533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/cartTrackDb.c src/hg/cgilib/cartTrackDb.c
new file mode 100644
index 0000000..702d4d8
--- /dev/null
+++ src/hg/cgilib/cartTrackDb.c
@@ -0,0 +1,447 @@
+/* cartTrackDb - Combine custom tracks, hub tracks & hTrackDb to get unified groups/tracks/tables */
+
+#include "common.h"
+#include "cartTrackDb.h"
+#include "cheapcgi.h"
+#include "customTrack.h"
+#include "hash.h"
+#include "hCommon.h"
+#include "hdb.h"
+#include "hgConfig.h"
+#include "hgMaf.h"
+#include "hubConnect.h"
+#include "joiner.h"
+#include "trackHub.h"
+#include "wikiTrack.h"
+
+/* Static globals */
+static boolean useAC = FALSE;
+static struct slRef *accessControlTrackRefList = NULL;
+
+static struct trackDb *getFullTrackList(struct cart *cart, char *db, struct grp **pHubGroups)
+{
+struct trackDb *list = hTrackDb(db);
+
+/* add wikiTrack if enabled */
+if (wikiTrackEnabled(db, NULL))
+    slAddHead(&list, wikiTrackDb());
+slSort(&list, trackDbCmp);
+
+// Add hub tracks at head of list
+struct trackDb *hubTdbList = hubCollectTracks(db, pHubGroups);
+list = slCat(list, hubTdbList);
+
+/* exclude any track with a 'tableBrowser off' setting */
+struct trackDb *tdb, *nextTdb, *newList = NULL;
+for (tdb = list;  tdb != NULL;  tdb = nextTdb)
+    {
+    nextTdb = tdb->next;
+    if (tdbIsDownloadsOnly(tdb) || tdb->table == NULL)
+        {
+        //freeMem(tdb);  // should not free tdb's.
+        // While hdb.c should and says it does cache the tdbList, it doesn't.
+        // The most notable reason that the tdbs are not cached is this hgTables CGI !!!
+        // It needs to be rewritten to make tdbRef structures for the lists it creates here!
+        continue;
+        }
+
+    char *tbOff = trackDbSetting(tdb, "tableBrowser");
+    if (useAC && tbOff != NULL &&
+        (startsWithWord("off", tbOff) || startsWithWord("noGenome", tbOff)))
+        {
+        slAddHead(&accessControlTrackRefList, slRefNew(tdb));
+        if (! startsWithWord("off", tbOff))
+            slAddHead(&newList, tdb);
+        }
+    else
+	slAddHead(&newList, tdb);
+    }
+slReverse(&newList);
+list = newList;
+
+// Add custom tracks at head of list
+struct customTrack *ctList, *ct;
+ctList = customTracksParseCart(db, cart, NULL, NULL);
+for (ct = ctList; ct != NULL; ct = ct->next)
+    {
+    slAddHead(&list, ct->tdb);
+    }
+
+return list;
+}
+
+static struct grp *makeGroupList(char *db, struct trackDb *trackList, struct grp **pHubGrpList,
+                                 boolean allTablesOk)
+/* Get list of groups that actually have something in them. */
+{
+struct grp *groupsAll, *groupList = NULL, *group;
+struct hash *groupsInTrackList = newHash(0);
+struct hash *groupsInDatabase = newHash(0);
+struct trackDb *track;
+
+/* Do some error checking for tracks with group names that are not in database.
+ * Warnings at this stage mess up CGIs that may produce text output like hgTables & hgIntegrator,
+ * so don't warn, just put CTs in group user and others in group x. */
+groupsAll = hLoadGrps(db);
+if (!trackHubDatabase(db))
+    {
+    struct hash *allGroups = hashNew(0);
+    for (group = groupsAll;  group != NULL; group = group->next)
+        hashAdd(allGroups, group->name, group);
+    for (track = trackList; track != NULL; track = track->next)
+        {
+        /* If track isn't in a track up, and has a group we don't know about, change it to one we do. */
+        if (!startsWith("hub_", track->grp) && !hashLookup(allGroups, track->grp))
+            {
+            fprintf(stderr, "Track %s has group %s, which isn't in grp table\n",
+                    track->table, track->grp);
+            if (isCustomTrack(track->track))
+                track->grp = cloneString("user");
+            else
+                track->grp = cloneString("x");
+            }
+        }
+    hashFree(&allGroups);
+    }
+
+/* Stream through track list building up hash of active groups. */
+for (track = trackList; track != NULL; track = track->next)
+    {
+    if (!hashLookup(groupsInTrackList,track->grp))
+        hashAdd(groupsInTrackList, track->grp, NULL);
+    }
+
+/* Scan through group table, putting in ones where we have data. */
+for (group = slPopHead(&groupsAll); group != NULL; group = slPopHead(&groupsAll))
+    {
+    if (hashLookup(groupsInTrackList, group->name))
+	{
+	slAddTail(&groupList, group);
+	hashAdd(groupsInDatabase, group->name, group);
+	}
+    else
+        grpFree(&group);
+    }
+
+/* if we have custom tracks, we want to add the track hubs
+ * after that group */
+struct grp *addAfter = NULL;
+if ((groupList != NULL) && sameString(groupList->name, "user"))
+    addAfter = groupList;
+
+/* Add in groups from hubs. */
+for (group = slPopHead(pHubGrpList); group != NULL; group = slPopHead(pHubGrpList))
+    {
+    // if the group isn't represented in any track, don't add it to list
+    if (!hashLookup(groupsInTrackList,group->name))
+	continue;
+    /* check to see if we're inserting hubs rather than
+     * adding them to the front of the list */
+    struct grp *newGrp = grpDup(group);
+    if (addAfter != NULL)
+	{
+	newGrp->next = addAfter->next;
+	addAfter->next = newGrp;
+	}
+    else
+	slAddHead(&groupList, newGrp);
+    hashAdd(groupsInDatabase, newGrp->name, newGrp);
+    }
+
+/* Create dummy group for all tracks. */
+AllocVar(group);
+group->name = cloneString("allTracks");
+group->label = cloneString("All Tracks");
+slAddTail(&groupList, group);
+
+/* Create another dummy group for all tables. */
+if (allTablesOk)
+    {
+    AllocVar(group);
+    group->name = cloneString("allTables");
+    group->label = cloneString("All Tables");
+    slAddTail(&groupList, group);
+    }
+
+hashFree(&groupsInTrackList);
+hashFree(&groupsInDatabase);
+return groupList;
+}
+
+void cartTrackDbInit(struct cart *cart, struct trackDb **retFullTrackList,
+                     struct grp **retFullGroupList, boolean useAccessControl)
+/* Get lists of all tracks and of groups that actually have tracks in them.
+ * If useAccessControl, exclude tracks with 'tableBrowser off' nor tables listed
+ * in the table tableAccessControl. */
+{
+char *db = cartString(cart, "db");
+useAC = useAccessControl;
+struct grp *hubGrpList = NULL;
+struct trackDb *fullTrackList = getFullTrackList(cart, db, &hubGrpList);
+boolean allTablesOk = hAllowAllTables() && !trackHubDatabase(db);
+struct grp *fullGroupList = makeGroupList(db, fullTrackList, &hubGrpList, allTablesOk);
+if (retFullTrackList != NULL)
+    *retFullTrackList = fullTrackList;
+if (retFullGroupList != NULL)
+    *retFullGroupList = fullGroupList;
+}
+
+static char *chopAtFirstDot(char *string)
+/* Terminate string at first '.' if found.  Return string for convenience. */
+{
+char *ptr = strchr(string, '.');
+if (ptr != NULL)
+    *ptr = '\0';
+return string;
+}
+
+struct accessControl
+/* Restricted permission settings for a table */
+    {
+    struct slName *hostList;       // List of hosts that are allowed to view this table
+    boolean isNoGenome;            // True if it's OK for position range but not genome-wide query
+    };
+
+void accessControlAddHost(struct accessControl *ac, char *host)
+/* Alloc an slName for host (unless NULL or empty) and add it to ac->hostList. */
+{
+if (isNotEmpty(host))
+    slAddHead(&ac->hostList, slNameNew(host));
+}
+
+struct accessControl *accessControlNew(char *host, boolean isNoGenome)
+/* Alloc, init & return accessControl. */
+{
+struct accessControl *ac;
+AllocVar(ac);
+accessControlAddHost(ac, host);
+ac->isNoGenome = isNoGenome;
+return ac;
+}
+
+static void acHashAddOneTable(struct hash *acHash, char *table, char *host, boolean isNoGenome)
+/* If table is already in acHash, update its accessControl fields; otherwise store a
+ * new accessControl for table. */
+{
+struct hashEl *hel = hashLookup(acHash, table);
+if (hel == NULL)
+    {
+    struct accessControl *ac = accessControlNew(host, isNoGenome);
+    hashAdd(acHash, table, ac);
+    }
+else
+    {
+    struct accessControl *ac = hel->val;
+    ac->isNoGenome = isNoGenome;
+    accessControlAddHost(ac, host);
+    }
+}
+
+static struct hash *accessControlInit(char *db)
+/* Return a hash associating restricted table/track names in the given db/conn
+ * with virtual hosts -- hash is empty if there is no tableAccessControl table and no
+ * accessControlTrackRefList (see getFullTrackList). */
+{
+struct hash *acHash = hashNew(0);
+if (! trackHubDatabase(db))
+    {
+    struct sqlConnection *conn = hAllocConn(db);
+    if (sqlTableExists(conn, "tableAccessControl"))
+        {
+        struct sqlResult *sr = NULL;
+        char **row = NULL;
+        acHash = newHash(0);
+        sr = sqlGetResult(conn, NOSQLINJ "select name,host from tableAccessControl");
+        while ((row = sqlNextRow(sr)) != NULL)
+            acHashAddOneTable(acHash, row[0], chopAtFirstDot(row[1]), FALSE);
+        sqlFreeResult(&sr);
+        }
+    hFreeConn(&conn);
+    }
+struct slRef *tdbRef;
+for (tdbRef = accessControlTrackRefList; tdbRef != NULL; tdbRef = tdbRef->next)
+    {
+    struct trackDb *tdb = tdbRef->val;
+    char *tbOff = cloneString(trackDbSetting(tdb, "tableBrowser"));
+    if (isEmpty(tbOff))
+        errAbort("accessControlInit bug: tdb for %s does not have tableBrowser setting",
+                 tdb->track);
+    // First word is "off" or "noGenome":
+    char *type = nextWord(&tbOff);
+    boolean isNoGenome = sameString(type, "noGenome");
+    // Add track table to acHash:
+    acHashAddOneTable(acHash, tdb->table, NULL, isNoGenome);
+    // Remaining words are additional table names to add:
+    char *tbl;
+    while ((tbl = nextWord(&tbOff)) != NULL)
+        acHashAddOneTable(acHash, tbl, NULL, isNoGenome);
+    }
+return acHash;
+}
+
+static struct hash *getCachedAcHash(char *db)
+/* Returns a hash that maps table names to accessControl, creating it if necessary. */
+{
+static struct hash *dbToAcHash = NULL;
+if (dbToAcHash == NULL)
+    dbToAcHash = hashNew(0);
+struct hash *acHash = hashFindVal(dbToAcHash, db);
+if (acHash == NULL)
+    {
+    acHash = accessControlInit(db);
+    hashAdd(dbToAcHash, db, acHash);
+    }
+return acHash;
+}
+
+static char *getCachedCurrentHost()
+/* Return the current host name chopped at the first '.' or NULL if not in the CGI environment. */
+{
+static char *currentHost = NULL;
+if (currentHost == NULL)
+    {
+    currentHost = cloneString(cgiServerName());
+    if (currentHost == NULL)
+	return NULL;
+    else
+	chopAtFirstDot(currentHost);
+    }
+return currentHost;
+}
+
+boolean cartTrackDbIsAccessDenied(char *db, char *table)
+/* Return TRUE if useAccessControl=TRUE was passed to cartTrackDbInit and
+ * if access to table is denied (at least on this host) by 'tableBrowser off'
+ * or by the tableAccessControl table. */
+{
+if (!useAC)
+    return FALSE;
+
+struct hash *acHash = getCachedAcHash(db);
+struct accessControl *ac = hashFindVal(acHash, table);
+if (ac == NULL)
+    return FALSE;
+if (ac->isNoGenome && ac->hostList == NULL)
+    return FALSE;
+char *currentHost = getCachedCurrentHost();
