c9cb558b37ad87c86ca3a0f1efb1a75c1b83465c
braney
  Tue May 7 11:08:19 2024 -0700
strip off hub_#_ for genark hubs when sending to Galaxy

diff --git src/hg/hgTables/galaxy.c src/hg/hgTables/galaxy.c
index 85162a3..2f4e2ac 100644
--- src/hg/hgTables/galaxy.c
+++ src/hg/hgTables/galaxy.c
@@ -1,159 +1,164 @@
 /* galaxy - stuff related to galaxy simple queries and db info. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "trackDb.h"
 #include "customTrack.h"
 #include "hdb.h"
 #include "web.h"
 #include "portable.h"
 #include "hui.h"
 #include "featureBits.h"
 #include "hgTables.h"
 #include "obscure.h"
 #include "cart.h"
 #include "grp.h"
 #include "net.h"
 #include "htmlPage.h"
 #include "wiggle.h"
 #include "trashDir.h"
 #include "hgConfig.h"
+#include "trackHub.h"
 
 
 char *getGalaxyUrl()
 /* Returns the url for the galaxy cgi; default can be overriden by cart var GALAXY_URL.
  * Don't free result. */
 {
 char *url = NULL;
 /* use parameter if available */
 if (cartVarExists(cart, "GALAXY_URL"))
     url = cartString(cart, "GALAXY_URL");
 else 
     {
     if (cfgOption("galaxyUrl"))
         url = cfgOption("galaxyUrl");
     else
         url = GALAXY_URL_APP;
     }
 return url;
 }
 
 void galaxyHandler (char *format, va_list args)
 /* error Handler that passes error on to Galaxy */
 {
 char msg[512];
 sprintf(msg, format, args);
 noWarnAbort();
 }
 
 void sendParamsToGalaxy(char *doParam, char *paramVal)
 /* intermediate page for formats printed directly from top form */
 {
 char *shortLabel = curTable;
 char *output = cartString(cart, hgtaOutputType);
 
 if (curTrack != NULL)
     shortLabel = curTrack->shortLabel;
 htmlOpen("Output %s as %s", "results to Galaxy", shortLabel);
 if (sameString(output, outPrimaryTable) || sameString(output, outSelectedFields))
     {
     if (anySubtrackMerge(database, curTable))
         errAbort("Can't do all fields output when subtrack merge is on. "
         "Please go back and select another output type (BED or custom track is good), or clear the subtrack merge.");
     if (anyIntersection())
         errAbort("Can't do all fields output when intersection is on. "
         "Please go back and select another output type (BED or custom track is good), or clear the intersection.");
 
     }
 if (isMafTable(database, curTrack, curTable))
     {
     hPrintf("You are about to download a VERY large dataset to Galaxy. "
             "For most usage scenarios it is not necessary as Galaxy already "
             "stores alignments locally. Click here ("
             "<A HREF=\"https://galaxyproject.org/main/maf-analysis/\" TARGET=_blank>https://galaxyproject.org/main/maf-analysis/</A>"
             ") for more information on how to analyze multiple alignments "
             "through Galaxy.\n<BR><BR>");
     }
 startGalaxyForm();
 /* send the hgta_do parameter that won't be in the cart */
 cgiMakeHiddenVar(doParam, paramVal);
 /* need to send sessionId */
 cgiMakeHiddenVar(cartSessionVarName(cart), cartSessionId(cart));
 printGalaxySubmitButtons();
 htmlClose();
 }
 
 void startGalaxyForm ()
 /* start form to send parameters to Galaxy, also send required params */
 {
 char selfUrl[256];
 char *hguid = cartUserId(cart);
 
 hPrintf("<FORM ACTION=\"%s\" METHOD=POST>\n", getGalaxyUrl());
 /* copy cart parameters into hidden fields to send to Galaxy */
 hPrintf("\n"); /* make more readable */
 /* Galaxy requires tool_id and URL */
 /* set default if no tool_id for Galaxy */
 if (!cartVarExists(cart, "tool_id"))
     cgiMakeHiddenVar("tool_id", "ucsc_table_direct1");
 else
     cgiMakeHiddenVar("tool_id", cartString(cart, "tool_id"));
 safef(selfUrl, sizeof(selfUrl), "http%s://%s%s", cgiAppendSForHttps(), cgiServerNamePort(), cgiScriptName());
 cgiMakeHiddenVar("URL", selfUrl);
 hPrintf("\n");
 /* forward user parameters */
 if (hguid)
     {
     cgiMakeHiddenVar("hguid", hguid);
     hPrintf("\n");
     }
-/* send database and organism and table for Galaxy's info */
-cgiMakeHiddenVar("db", database);
+/* send database and organism and table for Galaxy's info. If hub is genark, strip off hub_#_ prefix */
+char *galaxyDb = database;
+char *skipHubDb = trackHubSkipHubName(galaxyDb);
+if ((skipHubDb != NULL) && startsWith("GC",  skipHubDb))
+    galaxyDb = skipHubDb;
+cgiMakeHiddenVar("db", galaxyDb);
 if (cartVarExists(cart, "org"))
     cgiMakeHiddenVar("org", cartString(cart, "org"));
 cgiMakeHiddenVar("hgta_table", curTable);
 cgiMakeHiddenVar(hgtaTrack, cartString(cart, hgtaTrack));
 if (cartVarExists(cart, "hgta_regionType"))
     cgiMakeHiddenVar("hgta_regionType", cartString(cart, "hgta_regionType"));
 if (cartVarExists(cart, "hgta_outputType"))
     cgiMakeHiddenVar("hgta_outputType", cartString(cart, "hgta_outputType"));
 if (cartVarExists(cart, "position"))
     cgiMakeHiddenVar("position", cartString(cart, "position"));
 }
 
 void printGalaxySubmitButtons ()
 /* print submit button to send query results to Galaxy */
 {
 cgiMakeButton(hgtaDoGalaxyQuery, "Send query to Galaxy");
 hPrintf("</FORM>\n");
 hPrintf(" ");
 /* new form as action is different */
 hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
 cgiMakeButton(hgtaDoMainPage, "Cancel");
 hPrintf("</FORM>\n");
 }
 
 void verifyGalaxyFormat(const char *output)
 /* print warning about not using hyperlinks output formtat with Galaxy */
 {
 if (sameString(output, outHyperlinks))
     {
     htmlOpen("Sorry!");
     errAbort("Galaxy does not use hyperlinks output format.\n"
          "Please go back and ensure that hyperlinks output format is not chosen.");
     htmlClose();
     }
 }
 
 
 boolean doGalaxy ()
 /* has the send to Galaxy checkbox been selected? */
 {
 return cartUsualBoolean(cart, "sendToGalaxy", FALSE);
 }