6f949e90b1ba3de976455fbcf9da21897761d134
markd
  Fri Oct 29 16:11:58 2021 -0700
add timeout option to pipeline to allow kill long-running pipelines, especially ones run from CGIs

diff --git src/hg/hgGene/rnaStructure.c src/hg/hgGene/rnaStructure.c
index 59ee699..e3327ed 100644
--- src/hg/hgGene/rnaStructure.c
+++ src/hg/hgGene/rnaStructure.c
@@ -1,250 +1,250 @@
 /* rnaStructure - do section on 3' and 5' UTR structure. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "rnaFold.h"
 #include "hui.h"
 #include "web.h"
 #include "portable.h"
 #include "hgGene.h"
 #include "hgConfig.h"
 #include "pipeline.h"
 
 
 static void rnaTrashDirsInit(char **tables, int count)
 /*	create trash directories if necessary */
 {
 for ( count--; count > -1; count--)
     mkdirTrashDirectory(tables[count]);
 }
 
 static boolean rnaStructureExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if tables exists and have our gene. */
 {
 if (sqlTableExists(conn, "foldUtr3") && 
 	sqlRowExists(conn, "foldUtr3", "name", geneId))
     return TRUE;
 if (sqlTableExists(conn, "foldUtr5") && 
 	sqlRowExists(conn, "foldUtr5", "name", geneId))
     return TRUE;
 return FALSE;
 }
 
 static void rnaStructurePrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out rnaStructure table. */
 {
 static boolean firstTime = TRUE;
 static char *names[2] = 
 	{"5' UTR", "3' UTR"};
 static char *tables[2] = {"foldUtr5", "foldUtr3"};
 int side;
 
 if (firstTime)
     {
     rnaTrashDirsInit(tables, ArraySize(tables));
     firstTime = FALSE;
     }
 
 webPrintLinkTableStart();
 webPrintLabelCell("Region");
 webPrintLabelCell("Fold Energy");
 webPrintLabelCell("Bases");
 webPrintLabelCell("Energy/Base");
 webPrintWideCenteredLabelCell("Display As", 3);
 
 char *rnaPlotPath = cfgOptionDefault("rnaPlotPath", "../cgi-bin/RNAplot");
 
 for (side = 0; side < ArraySize(names); ++side)
     {
     char *table = tables[side];
     struct sqlResult *sr;
     char query[256], **row;
     sqlSafef(query, sizeof(query), "select * from %s where name = '%s'",
     	table, geneId);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL)
 	{
 	struct rnaFold fold;
 	int bases;
 	char psName[128];
 
 	/* Load fold and save it as postScript. */
 	rnaFoldStaticLoad(row, &fold);
 	safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, geneId);
         bool plotDone = FALSE;
 	if (fileExists(psName))
             plotDone = TRUE;
         else
 	    {
 	    FILE *f;
 
             if (!fileExists(rnaPlotPath))
                 {
                 plotDone = FALSE;
                 fprintf(stderr, "Could not find %s", rnaPlotPath);
                 }
             else
                 {
                 char *plotCmd[] = {rnaPlotPath, NULL};
-                struct pipeline *plStruct = pipelineOpen1(plotCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL);
+                struct pipeline *plStruct = pipelineOpen1(plotCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
                 f = pipelineFile(plStruct);
                 if (f != NULL)
                     {
                     fprintf(f, ">%s\n", psName);	/* This tells where to put file. */
                     fprintf(f, "%s\n%s\n", fold.seq, fold.fold);
                     plotDone = TRUE;
                     }
                 pipelineClose(&plStruct);
                 }
             }
 
         // newer versions of RNAplot add _ss.ps to the file name
         if (!fileExists(psName))
             safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps_ss.ps", table, table, geneId);
             
 	/* Print row of table, starting with energy terms . */
 	hPrintf("</TR><TR>");
 	bases = strlen(fold.seq);
 	webPrintLinkCell(names[side]);
 	webPrintLinkCellStart();
 	hPrintf("%1.2f", fold.energy);
 	webPrintLinkCellEnd();
 	webPrintLinkCellStart();
 	hPrintf("%d", bases);
 	webPrintLinkCellEnd();
 	webPrintLinkCellStart();
 	hPrintf("%1.3f", fold.energy/bases);
 	webPrintLinkCellEnd();
 
         if (plotDone)
             {
             /* Print link to png image. */
             webPrintLinkCellStart();
             hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
                 geneCgi, cartSidUrlString(cart), 
                 hggMrnaFoldRegion, table,
                 hggMrnaFoldPs, psName,
                 hggDoRnaFoldDisplay, "picture");
             hPrintf(" Picture ");
             hPrintf("</A>");
             webPrintLinkCellEnd();
 
             /* Print link to PostScript. */
             webPrintLinkCellStart();
             hPrintf("<A HREF=\"%s\" class=\"toc\">", psName);
             hPrintf(" PostScript ");
             hPrintf("</A>");
             webPrintLinkCellEnd();
             }
 
 	/* Print link to text. */
 	webPrintLinkCellStart();
 	hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
 	    geneCgi, cartSidUrlString(cart), 
 	    hggMrnaFoldRegion, table,
 	    hggDoRnaFoldDisplay, "text");
 	hPrintf(" Text ");
 	hPrintf("</A>");
 	webPrintLinkCellEnd();
 	}
     sqlFreeResult(&sr);
     }
 webPrintLinkTableEnd();
 hPrintf("<BR>The RNAfold program from the ");
 hPrintf("<A HREF=\"http://www.tbi.univie.ac.at/~ivo/RNA/\" TARGET=_blank>");
 hPrintf("Vienna RNA Package</A> is used to perform the ");
 hPrintf("secondary structure predictions and folding calculations. ");
 hPrintf("The estimated folding energy is in kcal/mol.  The more ");
 hPrintf("negative the energy, the more secondary structure the RNA ");
 hPrintf("is likely to have.");
 }
 
 struct section *rnaStructureSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create rnaStructure section. */
 {
 struct section *section = sectionNew(sectionRa, "rnaStructure");
 if (section != NULL)
     {
     section->exists = rnaStructureExists;
     section->print = rnaStructurePrint;
     }
 return section;
 }
 
 struct rnaFold *loadFold(struct sqlConnection *conn,
 	char *table, char *name)
 /* Load named fold from table. */
 {
 struct rnaFold *fold = NULL;
 struct sqlResult *sr;
 char query[256], **row;
 sqlSafef(query, sizeof(query), "select * from %s where name = '%s'",
     table, name);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     fold = rnaFoldLoad(row);
 sqlFreeResult(&sr);
 return fold;
 }
 
 void doRnaFoldDisplay(struct sqlConnection *conn, char *geneId, char *geneName)
 /* Show RNA folding somehow. */
 {
 char *table = cartString(cart, hggMrnaFoldRegion);
 char *how = cartString(cart, hggDoRnaFoldDisplay);
 struct rnaFold *fold = loadFold(conn, table, geneId);
 
 if (fold == NULL)
     {
     warn("Couldn't load %s from %s", geneId, table);
     return;
     }
 if (sameString(how, "text"))
     {
     hPrintf("<TT><PRE>");
     hPrintf("%s\n%s (%1.2f)\n", fold->seq, fold->fold, fold->energy);
     hPrintf("</PRE></TT>");
     }
 else if (sameString(how, "picture"))
     {
     char *psFile = cartString(cart, hggMrnaFoldPs);
     char *rootName = cloneString(psFile);
     char pngName[256];
     char pdfName[256];
 
     chopSuffix(rootName);
     safef(pngName, sizeof(pngName), "%s.png", rootName);
     safef(pdfName, sizeof(pngName), "%s.pdf", rootName);
     hPrintf("<H2>%s (%s) %s energy %1.2f</H2>\n", 
     	geneName, geneId, table, fold->energy);
     if (!fileExists(pdfName))
         {
         char *command[] = { "ps2pdf", psFile, pdfName, NULL};
-        struct pipeline *pl = pipelineOpen1(command, pipelineWrite | pipelineNoAbort, "/dev/null", NULL);
+        struct pipeline *pl = pipelineOpen1(command, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
         int sysRet = pipelineWait(pl);
         if (sysRet != 0)
             errAbort("System call returned %d for:\n  %s", sysRet, pipelineDesc(pl));
         }
     hPrintf("Click <A HREF=\"%s\">here for PDF version</A><BR>", pdfName);
     if (!fileExists(pngName))
         {
         char outputBuf[1024];
         safef(outputBuf, sizeof outputBuf, "-sOutputFile=%s", pngName);
         char *command[] = { "gs","-sDEVICE=png16m", outputBuf,"-dBATCH","-dNOPAUSE","-q", psFile, NULL};
-        struct pipeline *pl = pipelineOpen1(command, pipelineWrite | pipelineNoAbort, "/dev/null", NULL);
+        struct pipeline *pl = pipelineOpen1(command, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
         int sysRet = pipelineWait(pl);
         if (sysRet != 0)
             errAbort("System call returned %d for:\n  %s", sysRet, pipelineDesc(pl));
         }
     hPrintf("<IMG SRC=\"%s\">", pngName);
     }
 }