42379069550347d7135531a382a9a30958d106a2
galt
  Mon Jul 16 17:25:15 2012 -0700
fixed html error found by htmlCheck; added some newlines to make show source more legible
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index 4821ba5..d068f20 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -1,552 +1,551 @@
 /* hgHubConnect - the CGI web-based program to select track data hubs to connect with. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "errabort.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "hdb.h"
 #include "hui.h"
 #include "cart.h"
 #include "dbDb.h"
 #include "web.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "dystring.h"
 #include "hPrint.h"
 #include "jsHelper.h"
 #include "obscure.h"
 #include "hgConfig.h"
 
 #define hgHub             "hgHub_"  /* prefix for all control variables */
 #define hgHubDo            hgHub   "do_"    /* prefix for all commands */
 #define hgHubDoClear       hgHubDo "clear"
 #define hgHubDoDisconnect  hgHubDo "disconnect"
 #define hgHubDoReset       hgHubDo "reset"
 
 struct cart *cart;	/* The user's ui state. */
 struct hash *oldVars = NULL;
 
 static char *destUrl = "../cgi-bin/hgTracks";
 static char *pageTitle = "Track Data Hubs";
 char *database = NULL;
 char *organism = NULL;
 
 static void ourCellStart()
 {
 puts("<TD>");
 }
 
 static void ourCellEnd()
 {
 puts("</TD>");
 }
 
 static void ourPrintCell(char *str)
 {
 ourCellStart();
 if (str != NULL)
     puts(str);
 ourCellEnd();
 }
 
 static char *removeLastComma(char *string)
 {
 if (string != NULL)
     {
     int len = strlen(string);
 
     if ( string[len - 1] == ',')
 	string[len - 1]  = 0;
     }
 return string;
 }
 
 static void addGenomesToHash(struct hubConnectStatus *hub, struct hash *hash)
 /* add supported assembly names from trackHub to hash */
 {
 if (hub == NULL)
     return;
 
 struct trackHub *thub = hub->trackHub;
 if (thub != NULL)
     {
     /* List of associated genomes. */
     struct trackHubGenome *genomes = thub->genomeList;	
 
     for(; genomes; genomes = genomes->next)
 	hashStore(hash, genomes->name);
     }
 }
 
 static void hgHubConnectUnlisted(struct hubConnectStatus *hubList, 
     struct hash *publicHash)
 /* Put up the list of unlisted hubs and other controls for the page. */
 /* uses publicHash to distingusih public hubs from unlisted ones */
 /* NOTE: Destroys hubList */
 {
 // put out the top of our page
-printf("<div id=\"unlistedHubs\" class=\"hubList\"> "
-    "<table id=\"unlistedHubsTable\"> "
-    "<thead><tr> "
-	"<th colspan=\"6\" id=\"addHubBar\"><label for=\"hubUrl\">URL:</label> "
+printf("<div id=\"unlistedHubs\" class=\"hubList\"> \n"
+    "<table id=\"unlistedHubsTable\"> \n"
+    "<thead><tr> \n"
+	"<th colspan=\"6\" id=\"addHubBar\"><label for=\"hubUrl\">URL:</label> \n"
 	"<input name=\"hubText\" id=\"hubUrl\" class=\"hubField\""
-	    "type=\"text\" size=\"65\"> "
+	    "type=\"text\" size=\"65\"> \n"
 	"<input name=\"hubAddButton\""
 	    "onClick=\"if(validateUrl($('#hubUrl').val())) { document.addHubForm.elements['hubUrl'].value=hubText.value;"
 		"document.addHubForm.submit();return true;} else { return false;}\" "
-		"class=\"hubField\" type=\"button\" value=\"Add Hub\">"
-	"</th> "
-    "</tr> ");
+		"class=\"hubField\" type=\"button\" value=\"Add Hub\">\n"
+	"</th> \n"
+    "</tr> \n");
 
 // count up the number of unlisted hubs we currently have
 int unlistedHubCount = 0;
 struct hubConnectStatus *unlistedHubList = NULL;
 struct hubConnectStatus *hub, *nextHub;
 struct hash *assHash = newHash(5);
 
 for(hub = hubList; hub; hub = nextHub)
     {
     nextHub = hub->next;
     // if url is not in publicHash, it's unlisted */
     if (!((publicHash != NULL) && hashLookup(publicHash, hub->hubUrl)))
 	{
 	addGenomesToHash(hub, assHash);
 	unlistedHubCount++;
 	slAddHead(&unlistedHubList, hub);
 	}
     }
 
 hubList = NULL;  // hubList no longer valid
 
 struct hashCookie cookie = hashFirst(assHash);
 struct dyString *dy = newDyString(100);
 struct hashEl *hel;
 int numAssemblies = 0;
 while ((hel = hashNext(&cookie)) != NULL)
     {
     dyStringPrintf(dy,"%s,", hel->name);
     numAssemblies++;
     }
 
 char *dbList = NULL;
 if (numAssemblies)   
     dbList = dyStringCannibalize(&dy);
 
 if (unlistedHubCount == 0)
     {
     // nothing to see here
-    printf(
-	"<tr><td>No Unlisted Track Hubs</td></tr>"
-	"</td>");
-    printf("</table></thead></div>");
+    printf("<tr><td>No Unlisted Track Hubs</td></tr>");
+    printf("</thead></table></div>");
     return;
     }
 
 // time to output the big table.  First the header
 printf(
     "<tr> "
 	"<th>Display</th> "
 	"<th>Hub Name</th> "
 	"<th>Description</th> "
 	"<th>Assemblies</th> "
 	"<th>URL</th> "
 	"<th>Disconnect</th> "
-    "</tr></thead>\n");
+    "</tr>\n"
+    "</thead>\n");
 
 // start first row
 printf("<tbody><tr>");
 
 int count = 0;
 for(hub = unlistedHubList; hub; hub = hub->next)
     {
     if (count)
 	webPrintLinkTableNewRow();  // ends last row and starts a new one
     count++;
 
     // if there's an error message, we don't let people select it
     if (isEmpty(hub->errorMessage))
 	{
 	ourCellStart();
 	char hubName[32];
 	safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, hub->id);
 	cartMakeCheckBox(cart, hubName, FALSE);
 	ourCellEnd();
 	}
     else
 	{
 	// give people a chance to clear the error 
 	ourCellStart();
 	printf(
 	"<input name=\"hubClearButton\""
 	    "onClick=\"document.resetHubForm.elements['hubUrl'].value='%s';"
 		"document.resetHubForm.submit();return true;\" "
-		"class=\"hubField\" type=\"button\" value=\"check hub\">"
+		"class=\"hubField\" type=\"button\" value=\"check hub\">\n"
 		, hub->hubUrl);
 	ourCellEnd();
 	}
     if (hub->trackHub != NULL)
 	ourPrintCell(hub->trackHub->shortLabel);
     else
 	ourPrintCell("");
 
     if (!isEmpty(hub->errorMessage))
 	printf("<TD><span class=\"hubError\">ERROR: %s </span>"
-	    "<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug</a></TD>", 
+	    "<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug</a></TD>\n", 
 	    hub->errorMessage);
     else if (hub->trackHub != NULL)
 	ourPrintCell(hub->trackHub->longLabel);
     else
 	ourPrintCell("");
 
     ourPrintCell(removeLastComma(dbList));
     ourPrintCell(hub->hubUrl);
 
     ourCellStart();
     printf(
     "<input name=\"hubDisconnectButton\""
 	"onClick=\"document.disconnectHubForm.elements['hubId'].value='%d';"
 	    "document.disconnectHubForm.submit();return true;\" "
-	    "class=\"hubField\" type=\"button\" value=\"X\">"
+	    "class=\"hubField\" type=\"button\" value=\"X\">\n"
 	    , hub->id);
     ourCellEnd();
     }
 
 printf("</TR></tbody></TABLE>\n");
 printf("</div>");
 }
 
 static struct hash *outputPublicTable(struct sqlConnection *conn, char *publicTable)
 /* Put up the list of public hubs and other controls for the page. */
 {
 struct hash *publicHash = NULL;
 char query[512];
 safef(query, sizeof(query), "select hubUrl,shortLabel,longLabel,dbList from %s", 
 	publicTable); 
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 
 boolean gotAnyRows = FALSE;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *url = row[0], *shortLabel = row[1], *longLabel = row[2], 
     	  *dbList = row[3];
     if (gotAnyRows)
 	webPrintLinkTableNewRow();
     else
 	{
 	/* output header */
 	printf("<div id=\"publicHubs\" class=\"hubList\"> \n");
 	printf("<table id=\"publicHubsTable\"> "
 	    "<thead><tr> "
 		"<th>Display</th> "
 		"<th>Hub Name</th> "
 		"<th>Description</th> "
 		"<th>Assemblies</th> "
 		"<th>URL</th> "
 	    "</tr></thead>\n");
 
