global job_params
global system
#
#
# Source file with utility procedures
# source [SearchPath TOP src CCP4_utils.tcl]
  source [SearchPath TOP utils map_utils.tcl]
# Read the crystal parameters files
#  ReadSymops [FileJoin [GetEnvPath CLIBD] symop.lib]
#  ReadCrystalData [SearchPath TOP etc crystal.lib]
#
# Write the arp .par file

  set logfile $job_params(LOG_FILE)
  set arpwarpdir $job_params(JOB_ID)_$job_params(TASKNAME) 
  set workdir [GetDefaultDirPath]

  set parfile "$workdir/$arpwarpdir.par"

  append partext "set parfile = $parfile \n"

  append partext "set warpbin = [GetEnvPath warpbin]\n"
  append partext "set version = 7.6 \n"

  append partext "set WORKDIR = [GetDefaultDirPath]\n"
  append partext "set PROJECT = CCP4GUI \n"
  append partext "set JOB_ID = $job_params(JOB_ID) \n"
  append partext "set arpwarpdir = $arpwarpdir \n"

# Put the name of the CCP4i def file  inot the par file
  append partext "set CCP4I_DEFFILE = " [FileJoin [GetDefaultDirPath]  \
     CCP4_DATABASE $job_params(JOB_ID)_$job_params(TASKNAME).def ] \n

  
# Handle file names

  foreach par [list HKLIN    MODELIN SEQIN HEAVYIN COMPARETO] \
       arppar [list datafile modelin seqin heavyin compareto] {
    set file [subst $[subst $par]]
    set dir [subst DIR_$[subst $par]]
    set value [GetFullFileName1 $file $dir]
#    if { $value == "" } {
#      append partext "set $arppar = ''" \n
#    } else {
      append partext "set $arppar = $value" \n
#    }
  }

# Protein size
# Naive approach to start with
  
    set value [ expr $NRES * 8]
    append partext "set protsize = $value" \n

# More basic params

    foreach \
       par [ list WILSON_B SOLVENTC FP SIGFP FBEST PHIB FOM ] \
    arppar [ list wilsonb  solventc fp sigfp fbest phibest fom ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

# cycling

    foreach \
       par [ list TOTAL_CYCLES SMALL_CYCLES NMOL WEIGHT WEIGHTVAL NMODELS SOLVENT RIDGE_RESTRAINTS FLATTEN FREEBUILD] \
    arppar [ list restrcyc     restrref     cgr  wmat   weightv   models  solvent ridgerestraints  flatten freebuild] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

  GetCellfromMtz $HKLIN mtz_space_group cell lattice
  set space_gp_number [GetSpaceGroupNumber $SPACE_GROUP]

#  puts $space_gp_number
  
  append partext "set sym = $space_gp_number" \n
  append partext "set cell = '$cell'" \n
  append partext "set scanis = Y" \n

#
# Dipvali flag
  append partext "set dipvali = $DIPVALI" \n 

# FAKE DATA values
if {$FAKE_DATA == "1"} {
  append partext "set fakedata = '0.33 0.75 1'" \n
} else {
  append partext "set fakedata = '0 0 0'" \n
}

# NCS settings
  append partext "set ncsrestraints = $NCS_RESTRAINTS" \n 
  append partext "set ncsextension = $NCS_EXTENSION" \n 

# hmainpostfit is always set to 1
  append partext "set hmainpostfit = 1" \n 

# Keep Junk
  append partext "set keepjunk = $KEEP_JUNK" \n

# Params not requiring quotes
    foreach \
       par [ list ALBE TWIN RESTRAINTS LOOPS SAD ] \
    arppar [ list albe twin restraints loops sad ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
    }

# These are params that have to be included in quotes !!!

    foreach \
       par [ list XYZLIM DAMP RESOL SCALEOPT FREELABIN SCALML SCALE PHASELABIN PHASEREF SADCARD] \
    arppar [ list xyzlim damp resol scaleopt freelabin scalml scale phaselabin phaseref sadcard] {
	set value [subst $[subst $par]]
        if { $value == "" } {
          append partext "set $arppar = " \n
        } else {
          append partext "set $arppar = '$value'" \n
	}
    }
#
    foreach \
       par [ list REFMAX EXCLUDE_FREER REFMAC_REF_SET NCYCLES ] \
    arppar [ list refmax freer freerml rrcyc ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

    foreach \
       par [ list CYCSKIP SKIP_CYCLES MULTITRACE UP_UPDATE SIDE IS_SEMET] \
    arppar [ list cycskip skip multit upmore side is_semet] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

    foreach \
       par [ list ADDATOM_SIGMA REMATOM_SIGMA ARP_MODE ] \
    arppar [ list fsig          rsig          modeccp4i ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

    foreach \
       par [ list RANDTIMES RAND1 RANDSHIFT1 BCUT1 RAND2 RANDSHIFT2 BCUT2 RAND3 RANDSHIFT3 BCUT3 ] \
    arppar [ list randtimes rand1 randshift1 bcut1 rand2 randshift2 bcut2 rand3 randshift3 bcut3 ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}


    foreach \
       par [ list DATAKEEP_MODE REMOTE_JOB USER_EMAIL ] \
    arppar [ list keepdata remote remoteemail ] {
	set value [subst $[subst $par]]
        append partext "set $arppar = $value" \n
	}

if { [file exists $parfile] } {
	   file delete -force -- $parfile
}

   WriteFile $parfile $partext
 
   file attributes $parfile -permissions 0740

    AddOutputFile $parfile PROJECT
    AddOutputFile $WILSON_LOG PROJECT

#  puts "Par file: $parfile\n $partext\n"

   set TheOS $system(OPSYS)
#   puts $TheOS

if { $REMOTE_JOB == "0" && $TheOS == "WINDOWS" } {
   WriteToLog {You can not submit jobs on your local Windows machine} -nofoot -nohead
   WriteToLog {You can however submit the job remotely at the Hamburg cluster} -nofoot -nohead
   WriteToLog {Use the options at the last panel of the ARp/wARP CCP4i interface} -nofoot -nohead
   TerminateScript 0 -report {Local submisison not allowed in Windows}
}

if { $REMOTE_JOB == "0" } {

   catch {exec [GetEnvPath warpbin]/warp_tracing.sh $parfile >> $logfile}

} else {

   WriteToLog  {The ARP/wARP job is now ready to run remotely on the 300 cores Cluster at Hamburg} -nofoot -nohead
   WriteToLog  {<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> } -nofoot -nohead 
   WriteToLog  {Further instructions will be sent to the Email address: } -nofoot -nohead 
   WriteToLog  $USER_EMAIL -nofoot -nohead 
   WriteToLog  {Please check your mailbox for further instructions and to start the job ! } -nofoot -nohead 
   WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead 

   if { $DATAKEEP_MODE == "CONFIDENTIAL" } {
      WriteToLog  {Your data and results will be automatically erased \
      after you downloaded the results. Only the minimum information will be \
      stored in the ARP/wARP database, i.e. the short log file, the Wilson log file \
      and the parameter file.} -nofoot -nohead 
   } else {      
      WriteToLog {Your files will be made available to:} -nofoot -nohead
      if { $DATAKEEP_MODE == "WARPTEAM" } { WriteToLog {    ARP/wARP-AutoRickshaw-Refmac developers.}  -nofoot -nohead }
      if { $DATAKEEP_MODE == "EUFW6" } { WriteToLog {    Participants of the BIOXHIT and SPINE EU networks.} -nofoot -nohead }
      if { $DATAKEEP_MODE == "WORLD" } { WriteToLog {    Any developer that requests them.} -nofoot -nohead  }
   }


   WriteToLog {Your data will now get packed and transferred to the Hamburg server.} -nofoot -nohead 

   set taridList [GetUserId] 
   lappend taridList [GetHostname]
#   lappend taridList [exec date -u +%j%Y%H%M]
   lappend taridList [exec date -u +%j%Y%H%M%S]

   set tmpDir [join $taridList "_"]
   set tarName "$tmpDir.tar"

   set WorkPath [GetDefaultDirPath]

#   puts $tmpDir
#   puts $tarName
#   puts $WorkPath

   if {![file isdirectory $WorkPath/$tmpDir]} {
    file mkdir $WorkPath/$tmpDir
   } 

   file copy -force $parfile $WorkPath/$tmpDir
   file copy -force $HKLIN $WorkPath/$tmpDir

   file copy -force $WILSON_LOG $WorkPath/$tmpDir

   if { $SEQIN != "" } {
      file copy -force $SEQIN $WorkPath/$tmpDir
   }  

   if { $MODELIN != "" } {
      file copy -force $MODELIN $WorkPath/$tmpDir
   }  

   if { $COMPARETO != "" } {
      file copy -force $COMPARETO $WorkPath/$tmpDir
   }  

   cd $WorkPath


    if { [ catch { exec tar -cf $tarName $tmpDir } ] } {
    WriteToLog {Error While Creating TarFile for remote submission.}
      TerminateScript 0 -report {Creation of Tar file has failed.}
   } else {
      WriteToLog {Archive (tar file) with needed data created.} -nohead -nofoot
   }
 
    set logFile [open "./$tarName.log" "w"]
    puts $logFile "EOF"
    close $logFile
    
#    source [file join [GetEnvPath warpbin] ftp_lib.tcl ] 
#    set spass [exec [file join [GetEnvPath warpbin] arp_warp] -r]
#    set server [lindex "$spass" 0]
#    set user [lindex "$spass" 1]
#    set passwd [lindex "$spass" 2]
#    set pno [lindex "$spass" 3]
 
#    puts $spass
#    puts $server
#    puts $user
#    puts $passwd
#    puts $pno

   WriteToLog {Attempting http connection using curl.}  -nohead -nofoot

   if [ catch [GetEnvPath HTTP_PROXY] ] {
	set http_proxy [GetEnvPath HTTP_PROXY]
   } else {
   	set http_proxy "0"
   }


   if { $http_proxy == "0" } {
        WriteToLog {No proxy server is in use.}  -nohead -nofoot
      if { [ catch { exec curl --url http://cluster.embl-hamburg.de/upload.php --form userfile=@$tarName --silent --fail --connect-timeout 30 } ] } {
         WriteToLog  {<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> } -nofoot -nohead 
         WriteToLog {HTTP connection could not be established.} -nohead -nofoot
         WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead 
         WriteToLog {Either HTTP_PROXY is needed or the Cluster at Hamburg is not responding.} -nohead -nofoot
         WriteToLog {HTTP_PROXY is NOT set. Do you need an HTTP_PROXY ?} -nohead -nofoot
         WriteToLog {Did you get any warning messages during installation?} -nohead -nofoot
	 TerminateScript 0 -report {Remote submission failed.}
      } else {
         WriteToLog  {<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> } -nofoot -nohead 
         WriteToLog {HTTP connection established and files transferred. } -nohead -nofoot
         WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead 
  	 exec curl --url http://cluster.embl-hamburg.de/upload.php --form userfile=@$tarName.log --silent --fail --connect-timeout 30
      }
   } else {
      WriteToLog {Using proxy server defined in HTTP_PROXY}  -nohead -nofoot
      if { [ catch { exec curl --proxy $http_proxy --url http://cluster.embl-hamburg.de/upload.php --form userfile=@$tarName --silent --fail --connect-timeout 30 } ] } {
         WriteToLog  {<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> } -nofoot -nohead 
         WriteToLog {HTTP connection could not be established.} -nohead -nofoot
         WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead 
         WriteToLog {Either HTTP_PROXY is not set correctly or the Cluster at Hamburg is not responding.} -nohead -nofoot
         WriteToLog {HTTP_PROXY is set. Is the value in the next line correct ?} -nohead -nofoot
	 WriteToLog $http_proxy  -nohead -nofoot
         WriteToLog {Did you get any warning messages during installation?} -nohead -nofoot
	 TerminateScript 0 -report {Remote submission failed.}
      } else {
         WriteToLog  {<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> } -nofoot -nohead 
         WriteToLog {HTTP connection established and files transferred. } -nohead -nofoot
         WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead 
  	 exec curl --proxy $http_proxy --url http://cluster.embl-hamburg.de/upload.php --form userfile=@$tarName.log --silent --fail --connect-timeout 30
      }
   }


TerminateScript 1 -report {Remote submission done}

}

   WriteToLog  {<!--SUMMARY_END--></FONT></B>} -nofoot -nohead