[Swift-commit] r7857 - SwiftApps/swift-galaxy/swift

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-05-12 11:05:37 -0500 (Mon, 12 May 2014)
New Revision: 7857

Modified:
   SwiftApps/swift-galaxy/swift/swiftforeach.py
Log:
python version of Swift-Galaxy driver passes tests. So, will switch to python from now. This will give advantage working with existing Galaxy tools

Modified: SwiftApps/swift-galaxy/swift/swiftforeach.py
===================================================================
--- SwiftApps/swift-galaxy/swift/swiftforeach.py	2014-05-12 16:01:47 UTC (rev 7856)
+++ SwiftApps/swift-galaxy/swift/swiftforeach.py	2014-05-12 16:05:37 UTC (rev 7857)
@@ -6,6 +6,7 @@
 import distutils.spawn
 import traceback
 import fnmatch
+import re
 
 def setwdir():
     return subprocess.check_output(["mktemp", "-d", "/tmp/swift-gal.XXXX"])
@@ -51,7 +52,7 @@
             rstart = next(myargs)
             rend = next(myargs)
             stepsize = next(myargs)
-            n = (rend - rstart)/stepsize
+            n = (int(rend) - int(rstart))/int(stepsize)
             
         outloc = next(myargs)
         outlistfile = next(myargs)
@@ -84,7 +85,7 @@
         
     # workout the stringargs
     if stringargs:
-        stringarrayexpr="string stringargs[]="+str(stringargs.split())+";\n"
+        stringarrayexpr="string stringargs[]="+re.sub('\'','"',str(stringargs.split()))+";\n"
     else:
         stringarrayexpr="string stringargs[];\n"
     
@@ -95,10 +96,10 @@
         #print "stdin"
         if k_or_t == "swiftK":
             #print "stdinK"
-            stdinfilexpr = "file stdinfile<"+stdin+">;\n"
+            stdinfilexpr = "file stdinfile<\""+stdin+"\">;\n"
         else:
             #print "stdinT"
-            stdinfilexpr = "file stdinfile = input("+stdin+");\n"
+            stdinfilexpr = "file stdinfile = input(\""+stdin+"\");\n"
     else:
         #print "no stdin"
         if k_or_t == "swiftK":
@@ -169,7 +170,7 @@
         f.write(stringarrayexpr + " \n");
         f.write(filearrayexpr + " \n");
         f.write(stdinfilexpr + " \n");
-        f.write("file exec = input("+executable+");\n");
+        f.write("file exec = input(\""+executable+"\");\n");
         
         if range_or_list == "list":
         
@@ -213,11 +214,11 @@
             stc=distutils.spawn.find_executable("stc")
             turbine= distutils.spawn.find_executable("turbine")
             with open(logfile, "wb") as errfile:
-                exitcode=subprocess.check_call([stc, "-j", "$(\which java)", wdir+"/script.swift"], stderr=errfile)
+                exitcode=subprocess.check_call([stc, "-j", "/homes/ketan/jdk1.7.0_07/bin/java", wdir+"/script.swift"], stderr=errfile)
 
             if exitcode == 0:
                 with open(logfile, "wb") as errfile:
-                    exitcode=subprocess.check_call([turbine, "-n", n, wdir+"/script.swift"], stderr=errfile)
+                    exitcode=subprocess.check_call([turbine, "-n", str(n), wdir+"/script.tcl"], stderr=errfile)
                     
 
         elif sites == "Vesta":
@@ -266,6 +267,5 @@
     f.close()
 
 
-
 if __name__=='__main__':
     main()