 	// start first row
 	printf("<tbody> <tr>");
 	gotAnyRows = TRUE;
 
 	// allocate the hash to store hubUrl's
 	publicHash = newHash(5);
 	}
 
     char *errorMessage = NULL;
     // get an id for this hub
     unsigned id = hubFindOrAddUrlInStatusTable(database, cart, 
 	url, &errorMessage);
 
     if ((id != 0) && isEmpty(errorMessage)) 
 	{
 	ourCellStart();
 	char hubName[32];
 	safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
 	cartMakeCheckBox(cart, hubName, FALSE);
 	ourCellEnd();
 	}
     else if (!isEmpty(errorMessage))
 	{
 	// give user a chance to clear the error
 	ourCellStart();
 	printf(
 	"<input name=\"hubClearButton\""
 	    "onClick=\"document.resetHubForm.elements['hubUrl'].value='%s';"
 		"document.resetHubForm.submit();return true;\" "
 		"class=\"hubField\" type=\"button\" value=\"check hub\">"
 		, url);
 	ourCellEnd();
 	}
     else
 	errAbort("cannot get id for hub with url %s\n", url);
 
     ourPrintCell(shortLabel);
     if (isEmpty(errorMessage))
 	ourPrintCell(longLabel);
     else
 	printf("<TD><span class=\"hubError\">ERROR: %s </span>"
 	    "<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug</a></TD>", 
 	    errorMessage);
 
     ourPrintCell(removeLastComma(dbList));
     ourPrintCell(url);
     hashStore(publicHash, url);
     }
 sqlFreeResult(&sr);
 
 if (gotAnyRows)
     {
     printf("</TR></tbody></TABLE>\n");
     printf("</div>");
     }
 return publicHash;
 }
 
 
 struct hash *hgHubConnectPublic()
 /* Put up the list of public hubs and other controls for the page. */
 {
 struct hash *retHash = NULL;
 struct sqlConnection *conn = hConnectCentral();
 char *publicTable = cfgOptionEnvDefault("HGDB_HUB_PUBLIC_TABLE", 
 	hubPublicTableConfVariable, defaultHubPublicTableName);
 if (!(sqlTableExists(conn, publicTable) && 
 	(retHash = outputPublicTable(conn, publicTable)) != NULL ))
     {
     printf("<div id=\"publicHubs\" class=\"hubList\"> \n");
     printf("No Public Track Hubs for this genome assembly<BR>");
     printf("</div>");
     }
 hDisconnectCentral(&conn);
 
 return retHash;
 }
 
 static void tryHubOpen(unsigned id)
 /* try to open hub, leaks trackHub structure */
 {
 /* try opening this again to reset error */
 struct sqlConnection *conn = hConnectCentral();
 struct errCatch *errCatch = errCatchNew();
 struct hubConnectStatus *hub = NULL;
 if (errCatchStart(errCatch))
     hub = hubConnectStatusForId(conn, id);
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     hubUpdateStatus( errCatch->message->string, NULL);
 else
     hubUpdateStatus(NULL, hub);
 errCatchFree(&errCatch);
 
 hDisconnectCentral(&conn);
 }
 
 
 static void doResetHub(struct cart *theCart)
 {
 char *url = cartOptionalString(cart, hgHubDataText);
 
 if (url != NULL)
     {
     unsigned id = hubResetError(url);
     tryHubOpen(id);
     }
 else
     errAbort("must specify url in %s\n", hgHubDataText);
 }
 
 static void doClearHub(struct cart *theCart)
 {
 char *url = cartOptionalString(cart, hgHubDataText);
 
 printf("<pre>clearing hub %s\n",url);
 if (url != NULL)
     hubClearStatus(url);
 else
     errAbort("must specify url in %s\n", hgHubDataText);
 printf("<pre>Completed\n");
 }
 
 static void doDisconnectHub(struct cart *theCart)
 {
 char *id = cartOptionalString(cart, "hubId");
 
 if (id != NULL)
     {
     char buffer[1024];
     safef(buffer, sizeof buffer, "hgHubConnect.hub.%s", id);
     cartRemove(cart, buffer);
     }
 
 cartRemove(theCart, "hubId");
 }
 
 static void checkTrackDbs(struct hubConnectStatus *hubList)
 {
 struct hubConnectStatus *hub = hubList;
 struct trackHub *trackHubList = NULL;
 
 for(; hub; hub = hub->next)
     {
     struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
 	{
 	hubAddTracks(hub, database, &trackHubList);
 	}
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	{
 	hub->errorMessage = cloneString(errCatch->message->string);
 	hubUpdateStatus( errCatch->message->string, hub);
 	}
     else
 	hubUpdateStatus(NULL, hub);
     }
 }
 
