src/hg/hgc/hgdpClick.c 1.5
1.5 2009/02/09 22:30:25 angie
Use hg.conf settings to determine GMT executable paths and enable/disable images, instead of hIsPrivateHost.
Index: src/hg/hgc/hgdpClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgdpClick.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/hgc/hgdpClick.c 9 Feb 2009 18:52:35 -0000 1.4
+++ src/hg/hgc/hgdpClick.c 9 Feb 2009 22:30:25 -0000 1.5
@@ -1,378 +1,393 @@
/* hgdpClick -- handlers for Human Genome Variation Project tracks */
#include "common.h"
#include "hgc.h"
#include "hgdpGeo.h"
+#include "hgConfig.h"
#include "trashDir.h"
#include "pipeline.h"
#include "obscure.h"
#include "htmshell.h"
static char const rcsid[] = "$Id$";
struct hgdpPopInfo
{
char *name;
float longitude;
float latitude;
};
// auto-generated -- see makeDb/doc/hgdpGeo.txt
struct hgdpPopInfo pops[] =
{
{ "Adygei", 44, 39 },
{ "Balochi", 30, 73 },
{ "BantuKenya", -3, 37 },
{ "BantuSouthAfrica", -25.56926433, 24.25 },
{ "Basque", 43, 0 },
{ "Bedouin", 29, 40 },
{ "BiakaPygmy", 4, 17 },
{ "Brahui", 32, 63 },
{ "Burusho", 39, 78 },
{ "Cambodian", 12, 105 },
{ "Colombian", 3, -68 },
{ "Dai", 20, 97 },
{ "Daur", 46.5, 122 },
{ "Druze", 30, 30 },
{ "French", 47, 1 },
{ "Han", 31, 116 },
{ "Han-NChina", 35, 114 },
{ "Hazara", 37, 65 },
{ "Hezhen", 47.4976192, 133.5 },
{ "Italian", 46, 10 },
{ "Japanese", 38, 138 },
{ "Kalash", 42, 68 },
{ "Karitiana", -7, -66 },
{ "Lahu", 22, 103 },
{ "Makrani", 26, 62 },
{ "Mandenka", 12, -12 },
{ "Maya", 19, -91 },
{ "MbutiPygmy", 1, 29 },
{ "Melanesian", -6, 155 },
{ "Miao", 27, 110 },
{ "Mongola", 45, 111 },
{ "Mozabite", 32, 3 },
{ "Naxi", 26, 97 },
{ "Orcadian", 59, -3 },
{ "Oroqen", 52, 128 },
{ "Palestinian", 35, 38 },
{ "Papuan", -4, 143 },
{ "Pathan", 34, 77 },
{ "Pima", 29, -108 },
{ "Russian", 61, 40 },
{ "San", -21, 20 },
{ "Sardinian", 39, 7 },
{ "She", 26, 120 },
{ "Sindhi", 24.49, 69 },
{ "Surui", -14, -59 },
{ "Tu", 37, 100 },
{ "Tujia", 31.4, 108.5 },
{ "Tuscan", 40.5, 14 },
{ "Uygur", 44, 76.5 },
{ "Xibo", 43.497, 84 },
{ "Yakut", 62.98287845, 129.5 },
{ "Yi", 28, 103 },
{ "Yoruba", 7.995094727, 5 }
};
// PostScript printf format for adding labels to map image.
