05e67c59a20a5d00b810a981aef3b00c5bef82e1
max
Fri Sep 20 06:03:18 2024 -0700
more features to hubtools: search in both parent and subdirs, better docs
diff --git src/hg/hgMirror/hgMirror src/hg/hgMirror/hgMirror
index 396bd17..98e25fb 100755
--- src/hg/hgMirror/hgMirror
+++ src/hg/hgMirror/hgMirror
@@ -1,86 +1,81 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
# A little CGI interface to download the tables for a set of tracks via udr
# to local machine. This is mostly useful when setting up a mirror or a VM
# of the browser. It does not run on hgwdev.
# This script does the following:
# - get trackDb and grp table from hgDownload
# - get table and gbdb sizes from ucsc rsync server
# - get list with track<->filename for all bigfile tracks from hgwdev
# - try to assign table names to gbdb files using this list and some hacky rules
# - parse hg.conf to find mysql server and hide a few tracks in its trackDb
# - infer track/subtrack hierarchy by parsing trackDb
# - generate HTML table with labels/sizes/tablecounts for all tracks and their child tracks
# - when user clicks submit, start rsync transfer and redirect to page that shows progress
# - handles non-existing tables and some hgFixed tables
# When run from the command line, this CGI hides some tracks and removes tracks from
# track search on hg19. This is usually run from a cronjob after trackDb updates.
# This script requires the following setup
-# - mysqldb python module
# - "rsync" in path
# - "at" in path
# To allow this on ubuntu, add these lines to /etc/sudoers:
#www-data ALL = (mysql:mysql) NOPASSWD: /bin/ls,/usr/bin/rsync,/bin/rm
#www-data ALL = (root:root) NOPASSWD: /bin/mkdir /gbdb
#www-data ALL = (root:root) NOPASSWD: /bin/chown www-data.www-data /gbdb
# - the apache user has to be able to run 'at' jobs.
# To allow this on ubuntu, need to run this command to remove www-data from /etc/at.deny
# sudo sed -i s/www-data//g /etc/at.deny
# This script does not handle:
# tables joined to other tables are not downloaded. Would have to parse all.joiner for that.
# format python errors in html, as we're a CGI script
import cgi
import cgitb; cgitb.enable()
# these are default python modules on python 2.7, no errors expected here
-import urllib, urllib2, zlib, collections, StringIO, gzip, string, sys, os, random, \
- subprocess, re, types, socket, cPickle, copy, glob, tempfile, Cookie
+import urllib.request, urllib.parse, urllib.error, urllib.request, urllib.error, urllib.parse, zlib, collections, io, gzip, string, sys, os, random, \
+ subprocess, re, types, socket, pickle, copy, glob, tempfile, http.cookies
from collections import defaultdict, namedtuple
from os.path import *
from distutils import spawn
# import the UCSC-specific library
sys.path.append(join(dirname(__file__), "pyLib"))
try:
- from hgLib import getNonce, getCspMetaHeader, jsOnEventByIdF, jsInlineFinish
+ from hgLib3 import getNonce, getCspMetaHeader, jsOnEventByIdF, jsInlineFinish
# cgiArgs, cgiSetup, cgiString, printContentType, printMenuBar, \
# sqlConnect, sqlQuery, errAbort, cfgOption, runCmd, cgiGetAll, printHgcHeader, \
# printHgcSection,
# webStartGbNoBanner, htmlPageEnd, hConnectCentral, sqlTableExists, \
# readSmallFile
except:
print("Content-type: text/html\n")
print("Cannot find the directory cgi-bin/pyLib in Apache. This is an installation error.")
print("All all parts of cgi-bin installed? Did you do 'make' in kent/src/hg/pyLib?")
defaultDb = "hg19"
-# the mysqldb module has to be installed with one of these commands:
-# - many common linuxes and OSX: pip install mysqldb
-# - debian: sudo apt-get install python-mysqldb
-# - fedora/centos/redhat: sudo yum install python-mysqldb
-# The script works without the mysqldb module but cannot auto-hide some tracks.
+# The script works without mysql module but cannot auto-hide some tracks.
mysqlDbLoaded = True
try:
- import MySQLdb
+ import pymysql.cursors
except:
mysqlDbLoaded = False
# default mysql data dir on debian-based distros
MYSQLDIR = "/var/lib/mysql"
# can probably autodetect this, but hardcoded here
APACHEUSER = "www-data"
# optional file with rows to add to tableList
TABLELISTADD = "/root/tableListAdd.hg19.tab"
# directory for temporary files, keep trailing slash
TMPDIR = "/tmp/hgMirror/"
@@ -156,95 +151,95 @@
return hgConf
def sqlConnect(db, name):
""" connect to sql """
if name=="public":
host, user, passwd = "genome-mysql.soe.ucsc.edu", "genomep", "password"
elif name=="local":
cfg = parseHgConf()
host, user, passwd = cfg["db.host"], cfg["db.user"], cfg["db.password"]
conn = MySQLdb.connect(host=host, user=user, passwd=passwd, db=db)
return conn
def debug(msg):
if DEBUG:
- print(msg+" ")
+ print((msg+" "))
sys.stdout.flush()
def runningAtUcsc():
if "hgwdev" in socket.gethostname():
return True
return False
def runCmd(cmd, mustRun=True):
" wrapper around os.system that makes sure sudo is not called "
if runningAtUcsc() and cmd.startswith("sudo"):
return 0
ret = os.system(cmd)
if ret!=0 and mustRun:
- print "Could not run command %s" % cmd
+ print("Could not run command %s" % cmd)
sys.exit(0)
return ret
def loadGroups(db):
""" load grp table via mysql and return as a list of tuples (name, label)"""
groups = []
if mysqlDbLoaded:
conn = sqlConnect(db, "public")
cur = conn.cursor()
cur.execute("SELECT name, label from grp order by priority")
groups = []
for row in cur.fetchall():
groups.append((row[0], row[1]))
cur.close()
conn.close()
else:
for row in downloadTable(db, "grp"):
groups.append((row[0], row[1]))
return groups
def downloadTable(db, table):
"""
download table from hgdownload by parsing sql file first to get the field
names, then the tab sep file. Returns a list of objects, with field names
as attributes and their values from the tab sep file.
"""
baseUrl = 'http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/' % db
# parse the .sql file and create a namedtuple "struct" for it
sqlUrl = baseUrl+table+".sql"
- sqlLines = urllib2.urlopen(sqlUrl).read().splitlines()
+ sqlLines = urllib.request.urlopen(sqlUrl).read().splitlines()
fieldNames = []
for l in sqlLines:
if l.strip().startswith("PRIMARY KEY"):
continue
if l.startswith(" "):
fieldName = l.split()[0].strip("`")
fieldNames.append(fieldName)
Struct = namedtuple("rec", fieldNames)
# read the tab-sep data
# can use a cached copy from /tmp
tmpFname = TMPDIR+db+"."+table+".txt.gz"
if isfile(tmpFname):
data = open(tmpFname)
else:
dataUrl = baseUrl+table+".txt.gz"
- remoteData = urllib2.urlopen(dataUrl).read()
- data = StringIO.StringIO(remoteData) # gunzipping requires to wrap a pseudo-file around the gzip data
+ remoteData = urllib.request.urlopen(dataUrl).read()
+ data = io.StringIO(remoteData) # gunzipping requires to wrap a pseudo-file around the gzip data
# write to cache file
tmpFh = open(tmpFname, "w")
tmpFh.write(remoteData)
tmpFh.close()
data = gzip.GzipFile(fileobj=data).read()
data = data.replace("\\\n", "\a") # translate escaped mysql newline to \a
data = data.replace("\\\t", "\b") # translate escaped mysql tab to \b
lines = data.split("\n")
# convert tab-sep lines to namedtuples (=objects)
rows = []
for line in lines:
if len(line)==0:
continue
fields = line.split("\t")
@@ -410,79 +405,79 @@
trackTables[track] = [track]
# same for bigGeneDataUrl, only used on knownGene right now
if "bigGeneDataUrl" in settings:
trackBigDataFiles[track] = settings["bigGeneDataUrl"]
trackTables[track] = [track]
if track=="bacEndPairs":
trackTables[track].add("all_bacends")
return trackLabels, trackTables, trackParents, groups, pseudos, \
trackVis, superTracks, trackBigDataFiles
def htmlHeader():
" print start of page "
- print """
+ print("""
%s
UCSC Genome Browser mirror tool
- """ % (getCspMetaHeader())
- print open("../htdocs/inc/globalNavBar.inc").read()
+ """ % (getCspMetaHeader()))
+ print(open("../htdocs/inc/globalNavBar.inc").read())
sys.stdout.flush()
def htmlFooter():
" print end of page "
- print """
+ print("""
- """
+ """)
def findTopParent(trackParents, trackName):
" recursively search for the top level parent of a track "
if trackName not in trackParents:
return trackName
return findTopParent(trackParents, trackParents[trackName])
def makeTrackHierarchy(trackParents):
""" given a dict with track->parent return dict with parent->list of child tracks.
"""
debug("hierarchy")
trackChildren = dict()
- for track, parent in trackParents.iteritems():
+ for track, parent in trackParents.items():
if parent not in trackChildren:
trackChildren[parent] = []
trackChildren[parent].append(track)
return trackChildren
def getAllChildren(trackName, trackChildren):
""" given track name and hierarchy info, return list of all children (recursive)
"""
if trackName not in trackChildren:
return []
children = trackChildren[trackName]
- assert(type(children) is types.ListType)
+ assert(type(children) is list)
tracks = []
tracks.extend(children)
for child in children:
grandkids = getAllChildren(child, trackChildren)
tracks.extend(grandkids)
return tracks
def getTrackTables(trackName, trackTables, trackChildren):
""" return list of all track or table names required for a track,
this includes:
- tables that are split or specified via the trackDb "table" statement
- track names that do not have a table associated with them
- the same for all sub tracks of the track
"""
@@ -521,31 +516,31 @@
return sizeStr
#def freespace(p):
#""" Returns the number of free bytes on the drive that p is on """
# does not make a lot of sense in virtual box, with a virtual disk that is auto-extending
#s = os.statvfs(p)
#return s.f_bsize * s.f_bavail
def trackToFiles(trackName, trackTables, trackChildren, tableSizes, tableToGbdbFiles, noTableTracks, gbdbSizes):
" return list of mysql tables and gbdb files for a given trackName "
tableNames = []
gbdbFiles = []
# these tracks don't have any tables, but all gbdb files
if trackName=="allGbdb":
- return [], gbdbSizes.keys()
+ return [], list(gbdbSizes.keys())
elif trackName=="liftOver":
return [], tableToGbdbFiles.get("liftOver", [])
elif trackName=="nonTrackTables":
return trackChildren.get("nonTrackTables", []), []
trackTableNames = getTrackTables(trackName, trackTables, trackChildren)
# this predef track doesn't have any gbdb files
if trackName=="allTables":
return trackTableNames, []
for table in trackTableNames:
if table in noTableTracks:
continue
tableNames.append(table)
@@ -652,31 +647,31 @@
gbdbSizeStr = humanReadable(gbdbSize)
gbdbFCount = len(gbdbFnames)
gbdbStr=""
if gbdbFCount!=0:
gbdbStr = " + %(gbdbFCount)d gbdb files, %(gbdbSizeStr)s" % locals()
debug("tables: "+str(trackTableNames))
debug("gbdbFiles: "+str(gbdbFnames))
outStr = '%(indentStr)s'\
'%(label)s ' \
'(%(trackName)s): %(tableStr)s, %(sizeStr)s%(gbdbStr)s%(status)s %(addNote)s ' % locals()
if isGrey:
outStr = ''+outStr+''
- print outStr
+ print(outStr)
indent += 1
if showSubtracks:
for subTrack in trackChildren.get(trackName, []):
printTrackInfo(db, subTrack, trackTables, trackLabels, localSizes, trackChildren, \
tableSizes, trackToGbdbFiles, gbdbSizes, \
showSubtracks, indent, noTableTracks)
def getRevokedTracks(db):
" many encode tracks have been revoked or renamed. We ignore them. "
outFname = join(TMPDIR,"%s.revokedTrackes" % db)
if isfile(outFname):
tables = set(open(outFname).read().splitlines())
else:
@@ -701,71 +696,71 @@
return tables
def htmlDropBox(selName, elList, selKey):
"""
print html dropdown box with a selected default element and auto-reload on selection
print html dropbox box with (key, desc) elList, selKey is the key of the selected element.
the name of the dropbox variable is selName and upon selection, a page refresh will be issued
with the new value in selName
"""
addStr = ""
if selName=="clade":
addStr += "document.orgForm.org.value = 0; "
if selName=="org" or selName=="clade":
addStr += "document.orgForm.db.value = 0; "
- print '''')
def printHiddenForm(clade, org, db):
" hidden form is needed for javascript "
- print """
+ print("""
- """ % (clade, org, db)
+ """ % (clade, org, db))
def getHgDownloadDbs():
" get all dbs available from hgdownload "
fname = TMPDIR+"hgdownload.dbs.txt"
if not isfile(fname):
proc = subprocess.Popen(['rsync','hgdownload.soe.ucsc.edu::mysql'],stdout=subprocess.PIPE)
dbs = set()
for line in proc.stdout:
db = line.rstrip("\n").split()[-1]
dbs.add(db)
open(fname, "w").write("\n".join(dbs))
else:
dbs = set(open(fname).read().splitlines())
return dbs
def getOrgInfo(validDbs):
" get db info, either from local db or cached version "
fname = TMPDIR+"orgInfo.cache"
if isfile(fname):
- return cPickle.load(open(fname))
+ return pickle.load(open(fname))
defaultClade = "mammal"
conn = sqlConnect(hgConf.get("central.db", "hgcentral"), "local")
cur = conn.cursor()
# list of all clade descriptions ("mammal", "Mammal"), ...
cladeList = []
cur.execute("SELECT name, label FROM clade ORDER BY priority")
for row in cur.fetchall():
cladeList.append((row[0], row[1]))
# dict of clade -> list (orgName, orgName)
cladeToOrgs = defaultdict(list)
#cur.execute('SELECT clade, genome FROM genomeClade ORDER BY genome')
cur.execute('SELECT clade, genomeClade.genome, name FROM genomeClade, dbDb where dbDb.genome=genomeClade.genome AND active=1 ORDER BY orderKey;')
doneOrgs = set()
@@ -798,177 +793,177 @@
# dict of db -> description
orgToDbs = defaultdict(list)
cur.execute('SELECT genome, name, description FROM dbDb WHERE active=1 order by orderKey;')
for row in cur.fetchall():
rowDb = row[1]
if rowDb not in validDbs:
continue
orgToDbs[row[0]].append((row[1], row[2]))
# default db per orgName, {"Human":"hg19"}
orgToBestDb = {}
cur.execute('SELECT genome, name FROM defaultDb')
for row in cur.fetchall():
orgToBestDb[row[0]] = row[1]
# add every genome that has only one db
- for org, dbs in orgToDbs.iteritems():
+ for org, dbs in orgToDbs.items():
if len(dbs)==1 and org not in orgToBestDb:
orgToBestDb[org] = dbs[0][0]
cur.close()
conn.close()
orgInfo = {}
orgInfo["clades"] = cladeList
#orgInfo["orgs"] = orgList
orgInfo["cladeToOrgs"] = cladeToOrgs
orgInfo["orgToDbs"] = orgToDbs
orgInfo["orgToBestDb"] = orgToBestDb
orgInfo["cladeToBestOrg"] = cladeToBestOrg
orgInfo["defaultClade"] = defaultClade
- cPickle.dump(orgInfo, open(fname, "w"))
+ pickle.dump(orgInfo, open(fname, "w"))
return orgInfo
def getCladeAssemblyDb(clade, org, db):
""" return the list of clades, organisms and assemblies and default DBs.
any of clade, org or db can be None.
Return values for clade, org, db so all are valid strings
"""
if not mysqlDbLoaded:
print("info: MySQLDb not installed, cannot retrieve hgcentral.dbDb, using internal defaults")
orgInfo = {}
orgInfo["clades"] = [("mammal", "Mammal")]
orgInfo["cladeToOrgs"] = {"mammal":[("Human", "Human")]}
orgInfo["cladeToBestOrg"] = {"mammal":"Human"}
orgInfo["orgToDbs"] = {"Human":["hg19"]}
orgInfo["dbs"] = [("hg19", "Human (GrCh37)"), ("mm9", "Mouse (NCBI37)")]
return orgInfo, "mammal", "Human", "hg19"
validDbs = getHgDownloadDbs()
orgInfo = getOrgInfo(validDbs)
if db is not None and clade is None and org is None:
dbToClade = dict()
# search for the right org for this db
- for o, dbList in orgInfo["orgToDbs"].items():
+ for o, dbList in list(orgInfo["orgToDbs"].items()):
for orgDb, desc in dbList:
if orgDb==db:
org = o
break
# search for the right clade for this org
- for c, orgList in orgInfo["cladeToOrgs"].items():
+ for c, orgList in list(orgInfo["cladeToOrgs"].items()):
for o, _ in orgList:
if o==org:
clade = c
break
if clade is None or clade=="0":
clade = orgInfo["defaultClade"]
if org is None or org=="0" and clade not in [None, "0"]:
org = orgInfo["cladeToBestOrg"][clade]
if (db==None or db=="0"):
if org not in orgInfo["orgToBestDb"]:
- print "organism is not valid:", org
+ print("organism is not valid:", org)
sys.exit(0)
db = orgInfo["orgToBestDb"][org]
if not db in validDbs:
- print "error: db %s does not exist on hgdownload" % db
+ print("error: db %s does not exist on hgdownload" % db)
org = "Human"
clade = "mammal"
db = "hg19"
return orgInfo, clade, org, db
def htmlDbSelector(orgInfo, clade, org, db):
" print dropdown boxes with clade, assembly, DBs and refresh when selected "
- print ''
+ print('')
+ print('')
printHiddenForm(clade, org, db)
def htmlTrackTable(db, trackLabels, trackTables, \
trackParents, trackChildren, groupList, groupToTopTracks, \
tableSizes, localSizes, gbdbSizes, trackToGbdbFiles, showSubtracks, noTableTracks):
" print list of track sizes/tablecount as a html form, sorted by group "
myUrl = basename(__file__)
- print 'Locally mirrored tracks are faster to browse than tracks that are accessed through the internet. '
- print 'Select any number of tracks from the list below and click "Download" when finished. '
- print 'The data will be downloaded from the UCSC servers with rsync and copied to the local mysql database and %s.
' % getGbdbDir()
+ print('Locally mirrored tracks are faster to browse than tracks that are accessed through the internet. ')
+ print('Select any number of tracks from the list below and click "Download" when finished. ')
+ print('The data will be downloaded from the UCSC servers with rsync and copied to the local mysql database and %s.
')
+ print('' % db)
+ print('')
+ print('')
def downloadCache(url, cacheFname):
" download file from url or open local cached copy. Return list of lines "
cachePath = TMPDIR+cacheFname
if isfile(cachePath):
return open(cachePath).read().splitlines()
try:
- data = urllib2.urlopen(url).read()
- except urllib2.HTTPError:
- print "info: Could not find %s. bigWig/bigBed/bam files will be skipped. " % url
+ data = urllib.request.urlopen(url).read()
+ except urllib.error.HTTPError:
+ print("info: Could not find %s. bigWig/bigBed/bam files will be skipped. " % url)
data = None
if data is not None and url.endswith(".gz"):
- data = StringIO.StringIO(data) # gunzipping requires to wrap a pseudo-file around the gzip data
+ data = io.StringIO(data) # gunzipping requires to wrap a pseudo-file around the gzip data
data = gzip.GzipFile(fileobj=data).read()
# only create cache file if we got some data
if data == None:
data = ""
else:
cacheFh = open(cachePath, "wb")
cacheFh.write(data)
cacheFh.close()
return data.splitlines()
def linkTrackToGbdb(fnames, db, tableNames, bigDataFiles):
"""
do some educated guessing on the gbdb files<->track links. returns a dict track -> list of files
@@ -1053,61 +1048,61 @@
#if "liftOver" in fname:
#print fname, " "
#print "table", table, " "
orphanFnames = set(fnames) - set(assignedFnames)
for fname in sorted(orphanFnames):
debug("unassigned gbdb file: "+fname)
#print assignedFnames
misassignedTables = set(tableFiles) - set(tableNames)
for table in sorted(misassignedTables):
debug("not existing table: "+table)
debug("for files: "+",".join(tableFiles[table]))
# add the bigDataUrl files from trackDb
- for trackName, bigDataFile in bigDataFiles.iteritems():
+ for trackName, bigDataFile in bigDataFiles.items():
fname = bigDataFile.replace("/gbdb/%s/" % db, "")
tableFiles[trackName].append(fname)
# also add indexes for vcf or bam files
tbiFname = fname+".tbi"
baiFname = fname+".bai"
if tbiFname in fnames:
tableFiles[trackName].append(tbiFname)
if baiFname in fnames:
tableFiles[trackName].append(baiFname)
return tableFiles
def getRsyncSizes(dataType, db):
"""
debug("rsync sizes")
if dataType is "mysql: return dict with tableName:size for given db (includes indexes, frm + data)
if dataType is "gbdb": return dict with filaname:size for given db
"""
# run rsync command
tmpFname = TMPDIR+"%s_%s.rsync.txt" % (dataType, db)
if not isfile(tmpFname):
cmd = "rsync -nav rsync://hgdownload.soe.ucsc.edu/%s/%s/ > %s.new && mv %s.new %s" % (dataType, db, tmpFname, tmpFname, tmpFname)
ret = runCmd(cmd, mustRun=False)
if ret!=0:
- print "
"
- print "Cannot run %s " % cmd
- print "
"
- print "It seems that the rsync server hgdownload.soe.ucsc.edu is not available "
- print "Please check your network connection. If this problem persists send email to genome@soe.ucsc.edu "
+ print("
")
+ print("Cannot run %s " % cmd)
+ print("
")
+ print("It seems that the rsync server hgdownload.soe.ucsc.edu is not available ")
+ print("Please check your network connection. If this problem persists send email to genome@soe.ucsc.edu ")
sys.exit(0)
# parse rsync output file
tableSizes = collections.defaultdict(int)
for line in open(tmpFname):
## rsync output looks like this:
# receiving incremental file list
# drwxr-xr-x 1875968 2013/11/23 23:37:59 .
# -rw-rw-r-- 2031084 2011/01/04 14:55:26 HInv.MYD
fields = line.rstrip("\n").split()
if len(fields)!=5:
continue
if fields[0][0]=="d":
continue
@@ -1141,31 +1136,31 @@
#var = fields[1]
#targets = set(fields[-1].split(","))
#resolvedTargets = []
#for t in targets:
#if t.startswith("$"):
#resolvedTargets.extend(sets[t[1:]])
#else:
#resolvedTargets.append(t)
#sets[var] = resolvedTargets
def udrIsUsable():
" return true if we can use udr "
# http://stackoverflow.com/a/12611523/233871
# this is doing he same as the unix which command
if spawn.find_executable("rsync") is None:
- print "ERROR: could not find the rsync executable in the PATH"
+ print("ERROR: could not find the rsync executable in the PATH")
sys.exit(0)
# we currently don't use udr: it often fails as the port is not open
# it's very hard to detect if it fails or not
# return False
# check if we can find udr binary
udrPath = spawn.find_executable("udr")
if udrPath is None:
return False
# created by /etc/rc.local
if isfile(TMPDIR+"useUdr"):
return True
@@ -1239,156 +1234,156 @@
logFh.write("\nrsync output:\n")
logFh.close()
# write jobId to status file
idFh = open(TMPDIR+"lastJob.log", "w")
idFh.write(str(jobId))
idFh.close()
# run commands
print("Starting udr/rsync command script...")
runCmd(cmd)
def refreshPage(paramStr, delay=5, addNote=False):
" refresh current CGI page using javascript "
newUrl = basename(__file__)+"?"+paramStr
- print """
+ print("""
- """ % (getNonce(), newUrl, delay)
+ """ % (getNonce(), newUrl, delay))
if addNote:
- print("""Redirecting to %s""" % (newUrl, newUrl))
+ print(("""Redirecting to %s""" % (newUrl, newUrl)))
def jobsAreDone():
" True if no jobs currently in the 'at' queue "
cmd = "at -l | wc -l > %satWc.txt" % TMPDIR
runCmd(cmd)
lineCount = int(open(TMPDIR+"atWc.txt").read().strip())
os.remove(TMPDIR+"atWc.txt")
return lineCount==0
def printLog(jobId):
" print rsync log for given jobId to stdout "
jobFname = TMPDIR+"%d.log" % int(jobId)
- print "rsync download commands:
"
- print "
"
+ print("rsync download commands:
")
+ print("
")
if not isfile(jobFname):
- print "This download job is not active anymore.
"
- print 'Start a new download'
+ print("This download job is not active anymore.
")
+ print('Start a new download')
sys.exit(0)
lines = open(jobFname).read().splitlines()
for line in lines[-30:]:
- print line
+ print(line)
- print "
')
+ print('Download more tracks')
else:
- print 'Downloading files... Page will reload every 4 seconds until download is complete.'
- print 'Cancel download now'
+ print('Downloading files... Page will reload every 4 seconds until download is complete.')
+ print('Cancel download now')
refreshPage("jobId=%d" % jobId, delay=4000, addNote=False)
def removeSomeTracksFromSearch(conn):
cur = conn.cursor()
for table in REMOVESEARCH:
query = "DELETE FROM hgFindSpec WHERE searchTable='%s';" % table
try:
cur.execute(query)
except MySQLdb.ProgrammingError:
pass
cur.close()
def hideSomeTracks(db, conn, trackNames):
"""
hide some notoriously slow tracks by default
"""
if not mysqlDbLoaded:
- print "warning: cannot hide some tracks, module mysqldb not installed"
+ print("warning: cannot hide some tracks, module mysqldb not installed")
return
# do we need this?
# if "trackDb" not in localTables:
#return
# find all conservation tracks
hideTracks = []
for t in trackNames:
if (t.startswith("multiz") or t.startswith("cons")) and t.endswith("way"):
hideTracks.append(t)
elif t in FORCEHIDE:
hideTracks.append(t)
hideList = ["'"+s+"'" for s in hideTracks]
hideStr = ", ".join(hideList)
hideStr = "(%s)" % hideStr
cur = conn.cursor()
try:
cur.execute("SELECT 1 FROM trackDb LIMIT 1;")
except:
return
query = "UPDATE trackDb SET visibility=0 WHERE tableName in %s" % hideStr
try:
cur.execute(query)
except:
- print "could not execute query %s in database %s" % (query, db)
+ print("could not execute query %s in database %s" % (query, db))
cur.close()
def getGbdbDir():
" return local gbdb dir without trailing slash "
gbdbLoc = parseHgConf().get("gbdbLoc1", "/gbdb")
gbdbLoc = gbdbLoc.rstrip("/")
return gbdbLoc
def getLocalSizes(db):
"""
return a dict with table name -> total size of a mysql directory and filename -> size for the gbdb dir
(gbdb filenames are relative to the gbdb/db directory)
"""
path = join(MYSQLDIR, db)
sizes = defaultdict(int)
if runningAtUcsc():
return sizes
sqlFh = tempfile.NamedTemporaryFile()
sqlFname = sqlFh.name
cmd = 'sudo -u mysql /bin/ls -l %s > %s' % (path, sqlFname)
ret = runCmd(cmd, mustRun=False)
if ret!=0:
if runningAtUcsc():
- print "info: cannot read file sizes from %s, local file sizes unknown " % path
+ print("info: cannot read file sizes from %s, local file sizes unknown " % path)
return sizes
for line in open(sqlFname):
fields = line.strip().split()
if len(fields)<4:
continue
size = int(fields[4])
fname = fields[-1]
fileNoExt = splitext(basename(fname))[0]
sizes[fileNoExt] += size
if len(sizes)==0:
- print "(warning: local directory %s seems to be empty)" % path
+ print("(warning: local directory %s seems to be empty)" % path)
gbdbDir = join(getGbdbDir(), db)
if isdir(gbdbDir):
# get the size of all gbdb files
gbdbFh = tempfile.NamedTemporaryFile()
gbdbFname = gbdbFh.name
# trailing slash is important
cmd = 'find %s/ -type f > %s ' % (gbdbDir, gbdbFname)
runCmd(cmd)
fnames = open(gbdbFname).read().splitlines()
for fname in fnames:
relName = fname.replace(gbdbDir+"/", "")
sizes[relName] = getsize(fname)
return sizes
@@ -1401,61 +1396,61 @@
runCmd(cmd)
def checkGbdbMysqlAccess():
""" check if we have write access to gbdb and mysql dir and can run the at command """
msg = """
www-data ALL = (mysql:mysql) NOPASSWD: /usr/local/bin/udr,/bin/ls,/usr/bin/rsync,/bin/rm
www-data ALL = (root:root) NOPASSWD: /bin/mkdir /data/gbdb
www-data ALL = (root:root) NOPASSWD: /bin/chown www-data.www-data /data/gbdb
"""
# check if we can write to gbdb
tmpFname = "%s/test.tmp" % getGbdbDir()
try:
open(tmpFname, "w")
except IOError:
- print "This program cannot write to the %s directory. Please make sure that the apache user has permission to write to %s " % (getGbdbDir(), getGbdbDir())
- print 'Use "sudo visudo" to add these lines to /etc/sudoers: '
- print msg
- print 'Or check the directory permissions if the directory already exists. '
+ print("This program cannot write to the %s directory. Please make sure that the apache user has permission to write to %s " % (getGbdbDir(), getGbdbDir()))
+ print('Use "sudo visudo" to add these lines to /etc/sudoers: ')
+ print(msg)
+ print('Or check the directory permissions if the directory already exists. ')
sys.exit(0)
# check if we can rsync to mysql
tmpFname2= "%s/test.tmp" % MYSQLDIR
cmd = "sudo -u mysql rsync %s %s" % (tmpFname, tmpFname2)
ret = runCmd(cmd, mustRun=False)
if ret!=0:
- print "Could not run %s " % cmd
- print """Cannot run rsync as the mysql user. Please make sure that you have these lines in /etc/sudoers: """
- print msg
+ print("Could not run %s " % cmd)
+ print("""Cannot run rsync as the mysql user. Please make sure that you have these lines in /etc/sudoers: """)
+ print(msg)
sys.exit(0)
# cleanup the two tmp files
os.remove(tmpFname)
cmd = "sudo -u mysql rm %s" % tmpFname2
ret = runCmd(cmd, mustRun=False)
if ret!=0:
os.remove(tmpFname2)
# check if we can run "at"
cmd = "echo echo hi | at -M now"
ret = runCmd(cmd, mustRun=False)
if ret != 0:
- print "Could not run %s " % cmd
- print "It looks like we cannot run the 'at' command "
- print "You might have to remove %s from /etc/at.deny" % APACHEUSER
+ print("Could not run %s " % cmd)
+ print("It looks like we cannot run the 'at' command ")
+ print("You might have to remove %s from /etc/at.deny" % APACHEUSER)
sys.exit(0)
def trackToTableNames(tableNames):
" handle split tables and some spec cases by creating a dictionary trackName -> tableNames "
# as a heuristic to detect split tables, first get the counts of all suffixes
# after the underscore
suffixCounts = defaultdict(int)
for t in tableNames:
if "_" in t and not t.startswith("uniGene"):
prefix, track = string.split(t, "_", maxsplit=1)
suffixCounts[track] += 1
suffixDict = defaultdict(set)
for t in tableNames:
if "_" in t and not t.startswith("uniGene"):
@@ -1487,149 +1482,149 @@
def findImportantTables(trackSizes):
"""
some tables are important for some assemblies, we always add them
"""
tables = set()
for t in FORCETABLES:
if t in trackSizes:
tables.add(t)
return tables
def htmlStats(localSizes, gbdbSizes, tableSizes):
locTotal = humanReadable(sum(localSizes.values()))
gbdbTotal = humanReadable(sum(gbdbSizes.values()))
tableTotal = humanReadable(sum(tableSizes.values()))
- print("Total size at UCSC: mysql tables %(tableTotal)s, gbdb files %(gbdbTotal)s " % locals())
- print("Total size of tables and gbdb on local disk: %(locTotal)s
" % locals())
+ print(("Total size at UCSC: mysql tables %(tableTotal)s, gbdb files %(gbdbTotal)s " % locals()))
+ print(("Total size of tables and gbdb on local disk: %(locTotal)s
" % locals()))
def addPredefined(trackVis, superTracks, groupList, groupToTopTracks, trackLabels, \
trackChildren, tableToGbdbFiles, trackTables, tableSizes, revokedTracks):
""" add special predefined track groups in place, modifies the last five parameters
These groups are special "tracks" that don't exist, their children are the real tracks
"""
# get all track that are not hidden
defaultTracks = []
- for track, vis in trackVis.iteritems():
+ for track, vis in trackVis.items():
if vis!="hide":
defaultTracks.append(track)
# go down the hierarchy and let "hide" on higher levels override the lower ones
# remove all tracks that are somehow hidden by higher tracks from the first list
defaultTracks = set(defaultTracks)
- for topTracks in groupToTopTracks.values():
+ for topTracks in list(groupToTopTracks.values()):
for topTrack in topTracks:
if trackVis.get(topTrack, None)=="hide":
for child in getAllChildren(topTrack, trackChildren):
if child in defaultTracks:
defaultTracks.remove(child)
# also remove all superTracks from this list, otherwise will pull in all of encode again
# somehow visibility/inheritance works this way
defaultTracks = defaultTracks-set(superTracks)
# need lists, not sets
defaultTracks = list(defaultTracks)
debug(",".join(defaultTracks))
# create the two other sets of tracks, based on defaultTracks:
defaultNoCons = []
for t in defaultTracks:
if "multiz" not in t and not t.startswith("cons"):
defaultNoCons.append(t)
nonEncode = []
for track in trackVis:
if track in defaultTracks or not track.startswith("wgEncode"):
nonEncode.append(track)
#nonEncAllTables = [t for t in tableSizes.keys() if not t.startswith("wgEncode")]
# create a set of table names that are not linked to any trackDb entry
# e.g. gbExtFile or extFile tables
allTrackTables = set()
- for tableList in trackTables.values(): # flatten list
+ for tableList in list(trackTables.values()): # flatten list
allTrackTables.update(tableList)
#print "
", revokedTracks
nonTrackTables = list(set(tableSizes) - set(allTrackTables) - revokedTracks)
# hack to remove the ATTIC removed encode files, they're not in metaDb
nonTrackTables = [t for t in nonTrackTables if not t.startswith("wgEncode") and not "Gencode" in t]
#print "", nonTrackTables # XX
groupList.insert(0, ("special", "Predefined tracks sets"))
groupToTopTracks["special"] = ["defaultNoCons", "defaultConsTables", \
"default", "nonEncode", "liftOver", "nonTrackTables", "allTables", "allGbdb"]
trackLabels["defaultNoCons"] = "Default tracks without conservation"
trackLabels["defaultConsTables"] = "Default tracks with conservation tables, but no alignments"
trackLabels["default"] = "Default tracks"
trackLabels["nonEncode"] = "Default tracks plus all non-Encode tracks"
trackLabels["liftOver"] = "Liftover files"
#trackLabels["nonEncAllTables"] = "Non-Encode tracks"
trackLabels["nonTrackTables"] = "Secondary database tables not assigned to any track"
trackLabels["allTables"] = "All database tables"
trackLabels["allGbdb"] = "All non-database binary/text files"
trackChildren["defaultNoCons"] = defaultNoCons
trackChildren["defaultConsTables"] = defaultTracks
trackChildren["default"] = defaultTracks
trackChildren["nonEncode"] = nonEncode
#trackChildren["liftOver"] = trackToGbdbFiles["liftOver"]
#trackChildren["nonEncAllTables"] = nonEncAllTables
trackChildren["nonTrackTables"] = nonTrackTables
- trackChildren["allTables"] = tableSizes.keys()
+ trackChildren["allTables"] = list(tableSizes.keys())
def stopAllJobs():
""" stop all waiting at jobs and the currently running download job """
cmd = "atrm `at -l | cut -f1`"
runCmd(cmd)
if isfile(TMPDIR+"lastJob.pid"):
lastPid = open(TMPDIR+"lastJob.pid").read().strip()
cmd = "sudo kill -- -%s" % lastPid
runCmd(cmd)
# make sure mysql is started again
cmd = 'sudo service mysql start'
runCmd(cmd)
def assertEmptyQueue():
""" if the at queue is not empty, show link to log file of running job and stop program """
if jobsAreDone():
return
jobId = open(TMPDIR+"lastJob.log").read()
- print "There is still a download job running "
- print 'Show download job' % jobId
+ print("There is still a download job running ")
+ print('Show download job' % jobId)
sys.exit(0)
# the list of allowed chars in cgi args: digits, letters and dashes
legalChars = set(string.digits)
-legalChars.update(set(string.letters))
+legalChars.update(set(string.ascii_letters))
legalChars.update("_-.()/: ")
def mustBeClean(str):
""" make sure a string contains only letters and digits """
if str==None:
return str
- str = urllib.unquote(str)
+ str = urllib.parse.unquote(str)
str = str.strip()
for s in str:
if s not in legalChars:
- print "illegal character in CGI parameter"
+ print("illegal character in CGI parameter")
sys.exit(0)
return str
#def getDb(args, org):
#""" get Db from either CGI args or hgcentral, makes sure that DB actually exists """
#db = mustBeClean(args.getvalue("db", default=None))
#if db=="0":
#db = None
#
#if db!=None:
#if mysqlDbLoaded:
#import _mysql_exceptions
#try:
#conn = sqlConnect(db, "public")
#except _mysql_exceptions.OperationalError:
@@ -1671,173 +1666,173 @@
cur.execute(query)
except MySQLdb.ProgrammingError:
return None
for row in cur.fetchall():
names.append(row[0])
return names
def postRsyncChanges(db, localSizes):
" remove some tracks from trackDb, others from hgFindSpec and add a few row to tableList"
if not mysqlDbLoaded:
return
try:
conn = sqlConnect(db, "local")
tracks = getAllTrackNames(conn)
if tracks is None:
- print("mysql database %s has no trackDb" % db)
+ print(("mysql database %s has no trackDb" % db))
else:
hideSomeTracks(db, conn, tracks)
removeSomeTracksFromSearch(conn)
addTableList(db, conn)
conn.close()
- except MySQLdb.OperationalError, e:
- print "Could not run postRsyncChanges on db %s" % db
+ except MySQLdb.OperationalError as e:
+ print("Could not run postRsyncChanges on db %s" % db)
return
def reloadPage():
" trigger page reload with javascript "
- print """
+ print("""
-