c2e376e7b6d980f41ff903e6374378d668f11770
kate
  Thu Oct 22 14:41:52 2020 -0700
Multi-region features for sparse tracks.  With virt->multi, needs debug. refs #26385

diff --git src/hg/hgTracks/extTools.c src/hg/hgTracks/extTools.c
index f28eb44..fa4da67 100644
--- src/hg/hgTracks/extTools.c
+++ src/hg/hgTracks/extTools.c
@@ -1,335 +1,335 @@
 // Code to parse list of external tools and redirect to it via a hidden form */
 //
 // The link from hgTracks has the form ?hgt.redirectTool=<name>
 // Note that you can add the parameter &debug=1 to the URL to see and modify the hidden form
 // cgi-bin/extTools.ra defines the parameters and labels of the tools
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "dystring.h"
 #include "hCommon.h"
 #include "htmshell.h"
 #include "hash.h"
 #include "web.h"
 #include "ra.h"
 #include "hgTracks.h"
 #include "extTools.h"
 #include "hgFind.h"
 #include "obscure.h"
 #include "net.h"
 
 boolean extToolsEnabled()
 /* Return TRUE if we can display the external tools menu. */
 {
 return fileExists("extTools.ra");
 }
 
 void printExtMenuData(char *chromName) 
 /* print the external tools aka "send to" menu entries as a javascript list to stdout */
 {
 if (!extToolsEnabled())
     return;
 
 struct extTool *extTools = NULL;
 
 // we allow an alternative location in /gbdb/hgFixed
 // This means that we do not have to do a build patch when 
 // we have to change this .ra file and can do it with a simple
 // file push to the RR
 if (fileExists("/gbdb/hgFixed/extTools.ra"))
     extTools = readExtToolRa("/gbdb/hgFixed/extTools.ra");
 else
     extTools = readExtToolRa("extTools.ra");
 
 struct extTool *et;
 struct dyString *dy = dyStringNew(1024);
 dyStringAppend(dy, "extTools = [\n");
 for(et = extTools; et != NULL; et = et->next)
     {
     // special case for alternate chroms on hg38, skip the Ensembl links
     if (chromName!=NULL && startsWith("ensembl", et->tool) && endsWith(chromName, "_alt"))
         continue;
 
     if (et->dbs!=NULL)
         {
         if (!slNameInList(et->dbs, database))
             continue;
         }
     if (et->notDbs!=NULL)
         {
         if (slNameInList(et->notDbs, database))
             continue;
         }
     char* tool = jsonStringEscape(et->tool);
     char* shortLabel = jsonStringEscape(et->shortLabel);
     char* longLabel = jsonStringEscape(et->longLabel);
     dyStringPrintf(dy, "    ['%s', '%s', '%s', %d]", tool, shortLabel, longLabel, et->maxSize);
     if (et->next)
         dyStringAppend(dy, ",");
     dyStringAppend(dy, "\n");
     }
 dyStringAppend(dy, "];\n");
 
 jsInline(dy->string);
 dyStringFree(&dy);
 
 }
 
 static char *cloneRaSetting(struct hash *hash, char *name, struct lineFile *lf, bool mustExist)
 /* clone a setting out of the ra hash.  errAbort if mustExit and not found, otherwise NULL. */
 {
 char *str;
 if ((str = hashFindVal(hash, name)) == NULL) 
     {
     if (mustExist)
         errAbort("missing required setting '%s' on line %d in file %s\n",
             name, lf->lineIx, lf->fileName);
     else
         return NULL;
     }
 return cloneString(str);
 }
 
 struct extTool *readExtToolRa(char *raFileName) 
 /* parse the extTools.ra file. Inspired by trackHub.c:readGroupRa() */
 {
 struct lineFile *lf = udcWrapShortLineFile(raFileName, NULL, 1*1024*1024);
 struct extTool *list = NULL;
 //struct hash *ra;
 struct slPair *raList;
 while ((raList = raNextStanzAsPairs(lf)) != NULL)
     {
     struct extTool *et;
     AllocVar(et);
 
     struct slPair *paramList = NULL;
 
     struct hash *raHash;
     raHash = hashNew(0);
 