// auto-generated -- see makeDb/doc/hgdpGeo.txt
static const char *hgdpGeoLabelFormat =
"PSL_font_encode 0 get 0 eq {ISOLatin1+_Encoding /Helvetica /Helvetica PSL_reencode PSL_font_encode 0 1 put} if\n"
"0 setlinecap\n"
"0 setlinejoin\n"
"10 setmiterlimit\n"
"-2175 -1425 T\n"
"\n"
"%%%% PostScript produced by:\n"
"%%%%GMT: pstext -Jx1i -R0/9/0/6.5 -x-7.25i -y-4.75i -O -K\n"
"S 0 W\n"
"S 0 A\n"
"S V\n"
"0 0 M\n"
"2700 0 D\n"
"0 1950 D\n"
"-2700 0 D\n"
"P\n"
"eoclip N\n"
"PSL_font_encode 1 get 0 eq {ISOLatin1+_Encoding /Helvetica-Bold /Helvetica-Bold PSL_reencode PSL_font_encode 1 1 put} if\n"
"0 0 M 58 F1 (SNP: %s) E /PSL_dimx exch def YP /PSL_dimy exch def\n"
"75 1875 M 0 PSL_dimy neg G 58 F1 (SNP: %s) Z\n"
"S U\n"
"S [] 0 B\n"
"S 0 A\n"
"PSL_font_encode 0 get 0 eq {ISOLatin1+_Encoding /Helvetica /Helvetica PSL_reencode PSL_font_encode 0 1 put} if\n"
"0 setlinecap\n"
"0 setlinejoin\n"
"10 setmiterlimit\n"
"\n"
"%%%% PostScript produced by:\n"
"%%%%GMT: pstext -Jx1i -R0/9/0/6.5 -O -K -Gblue\n"
"S 0 W\n"
"S 0 A\n"
"S V\n"
"0 0 M\n"
"2700 0 D\n"
"0 1950 D\n"
"-2700 0 D\n"
"P\n"
"eoclip N\n"
"PSL_font_encode 1 get 0 eq {ISOLatin1+_Encoding /Helvetica-Bold /Helvetica-Bold PSL_reencode PSL_font_encode 1 1 put} if\n"
"S 0 0 1 C\n"
"0 0 M 58 F1 (Ancestral Allele: %c) E /PSL_dimx exch def YP /PSL_dimy exch def\n"
"75 1800 M 0 PSL_dimy neg G 58 F1 (Ancestral Allele: %c) Z\n"
"S U\n"
"S [] 0 B\n"
"S 0 A\n"
"PSL_font_encode 0 get 0 eq {ISOLatin1+_Encoding /Helvetica /Helvetica PSL_reencode PSL_font_encode 0 1 put} if\n"
"0 setlinecap\n"
"0 setlinejoin\n"
"10 setmiterlimit\n"
"\n"
"%%%% PostScript produced by:\n"
"%%%%GMT: pstext -Jx1i -R0/9/0/6.5 -O -K -Gorange\n"
"S 0 W\n"
"S 0 A\n"
"S V\n"
"0 0 M\n"
"2700 0 D\n"
"0 1950 D\n"
"-2700 0 D\n"
"P\n"
"eoclip N\n"
"PSL_font_encode 1 get 0 eq {ISOLatin1+_Encoding /Helvetica-Bold /Helvetica-Bold PSL_reencode PSL_font_encode 1 1 put} if\n"
"S 1 0.647 0 C\n"
"0 0 M 58 F1 (Derived Allele: %c) E /PSL_dimx exch def YP /PSL_dimy exch def\n"
"75 1725 M 0 PSL_dimy neg G 58 F1 (Derived Allele: %c) Z\n"
"S U\n"
"S [] 0 B\n"
"S 0 A\n";
// Parameters for running the Generic Mapping Tools psxy command to plot pie charts
// on two maps in one image: Africa+EurAsia (AEA) and Central/South America (AM).
// These are from scripts written by John Novembre, jnovembre at ucla.