+if (currentHost == NULL)
+    warn("accessControl: unable to determine current host");
+return (! slNameInList(ac->hostList, currentHost));
+}
+
+boolean cartTrackDbIsNoGenome(char *db, char *table)
+/* Return TRUE if range queries, but not genome-queries, are permitted for this table. */
+{
+struct hash *acHash = getCachedAcHash(db);
+struct accessControl *ac = hashFindVal(acHash, table);
+return (ac != NULL && ac->isNoGenome);
+}
+
+static void addTablesAccordingToTrackType(char *db, struct slName **pList, struct hash *uniqHash,
+                                          struct trackDb *track)
+/* Parse out track->type and if necessary add some tables from it. */
+{
+struct slName *name;
+char *trackDupe = cloneString(track->type);
+if (trackDupe != NULL && trackDupe[0] != 0)
+    {
+    char *s = trackDupe;
+    char *type = nextWord(&s);
+    if (sameString(type, "wigMaf"))
+        {
+	static char *wigMafAssociates[] = {"frames", "summary"};
+	int i;
+	for (i=0; i<ArraySize(wigMafAssociates); ++i)
+	    {
+	    char *setting = wigMafAssociates[i];
+	    char *table = trackDbSetting(track, setting);
+            if (table != NULL)
+                {
+                name = slNameNew(table);
+                slAddHead(pList, name);
+                hashAdd(uniqHash, table, NULL);
+                }
+	    }
+        /* include conservation wiggle tables */
+        struct consWiggle *wig, *wiggles = wigMafWiggles(db, track);
+        slReverse(&wiggles);
+        for (wig = wiggles; wig != NULL; wig = wig->next)
+            {
+            name = slNameNew(wig->table);
+            slAddHead(pList, name);
+            hashAdd(uniqHash, wig->table, NULL);
+            }
+	}
+    if (track->subtracks)
+        {
+        struct slName *subList = NULL;
+	struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
+	slSort(&tdbRefList, trackDbRefCmp);
+	struct slRef *tdbRef;
+	for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
+            {
+	    struct trackDb *subTdb = tdbRef->val;
+	    name = slNameNew(subTdb->table);
+	    slAddTail(&subList, name);
+	    hashAdd(uniqHash, subTdb->table, NULL);
+            }
+        pList = slCat(pList, subList);
+        }
+    }
+freez(&trackDupe);
+}
+
+struct slName *cartTrackDbTablesForTrack(char *db, struct trackDb *track, boolean useJoiner)
+/* Return list of all tables associated with track.  If useJoiner, the result can include
+ * non-positional tables that are related to track by all.joiner. */
+{
+static struct joiner *allJoiner = NULL;
+struct hash *uniqHash = newHash(8);
+struct slName *name, *nameList = NULL;
+char *trackTable = track->table;
+
+/* suppress for parent tracks -- only the subtracks have tables */
+if (track->subtracks == NULL)
+    {
+    name = slNameNew(trackTable);
+    slAddHead(&nameList, name);
+    hashAdd(uniqHash, trackTable, NULL);
+    }
+addTablesAccordingToTrackType(db, &nameList, uniqHash, track);
+if (useJoiner)
+    {
+    if (allJoiner == NULL)
+        allJoiner = joinerRead("all.joiner");
+    struct slName *joinedList = NULL, *t;
+    for (t = nameList;  t != NULL;  t = t->next)
+        {
+        struct joinerPair *jpList, *jp;
+        jpList = joinerRelate(allJoiner, db, t->name, db);
+        for (jp = jpList; jp != NULL; jp = jp->next)
+            {
+            struct joinerDtf *dtf = jp->b;
+            if (cartTrackDbIsAccessDenied(dtf->database, dtf->table))
+                continue;
+            char buf[256];
+            char *s;
+            if (sameString(dtf->database, db))
+                s = dtf->table;
+            else
+                {
+                safef(buf, sizeof(buf), "%s.%s", dtf->database, dtf->table);
+                s = buf;
+                }
+            if (!hashLookup(uniqHash, s))
+                {
+                hashAdd(uniqHash, s, NULL);
+                name = slNameNew(s);
+                slAddHead(&joinedList, name);
+                }
+            }
+	}
+    slNameSort(&joinedList);
+    nameList = slCat(nameList, joinedList);
+    }
+hashFree(&uniqHash);
+return nameList;
+}