void vgLoadJax(char *visiGeneDir, char *jaxDb, char *outDir)
/* vgLoadJax - Load visiGene database from jackson database. */
{
struct sqlConnection *conn = sqlConnect(jaxDb);
struct sqlConnection *conn2 = sqlConnect(jaxDb);
struct sqlConnection *connSp = sqlConnect("uniProt");
char inFull[PATH_LEN];
char *jaxPath = "inSitu/Mouse/jax";
char inJax[PATH_LEN];
#ifdef UNUSED
/* won't work yet */
char* host = "genome-test";
char* user = cfgOptionEnv("HGDB_USER", "db.user");
char* password = cfgOptionEnv("HGDB_PASSWORD", "db.password");
connSp = sqlConnectRemote(host, user, password, "uniProt");
#endif
safef(inFull, sizeof(inFull), "%s/full", visiGeneDir);
safef(inJax, sizeof(inJax), "%s/%s", inFull, jaxPath);
submitToDir(conn, conn2, connSp, outDir, inJax);
sqlDisconnect(&connSp);
sqlDisconnect(&conn2);
sqlDisconnect(&conn);
}
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
boolean gotDisconnect = FALSE;
cart = theCart;
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 is not 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(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", "Use Selected Hubs");
char *emailAddress = cfgOptionDefault("hub.emailAddress","*****@*****.**");
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();
}
