src/hg/hgTables/great.c 1.1

Index: src/hg/hgTables/great.c
===================================================================
RCS file: src/hg/hgTables/great.c
diff -N src/hg/hgTables/great.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgTables/great.c	22 Apr 2010 19:25:22 -0000	1.1
@@ -0,0 +1,142 @@
+/* great - stuff related to GREAT. */
+
+#include "common.h"
+#include "cheapcgi.h"
+#include "hgTables.h"
+#include "cart.h"
+#include "dystring.h"
+#include "textOut.h"
+#include "trashDir.h"
+
+static char const rcsid[] = "$Id$";
+
+static struct dyString *getRequestName()
+{
+char *track = cartString(cart, hgtaTrack);
+char *table = cartString(cart, hgtaTable);
+struct dyString *name;
+
+if (differentStringNullOk(track, table))
+    name = dyStringCreate("%s:%s", track, table);
+else
+    name = dyStringCreate("%s", track);
+return name;
+}
+
+void verifyGreatFormat(const char *output)
+{
+if (!sameString(output, outBed) && !sameString(output, outWigBed))
+    {
+    htmlOpen("Sorry!");
+    errAbort("GREAT requires that the output format be BED format.\n"
+         "Some tracks are not available in BED format and thus cannot be passed to GREAT.\n"
+         "Please go back and ensure that BED format is chosen.");
+    htmlClose();
+    }
+}
+
+void verifyGreatAssemblies()
+{
+if (differentStringNullOk(database, "hg18") && differentStringNullOk(database, "mm9"))
+    {
+    hPrintf("<script type='text/javascript'>\n");
+    hPrintf("function logSpecies() {\n");
+    hPrintf("try {\n");
+    hPrintf("var r = new XMLHttpRequest();\n");
+    hPrintf("r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n", database);
+    hPrintf("r.send(null);\n");
+    hPrintf("} catch (err) { }\n");
+    hPrintf("}\n");
+    hPrintf("window.onload = logSpecies;\n");
+    hPrintf("</script>\n");
+    errAbort("GREAT only supports the Human, Mar. 2006 (NCBI36/hg18) and Mouse, July 2007 (NCBI37/mm9) assemblies."
+    "\nPlease go back and ensure that one of those assemblies is chosen.");
+    htmlClose();
+    }
+}
+
+void doGreatTopLevel()
+/* intermediate page for formats printed directly from top form */
+{
+struct dyString *name = getRequestName();
+
+htmlOpen("Send BED data to GREAT as %s", dyStringContents(name));
+freeDyString(&name);
+verifyGreatAssemblies();
+startGreatForm();
+cgiMakeHiddenVar(hgtaDoTopSubmit, "get output");
+printGreatSubmitButtons();
+htmlClose();
+}
+
+void startGreatForm()
+/* Start form for GREAT */
+{
+hPrintf("<FORM ACTION=\"%s\" NAME='greatForm' METHOD=POST>\n", getScriptName());
+}
+
+void printGreatSubmitButtons()
+/* print submit button to create data and then send query results to GREAT. */
+{
+cartSetString(cart, hgtaCompressType, textOutCompressNone);
+cartSetString(cart, hgtaOutFileName, "");
+
+cgiMakeHiddenVar(hgtaCompressType, textOutCompressNone);
+cgiMakeHiddenVar(hgtaOutFileName, "");
+
+cgiMakeHiddenVar(hgtaDoGreatOutput, "on");
+cgiMakeHiddenVar(hgtaPrintCustomTrackHeaders, "on");
+cgiMakeButton(hgtaDoGreatQuery, "Send query to GREAT");
+hPrintf("</FORM>\n");
+hPrintf(" ");
+/* new form as action is different */
+hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
+cgiMakeButton(hgtaDoMainPage, "Cancel");
+hPrintf("</FORM>\n");
+}
+
+boolean doGreat()
+/* has the send to GREAT checkbox been selected? */
+{
+return cartUsualBoolean(cart, "sendToGreat", FALSE);
+}
+
+void doSubmitToGreat(const char *path)
+/* Send a URL to GREAT that it can use to retrieve the results. */
+{
+struct dyString *requestName = getRequestName();
+struct dyString *requestURL = dyStringCreate("http://%s/%s", cgiServerName(), path);
+struct dyString *greatRequest;
+
+greatRequest = dyStringCreate(
+    "<meta http-equiv='refresh' content='0;url=http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%20Table%20Browser'>",
+    dyStringContents(requestURL), database, dyStringContents(requestName));
+
+hPrintf("<b>GREAT</b> is processing BED data from \"%s\"...please wait.\n", dyStringContents(requestName));
+hPrintf(dyStringContents(greatRequest));
+freeDyString(&greatRequest);
+freeDyString(&requestName);
+freeDyString(&requestURL);
+}
+
+void doGetGreatOutput(void (*dispatch)())
+{
+char hgsid[64];
+struct tempName tn;
+FILE *saveStdout = stdout;
+
+safef(hgsid, sizeof(hgsid), "%u", cartSessionId(cart));
+trashDirFile(&tn, "great", hgsid, ".bed");
+stdout = fopen(tn.forCgi, "w");
+
+dispatch();
+
+fflush(stdout);
+fclose(stdout);
+cartSetBoolean(cart, hgtaDoGreatOutput, FALSE);
+stdout = saveStdout;
+htmlOpen("Table Browser integration with GREAT");
+doSubmitToGreat(tn.forCgi);
+htmlClose();
+}
+