7607fbec3f1c56d1a8b0a24317b87340292205bf wong Fri Feb 17 13:54:59 2012 -0800 changed the reporting of changed tables state to be a critical error diff --git python/lib/ucscgenomics/mkChangeNotes.py python/lib/ucscgenomics/mkChangeNotes.py index 00b76eb..5e26381 100644 --- python/lib/ucscgenomics/mkChangeNotes.py +++ python/lib/ucscgenomics/mkChangeNotes.py @@ -1,722 +1,720 @@ #!/hive/groups/encode/dcc/bin/python import sys, os, re, argparse, subprocess, math, datetime, time from ucscgenomics import ra, track, qa, ucscUtils 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 state == 'old' 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): errors=[] diff = set(self.oldMdb) - set(self.newMdb) for i in diff: if re.match('.*MAGIC.*', i): continue errors.append("%s: %s missing from %s" % (type, i, status)) return errors def __checkFilesForDropped(self): diff = set(self.oldReleaseFiles) - set(self.newReleaseFiles) 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) ### If MySQLdb ever gets installed ### #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()) ### END ### mdbobjectset = set(mdb.filter(lambda s: s['objType'] == 'table' and 'tableName' in s and 'attic' not in s, lambda s: s['metaObject'])) - revokedset mdbtableset = set(mdb.filter(lambda s: s['metaObject'] in mdbobjectset, 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) cmdoutput = p.stdout.read() 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'])) if missingTableNames: for i in missingTableNames: errors.append("table: %s is type obj, but missing tableName field called by %s" % (i, status)) missingFromDb = mdbtableset - sqltableset if missingFromDb: for i in missingFromDb: errors.append("table: %s table not found in Db called by %s" % (i, status)) return (mdbtableset, revokedtableset, missingFromDb, errors) def __checkGbdbFileStatus(self, i, set, errors, state): filelist = i['fileName'].split(',') #preprocess filelist, delete after bai in mdb issue is revoled #print filelist[0] if re.match('\S+.bam', filelist[0]) and filelist[0] in self.oldReleaseFiles and (filelist[0] + '.bai') not in filelist: filelist.append(filelist[0] + '.bai') for j in filelist: if ucscUtils.isGbdbFile(j, i['tableName'], self.database): set.add(j) else: errors.append("gbdb: %s%s does not exist in %s" % (state, j, self.gbdbPath)) return set, errors def getGbdbFiles(self, state): 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) filestanzas = mdb.filter(lambda s: s['tableName'] in gbdbtableset, lambda s: s) revokedstanzas = mdb.filter(lambda s: s['tableName'] in revokedtableset, lambda s: s) gbdbfileset = set() revokedfileset = set() for i in filestanzas: (gbdbfileset, errors) = self.__checkGbdbFileStatus(i, gbdbfileset, errors, "") for i in revokedstanzas: (revokedfileset, errors) = self.__checkGbdbFileStatus(i, revokedfileset, errors, "revoked gbdb ") 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,2) total_size_mb, ROUND(index_length,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) cmdoutput = p.stdout.read() for i in cmdoutput.split("\n")[1:-1]: fields = i.split() for j in fields: tablesize = tablesize + float(j) tablesize = tablesize/(1024 ** 2) return int(math.ceil(tablesize)) def __checkMd5sums(self): (newfiles, oldfiles, loose) = (self.newReleaseFiles, self.oldReleaseFiles, self.loose) errors = [] repush = set() for i in oldfiles: if i not in newfiles: pass elif re.match('wgEncode.*', i): if oldfiles[i].md5sum != newfiles[i].md5sum: repush.add(i) errors.append("file: %s have changed md5sums between releases. %s vs %s" % (i, oldfiles[i].md5sum, newfiles[i].md5sum)) if loose: for i in repush: del oldfiles[i] return list() else: return errors 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 __determineNiceSize(self, bytes): bytes = float(bytes) if bytes >= (1024**2): terabytes = bytes / (1024**2) size = '%.2f TB' % terabytes elif bytes >= (1024): gigabytes = bytes / (1024) size = '%.0f GB' % gigabytes else: return 0 return size def __printSize(self, size, output, totalsize, type): nicesize = self.__determineNiceSize(size) if nicesize: output.append("%s: %d MB (%s)" % (type, size, nicesize)) else: output.append("%s: %d MB" % (type, size)) totalsize = totalsize + size return (output, totalsize, str(size)) def __printSection(self, new, untouched, revoked, all, title, path, summary): output = [] removeline = "Revoked/Replaced/Renamed" totaline = "Total (New + Untouched + Revoked/Replaced/Renamed)" caps = title.upper() - change = set() - if title == "tables": - change = self.changedTables - elif title == "supplemental": + if title == "supplemental": removeline = "Removed" totaline = "Total" title = title + " files" caps = title.upper() elif title == 'gbdbs': caps = "GBDBS" title = "gbdb files" - change = self.changedGbdbs elif title == "download": title = title + " files" caps = title.upper() if all: output.append("") output.append("%s:" % caps) output.append("New: %s" % len(new)) output.append("Untouched: %s" % len(untouched)) output.append("%s: %s" % (removeline, len(revoked))) output.append("New + Untouched: %s" % len(new | untouched)) output.append("%s: %s" % (totaline, len(all))) intersect = new & revoked if intersect: output.append("") output.append("These %s objects exist in both new and revoked %s:" % (len(intersect), title)) for i in intersect: output.append("%s" % i) - if change: - output.append("") - output.append("These %s objects changed state between public and alpha" % len(change)) - for i in change: - output.append("%s" % i) if all and not summary: output.append("") output.append("New %s (%s):" % (title.title(), len(new))) output.extend(ucscUtils.printIter(new, path)) output.append("") output.append("Untouched %s (%s):" % (title.title(), len(untouched))) output.extend(ucscUtils.printIter(untouched, path)) output.append("") output.append("%s %s (%s):" % (removeline, title.title(), len(revoked))) output.extend(ucscUtils.printIter(revoked, path)) if all: output.append("") return output def __qaHeader(self, output, newTableSet, filesNoRevoke, newGbdbSet, newSupp, additionalList, revokedTables, revokedFiles, revokedGbdbs, pushFiles, pushGbdbs, args, c): output = [] tableSize = self.__getTableSize() output.append("mkChangeNotes v2") title = "%s %s Release %s" % (args['database'], args['composite'], args['releaseNew']) if args['releaseOld'] != "solo": title = title + " vs Release %s" % args['releaseOld'] if args['summary']: title = "Summary for " + title output.append(title) d = datetime.date.today() output.append("%s" % str(d)) 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(filesNoRevoke))) output.append("Gbdbs: %d" % int(len(newGbdbSet))) output.append("Supplemental: %d" % int(len(newSupp))) 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("") output.append("Sizes of New:") totalsize = 0 (output, totalsize, strout) = self.__printSize(tableSize, output, totalsize, "Table") self.totalTableSize = strout (output, totalsize, strout) = self.__printSize(int(ucscUtils.makeFileSizes(pushFiles, self.releasePath)), output, totalsize, "Files") self.totalFilesSize = strout (output, totalsize, strout) = self.__printSize(int(ucscUtils.makeFileSizes(pushGbdbs, self.releasePath)), output, totalsize, "Gbdbs") self.totalGbdbsSize = strout (output, totalsize, strout) = self.__printSize(int(ucscUtils.makeFileSizes(newSupp, self.releasePath)), output, totalsize, "Supplemental") self.totalSupplementalSize = strout (output, totalsize, strout) = self.__printSize(int(ucscUtils.makeFileSizes(additionalList, self.releasePath)), output, totalsize, "Other") self.totalAdditionalSize = strout (output, totalsize, strout) = self.