-#define PSXY_PATH "/hive/data/outside/GMT4.3.1/bin/psxy"
#define PSXY_PIX "-W0.5p"
#define PSXY_CIRCLE "-Sc"
#define PSXY_WEDGE "-Sw"
#define PSXY_CONT_PLOT "-O"
#define PSXY_CONT_PS "-K"
#define AEA_REGION "-R-20/160/-35/72"
#define AEA_PROJ "-JKs70/7.5i"
#define AEA_X "-X0.4i"
#define AEA_Y "-Y0.5i"
#define AM_REGION "-R245/310/-20/35"
#define AM_PROJ "-JKs275.5/1.5i"
#define AM_X "-X6.85i"
#define AM_Y "-Y4.25i"
static char *psxyOrangeAeaCmd[] =
- {PSXY_PATH, "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
+ {"", "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
PSXY_CIRCLE, "-Gorange", AEA_X, AEA_Y, NULL};
static char *psxyPieAeaCmd[] =
- {PSXY_PATH, "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
+ {"", "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
PSXY_WEDGE, "-Gblue", NULL};
static char *psxyBlueAeaCmd[] =
- {PSXY_PATH, "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
+ {"", "", AEA_REGION, AEA_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
PSXY_CIRCLE, "-Gblue", NULL};
static char *psxyOrangeAmCmd[] =
- {PSXY_PATH, "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
+ {"", "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
PSXY_CIRCLE, "-Gorange", AM_X, AM_Y, NULL};
static char *psxyPieAmCmd[] =
- {PSXY_PATH, "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
+ {"", "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT, PSXY_CONT_PS,
PSXY_WEDGE, "-Gblue", NULL};
static char *psxyBlueAmCmd[] =
- {PSXY_PATH, "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT,
+ {"", "", AM_REGION, AM_PROJ, PSXY_PIX, PSXY_CONT_PLOT,
PSXY_CIRCLE, "-Gblue", NULL};
-// We use the Generic Mapping Tools ps2raster command to convert the generated
-// Encapsulated PostScript imange to PNG.
-#define PS2RASTER_PATH "/hive/data/outside/GMT4.3.1/bin/ps2raster"
-#define GHOSTSCRIPT_PATH "-G/usr/bin/ghostscript"
-
-static void runCommandAppend(char *cmd[], char *inFile, char *outFile)
+static void runCommandAppend(char *cmd[], char *program, char *inFile, char *outFile)
/* Use the pipeline module to run a single command pipelineWrite|pipelineAppend. */
{
char **cmds[2];
cmds[0] = cmd;
cmds[1] = NULL;
+cmd[0] = program;
cmd[1] = inFile;
struct pipeline *pl = pipelineOpen(cmds, pipelineWrite|pipelineAppend, outFile, NULL);
pipelineWait(pl);
pipelineFree(&pl);
}
static void mustRename(char *oldName, char *newName)
/* Rename a file or errAbort if there's a problem. */
{
if (rename(oldName, newName))
errAbort("Cannot rename %s to %s", oldName, newName);
}
static void generateImgFiles(struct hgdpGeo *geo, char finalEpsFile[PATH_LEN],
char finalPdfFile[PATH_LEN], char finalPngFile[PATH_LEN])
/* Using the frequencies given in geo and the population latitude and longitude
* given above, plot allele frequency pie charts for each population on a world map.
* Work in a temporary trash dir and then move result files to the given paths. */
{
// The Generic Mapping Tools commands must have a writeable ./ and $HOME.
// Use trashDirFile as a directory name, cd to that and work there.
char cwd[PATH_LEN];
if (getcwd(cwd, sizeof(cwd)) == NULL)
errAbort("PATH_LEN (%d) is too short.", PATH_LEN);
struct tempName dirTn;
trashDirFile(&dirTn, "hgc", "hgdpGeo", "");
makeDirs(dirTn.forCgi);
chdir(dirTn.forCgi);
char *realHome = getenv("HOME");
setenv("HOME", ".", TRUE);
// Make trash files with coordinate specs for pie charts and full circles:
char rootName[FILENAME_LEN];
splitPath(dirTn.forCgi, NULL, rootName, NULL);
char pieFile[FILENAME_LEN], circleFile[FILENAME_LEN];
safef(pieFile, sizeof(pieFile), "%s_pie.txt", rootName);
safef(circleFile, sizeof(circleFile), "%s_circle.txt", rootName);
FILE *fPie = mustOpen(pieFile, "w");
FILE *fCir = mustOpen(circleFile, "w");
int i;
for (i = 0; i < HGDPGEO_POP_COUNT; i++)
{
FILE *f = (geo->popFreqs[i] == 1.0) ? fCir : fPie;
fprintf(f, "%.4f %.4f 0.65 0 %.4f\n",
pops[i].latitude, pops[i].longitude, geo->popFreqs[i]*360);
}
fclose(fPie);
fclose(fCir);
// Build up an EPS image: copy a baseline EPS (map background), add SNP and allele labels,
// and use ps2xy commands to allele frequency pie charts.
char epsFile[FILENAME_LEN];
safef(epsFile, sizeof(epsFile), "%s.eps", rootName);
char mapBgEps[PATH_LEN];
safef(mapBgEps, sizeof(mapBgEps), "%s/hgcData/hgdpGeoMap.eps", cwd);
copyFile(mapBgEps, epsFile);
FILE *fEps = mustOpen(epsFile, "a");
fprintf(fEps, hgdpGeoLabelFormat, geo->name, geo->name,
geo->ancestralAllele, geo->ancestralAllele, geo->derivedAllele, geo->derivedAllele);
fclose(fEps);
//- run psxy on circle/pie spec trash files for AfrEurAsia and America
-runCommandAppend(psxyOrangeAeaCmd, pieFile, epsFile);
-runCommandAppend(psxyPieAeaCmd, pieFile, epsFile);
-runCommandAppend(psxyBlueAeaCmd, circleFile, epsFile);
-runCommandAppend(psxyOrangeAmCmd, pieFile, epsFile);
-runCommandAppend(psxyPieAmCmd, pieFile, epsFile);
-runCommandAppend(psxyBlueAmCmd, circleFile, epsFile);
+char *psxy = cfgOption("hgc.psxyPath");
+if (isEmpty(psxy))
+ errAbort("How did this get called? hg.conf doesn't have hgc.psxyPath.");
+runCommandAppend(psxyOrangeAeaCmd, psxy, pieFile, epsFile);
+runCommandAppend(psxyPieAeaCmd, psxy, pieFile, epsFile);
+runCommandAppend(psxyBlueAeaCmd, psxy, circleFile, epsFile);
+runCommandAppend(psxyOrangeAmCmd, psxy, pieFile, epsFile);
+runCommandAppend(psxyPieAmCmd, psxy, pieFile, epsFile);
+runCommandAppend(psxyBlueAmCmd, psxy, circleFile, epsFile);
// Make PDF and PNG:
struct pipeline *pl;
char pdfFile[FILENAME_LEN], pngFile[FILENAME_LEN];
safef(pdfFile, sizeof(pdfFile), "%s.pdf", rootName);
safef(pngFile, sizeof(pngFile), "%s.png", rootName);
char *ps2pdfCmd[] = {"ps2pdf", epsFile, pdfFile, NULL};
char **cmdsPdf[] = {ps2pdfCmd, NULL};
pl = pipelineOpen(cmdsPdf, pipelineWrite, "/dev/null", NULL);
pipelineWait(pl);
pipelineFree(&pl);
-char *ps2RasterPngCmd[] = {PS2RASTER_PATH, GHOSTSCRIPT_PATH, "-P", "-A", "-Tg", "-E150",
- epsFile, NULL};
+char *ps2raster = cfgOption("hgc.ps2rasterPath");
+char *ghostscript = cfgOption("hgc.ghostscriptPath");
+char gsOpt[PATH_LEN];
+safef(gsOpt, sizeof(gsOpt), "-G%s", ghostscript);
+char *ps2RasterPngCmd[] = {ps2raster, gsOpt, "-P", "-A", "-Tg", "-E150", epsFile, NULL};
char **cmdsPng[] = {ps2RasterPngCmd, NULL};
pl = pipelineOpen(cmdsPng, pipelineRead, "/dev/null", NULL);
pipelineWait(pl);
pipelineFree(&pl);
// Back to our usual working directory and $HOME:
if (realHome == NULL)
unsetenv("HOME");
else
setenv("HOME", realHome, TRUE);
chdir(cwd);
// Move the result files into place:
char tmpPath[PATH_LEN];
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, epsFile);
mustRename(tmpPath, finalEpsFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pdfFile);
mustRename(tmpPath, finalPdfFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pngFile);
mustRename(tmpPath, finalPngFile);
}
+static boolean canMakeImages()
+/* Determine whether we have the necessary command line programs for
+ * creating images above. */
+{
+char *psxy = cfgOption("hgc.psxyPath");
+char *ps2raster = cfgOption("hgc.ps2rasterPath");
+char *ghostscript = cfgOption("hgc.ghostscriptPath");
+if (isEmpty(psxy) || isEmpty(ps2raster) || isEmpty(ghostscript))
+ return FALSE;
+if (!fileExists(psxy) || !fileExists(ps2raster) || !fileExists(ghostscript))
+ return FALSE;
+return TRUE;
+}
+
void hgdpGeoImg(struct hgdpGeo *geo)
/* Generate a PNG image: world map with pie charts for population allele frequencies. */
{
-// Disable this past hgwdev until we fix the /hive paths...