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 boolean gotDisconnect = FALSE;
 
 cart = theCart;
 setUdcCacheDir();
 
 if (cartVarExists(cart, hgHubDoClear))
     {
     doClearHub(cart);
     cartWebEnd();
     return;
     }
 
 if (cartVarExists(cart, hgHubDoDisconnect))
     {
     gotDisconnect = TRUE;
     doDisconnectHub(cart);
 
     // now rebuild the cart variable ("trackHubs") that has which lists which
     // hubs are on.
     hubConnectHubsInCart(cart);
     }
 
 if (cartVarExists(cart, hgHubDoReset))
     {
     doResetHub(cart);
     }
 
 cartWebStart(cart, NULL, "%s", pageTitle);
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("jquery-ui.js", NULL);
 
 webIncludeResourceFile("jquery-ui.css");
 
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("hgHubConnect.js", NULL);
 jsIncludeFile("jquery.cookie.js", NULL);
 
 printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n");
 printf(
    "<P>Track data hubs are collections of tracks from outside of UCSC that "
    "can be imported into the Genome Browser.  To import a public hub check "
    "the box in the list below. "
    "After import the hub will show up as a group of tracks with its own blue "
    "bar and label underneath the main browser graphic, and in the "
    "configure page. For more information, see the "
    "<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>"
    "User's Guide</A>.</P>\n"
    "<P><B>NOTE: Because Track Hubs are created and maintained by external sources,"
    " UCSC cannot be held responsible for their content.</B></P>"
    );
 printf("</div>\n");
 
 getDbAndGenome(cart, &database, &organism, oldVars);
 
 char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
 char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
 
 if (survey && differentWord(survey, "off"))
     hPrintf("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey");
 hPutc('\n');
 
 // check to see if we have any new hubs
 hubCheckForNew(database, cart);
 
 // grab all the hubs that are listed in the cart
 struct hubConnectStatus *hubList =  hubConnectStatusListFromCartAll(cart);
 
 checkTrackDbs(hubList);
 
 // here's a little form for the add new hub button
 printf("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubUrl", "");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 puts("</FORM>");
 
 // this the form for the disconnect hub button
 printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubId", "");
 cgiMakeHiddenVar(hgHubDoDisconnect, "on");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 puts("</FORM>");
 
 // this the form for the reset hub button
 printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubUrl", "");
 cgiMakeHiddenVar(hgHubDoReset, "on");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 puts("</FORM>");
 
 
 // ... and now the main form
 if (cartVarExists(cart, hgHubConnectCgiDestUrl))
     destUrl = cartOptionalString(cart, hgHubConnectCgiDestUrl);
 printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
 cartSaveSession(cart);
 
 // we have two tabs for the public and unlisted hubs
 printf("<div id=\"tabs\">"
        "<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>"
        "<li><a href=\"#unlistedHubs\">My Hubs</a></li> "
        "</ul> ");
 
 struct hash *publicHash = hgHubConnectPublic();
 hgHubConnectUnlisted(hubList, publicHash);
 printf("</div>");
 
 printf("<div class=\"tabFooter\">");
 cgiMakeButton("Submit", "Load Selected Hubs");
 
 char *emailAddress = cfgOptionDefault("hub.emailAddress","genome@soe.ucsc.edu");
 printf("<span class=\"small\">"
     "Contact <A HREF=\"mailto:%s\">%s</A> to add a public hub."
     "</span>\n", emailAddress,emailAddress);
 printf("</div>");
 
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 
 printf("</div>\n");
 puts("</FORM>");
 cartWebEnd();
 }
 
 char *excludeVars[] = {"Submit", "submit", "hc_one_url", 
     hgHubDoReset, hgHubDoClear, hgHubDoDisconnect, hgHubDataText, 
     hgHubConnectRemakeTrackHub, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }