46be8ee0e162296c4a15954f967797e389f88b0e
braney
  Thu Aug 18 16:07:51 2011 -0700
add a note about the data not being QA'ed by UCSC  #3260
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index a8a5656..ffce0cf 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -1,448 +1,450 @@
 /* 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"
 
 #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 = "Import Tracks from Data Hubs";
 char *database = NULL;
 char *organism = NULL;
 
 static void ourCellStart()
 {
 puts("<TD>");
 }
 
 static void ourCellEnd()
 {
 puts("</TD>");
 }
 
 static void ourPrintCell(char *str)
 {
 ourCellStart();
 puts(str);
 ourCellEnd();
 }
 
 static void hgHubConnectUnlisted()
 /* Put up the list of unlisted hubs and other controls for the page. */
 {
 // put out the top of our page
 printf("<div id=\"unlistedHubs\" class=\"hubList\"> "
     "<table id=\"unlistedHubsTable\"> "
     "<thead><tr> "
 	"<th colspan=\"5\" id=\"addHubBar\"><label>URL:</label> "
 	"<input name=\"hubText\" id=\"hubUrl\" class=\"hubField\""
 	    "type=\"text\" size=\"65\"> "
 	"<input name=\"hubAddButton\""
 	    "onClick=\"document.addHubForm.elements['hubUrl'].value=hubText.value;"
 		"document.addHubForm.submit();return true;\" "
 		"class=\"hubField\" type=\"button\" value=\"Add Hub\">"
 	"</th> "
     "</tr> ");
 
 // count up the number of unlisted hubs we currently have
 int count = 0;
 struct hubConnectStatus *hub, *hubList =  hubConnectStatusListFromCartAll(cart);
 for(hub = hubList; hub; hub = hub->next)
     {
     if (isHubUnlisted(hub))
 	count++;
     }
 
 if (count == 0)
     {
     // nothing to see here
     printf(
 	"<tr><td>No Track Hubs for this genome assembly</td></tr>"
 	"</td></table>");
     printf("</thead></div>");
     return;
     }
 
 // time to output the big table.  First the header
 printf(
     "<tr> "
 	"<th>Display</th> "
 	"<th>Hub Name</th> "
 	"<th>Description</th> "
 	"<th>URL</th> "
 	"<th>Disconnect</th> "
     "</tr></thead>\n");
 
 // start first row
 printf("<tbody><tr>");
 
 count = 0;
 for(hub = hubList; hub; hub = hub->next)
     {
     /* if the hub is public, then don't list it here */
     if (!isHubUnlisted(hub))
 	continue;
 
     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=\"clear error\">"
 		, hub->hubUrl);
 	ourCellEnd();
 	}
     ourPrintCell(hub->shortLabel);
     if (isEmpty(hub->errorMessage))
 	ourPrintCell(hub->longLabel);
     else
 	printf("<TD><span class=\"hubError\">ERROR: %s</span>"
 	    "<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug</a></TD>", 
 	    hub->errorMessage);
 
     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\">"
 	    , hub->id);
     ourCellEnd();
     }
 
 printf("</TR></tbody></TABLE>\n");
 printf("</div>");
 }
 
 static void makeGenomePrint()
 /* print out the name of the current database etc. */
 {
 getDbAndGenome(cart, &database, &organism, oldVars);
 printf("<div id=\"assemblyInfo\"> \n");
 printf("<B>genome:</B> %s &nbsp;&nbsp;&nbsp;<B>assembly:</B> %s  ",
 	organism, hFreezeDate(database));
 printf("</div>\n");
 }
 
 
 void hgHubConnectPublic()
 /* Put up the list of public hubs and other controls for the page. */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 safef(query, sizeof(query), "select hubUrl,shortLabel,longLabel,dbList from %s", 
 	hubPublicTableName); 
 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 (nameInCommaList(database, dbList))
 	{
 	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>URL</th> "
 		"</tr></thead>\n");
 
 	    // start first row
 	    printf("<tbody> <tr>");
 	    gotAnyRows = TRUE;
 	    }
 
 	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=\"clear error\">"
 		    , url);
 	    ourCellEnd();
 	    }
 	else
 	    errAbort("cannot get id for hub with url %s\n", url);
 
 	ourPrintCell(shortLabel);
 	if (isEmpty(errorMessage))
 	    ourPrintCell(longLabel);
 	else
 	    printf("<TD>ERROR: %s</TD>", errorMessage);
 
 	ourPrintCell(url);
 	}
     }
 sqlFreeResult(&sr);
 
 if (gotAnyRows)
     {
     printf("</TR></tbody></TABLE>\n");
     }
 else
     {
     printf("<div id=\"publicHubs\" class=\"hubList\"> \n");
     printf("No Public Track Hubs for this genome assembly<BR>");
     }
 
 printf("</div>");
 
 hDisconnectCentral(&conn);
 }
 
 static void tryHubOpen(unsigned id)
 /* try to open hub, leaks trackHub structure */
 {
 /* try opening this again to reset error */
 struct errCatch *errCatch = errCatchNew();
 struct trackHub *tHub;
 if (errCatchStart(errCatch))
     tHub = trackHubFromId(id);
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     hubSetErrorMessage( errCatch->message->string, id);
 else
     hubSetErrorMessage(NULL, id);
 errCatchFree(&errCatch);
 
 tHub = NULL;
 }
 
 
 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");
 }
 
 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);
     }
 
 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);
 webIncludeResourceFile("hgHubConnect.css");
 
 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>NOTE: Because Track Hubs are created and maintained by external sources,"
+   " UCSC cannot be held responsible for their content.</P>"
    );
 printf("</div>\n");
 
 // figure out and print out genome name
 makeGenomePrint();
 
 // check to see if we have any new hubs
 unsigned newId = hubCheckForNew(database, cart);
 
 if (newId)
     tryHubOpen(newId);
 
 // 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> ");
 
 hgHubConnectPublic();
 hgHubConnectUnlisted();
 printf("</div>");
 
 printf("<div class=\"tabFooter\">");
 cgiMakeButton("Submit", "Load Selected Hubs");
 printf("<span class=\"small\">Contact <A HREF=\"mailto:genome@soe.ucsc.edu\">genome@soe.ucsc.edu</A> to add a public hub.</span>\n");
 printf("</div>");
 
 if ((newId != 0) || gotDisconnect) // make MyHubs the default tab
     {
     printf("<script type='text/javascript'>\n ");
     printf("var $tabs = $('#tabs').tabs();\n");
     printf(" $tabs.tabs('select',1);\n");
     printf("</script>\n");
     }
 
 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;
 }