew'])) if not args['summary']: output.append("") if len(newTableSet - revokedTables): output.append("New Tables (%s):" % len(self.newTables)) output.extend(sorted(list(self.newTables))) output.append("\n") if len(totalFiles - revokedFiles): output.append("New Download Files (%s):" % len(self.newFiles)) output.extend(sorted(list(self.newFiles))) output.append("\n") if len(newGbdbSet - revokedGbdbs): output.append("New Gbdb Files (%s):" % len(newGbdbSet - revokedGbdbs)) output.extend(sorted(list(self.newGbdbs))) output.append("\n") if len(newSupplementalSet): output.append("New Supplemental Files (%s):" % len(newSupplementalSet)) output.extend(sorted(list(self.newSupplemental))) output.append("\n") if len(additionalList): output.append("New Other Files (%s):" % len(additionalList)) output.extend(sorted(list(self.newOthers))) output.append("\n") if len(revokedTables): output.append("Revoked Tables (%s):" % len(revokedTables)) output.extend(self.__printIter(revokedTables)) output.append("\n") if len(revokedFiles): output.append("Revoked Files (%s):" % len(revokedFiles)) output.extend(self.__printWithPath(revokedFiles, c, args['releaseNew'])) output.append("\n") if len(revokedGbdbs): output.append("Revoked Gbdbs (%s):" % len(revokedGbdbs)) output.extend(self.__printGbdbPath(revokedGbdbs, args['database'])) output.append("\n") if not args['ignore']: output.append("No Errors") return output def printErrors(self, errors): errorsDict = {} output = [] for i in errors: line = i.split(":", 1) try: errorsDict[line[0]].append(line[1]) except: errorsDict[line[0]] = [] errorsDict[line[0]].append(line[1]) output.append("Errors (%s):" % len(errors)) for i in sorted(errorsDict.keys()): output.append("%s:" % i) for j in sorted(errorsDict[i]): output.append("%s" % j) return output def __init__(self, args): self.releaseNew = args['releaseNew'] self.releaseOld = args['releaseOld'] self.database = args['database'] self.composite = args['composite'] self.loose = args['loose'] self.ignore = args['ignore'] self.summary = args['summary'] self.args = args errors = [] c = track.CompositeTrack(self.database, self.composite) #sanitize arguments if not self.releaseOld.isdigit(): self.releaseOld = 'solo' elif int(self.releaseOld) <= 0: self.releaseOlf = 'solo' elif self.releaseOld > self.releaseNew: self.releaseOld = 'solo' if int(self.releaseNew) > 1 and str(self.releaseOld) != 'solo': self.newReleaseFiles = c.releases[int(self.releaseNew)-1] self.oldReleaseFiles = c.releases[int(self.releaseOld)-1] self.newMdb = c.alphaMetaDb self.oldMdb = c.publicMetaDb #check if all files listed in release directories have associated metaDb entries (self.newMdb, self.revokedSet, self.revokedFiles, self.atticSet, self.newSupplementalSet, newFileErrors) = self.checkMetaDbForFiles("alpha metaDb", "new") (self.oldMdb, spam, eggs, ham, self.oldSupplementalSet, oldFileErrors) = self.checkMetaDbForFiles("public metaDb", "old") errors.extend(newFileErrors) errors.extend(oldFileErrors) #checks to see that nothing has disappeared between public and alpha errors.extend(self.__checkAlphaForDropped("alpha metaDb", "stanza")) self.missingFiles = self.__checkFilesForDropped() errors.extend(self.__checkMd5sums()) #checks and gets tables that are present, also returns a revoked set of tables for new (self.newTableSet, self.revokedTableSet, newTableError) = self.checkTableStatus("alpha metaDb", "new") (self.oldTableSet, spam, oldTableError) = self.checkTableStatus("public metaDb", "old") errors.extend(newTableError) errors.extend(oldTableError) #same as above except for gbdbs (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new") (self.oldGbdbSet, eggs, oldGbdbError) = self.getGbdbFiles("old") errors.extend(newGbdbError) errors.extend(oldGbdbError) #for ease of typing totalFiles = set(self.newReleaseFiles) oldTotalFiles = set(self.oldReleaseFiles) #these could honestly be moved earlier, get a file list processing section or something #they clean out special fiels out and separated the master fiels list into the 3 required #ones: wgEncode, supplemental and additional. self.totalFiles = self.__cleanSpecialFiles(totalFiles) self.oldTotalFiles = self.__cleanSpecialFiles(oldTotalFiles) (self.oldTotalFiles, self.additionalList, self.oldAdditionalList, self.totalFiles) = self.__separateOutAdditional() #get the stuff you need to push, also table sizes self.pushTables = set(sorted((self.newTableSet - self.oldTableSet))) self.pushFiles = set(sorted((self.totalFiles - self.oldTotalFiles))) self.pushGbdbs = set(sorted((self.newGbdbSet - self.oldGbdbSet))) self.tableSize = self.__getTableSize() #don't output.append(report unless ignore option is on or no errors if (not errors) or self.ignore: self.output = self.printReport(args, c) else: self.output = self.printErrors(errors) elif self.releaseOld == 'solo': self.newReleaseFiles = c.releases[int(self.releaseNew)-1] self.newMdb = c.alphaMetaDb (self.newMdb, self.revokedSet, self.revokedFiles, self.atticSet, self.newSupplementalSet, newFileErrors) = self.checkMetaDbForFiles("alpha metaDb", "new") errors.extend(newFileErrors) (self.newTableSet, self.revokedTableSet, newTableError) = self.checkTableStatus("alpha metaDb", "new") errors.extend(newTableError) self.tableSize = self.__getTableSize() (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new") errors.extend(newGbdbError) #set for easy operations totalFiles = set(self.newReleaseFiles) #clean out special fiels we don't push i.e. md5sum.history self.totalFiles = self.__cleanSpecialFiles(totalFiles) #makes list for additional files (self.oldTotalFiles, self.oldSupplementalSet) = (set(), set()) (self.oldReleaseFiles, self.additionalList, self.oldAdditionalList, self.totalFiles) = self.__separateOutAdditional() if (not errors) or self.ignore: self.output = self.printReportOne(args, c) else: self.output = self.printErrors(errors) def main(): parser = argparse.ArgumentParser( prog='mkChangeNotes', formatter_class=argparse.RawDescriptionHelpFormatter, description='Writes out notes file for packing to QA', epilog= """Examples: mkChangeNotes hg19 wgEncodeUwDnase 3 2 --loose mkChangeNotes hg19 wgEncodeSydhTfbs 1 - --full mkChangeNotes hg19 wgEncodeCshlLongRnaSeq 1 - """ ) parser.add_argument('-l', '--loose', action="store_true", default=0, help='Loose checking for legacy elements. Will be retired once all tracks go through a release cycle') parser.add_argument('-i', '--ignore', action="store_true", default=0, help='Ignore errors, output.append(out report.') parser.add_argument('-s', '--summary', action="store_true", default=0, help='output.append(summary stats only.') parser.add_argument('database', help='The database, typically hg19 or mm9') parser.add_argument('composite', help='The composite name, wgEncodeCshlLongRnaSeq for instance') parser.add_argument('releaseNew', help='The new release to be released') parser.add_argument('releaseOld', nargs='?', default='-', help='The old release that is already released, if on release 1, or solo release mode, put anything here') if len(sys.argv) == 1: parser.print_help() return args = parser.parse_args(sys.argv[1:]) if not args.releaseNew.isdigit(): parser.print_help() return if not args.releaseOld.isdigit(): args.releaseOld = 'solo' elif int(args.releaseOld) > int(args.releaseNew): errors.append("Old Release is higher than New Release") args.releaseOld = args.releaseNew printErrors(errors) return argsdict = {'database': args.database, 'composite': args.composite, 'releaseNew': args.releaseNew, 'releaseOld': args.releaseOld, 'loose': args.loose, 'ignore': args.ignore, 'summary': args.summary} notes = makeNotes(argsdict) for line in notes.output: print line if __name__ == '__main__': main()