     // the "param" field is there more than once, so cannot use a hash for it
     struct slPair *raPair;
     for (raPair = raList; raPair != NULL; raPair = raPair->next)
         {
         if (sameWord(raPair->name, "param"))
             {
             // split the val into parameter name and value
             char *paramArr[2];
             int fCount = chopByWhite(raPair->val, paramArr, 2);
             // hacky way to allow spaces in parameter names and values
             char *name = replaceChars(paramArr[0], "%20", " ");
             char *val;
             if (fCount==2)
                 val = cloneString(paramArr[1]);
             else
                 val = cloneString("");
             val = replaceChars(val, "%20", " ");
             slPairAdd(&paramList, name, val);
             }
         else
             // add all other name/val pairs to the hash
             hashAdd(raHash, raPair->name, cloneString(raPair->val));
         }
 
     // pull out the required fields from the hash
     et->tool = cloneRaSetting(raHash, "tool", lf, TRUE);
     et->shortLabel = cloneRaSetting(raHash, "shortLabel", lf, TRUE);
     et->longLabel = cloneRaSetting(raHash, "longLabel", lf, TRUE);
     et->url = cloneRaSetting(raHash, "url", lf, TRUE);
     et->dbs = NULL;
 
     // optional fields
     et->email = cloneRaSetting(raHash, "email", lf, FALSE);
     if (hashFindVal(raHash, "onlyDbs"))
         et->dbs = commaSepToSlNames(hashFindVal(raHash, "onlyDbs"));
     if (hashFindVal(raHash, "notDbs"))
         et->notDbs = commaSepToSlNames(hashFindVal(raHash, "notDbs"));
 
     char *isHttpGet = hashFindVal(raHash, "isHttpGet");
     if (isHttpGet && \
      (sameString(isHttpGet, "yes") || sameString(isHttpGet, "on") || sameString(isHttpGet, "true")))
             et->isHttpGet = TRUE;
 
     char *maxSize = hashFindVal(raHash, "maxSize");
     if (maxSize!=NULL)
         et->maxSize = sqlUnsignedOrError(maxSize, "Error: maxSize %s for tool %s is not a number", \
                 maxSize, et->tool);
 
     slReverse(&paramList);
     et->params = paramList;
 
     slAddHead(&list, et);
     freeHashAndVals(&raHash);
     slPairFree(&raList);
     }
 
 if (list)
     slReverse(&list);
 lineFileClose(&lf);
 return list;
 }
 
 void extToolRedirect(struct cart *cart, char *tool)
 /* redirect to an external tool, sending the data specified in the ext tools config file */
 {
 bool debug = cgiVarExists("debug");
 
 struct extTool *extTools = readExtToolRa("extTools.ra");
 struct extTool *et;
 for (et = extTools; et != NULL; et = et->next)
     if (sameWord(et->tool, tool))
         break;
 if (et==NULL)
     errAbort("No configuration found for tool %s", tool);
 
 
 // construct an invisible CGI form with the given parameters
 printf("<html>\n<head>\n");
 generateCspMetaHeader(stdout);
 printf("</head>\n<body>\n");
 
 if (debug)
     printf("Target URL: %s<p>", et->url);
 
 char *chromName;
 int winStart, winEnd;
 char *db = cartString(cart, "db");
 char *pos = cartString(cart, "position");
 
 // Try to deal with virt chrom position used by hgTracks.
-if (startsWith("virt:", cartUsualString(cart, "position", "")))
+if (startsWith(MULTI_REGION_CHROM, cartUsualString(cart, "position", "")))
     pos = cartString(cart, "nonVirtPosition");
 
 if (!parsePosition(pos, &chromName, (uint *)&winStart, (uint *)&winEnd))
     errAbort("Can't parse position '%s'", pos);
 int len = winEnd-winStart;
 
 char start1[255];
 safef(start1, sizeof(start1), "%d", winStart+1);
 
 char *url = replaceInUrl(et->url, "", cart, db, chromName, winStart, winEnd, NULL, TRUE, NULL);
 
 char *method = "POST";
 if (et->isHttpGet)
     method = "GET";
 
 printf("<form id=\"redirForm\" method=\"%s\" action=\"%s\">\n", method, url);
 
 struct slPair *slp;
 
 if (et->maxSize!=0 && len > et->maxSize)
     {
     printf("Sorry, this tool accepts only a sequence with less than %d base pairs<p>\n"
       "Please zoom in some more.<p>\n", et->maxSize);
     return;
     }
 
 printf("You're being redirected from the UCSC Genome Browser to the site %s<br>\n", url);
 if (et->email)
     printf("Please contact %s for questions on this tool.<br>\n", et->email);
 
 boolean submitDone = FALSE;
 for (slp=et->params; slp!=NULL; slp=slp->next)
     {
     char* val = slp->val;
     if (sameWord(val, "$db"))
         val = db;
     else if (sameWord(val, "$position"))
         val = pos;
     else if (sameWord(val, "$start1"))
         val = start1;
     else if (sameWord(val, "$returnUrl"))
         {
         // get the full URL of this hgTracks page, so external page can construct a custom track
         // and link back to us
         char* host = getenv("HTTP_HOST");
         char* reqUrl = getenv("REQUEST_URI");
         // remove everything after ? in URL
         char *e = strchr(reqUrl, '?');
         if (e) *e = 0; 
 
         char url[4000];
         // cannot find a way to find out if the request came in via http or https
         safef(url, sizeof(url), "http://%s%s", host, reqUrl);
         val = url;
         }
     // half the current window size
     else if (stringIn("$halfLen", val))
         {
         char buf[64];
         safef(buf, sizeof(buf), "%d", len/2);
         val = replaceChars(val, "$halfLen", buf);
         }
     else if (sameWord(val, "$seq") || sameWord(val, "$faSeq"))
         {
         static struct dnaSeq *seq = NULL;
         seq = hDnaFromSeq(db, chromName, winStart, winEnd, dnaLower);
         if (sameWord(val, "$seq"))
             val = seq->dna;
         else
             {
             val = catTwoStrings(">sequence\n",seq->dna);
             freez(&seq);
             }
         }
     else if (sameWord(val, "$ncbiGca"))
         {
         char *gca = hNcbiGcaId(db);
         if (gca)
             val = gca;
         else
             // Really we shouldn't be making this entire form... pass db as hail-mary
             val = db;
         }
     else if (sameWord(val, "$ncbiGcf"))
         {
         char *gcf = hNcbiGcfId(db);
         if (gcf)
             val = gcf;
         else
             // Really we shouldn't be making this entire form... pass db as hail-mary
             val = db;
         }
     // any remaining $-expression might be one of the general ones
     else if (stringIn("$", val))
         {
         val = replaceInUrl(val, "", cart, db, chromName, winStart, winEnd, NULL, TRUE, NULL);
         }
 
     // output
     if (debug)
         {
         printf("%s: ", slp->name);
         printf("<input name=\"%s\" value=\"%s\"><p>\n", slp->name, val);
         }
     else
         {
         // parameter named submit is a special case
         if (sameWord(slp->name, "submit"))
             {
             submitDone = TRUE;
             printf("<input type=\"submit\" value=\"%s\" style=\"position: absolute; left: -9999px; "
                 "width: 1px; height: 1px;\">\n", val);
             }
         else
             printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">\n", slp->name, val);
         }
     }
 
 // a hidden submit button, see
 // http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button
 if (debug)
     printf("<input type=\"submit\">\n");
 else if (!submitDone)
     printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n");
 printf("</form>\n");
 // a little javascript that clicks the submit button
 if (!debug)
     {
     jsInline("document.getElementById(\"redirForm\").submit();\n");
     }
 jsInlineFinish();
 printf("</body></html>\n");
 }