ef2869665d8c2d4fe59743faabe050de406a5278
braney
  Wed Apr 13 18:00:32 2011 -0700
add support for private hubs.  Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index a965529..3aa0b1b 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -5,84 +5,148 @@
 #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 "trashDir.h"
+#include "hPrint.h"
+
+#define TEXT_ENTRY_ROWS 7
+#define TEXT_ENTRY_COLS 73
+#define CONFIG_ENTRY_ROWS 3
+#define SAVED_LINE_COUNT  50
+
+#define HUB_CUSTOM_TEXT_ALT_VAR  "hghub_customText"
+#define HUB_CUSTOM_FILE_VAR      "hghub.customFile"
+#define HUB_UPDATED_ID           "hghub_updatedId"
+
+
+
+#define hgHubDataText      HUB_CUSTOM_TEXT_ALT_VAR
+#define hgHubDataFile      HUB_CUSTOM_FILE_VAR
+#define hgHubUpdatedId     HUB_UPDATED_ID
+
+#define hgHub             "hgHub_"  /* prefix for all control variables */
+#define hgHubDo            hgHub   "do_"    /* prefix for all commands */
+#define hgHubDoAdd         hgHubDo "add"
 
-static char const rcsid[] = "$Id: hgPcr.c,v 1.29 2009/09/23 18:42:17 angie Exp $";
 
 struct cart *cart;	/* The user's ui state. */
 struct hash *oldVars = NULL;
 
 static char *destUrl = "../cgi-bin/hgTracks";
-static char *pageTitle = "Import Tracks from External Data Hubs";
+static char *pageTitle = "Import Tracks from Data Hubs";
 char *database = NULL;
 char *organism = NULL;
 
 boolean nameInCommaList(char *name, char *commaList)
 /* Return TRUE if name is in comma separated list. */
 {
 if (commaList == NULL)
     return FALSE;
 int nameLen = strlen(name);
 for (;;)
     {
     char c = *commaList;
     if (c == 0)
         return FALSE;
     if (memcmp(name, commaList, nameLen) == 0)
         {
 	c = commaList[nameLen];
 	if (c == 0 || c == ',')
 	    return TRUE;
 	}
     commaList = strchr(commaList, ',');
     if (commaList == NULL)
         return FALSE;
     commaList += 1;
     }
 }
 
-void hgHubConnect()
-/* Put up the list of hubs and other controls for the page. */
+void hgHubConnectPrivate()
+/* Put up the list of private hubs and other controls for the page. */
+{
+printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", "../cgi-bin/hgHubConnect");
+cartSaveSession(cart);
+cgiMakeHiddenVar(hgHubDoAdd, "on");
+printf("<B>List of Private Hubs</B><BR>");
+struct hubConnectStatus *hub, *hubList =  hubConnectStatusListFromCart(cart);
+int count = 0;
+for(hub = hubList; hub; hub = hub->next)
+    {
+    if (hub->id > 0)
+	continue;
+    count++;
+    if (hub != hubList)
+	webPrintLinkTableNewRow();
+    else
+	webPrintLinkTableStart();
+
+    if (isEmpty(hub->errorMessage))
+	{
+	webPrintLinkCellStart();
+	char hubName[32];
+	safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
+	cartMakeCheckBox(cart, hubName, FALSE);
+	webPrintLinkCellEnd();
+	}
+    else
+	webPrintLinkCell("error");
+    webPrintLinkCell(hub->shortLabel);
+    if (isEmpty(hub->errorMessage))
+	webPrintLinkCell(hub->longLabel);
+    else
+	webPrintLinkCell(hub->errorMessage);
+    webPrintLinkCell(hub->hubUrl);
+    }
+if (count)
+    webPrintLinkTableEnd();
+else
+    printf("No Private Track Hubs for this genome assembly<BR>");
+cgiMakeButton("add", "add new private hub");
+}
+
+void hgHubConnectPublic()
+/* Put up the list of external hubs and other controls for the page. */
 {
 destUrl = cartUsualString(cart, hgHubConnectCgiDestUrl, destUrl);
 printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
 cartSaveSession(cart);
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 printf(
    "<P>Track data hubs are collections of tracks from outside of UCSC that can be imported into "
-   "the Genome Browser.  To import a hub check the box in the list below. "
+   "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. To arrange "
    "for your own track data hub to appear in this list, please contact genome@soe.ucsc.edu.</P>\n"
    );
 getDbAndGenome(cart, &database, &organism, oldVars);
 printf("<B>genome:</B> %s &nbsp;&nbsp;&nbsp;<B>assembly:</B> %s &nbsp;&nbsp;&nbsp;[%s] ", 
 	organism, hFreezeDate(database), database);
 cgiMakeButton("submit", "submit");
 printf("<BR>");
+printf("<B>List of Public Hubs</B><BR>");
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 safef(query, sizeof(query), "select id,shortLabel,longLabel,errorMessage,hubUrl,dbList from %s", 
 	hubConnectTableName); 
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 
 boolean gotAnyRows = FALSE;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *id = row[0], *shortLabel = row[1], *longLabel = row[2], *errorMessage = row[3],
     	 *url = row[4], *dbList = row[5];
     if (nameInCommaList(database, dbList))
 	{
 	if (gotAnyRows)
@@ -107,36 +171,168 @@
 	    webPrintLinkCell(longLabel);
 	else
 	    webPrintLinkCell(errorMessage);
 	webPrintLinkCell(url);
 	}
     }
 sqlFreeResult(&sr);
 if (gotAnyRows)
     webPrintLinkTableEnd();
 else
     printf("No Track Hubs for this genome assembly");
 printf("</FORM>\n");
 hDisconnectCentral(&conn);
 }
 
+static void addIntro()
+{
+}
+
+void makeClearButton(char *field)
+/* UI button that clears a text field */
+{
+char javascript[1024];
+safef(javascript, sizeof javascript,
+        "document.mainForm.%s.value = '';", field);
+cgiMakeOnClickButton(javascript, "&nbsp;Clear&nbsp;");
+}
+
+void addPrivateHubForm(struct hubConnectStatus *hub, char *err)
+/* display UI for adding private hubs by URL or pasting data */
+{
+getDbAndGenome(cart, &database, &organism, oldVars);
+boolean gotClade = FALSE;
+boolean isUpdateForm = FALSE;
+if (hub)
+    {
+    isUpdateForm = TRUE;
+    }
+else
+    /* add form needs clade for assembly menu */
+    gotClade = hGotClade();
+
+/* main form */
+printf("<FORM ACTION=\"%s\" METHOD=\"%s\" "
+    " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n",
+    "../cgi-bin/hgHubConnect", cartUsualString(cart, "formMethod", "POST"));
+cartSaveSession(cart);
+cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
+
+/* intro text */
+puts("<P>");
+puts("Add your own private data hub for the browser.");
+addIntro();
+puts("<P>");
+
+/* row for error message */
+if (err)
+    printf("<P><B>&nbsp;&nbsp;&nbsp;&nbsp;<I><FONT COLOR='RED'>Error</I></FONT>&nbsp;%s</B><P>", err);
+
+printf("Enter URL:");
+
+hTextVar(hgHubDataText, "", 60);
+cgiMakeSubmitButton();
+
+puts("</FORM>");
+}
+
+void helpPrivateHub()
+{
+}
+
+void doAddPrivateHub(struct cart *theCart, char *err)
+/* Write header and body of html page. */
+{
+cartWebStart(cart, database, "Add Private Hub");
+addPrivateHubForm(NULL, err);
+helpPrivateHub();
+cartWebEnd(cart);
+}
+
+void hubSaveInCart(struct cart *cart, struct hubConnectStatus *hub)
+{
+char hubName[1024];
+char *oldHubTrashName = cartOptionalString(cart, hubFileVar());
+static struct tempName tn;
+trashDirFile(&tn, "hub", "hub_", ".txt");
+char *hubTrashName = tn.forCgi;
+FILE *f = mustOpen(hubTrashName, "w");
+
+if (oldHubTrashName == NULL)
+    {
+    hub->id = -1;
+    }
+else
+    {
+    struct lineFile *lf = lineFileOpen(oldHubTrashName, TRUE);
+    int lineSize;
+    char *line;
+    int count = 1;
+
+    while (lineFileNext(lf, &line, &lineSize))
+	{
+	count++;
+	fprintf(f, "%s\n", line);
+	}
+    lineFileClose(&lf);
+    hub->id = -count;
+    }
+hubWriteToFile(f, hub);
+carefulClose(&f);
+
+safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
+cartSetString(cart, hubName, "1");
+
+cartSetString(cart, hubFileVar(), hubTrashName);
+}
+
+void checkForNewHub(struct cart *cart)
+{
+char *url = cartOptionalString(cart, hgHubDataText);
+
+if (url != NULL)
+    {
+    struct hubConnectStatus *hub = NULL;
+    struct trackHub *tHub = trackHubOpen(url, "1");
+    AllocVar(hub);
+
+    hub->hubUrl = cloneString(url);
+    hub->errorMessage = "";
+    hub->shortLabel = tHub->shortLabel;
+    hub->longLabel = tHub->longLabel;
+    hub->dbCount = 0;
+    AllocArray(hub->dbArray, 1);
+    hub->dbArray[0] = database;
+
+    hubSaveInCart(cart, hub);
+    cartRemove(cart, hgHubDataText);
+    }
+}
+
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 cart = theCart;
 setUdcCacheDir();
+if (cartVarExists(cart, hgHubDoAdd))
+    doAddPrivateHub(cart, NULL);
+else
+    {
 cartWebStart(cart, NULL, pageTitle);
-hgHubConnect();
+    checkForNewHub(cart);
+    hgHubConnectPublic();
+    hgHubConnectPrivate();
+    }
 cartWebEnd();
 }
 
 char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubConnectCgiDestUrl, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }