9661f8ba9e015aef34e09240d677ac7978ec0766
braney
Wed May 18 12:33:41 2011 -0700
move hub connection stuff into hg/lib so hgTracks can add hubs on its own
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index 56ab99c..dc1d1f6 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -8,68 +8,45 @@
#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"
-#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;
-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;
- }
-}
+boolean nameInCommaList(char *name, char *commaList);
static void hgHubConnectUnlisted()
/* Put up the list of unlisted hubs and other controls for the page. */
{
printf("<B>Unlisted Hubs</B><BR>");
struct hubConnectStatus *hub, *hubList = hubConnectStatusListFromCart(cart);
int 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();
@@ -163,219 +140,59 @@
void helpUnlistedHub()
{
printf("Unlisted hubs are constructed the same way as public hubs, but they "
"aren't listed in hgcentral<BR>\n");
}
void doAddUnlistedHub(struct cart *theCart, char *err)
/* Write header and body of html page. */
{
cartWebStart(cart, database, "Add Unlisted Hub");
addUnlistedHubForm(NULL, err);
helpUnlistedHub();
cartWebEnd(cart);
}
-static void enterHubInStatus(struct trackHub *tHub, boolean unlisted)
-/* put the hub status in the hubStatus table */
-{
-struct sqlConnection *conn = hConnectCentral();
-
-/* calculate dbList */
-struct dyString *dy = newDyString(1024);
-struct hashEl *hel;
-struct hashCookie cookie = hashFirst(tHub->genomeHash);
-int dbCount = 0;
-
-while ((hel = hashNext(&cookie)) != NULL)
- {
- dbCount++;
- dyStringPrintf(dy,"%s,", hel->name);
- }
-
-
-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 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);
-
-struct sqlResult *sr = sqlGetResult(conn, query);
-
-while ((row = sqlNextRow(sr)) != NULL)
- {
- 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);
- }
-sqlFreeResult(&sr);
-
-hDisconnectCentral(&conn);
-
-return id;
-}
-
-static boolean hubHasDatabase(unsigned id, char *database)
-/* check to see if hub specified by id supports database */
-{
-struct sqlConnection *conn = hConnectCentral();
-char query[512];
-
-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 errCatch *errCatch = errCatchNew();
-struct trackHub *tHub = NULL;
-boolean gotWarning = FALSE;
-unsigned id = 0;
-
-if (errCatchStart(errCatch))
- tHub = trackHubOpen(url, "1"); // open hub.. it'll get renamed later
-errCatchEnd(errCatch);
-if (errCatch->gotError)
- {
- gotWarning = TRUE;
- warn(errCatch->message->string);
- }
-errCatchFree(&errCatch);
-
-if (gotWarning)
- {
- return 0;
- }
-
-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);
+ unsigned id = hubFindOrAddUrlInStatusTable(database, cart,
+ 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);
@@ -387,93 +204,62 @@
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);
+ hubClearStatus(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))
doAddUnlistedHub(cart, NULL);
else if (cartVarExists(cart, hgHubDoClear))
doClearHub(cart);
else
{
cartWebStart(cart, NULL, pageTitle);
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);
+ hubCheckForNew(database, cart);
printf("<BR><P>");
printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
cartSaveSession(cart);
hgHubConnectPublic();
printf("<BR>Contact <A HREF=\"mailto:genome@soe.ucsc.edu\"> genome@soe.ucsc.edu </A>to add a public hub.</P>\n");
puts("<BR>");
hgHubConnectUnlisted();
puts("<BR>");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
cgiMakeButton("Submit", "Use Selected Hubs");
puts("</FORM>");
makeNewHubButton();
}