6411d5f0ae8b75f54dc71f28a6c0690a9d567895
braney
  Mon May 16 11:29:37 2011 -0700
make private (now unlisted) hubs use the same status table as the public hubs, no trash use
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index 1ce9eb7..56ab99c 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -5,366 +5,489 @@
 #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 "dystring.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 hgHubDataText      "hgHub_customText"
 
 #define hgHub             "hgHub_"  /* prefix for all control variables */
 #define hgHubDo            hgHub   "do_"    /* prefix for all commands */
 #define hgHubDoAdd         hgHubDo "add"
-
+#define hgHubDoClear       hgHubDo "clear"
 
 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;
 
-boolean nameInCommaList(char *name, char *commaList)
+static 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 hgHubConnectPrivate()
-/* Put up the list of private hubs and other controls for the page. */
+static void hgHubConnectUnlisted()
+/* Put up the list of unlisted hubs and other controls for the page. */
 {
-printf("<B>List of Private Hubs</B><BR>");
+printf("<B>Unlisted Hubs</B><BR>");
 struct hubConnectStatus *hub, *hubList =  hubConnectStatusListFromCart(cart);
 int count = 0;
 for(hub = hubList; hub; hub = hub->next)
     {
-    if (hub->id > 0)
+    /* if the hub is public, then don't list it here */
+    if (!isHubUnlisted(hub))
 	continue;
+
     if (count)
 	webPrintLinkTableNewRow();
     else
 	webPrintLinkTableStart();
     count++;
 
     if (isEmpty(hub->errorMessage))
 	{
 	webPrintLinkCellStart();
 	char hubName[32];
-	safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
+	safef(hubName, sizeof(hubName), "%s%u", 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>");
+    printf("No Unlisted Track Hubs for this genome assembly<BR>");
 }
 
 static void makeNewHubButton()
 {
 printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"secondForm\">\n", "../cgi-bin/hgHubConnect");
 cartSaveSession(cart);
 cgiMakeHiddenVar(hgHubDoAdd, "on");
-cgiMakeButton("add", "Add new private hub");
+cgiMakeButton("add", "Add new unlisted hub");
 printf("</FORM>\n");
 }
 
 static void makeGenomePrint()
 {
 getDbAndGenome(cart, &database, &organism, oldVars);
 printf("<B>genome:</B> %s &nbsp;&nbsp;&nbsp;<B>assembly:</B> %s  ",
 	organism, hFreezeDate(database));
 }
 
-void hgHubConnectPublic()
-/* Put up the list of external hubs and other controls for the page. */
-{
-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)
-	    webPrintLinkTableNewRow();
-	else
-	    {
-	    webPrintLinkTableStart();
-	    gotAnyRows = TRUE;
-	    }
-	if (isEmpty(errorMessage))
-	    {
-	    webPrintLinkCellStart();
-	    char hubName[32];
-	    safef(hubName, sizeof(hubName), "%s%s", hgHubConnectHubVarPrefix, id);
-	    cartMakeCheckBox(cart, hubName, FALSE);
-	    webPrintLinkCellEnd();
-	    }
-	else
-	    webPrintLinkCell("error");
-	webPrintLinkCell(shortLabel);
-	if (isEmpty(errorMessage))
-	    webPrintLinkCell(longLabel);
-	else
-	    webPrintLinkCell(errorMessage);
-	webPrintLinkCell(url);
-	}
-    }
-sqlFreeResult(&sr);
-if (gotAnyRows)
-    webPrintLinkTableEnd();
-else
-    printf("No Track Hubs for this genome assembly");
-hDisconnectCentral(&conn);
-}
-
 static void addIntro()
 {
 printf("Enter URL to remote hub.<BR>\n");
 }
 
-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 */
+void addUnlistedHubForm(struct hubConnectStatus *hub, char *err)
+/* display UI for adding unlisted hubs by URL */
 {
 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.");
+puts("Add your own unlisted data hub for the browser.");
 addIntro();
 puts("<P>");
 
 /* row for error message */
 if (err)
     printf("<P><B>&nbsp;&nbsp;&nbsp;&nbsp;<span style='color:red; font-style:italic;'>Error</span>&nbsp;%s</B><P>", err);
 
 printf("Enter URL:");
 
 hTextVar(hgHubDataText, "", 60);
 cgiMakeSubmitButton();
 
 puts("</FORM>");
 }
 
-void helpPrivateHub()
+void helpUnlistedHub()
 {
-printf("Private hubs are constructed the same way as public hubs, but they "
+printf("Unlisted hubs are constructed the same way as public hubs, but they "
    "aren't listed in hgcentral<BR>\n");
 }
 
-void doAddPrivateHub(struct cart *theCart, char *err)
+void doAddUnlistedHub(struct cart *theCart, char *err)
 /* Write header and body of html page. */
 {
-cartWebStart(cart, database, "Add Private Hub");
-addPrivateHubForm(NULL, err);
-helpPrivateHub();
+cartWebStart(cart, database, "Add Unlisted Hub");
+addUnlistedHubForm(NULL, err);
+helpUnlistedHub();
 cartWebEnd(cart);
 }
 
-void hubSaveInCart(struct cart *cart, struct hubConnectStatus *hub)
+static void enterHubInStatus(struct trackHub *tHub, boolean unlisted)
+/* put the hub status in the hubStatus table */
 {
-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");
+struct sqlConnection *conn = hConnectCentral();
+
+/* calculate dbList */
+struct dyString *dy = newDyString(1024);
+struct hashEl *hel;
+struct hashCookie cookie = hashFirst(tHub->genomeHash);
+int dbCount = 0;
 
-if (oldHubTrashName == NULL)
+while ((hel = hashNext(&cookie)) != NULL)
     {
-    hub->id = -1;
+    dbCount++;
+    dyStringPrintf(dy,"%s,", hel->name);
     }
-else
+
+
+char query[512];
+safef(query, sizeof(query), "insert into %s (hubUrl,status,shortLabel, longLabel, dbList, dbCount) values (\"%s\",%d,\"%s\",\"%s\", \"%s\", %d)",
+    hubStatusTableName, tHub->url, unlisted ? 1 : 0,
+    tHub->shortLabel, tHub->longLabel,
+    dy->string, dbCount);
+sqlUpdate(conn, query);
+hDisconnectCentral(&conn);
+}
+
+static unsigned getHubId(char *url, char **errorMessage)
+/* find id for url in hubStatus table */
     {
-    struct lineFile *lf = lineFileOpen(oldHubTrashName, TRUE);
-    int lineSize;
-    char *line;
-    int count = 1;
+struct sqlConnection *conn = hConnectCentral();
+char query[512];
+char **row;
+boolean foundOne = FALSE;
+int id = 0;
+
+safef(query, sizeof(query), "select id,errorMessage from %s where hubUrl = \"%s\"", hubStatusTableName, url);
 
-    while (lineFileNext(lf, &line, &lineSize))
+struct sqlResult *sr = sqlGetResult(conn, query);
+
+while ((row = sqlNextRow(sr)) != NULL)
 	{
-	count++;
-	fprintf(f, "%s\n", line);
-	}
-    lineFileClose(&lf);
-    unlink(oldHubTrashName);
-    hub->id = -count;
+    if (foundOne)
+	errAbort("more than one line in %s with hubUrl %s\n", 
+	    hubStatusTableName, url);
+
+    foundOne = TRUE;
+
+    char *thisId = row[0], *thisError = row[1];
+
+    if (!isEmpty(thisError))
+	*errorMessage = cloneString(thisError);
+
+    id = sqlUnsigned(thisId);
     }
-hubWriteToFile(f, hub);
-carefulClose(&f);
+sqlFreeResult(&sr);
 
-safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
-cartSetString(cart, hubName, "1");
+hDisconnectCentral(&conn);
 
-cartSetString(cart, hubFileVar(), hubTrashName);
+return id;
 }
 
-void checkForNewHub(struct cart *cart)
+static boolean hubHasDatabase(unsigned id, char *database)
+/* check to see if hub specified by id supports database */
 {
-char *url = cartOptionalString(cart, hgHubDataText);
+struct sqlConnection *conn = hConnectCentral();
+char query[512];
 
-if (url != NULL)
+safef(query, sizeof(query), "select dbList from %s where id=%d", 
+    hubStatusTableName, id); 
+char *dbList = sqlQuickString(conn, query);
+boolean gotIt = FALSE;
+
+if (nameInCommaList(database, dbList))
+    gotIt = TRUE;
+
+hDisconnectCentral(&conn);
+
+freeMem(dbList);
+
+return gotIt;
+}
+
+static boolean fetchHub(char *url, boolean unlisted)
     {
-    struct hubConnectStatus *hub = NULL;
+struct errCatch *errCatch = errCatchNew();
     struct trackHub *tHub = NULL;
+boolean gotWarning = FALSE;
+unsigned id = 0;
 
-    struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
-	tHub = trackHubOpen(url, "1");
+    tHub = trackHubOpen(url, "1"); // open hub.. it'll get renamed later
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	{
+    gotWarning = TRUE;
 	warn(errCatch->message->string);
-	return;
 	}
     errCatchFree(&errCatch);
-    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;
+if (gotWarning)
+    {
+    return 0;
+    }
 
-    hubSaveInCart(cart, hub);
+if (hashLookup(tHub->genomeHash, database) != NULL)
+    {
+    enterHubInStatus(tHub, unlisted);
     }
+else
+    {
+    warn("requested hub at %s does not have data for %s\n", url, database);
+    return 0;
+    }
+
+trackHubClose(&tHub);
+
+char *errorMessage = NULL;
+id = getHubId(url, &errorMessage);
+return id;
+}
+
+static void getAndSetHubStatus(char *url, boolean set, boolean unlisted)
+{
+char *errorMessage = NULL;
+unsigned id;
+
+if ((id = getHubId(url, &errorMessage)) == 0)
+    {
+    if ((id = fetchHub(url, unlisted)) == 0)
+	return;
+    }
+else if (!hubHasDatabase(id, database))
+    {
+    warn("requested hub at %s does not have data for %s\n", url, database);
+    return;
+    }
+
+char hubName[32];
+safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
+if (set)
+    cartSetString(cart, hubName, "1");
+}
+
+static unsigned findOrAddUrlInStatusTable( char *url, char **errorMessage)
+/* find this url in the status table, and return its id and errorMessage (if an errorMessage exists) */
+{
+int id = 0;
+
+*errorMessage = NULL;
+
+if ((id = getHubId(url, errorMessage)) > 0)
+    return id;
+
+getAndSetHubStatus(url, FALSE, FALSE);
+
+if ((id = getHubId(url, errorMessage)) == 0)
+    errAbort("inserted new hubUrl %s, but cannot find it", url);
+
+return id;
+}
+
+void hgHubConnectPublic()
+/* Put up the list of external hubs and other controls for the page. */
+{
+printf("<B>Public Hubs</B><BR>");
+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
+	    {
+	    webPrintLinkTableStart();
+	    gotAnyRows = TRUE;
+	    }
+	char *errorMessage = NULL;
+	unsigned id = findOrAddUrlInStatusTable( url, &errorMessage);
+
+	if ((id != 0) && isEmpty(errorMessage)) 
+	    {
+	    webPrintLinkCellStart();
+	    char hubName[32];
+	    safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
+	    cartMakeCheckBox(cart, hubName, FALSE);
+	    webPrintLinkCellEnd();
+	    }
+	else if (!isEmpty(errorMessage))
+	    webPrintLinkCell("error");
+	else
+	    errAbort("cannot get id for hub with url %s\n", url);
+
+	webPrintLinkCell(shortLabel);
+	if (isEmpty(errorMessage))
+	    webPrintLinkCell(longLabel);
+	else
+	    {
+	    char errorBuf[4*1024];
+	    safef(errorBuf, sizeof errorBuf, "Error: %s", errorMessage);
+	    webPrintLinkCell(errorBuf);
+	    }
+	webPrintLinkCell(url);
+	}
+    }
+sqlFreeResult(&sr);
+
+if (gotAnyRows)
+    webPrintLinkTableEnd();
+else
+    printf("No Public Track Hubs for this genome assembly<BR>");
+hDisconnectCentral(&conn);
+}
+
+void checkForNewHub(struct cart *cart)
+/* see if the user just typed in a new hub url */
+{
+char *url = cartOptionalString(cart, hgHubDataText);
+
+if (url != NULL)
+    {
+    getAndSetHubStatus(url, TRUE, TRUE);
+    }
+}
+
+static void clearHubStatus(char *url)
+{
+struct sqlConnection *conn = hConnectCentral();
+char query[512];
+
+safef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", hubStatusTableName, url);
+unsigned id = sqlQuickNum(conn, query);
+
+if (id == 0)
+    errAbort("could not find url %s in status table (%s)\n", 
+	url, hubStatusTableName);
+
+safef(query, sizeof(query), "delete from %s where hubUrl = \"%s\"", hubStatusTableName, url);
+
+sqlUpdate(conn, query);
+hDisconnectCentral(&conn);
+
+printf("%s status has been cleared\n", url);
+}
+
+static void doClearHub(struct cart *theCart)
+{
+char *url = cartOptionalString(cart, hgHubDataText);
+
+if (url != NULL)
+    clearHubStatus(url);
+else
+    errAbort("must specify url in %s\n", hgHubDataText);
 }
 
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 cart = theCart;
 setUdcCacheDir();
 if (cartVarExists(cart, hgHubDoAdd))
-    doAddPrivateHub(cart, NULL);
+    doAddUnlistedHub(cart, NULL);
+else if (cartVarExists(cart, hgHubDoClear))
+    doClearHub(cart);
 else
     {
     cartWebStart(cart, NULL, pageTitle);
-    checkForNewHub(cart);
-
-    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 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. </P>\n"
        );
     makeGenomePrint();
 
+    checkForNewHub(cart);
     printf("<BR><P>");
+    printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
+    cartSaveSession(cart);
     hgHubConnectPublic();
-    printf("Contact <A HREF=\"mailto:genome@soe.ucsc.edu\"> genome@soe.ucsc.edu </A>to add a public hub.</P>\n");
+    printf("<BR>Contact <A HREF=\"mailto:genome@soe.ucsc.edu\"> genome@soe.ucsc.edu </A>to add a public hub.</P>\n");
     puts("<BR>");
-    hgHubConnectPrivate();
+    hgHubConnectUnlisted();
     puts("<BR>");
 
+    cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
     cgiMakeButton("Submit", "Use Selected Hubs");
     puts("</FORM>");
 
     makeNewHubButton();
-
     }
 cartWebEnd();
 }
 
-char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubConnectCgiDestUrl, hgHubDoAdd, hgHubDataText, NULL};
+char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubConnectCgiDestUrl, hgHubDoAdd, hgHubDoClear hgHubDataText, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }