UCSC %s

") + print("

") + +def printHgcSection(name, rightSideContent, id=None): + " print a section header for the hgc page " + print("") + if id is None: + print("

") + else: + print("

" % id) + print("

" % name) + print("

") + print(rightSideContent) + print("

") + print("

") + +def getGbHeader(): + " Python cannot include files with the preprocessor, so manually copied kent/src/hg/lib/gbHeader.h for now " + return """ + + + %s + + + + UCSC %s + + + + + + + + + + + + + + + + """ + +def webStartGbNoBanner(prefix, title): + " output the part, largely copied from web.c / webStartGbNoBanner " + print (getGbHeader() % (prefix, title)) + +def runCmd(cmd, mustRun=True): + " wrapper around system() that prints error messages. cmd preferably a list, not just a string. " + import subprocess + ret = subprocess.call(cmd) + if ret!=0 and mustRun: + errAbort("Could not run command %s" % cmd) + return ret + +def printContentType(contType="text/html", fname=None): + " print the HTTP Content-type header line with an optional file name " + global contentLineDone + contentLineDone = True + print("Content-type: %s; charset=utf-8" % contType) + if fname is not None: + print("Content-Disposition: attachment; filename=%s" % fname) + print + +def queryBottleneck(host, port, ip): + " contact UCSC-style bottleneck server to get current delay time. From hg/lib/botDelay.c " + # send ip address + import socket + s = socket.socket() + s.connect((host, int(port))) + msg = ip + d = chr(len(msg))+msg + s.send(d) + + # read delay time + expLen = ord(s.recv(1)) + totalLen = 0 + buf = list() + while True: + resp = s.recv(1024) + buf.append(resp) + totalLen+= len(resp) + if totalLen==expLen: + break + return int("".join(buf)) + +def hgBotDelay(): + """ + Implement bottleneck delay, get bottleneck server from hg.conf. + This behaves similar to the function src/hg/lib/botDelay.c:hgBotDelay + It does not use the hgsid, currently it always uses the IP address. + Using the hgsid makes little sense. It is more lenient than that C version. + """ + if "DOCUMENT_ROOT" not in os.environ: # skip if not called from Apache + return + global hgConf + hgConf = parseHgConf() + if "bottleneck.host" not in hgConf: + return + ip = os.environ["REMOTE_ADDR"] + delay = queryBottleneck(hgConf["bottleneck.host"], hgConf["bottleneck.port"], ip) + if delay>10000: + time.sleep(delay/1000.0) + if delay>20000: + errAbort("Too many queries. Your IP has been blocked. Please contact genome-www@soe.ucsc.edu to unblock your IP address.") + sys.exit(0) + +def parseRa(text): + " Parse ra-style string and return as dict name -> value " + lines = text.split("\n") + data = dict() + for l in lines: + if len(l)==0: + continue + key, val = string.split(l, " ", maxsplit=1) + data[key] = val + return data + +def lineFileNextRow(inFile): + """ + parses tab-sep file with headers in first line. Yields collection.namedtuples. + Strips "#"-prefix from header line. + Cannot parse headers with non-alpha characters and fields that are not ASCII. Code + for these cases is commented out, for performance reasons. + """ + + if isinstance(inFile, str): + if inFile.endswith(".gz"): + fh = gzip.open(inFile, 'rb') + else: + fh = open(inFile) + else: + fh = inFile + + line1 = fh.readline() + line1 = line1.rstrip("\n").lstrip("#") + headers = line1.split("\t") + #headers = [re.sub("[^a-zA-Z0-9_]","_", h) for h in headers] + #headers = [x if x!="" else "noName" for x in headers] + + #filtHeads = [] + #for h in headers: + #if h[0].isdigit(): + #filtHeads.append("x"+h) + #else: + #filtHeads.append(h) + #headers = filtHeads + + Record = namedtuple('tsvRec', headers) + for line in fh: + if line.startswith("#"): + continue + #line = line.decode("latin1") + line = line.rstrip("\n") + fields = string.split(line, "\t", maxsplit=len(headers)-1) + try: + rec = Record(*fields) + except Exception, msg: + logging.error("Exception occured while parsing line, %s" % msg) + logging.error("Filename %s" % fh.name) + logging.error("Line was: %s" % line) + logging.error("Does number of fields match headers?") + logging.error("Headers are: %s" % headers) + raise Exception("header count: %d != field count: %d wrong field count in line %s" % (len(headers), len(fields), line)) + yield rec + +def parseDict(fname): + """ Parse text file in format keyvalue and return as dict key->val. + Does not abort on duplicate keys, for performance reasons. """ + d = {} + + if fname.endswith(".gz"): + fh = gzip.open(fname) + else: + fh = open(fname) + + for line in fh: + key, val = line.rstrip("\n").split("\t") + d[key] = val + return d + +def cgiString(name, default=None): + " get named cgi variable as a string, like lib/cheapcgi.c " + val = cgiArgs.getfirst(name, default=default) + return val + +def cgiGetAll(): + return cgiArgs + +def makeRandomKey(numBits=128+33): + " copied line-by-line from kent/src/lib/htmlshell.c:makeRandomKey " + import base64 + numBytes = (numBits + 7) / 8 # round up to nearest whole byte. + numBytes = ((numBytes+2)/3)*3 # round up to the nearest multiple of 3 to avoid equals-char padding in base64 output + f = open("/dev/urandom", "r") # open random system device for read-only access. + binaryString = f.read(numBytes) + f.close() + return base64.b64encode(binaryString, "Aa") # replace + and / with characters that are URL-friendly. + +def cartDbLoadFromId(conn, table, cartId, oldCart): + " Like src/hg/lib/cart.c, opens cart table and parses cart contents given a cartId of the format 123123_csctac " + import urlparse + + if cartId==None: + return {} + cartFields = cartId.split("_") + if len(cartFields)!=2: + errAbort("Could not parse identifier %s for cart table %s" % (cgi.escape(cartId), table)) + idStr, secureId = cartFields + + query = "SELECT contents FROM "+table+" WHERE id=%(id)s and sessionKey=%(sessionKey)s" + rows = sqlQuery(conn, query, {"id":idStr, "sessionKey":secureId}) + if len(rows)==0: + # silently ignore invalid cart IDs for now. Future code may want to generate a new cart. + return {} + + cartList = urlparse.parse_qs(rows[0][0]) + + # by default, python returns a dict with key -> list of vals. We need only the first one + for key, vals in cartList.iteritems(): + oldCart[key] =vals[0] + return oldCart + +centralConn = None + +def hConnectCentral(): + " similar to src/hg/lib/hdb.c:hConnectCentral. We use a much simpler cache, because we usually read all rows into memory. " + global centralConn + if centralConn: + return centralConn + + centralDb = cfgOption("central.db") + if centralDb is None: + errAbort("Could not find central.db in hg.conf. Installation error.") + + centralUser = cfgOption("central.user") + if centralUser is None: + errAbort("Could not find central.user in hg.conf. Installation error.") + + centralPwd = cfgOption("central.password") + if centralPwd is None: + errAbort("Could not find central.password in hg.conf. Installation error.") + + centralHost = cfgOption("central.host") + if centralHost is None: + errAbort("Could not find central.host in hg.conf. Installation error.") + + conn = sqlConnect(centralDb, host=centralHost, user=centralUser, passwd=centralPwd) + + centralConn = conn + return conn + +def cartNew(conn, table): + " create a new cart and return ID " + sessionKey = makeRandomKey() + sqlQuery(conn, "INSERT %s VALUES(0,'',0,now(),now(),0,%s" % (table, sessionKey)); + sqlLastId = conn.insert_id() + newId = "%d_%s" % (sqlLastId, sessionKey) + return newId + +def cartAndCookieSimple(): + """ Make the cart from the user cookie (user settings) and the hgsid CGI parameter (session settings, e.g. a browser tab). + This is somewhat similar to cartAndCookie from hg/lib/cart.c + Two important differences: this cart does not add all CGI arguments automatically. + It also does not run cart.c:cartJustify, so track priorities are not applied. + Also, if there is no hgsid parameter or no cookie, we do not create a new cart. + """ + import Cookie + + # no cgiApoptosis yet - maybe needed in the future. see cart.c / cartNew + + if "HTTP_COOKIE" in os.environ: + cookies = Cookie.SimpleCookie(os.environ["HTTP_COOKIE"]) + cookieName = cfgOption("central.cookie", "hguid") + hguid = cookies.get(cookieName) + if hguid is not None: + hguid = hguid.value # cookies have values and other attributes. We only need the value + else: + hguid = None + + hgsid = cgiString("hgsid") + + conn = hConnectCentral() + + cart = {} + userInfo = cartDbLoadFromId(conn, "userDb", hguid, cart) + sessionInfo = cartDbLoadFromId(conn, "sessionDb", hgsid, cart) + return cart + +def cartString(cart, default=None): + " Get a string from the cart. For better readability for programmers used to the C code. " + return cart.get(cart, default) + +def cgiSetup(): + """ do the usual browser CGI setup: parse the hg.conf file, parse the CGI + variables, get the cart, do bottleneck delay. Returns the cart. + + This is not part of the C code (though it maybe should). + """ + parseHgConf() + global cgiArgs + cgiArgs = cgi.FieldStorage() # Python has built-in cgiSpoof support: sys.argv[1] is the query string if run from the command line + + hgBotDelay() + + if cgiString("debug"): + global verboseLevel + verboseLevel = int(cgiString("debug")) + + cart = cartAndCookieSimple() + return cart + +#if __file__=="__main__": + #pass