[Sashimi-commit] SF.net SVN: sashimi: [2794] trunk/trans_proteomic_pipeline/src

[<ds...@us...>]

Revision: 2794
          http://sashimi.svn.sourceforge.net/sashimi/?rev=2794&view=rev
Author:   dshteyn
Date:     2008-01-30 11:26:29 -0800 (Wed, 30 Jan 2008)

Log Message:
-----------
Fix problems with calling mktemp that were causing things to fail under linux.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/PvalueModel/PvalueModel.cxx
    trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp
    trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
    trunk/trans_proteomic_pipeline/src/common/util.c

Modified: trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/PvalueModel/PvalueModel.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/PvalueModel/PvalueModel.cxx	2008-01-30 17:19:17 UTC (rev 2793)
+++ trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/PvalueModel/PvalueModel.cxx	2008-01-30 19:26:29 UTC (rev 2794)
@@ -169,7 +169,7 @@
      get initial guess
   */
   if(pngFile != NULL) {
-    tmpFile1 += "tmp_raw_data.XXXXXX.dat"; 
+    tmpFile1 += "tmp_raw_data.dat.XXXXXX"; 
     // do this in designated tmp dir, if any
     replace_path_with_webserver_tmp(tmpFile1);
     stdstring_mktemp(tmpFile1);
@@ -361,7 +361,7 @@
   */
   if(pngFile != NULL) {
 
-    tmpFile2 += "tmp_gaussian_fit.XXXXXX.dat"; 
+    tmpFile2 += "tmp_gaussian_fit.dat.XXXXXX"; 
     // do this in designated tmp dir, if any
     replace_path_with_webserver_tmp(tmpFile2);
     stdstring_mktemp(tmpFile2);
@@ -381,7 +381,7 @@
 
     if(strstr(pngFile, ".ps") != NULL)
       psIndx = 1;
-    tmpFile3 += ".XXXXXX.gnuplot";
+    tmpFile3 += ".gnuplot.XXXXXX";
     // do this in designated tmp dir, if any
     replace_path_with_webserver_tmp(tmpFile3);
     stdstring_mktemp(tmpFile3);

Modified: trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp	2008-01-30 17:19:17 UTC (rev 2793)
+++ trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp	2008-01-30 19:26:29 UTC (rev 2794)
@@ -1193,7 +1193,7 @@
    datafile = OUTFILE+"_senserr.txt"; // populate the filename to get an output file
    if (PLOT_PNG && getIsInteractiveMode() && !PAPER_FIGURES) {
 	   // it's going to get deleted, so write to tmp dir
-	   datafile += ".XXXXXX.tmp";
+	   datafile += ".tmp.XXXXXX";
 	   replace_path_with_webserver_tmp(datafile); // write this in tmpdir
 	   stdstring_mktemp(datafile); // replace XXXXXX with unique random stuff
    }
@@ -2222,7 +2222,7 @@
       imagefile.erase(dot);
    }
    imagefile += ".png";
-   std::string scriptfile = imagefile + ".script.XXXXXX.tmp";
+   std::string scriptfile = imagefile + ".script.tmp.XXXXXX";
    replace_path_with_webserver_tmp(scriptfile); // write this in tmpdir
    stdstring_mktemp(scriptfile); // replace XXXXXX with unique random stuff
 

Modified: trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx	2008-01-30 17:19:17 UTC (rev 2793)
+++ trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx	2008-01-30 19:26:29 UTC (rev 2794)
@@ -229,14 +229,14 @@
 
 
 
-  char suffix[] = ".XXXXXX.tmp";
+  char suffix[] = ".tmp.XXXXXX";
   int olen = (int)(strlen(outfile_)+strlen(suffix)+1);
   char* tmp_outfile = new char[olen];
   strcpy(tmp_outfile, outfile_);
   strcat(tmp_outfile, suffix);
   // do this in designated tmp dir, if any
   replace_path_with_webserver_tmp(tmp_outfile,olen);
-  mktemp(tmp_outfile);
+  mkstemp(tmp_outfile);
 
   unlink(tmp_outfile); // sometimes old cygwin files won't reopen for write
   ofstream fout(tmp_outfile);

Modified: trunk/trans_proteomic_pipeline/src/common/util.c
===================================================================
--- trunk/trans_proteomic_pipeline/src/common/util.c	2008-01-30 17:19:17 UTC (rev 2793)
+++ trunk/trans_proteomic_pipeline/src/common/util.c	2008-01-30 19:26:29 UTC (rev 2794)
@@ -434,11 +434,11 @@
 }
 
 //
-// mktemp for std::string, should have XXXXXX in it somewhere for replacement
+// mktemp for std::string, should have XXXXXX in it at the end for replacement
 //
 void stdstring_mktemp(std::string &XXXXXX_template) {
 	char *c=strdup(XXXXXX_template.c_str());
-	mktemp(c);
+	mkstemp(c);
 	XXXXXX_template = c;
 	free(c);
 }
@@ -448,14 +448,14 @@
 // caller must delete[]
 //
 char *construct_tmpfile_name(const char *basename) {
-  char suffix[] = ".XXXXXX.tmp";
+  char suffix[] = ".tmp.XXXXXX";
   int olen=(int)(strlen(basename)+strlen(suffix)+1);
   char* outfile = new char[olen];
   strcpy(outfile, basename);
   strcat(outfile, suffix);
   // do this in designated tmp dir, if any
   replace_path_with_webserver_tmp(outfile,olen);
-  mktemp(outfile);
+  mkstemp(outfile);
   return outfile;
 }
 


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