[Swift-commit] r7853 - SwiftApps/swift-galaxy/swift

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-05-11 18:09:31 -0500 (Sun, 11 May 2014)
New Revision: 7853

Added:
   SwiftApps/swift-galaxy/swift/testpy.sh
Modified:
   SwiftApps/swift-galaxy/swift/swiftforeach.py
Log:
test and fixes for py

Modified: SwiftApps/swift-galaxy/swift/swiftforeach.py
===================================================================
--- SwiftApps/swift-galaxy/swift/swiftforeach.py	2014-05-11 19:32:48 UTC (rev 7852)
+++ SwiftApps/swift-galaxy/swift/swiftforeach.py	2014-05-11 23:09:31 UTC (rev 7853)
@@ -3,7 +3,8 @@
 import subprocess
 import sys
 import os
-import distutils.
+import distutils.spawn
+import traceback
 
 def setwdir():
     return subprocess.check_output(["mktemp", "-d", "/tmp/swift-gal.XXXX"])
@@ -12,7 +13,7 @@
     for a in args:
         yield a
 
-def buildcfg():
+def buildcfg(wdir):
     f=open(wdir+"/cf", 'w');
     f.write('use.provider.staging=true')
     f.write('wrapperlog.always.transfer=true')
@@ -26,13 +27,21 @@
 def main():
     myargs = genargs(sys.argv)
     try:
+        this=next(myargs)
         range_or_list = next(myargs)
+        #print "range or list=> "+ range_or_list
         k_or_t = next(myargs)
+        #print "k or t=> "+ k_or_t
         sites = next(myargs)
+        #print "sites=> " + sites
         swiftargs = next(myargs)
+        #print "swiftargs=> " + swiftargs
         interpreter = next(myargs)
+        #print "interpreter=> " + interpreter
         executable = next(myargs)
+        #print "executable=> " + executable
         stdin = next(myargs)
+        #print "stdin => " + stdin
 
         if range_or_list == "list":
             listfile = next(myargs)
@@ -41,17 +50,15 @@
             rstart = next(myargs)
             rend = next(myargs)
             stepsize = next(myargs)
-        
-        rstart = next(myargs)
-        rend = next(myargs)
-        stepsize = next(myargs)
+            
         outloc = next(myargs)
         outlistfile = next(myargs)
+        #print "outlistfile=>"+outlistfile
         logfile = next(myargs)
         stringargs = next(myargs)
     except:
+        traceback.print_exc()
         sys.exit(1)
-    
     swift = distutils.spawn.find_executable("swift")
     BASEDIR = os.path.dirname(os.path.realpath(__file__))
 
@@ -70,7 +77,7 @@
         filearrayexpr="file fileargs[];"
     
     # create outloc dir
-    if not os.path.exists(directory):
+    if not os.path.exists(outloc):
         os.makedirs(outloc)
         
     # workout the stringargs
@@ -134,7 +141,7 @@
         subprocess.call([basedir+"/buildsite.sh", sites, wdir])
 
         #build config
-        buildcfg()
+        buildcfg(wdir)
         
         #build tc
         tc=open(wdir+"/tc", 'w');
@@ -161,9 +168,9 @@
         if range_or_list == "list":
         
             f.write(" \n");
-            f.write("file listfile=input("$listfile");\n")
+            f.write("file listfile=input(\""+listfile+"\");\n")
             f.write("string list[] = split(read(listfile),);\n");
-            f.write("foreach l, i in list{"\n)
+            f.write("foreach l, i in list{\n")
             f.write("    file out <sprintf(\""+outloc+"/%s.%i.out\", l, i)>;\n")
             f.write("    file err <sprintf(\""+outloc+"/%s.%i.err\", l, i)>;\n")
         
@@ -175,14 +182,14 @@
         
         f.write("(out,err) = anapp(exec, i, stringargs, fileargs, stdinfile);\n")
         f.write("}\n");
-        f.write("printf("%s", "Done!");\n");
+        f.write("printf(\"%s\", \"Done!\");\n");
         f.write("}\n");
     
     f.close()  
     
     #Populate output file
     outlist=subprocess.check_output(["find", outloc, "-type", "f", "-iname", "*.out"])
-    f=open(outlistfile)
+    f=open(outlistfile, "w")
     f.write(outlist);
     f.close()
     #dum ditty dum ditty dum dum dum

Added: SwiftApps/swift-galaxy/swift/testpy.sh
===================================================================
--- SwiftApps/swift-galaxy/swift/testpy.sh	                        (rev 0)
+++ SwiftApps/swift-galaxy/swift/testpy.sh	2014-05-11 23:09:31 UTC (rev 7853)
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+#!/bin/bash
+
+cat << EOF > list.txt
+a
+b
+c
+EOF
+
+cat << EOF > x.sh
+#!/bin/bash
+
+echo \$\@
+EOF
+
+chmod 755 x.sh
+
+echo "List, no input parameters and files"
+./swiftforeach.py list swiftK localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
+
+echo "Range, no input parameters and files"
+./swiftforeach.py range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out ""
+
+echo "List, string input parameters"
+./swiftforeach.py range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hello there list!"
+
+echo "Range, string input parameters"
+./swiftforeach.py range swiftK localhost "" bash x.sh "" 0 9 1 tmpoutrange b.log list2.out "hi there range!"
+
+echo "List, no input parameters and files stdin /dev/null"
+./swiftforeach.py list swiftK localhost "" bash x.sh "/dev/null" list.txt tmpoutlist a.log list1.out ""
+
+echo "T list"
+./swiftforeach.py list swiftT localhost "" bash x.sh "" list.txt tmpoutlist a.log list1.out ""
+
+echo "T range"
+./swiftforeach.py range swiftT localhost "" bash x.sh "" 0 9 1 tmpoutlist a.log list1.out "hello there T"
+
+echo "Call from Galaxy"
+python /nfs2/ketan/galaxy-dist/tools/swift/swiftforeach.py "range" "swiftT" "localhost" "" "sh" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_1.dat" "None" "0" "9" "1" "$HOME/swift-sandbox" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_12.dat" "/nfs2/ketan/galaxy-dist/database/files/000/dataset_13.dat" "hello how are you"


Property changes on: SwiftApps/swift-galaxy/swift/testpy.sh
___________________________________________________________________
Added: svn:executable
   + *