-if (! hIsPrivateHost())
+if (! canMakeImages())
return;
struct tempName tn;
trashDirFile(&tn, "hgc", "", "");
char trashDir[FILENAME_LEN];
splitPath(tn.forCgi, trashDir, NULL, NULL);
char geoSnpEpsFile[PATH_LEN], geoSnpPdfFile[PATH_LEN], geoSnpPngFile[PATH_LEN];
safef(geoSnpEpsFile, sizeof(geoSnpEpsFile), "%shgdpGeo_%s.eps", trashDir, geo->name);
safef(geoSnpPdfFile, sizeof(geoSnpPdfFile), "%shgdpGeo_%s.pdf", trashDir, geo->name);
safef(geoSnpPngFile, sizeof(geoSnpPngFile), "%shgdpGeo_%s.png", trashDir, geo->name);
if (! (fileExists(geoSnpEpsFile) && fileExists(geoSnpPdfFile) && fileExists(geoSnpPngFile)))
generateImgFiles(geo, geoSnpEpsFile, geoSnpPdfFile, geoSnpPngFile);
printf("<A HREF=\"%s\" TARGET=_BLANK><IMG SRC=\"%s\" WIDTH=677 HEIGHT=490></A><BR>\n",
geoSnpPngFile, geoSnpPngFile);
printf("<A HREF=\"%s\" TARGET=_BLANK>PDF</A> ", geoSnpPdfFile);
printf("<A HREF=\"%s\" TARGET=_BLANK>EPS</A> ", geoSnpEpsFile);
printf("<A HREF=\"%s\" TARGET=_BLANK>PNG</A><BR>\n", geoSnpPngFile);
}
void hgdpGeoFreqTable(struct hgdpGeo *geo)
/* Print an HTML table of populations and allele frequencies. */
{
int i;
printf("<B>Ancestral Allele Frequencies for %s:</B>\n", geo->name);
printf("<TABLE CELLPADDING=1 CELLSPACING=0>\n");
for (i = 0; i < HGDPGEO_POP_COUNT; i++)
{
printf("<TR><TD>%s</TD><TD>%.4f</TD></TR>\n",
pops[i].name, geo->popFreqs[i]);
}
printf("</TABLE>\n");
}
void doHgdpGeo(struct trackDb *tdb, char *item)
/* Show details page for HGDP SNP with population allele frequencies
* plotted on a world map. */
{
struct sqlConnection *conn = hAllocConn(database);
char query[512];
struct sqlResult *sr;
char **row;
int start = cartInt(cart, "o");
genericHeader(tdb, item);
int hasBin=1;
safef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
tdb->tableName, item, seqName, start);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct hgdpGeo geo;
hgdpGeoStaticLoad(row+hasBin, &geo);
printCustomUrl(tdb, item, TRUE);
bedPrintPos((struct bed *)&geo, 4, tdb);
printf("<B>Ancestral Allele:</B> %c<BR>\n", geo.ancestralAllele);
printf("<B>Derived Allele:</B> %c<BR>\n", geo.derivedAllele);
printf("<BR>\n");
printf("<TABLE><TR><TD>\n");
hgdpGeoFreqTable(&geo);
printf("</TD><TD valign=top>\n");
hgdpGeoImg(&geo);
printf("</TD></TR></TABLE>\n");
}
else
errAbort("doHgdpGeo: no match in %s for %s at %s:%d", tdb->tableName, item, seqName, start);
sqlFreeResult(&sr);
printTrackHtml(tdb);
hFreeConn(&conn);
}