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
@@ -1,370 +1,493 @@
/* 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 "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("List of Private Hubs
");
+printf("Unlisted Hubs
");
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
");
+ printf("No Unlisted Track Hubs for this genome assembly
");
}
static void makeNewHubButton()
{
printf("\n");
}
static void makeGenomePrint()
{
getDbAndGenome(cart, &database, &organism, oldVars);
printf("genome: %s assembly: %s ",
organism, hFreezeDate(database));
}
-void hgHubConnectPublic()
-/* Put up the list of external hubs and other controls for the page. */
-{
-printf("List of Public Hubs
");
-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.
\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, " Clear ");
-}
-
-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("");
}
-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
\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("Public Hubs
");
+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
");
+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("");
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;
}