__printSize(totalsize, output, 0, "Total") self.totalEverythingSize = strout output.append("") return output def __addMissingToReport(self, missing, type, path=None): output = [] if missing: output.append("%s that dropped between releases (%s):" % (type, len(missing))) output.extend(ucscUtils.printIter(missing, path)) output.append("\n") return output def __checkAtticNotInTrackDb(self): errors = [] atticTables = self.newMdb.filter(lambda s: s['objType'] == 'table' and 'attic' in s, lambda s: s['tableName']) for i in atticTables: foo = self.trackDb.filter(lambda s: i in s['track'], lambda s: s['track']) if foo: errors.append("trackDb: %s is attic in metaDb, has an active trackDb entry" % i) return errors def printReport(self, args, c): (totalFiles, newGbdbSet, newTableSet, additionalList, oldAdditionalList, oldTableSet, oldReleaseFiles, oldGbdbSet, atticSet, revokedFiles, revokedTableSet, revokedGbdbs, missingFiles, newSupplementalSet, oldSupplementalSet, pushTables, pushFiles, pushGbdbs, newSupp) = (self.totalFiles, self.newGbdbSet, self.newTableSet, self.additionalList, self.oldAdditionalList, self.oldTableSet, self.oldTotalFiles, self.oldGbdbSet, self.atticSet, self.revokedFiles, self.revokedTableSet, self.revokedGbdbs, self.missingFiles, self.newSupplementalSet, self.oldSupplementalSet, self.pushTables, self.pushFiles, self.pushGbdbs, self.newSupp) #the groups here need to be predefined, I just copied and pasted after working out what they were sep = "\n" output = [] #maths allTables = newTableSet | oldTableSet | revokedTableSet untouchedTables = oldTableSet & newTableSet allFiles = totalFiles | oldReleaseFiles | revokedFiles newFiles = pushFiles - revokedFiles untouchedFiles = (totalFiles & oldReleaseFiles) - revokedFiles filesNoRevoke = totalFiles - revokedFiles allGbdbs = newGbdbSet | oldGbdbSet | revokedGbdbs untouchedGbdbs = (newGbdbSet & oldGbdbSet) - revokedGbdbs allSupp = newSupplementalSet | oldSupplementalSet removedSupp = oldSupplementalSet - newSupplementalSet untouchedSupp = oldSupplementalSet & newSupplementalSet allOther = additionalList | oldAdditionalList removedOther = oldAdditionalList - additionalList output.extend(self.__qaHeader(output, newTableSet, filesNoRevoke, newGbdbSet, newSupp, additionalList, revokedTableSet, revokedFiles, revokedGbdbs, pushFiles, pushGbdbs, args, c)) output.extend(self.__printSection(pushTables, untouchedTables, revokedTableSet, allTables, "tables", 0, args['summary'])) output.extend(self.__printSection(pushFiles, untouchedFiles, revokedFiles, allFiles, "download", self.releasePath, args['summary'])) output.extend(self.__printSection(pushGbdbs, untouchedGbdbs, revokedGbdbs, allGbdbs, "gbdbs", self.gbdbPath, args['summary'])) output.extend(self.__printSection(newSupp, untouchedSupp, removedSupp, allSupp, "supplemental", self.releasePath, args['summary'])) #These attributes are the critical ones that are used by qaInit, others could potentially use these also. otherprint = len(allOther) if otherprint: output.append("\n") output.append("OTHER FILES:") output.append("New: %s" % len(additionalList)) output.append("Revoked/Replace: %s" % len(removedOther)) output.append("Total: %s" % len(allOther)) 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(removedOther)) output.extend(ucscUtils.printIter((removedOther), self.releasePath)) output.append("\n") output.extend(self.__addMissingToReport(missingFiles, "Files", self.releasePathOld)) output.append("\n") output.extend(self.__addMissingToReport(self.droppedTables, "Tables")) output.append("\n") if self.atticSet: if self.newInAttic: output.append("New Attic Objects (%s):" % len(self.newInAttic)) output.extend(ucscUtils.printIter((self.newInAttic))) if self.stillInAttic: output.append("Untouched Attic Objects (%s):" % len(self.stillInAttic)) output.extend(ucscUtils.printIter((self.stillInAttic))) if self.noMoreAttic: output.append("Untouched Attic Objects (%s):" % len(self.noMoreAttic)) output.extend(ucscUtils.printIter((self.noMoreAttic))) output.append("\n") if not args['ignore']: output.append("No Errors") else: output.append("The counts here were generated by ignoring errors, they may not be correct") return output def __printSectionOne(self, output, set, title): output = [] if set: output.append("%s (%s):" % (title, len(set))) output.extend(sorted(list(set))) else: return output output.append("\n") 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 = [] newTables = newTableSet - revokedTables newFiles = totalFiles - revokedFiles newGbdbs = newGbdbSet - revokedGbdbs output.extend(self.__qaHeader(output, newTables, newFiles, newGbdbSet, newSupplementalSet, additionalList, revokedTables, revokedFiles, revokedGbdbs, totalFiles, newGbdbSet, args, c)) self.newTables = set(newTables) self.newFiles = set(ucscUtils.printIter(newFiles, self.releasePath)) self.newGbdbs = set(ucscUtils.printIter(newGbdbs, self.gbdbPath)) self.newSupplemental = set(ucscUtils.printIter(newSupplementalSet, self.releasePath)) self.newOthers = set(ucscUtils.printIter(additionalList, self.releasePath)) if not args['summary']: output.append("") output.extend(self.__printSectionOne(output, self.newTables, "New Tables")) output.extend(self.__printSectionOne(output, self.newFiles, "New Download Files")) output.extend(self.__printSectionOne(output, self.newGbdbs, "New Gbdb Files")) output.extend(self.__printSectionOne(output, self.newSupplemental, "New Supplemental Files")) output.extend(self.__printSectionOne(output, self.newOthers, "New Other Files")) output.extend(self.__printSectionOne(output, ucscUtils.printIter(revokedTables, 0), "Revoked Tables")) output.extend(self.__printSectionOne(output, ucscUtils.printIter(revokedFiles, self.releasePath), "Revoked Files")) output.extend(self.__printSectionOne(output, ucscUtils.printIter(revokedGbdbs, self.gbdbPath), "Revoked Gbdbs")) if self.atticSet: output.append("Attic Objects") output.extend(ucscUtils.printIter((self.atticSet), self.releasePath)) if not args['ignore']: output.append("No Errors") else: output.append("The counts here were generated by ignoring errors, they may not be correct") return output def printErrors(self, errors, missingFiles): 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) output.append("\n") if missingFiles: output.extend(self.__addMissingToReport(missingFiles, "Files", self.releasePathOld)) output.append("\n") if self.droppedTables: output.extend(self.__addMissingToReport(self.droppedTables, "Tables")) 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.specialMdb = args['specialMdb'] self.args = args if 'verbose' in args: self.verbose = args['verbose'] else: self.verbose = 0 errors = [] c = track.CompositeTrack(self.database, self.composite, None, self.specialMdb) #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 self.verbose >= 1: sys.stderr.write("Initializing MkChangeNotes\n") self.releasePath = c.httpDownloadsPath + 'release' + args['releaseNew'] self.gbdbPath = "/gbdb/%s/bbi" % args['database'] self.trackDbFile = c.currentTrackDb if not self.trackDbFile: self.trackDb = None errors.append("track: There is no entry in trackDb.wgEncode.ra for %s with the alpha tag" % self.composite) else: self.trackDb = ra.RaFile(self.trackDbFile, "track") if int(self.releaseNew) > 1 and str(self.releaseOld) != 'solo': if self.verbose >= 2: sys.stderr.write("Comparison mode\n") self.newReleaseFiles = c.releases[int(self.releaseNew)-1] self.oldReleaseFiles = c.releases[int(self.releaseOld)-1] self.releasePathOld = c.httpDownloadsPath + 'release' + args['releaseOld'] self.newMdb = c.alphaMetaDb self.oldMdb = c.publicMetaDb if self.verbose >= 2: sys.stderr.write("Checking for missing files\n") #make a list of missing files self.missingFiles = self.__checkFilesForDropped() #filter them out of old release files if self.verbose >= 1: sys.stderr.write("Scanning and parsing release directories\n") #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, self.oldAtticSet, self.oldSupplementalSet, oldFileErrors) = self.checkMetaDbForFiles("public metaDb", "old") self.expIds = set(self.newMdb.filter(lambda s: 'expId' in s, lambda s: s['expId'])) if self.verbose >= 2: sys.stderr.write("Checking for attic files\n") #check that attic fiels aren't in trackDb if self.trackDb: errors.extend(self.__checkAtticNotInTrackDb()) #checks to see that nothing has disappeared between public and alpha if self.verbose >= 1: sys.stderr.write("Checking new metaDb for missing stanzas\n") errors.extend(self.__checkAlphaForDropped("alpha metaDb", "stanza")) if self.verbose >=1: sys.stderr.write("Checking file md5sums across releases\n") errors.extend(self.__checkMd5sums()) #checks and gets tables that are present, also returns a revoked set of tables for new if self.verbose >= 1: sys.stderr.write("Checking table status\n") (self.newTableSet, self.revokedTableSet, self.newMissingTables, newTableError) = self.checkTableStatus("alpha metaDb", "new") (self.oldTableSet, spam, self.droppedTables, oldTableError) = self.checkTableStatus("public metaDb", "old") self.newInAttic = self.atticSet - self.oldAtticSet self.stillInAttic = self.oldAtticSet & self.atticSet self.oldTableSet = self.oldTableSet - self.atticSet self.noMoreAttic = self.oldAtticSet - self.atticSet self.changedTables = self.oldTableSet - self.newTableSet - self.revokedTableSet #same as above except for gbdbs if self.verbose >= 1: sys.stderr.write("Checking GBDB status\n") (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new") (self.oldGbdbSet, eggs, oldGbdbError) = self.getGbdbFiles("old") #remove missing files from gbdbs self.oldGbdbSet = self.oldGbdbSet - self.missingFiles self.oldGbdbSet = self.oldGbdbSet - self.atticSet self.changedGbdbs = self.oldGbdbSet - self.newGbdbSet for i in self.missingFiles: if i in self.oldReleaseFiles: del self.oldReleaseFiles[i] #fill in the errors errors.extend(newFileErrors) errors.extend(oldFileErrors) errors.extend(newTableError) errors.extend(oldTableError) errors.extend(newGbdbError) errors.extend(oldGbdbError) + if self.changedTables: + errors.append("These tables were tables in the old release, but are no longer tables in the new release:" + errors.extend(list(self.changedTables)) + if self.changedGbdbs: + errors.append("These GBDBs were GBDB tables in the old release, but are no longer GBDB tables in the new release:" + errors.extend(list(self.changedGbdbs)) + #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 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.newSupp = self.newSupplementalSet - self.oldSupplementalSet self.newTables = set(self.pushTables) self.newFiles = set(ucscUtils.printIter(self.pushFiles, self.releasePath)) self.newGbdbs = set(ucscUtils.printIter(self.pushGbdbs, self.gbdbPath)) self.newSupplemental = set(ucscUtils.printIter(self.newSupp, self.releasePath)) self.newOthers = set(ucscUtils.printIter(self.additionalList, self.releasePath)) self.fullFiles = sorted(self.totalFiles - self.revokedFiles) self.fullTables = self.oldTableSet & self.newTableSet self.errors = errors #don't output.append(report unless ignore option is on or no errors #module mode doesn't generate output by default if self.verbose >= 1: sys.stderr.write("Creating report\n") if (not errors) or self.ignore: self.output = self.printReport(args, c) else: self.output = self.printErrors(errors, self.missingFiles) elif self.releaseOld == 'solo': self.newReleaseFiles = c.releases[int(self.releaseNew)-1] self.oldReleaseFiles = set() self.newMdb = c.alphaMetaDb #check that attic fiels aren't in trackDb if self.trackDb: errors.extend(self.__checkAtticNotInTrackDb()) (self.newMdb, self.revokedSet, self.revokedFiles, self.atticSet, self.newSupplementalSet, newFileErrors) = self.checkMetaDbForFiles("alpha metaDb", "new") self.expIds = set(self.newMdb.filter(lambda s: 'expId' in s, lambda s: s['expId'])) (self.newTableSet, self.revokedTableSet, spam, newTableError) = self.checkTableStatus("alpha metaDb", "new") self.tableSize = self.__getTableSize() (self.newGbdbSet, self.revokedGbdbs, newGbdbError) = self.getGbdbFiles("new") #collect errors errors.extend(newFileErrors) errors.extend(newTableError) 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) self.pushTables = self.newTableSet self.pushFiles = self.totalFiles self.pushGbdbs = self.newGbdbSet self.newSupp = self.newSupplementalSet self.fullFiles = self.totalFiles self.fullTables = self.newTableSet #makes list for additional files (self.oldTotalFiles, self.oldSupplementalSet) = (set(), set()) (self.oldReleaseFiles, self.additionalList, self.oldAdditionalList, self.totalFiles) = self.__separateOutAdditional() self.errors = errors if (not errors) or self.ignore: self.output = self.printReportOne(args, c) else: self.droppedTables = set() self.output = self.printErrors(errors, set())