src/beacon/query 413eea60a2ca4d9c534a6750fcbf332ffa7e1e36

413eea60a2ca4d9c534a6750fcbf332ffa7e1e36
max
  Thu Nov 27 03:06:00 2014 -0800
moving bigbed files to a location that is less lame, refs #14427
diff --git src/beacon/query src/beacon/query
index 71a6970..e951874 100755
--- src/beacon/query
+++ src/beacon/query
@@ -1,51 +1,55 @@
 #!/usr/bin/env python
 # a beacon for LOVD, ClinVar, UniProt and HGMD, see ga4gh.org/#/beacon
 import cgi, subprocess, sys, cgitb, os, datetime, gdbm
+from os.path import join
 cgitb.enable()
 
+# dir for bigBed files
+DATADIR = "/gbdb/hg19/beacon"
+
 trackFnames = {
 "clinvar" : "clinvarMain.bb",
 "uniprot" : "spMut.bb",
 "hgmd" : "hgmd.bb",
 "lovd" : "lovd.bb"
 }
 
 MAXREQPERDAY=1000
 
 def checkReqCount():
     " check if IP address has exceeded max number of requests today "
     accCounts = gdbm.open("accCounts.gdbm", "c")
 
     ipAddr = os.environ["REMOTE_ADDR"]
     dateStr = datetime.date.today().isoformat()
     accKey = ipAddr+"|"+dateStr
     try:
         oldCount = int(accCounts[accKey])
     except KeyError:
         oldCount = 0
 
     newCount = oldCount+1
     if newCount > MAXREQPERDAY:
         print("No more requests left today")
         sys.exit(0)
 
     accCounts[accKey]=str(newCount)
     accCounts.close()
 
 def getTrackFromScript():
-    " check which track name occurs in script name, to make the track captured by symlinks "
+    " check which track name occurs in script name, allows symlinks to cgi that include the track name "
     name = sys.argv[0].lower()
     for trackName in trackFnames:
         if trackName in name:
             return trackName
 
 def errAbort(errMsg=None):
     print "<html><body><pre>"
     if errMsg is not None:
         print "error: "+errMsg
 
     host = os.environ.get("HTTP_HOST", "")
 
     print """
     A Genomics Alliance Beacon at UCSC. In collaboration with the Leiden Open Variation Database.
 
@@ -110,31 +114,31 @@
 if chrom not in insdcToUcsc.values():
     chrom = insdcToUcsc.get(chrom, None)
 if chrom==None:
     errAbort( "ERROR: illegal chrom identifier %s" % chrom)
     
 if track not in trackFnames:
     errAbort("illegal track name")
 
 if nucl==None or len(nucl)!=1 or nucl[0].lower() not in "actg":
     errAbort("invalid allele, can only be ACTG")
     
 checkReqCount()
 
 # change parameters slightly
 nucl = nucl.upper()
-fname = trackFnames[track]
+fname = join(DATADIR, trackFnames[track])
 pos = int(pos)
 
 # run tool
 args = ["./bigBedToBed", fname, "stdout", "-chrom=%s"%chrom, "-start=%d"%pos, "-end=%d"%(pos+1)]
 p = subprocess.Popen(args, stdout=subprocess.PIPE)
 
 # parse output
 isMaybe = False
 for line in p.stdout:
     fs = line.rstrip("\n").split("\t")
     if fs[-1]=="maybe":
         isMaybe=True
     if int(fs[2])-int(fs[1])!=1 and track != "uniprot":
         continue
     if fs[3][-1]==nucl or track in ["hgmd", "uniprot"]: