/* Make a track ixIxx file for the given to be used in the track search tool. */

#include "common.h"
#include "options.h"
#include "hdb.h"
#include "grp.h"
#include "hui.h"
#include "ra.h"
#include "jsHelper.h"


void usage()
/* Explain usage and exit. */
{
errAbort(
  "makeTrackIndex - make a ixIxx input file for the tracks in given assembly.\n"
  "usage:\n"
  "   makeTrackIndex database metaDataTableName cv.ra\n\n");
}

static void printTrack(struct sqlConnection *conn, struct trackDb *tdb, char *html,
                       struct hash *grpHash, struct hash *cvHash,struct hash *tdbHash, char *metaDbName)
{
// Don't duplicate superTracks
if (hashLookup(tdbHash,tdb->track))
    return;
hashAdd(tdbHash,tdb->track,tdb);

char query[256];
struct sqlResult *sr = NULL;
char **row = NULL;
char *metadataList[] = {"longLabel", NULL}; // include a fixed set of metadata (i.e. not stuff like subGroup).
int i;
char *grpLabel, *tmp;
boolean metaDbExists = sqlTableExists(conn, metaDbName);

printf("%s ", tdb->track);
printf("%s ", tdb->shortLabel);
if(metaDbExists)
    {
    safef(query, sizeof(query), "select val from %s where obj = '%s'",
        metaDbName, tdb->track);
    sr = sqlGetResult(conn, query);
    while ((row = sqlNextRow(sr)) != NULL)
        {
        printf("%s ", row[0]);
        }
    sqlFreeResult(&sr);
    }

// We include the long descriptions for these terms, b/c we assume people will search for the long labels.
// Jim want's cv data after short/long label

if(metaDbExists && cvHash)
    {
    sr = sqlGetResult(conn, query);
    while ((row = sqlNextRow(sr)) != NULL)
        {
        struct hash *hash = hashFindVal(cvHash, row[0]);
        if(hash != NULL)
            {
            // hand-curated list of which cv.ra fields to include in fulltext index.
            char *fields[] = {"description", "targetDescription", NULL};
            int i;
            for(i = 0; fields[i] != NULL; i++)
                {
                char *str = hashFindVal(hash, fields[i]);
                if(str)
                    printf("%s ", str);
                }
            }
        }
    sqlFreeResult(&sr);
    }

for(i = 0; metadataList[i] != NULL; i++)
    {
    char *str = trackDbLocalSetting(tdb, metadataList[i]);
    if(str != NULL)
        printf("%s ", str);
    }

grpLabel = tdb->grp;
tmp = hashFindVal(grpHash, grpLabel);
if(tmp != NULL)
    grpLabel = tmp;
printf("%s ", grpLabel);


if(html == NULL)
    {
    html = tdb->html;
    if(html != NULL)
        // strip out html markup
        html = stripRegEx(html, "<[^>]*>", REG_ICASE);
    }
if(html != NULL)
    {
    char *tmp = cloneString(html);
    char *val = nextWord(&tmp);
    while(val != NULL)
        {
        printf("%s ", val);
        val = nextWord(&tmp);
        }
    }
printf("\n");

if (tdbIsSuper(tdb->parent))
    printTrack(conn, tdb->parent, NULL, grpHash, cvHash, tdbHash, metaDbName);
if(tdb->subtracks != NULL)
    {
    struct trackDb *subtrack;
    for (subtrack = tdb->subtracks; subtrack != NULL; subtrack = subtrack->next)
        // We have decided NOT to populate html down to children.
        printTrack(conn, subtrack, NULL, grpHash, cvHash, tdbHash, metaDbName);
    }
}

int main(int argc, char *argv[])
{
struct trackDb *tdb, *tdbList = NULL;
struct hash *grpHash = newHash(0);
struct hash *tdbHash = newHash(0);
struct grp *grp, *grps;
char filePath[PATH_LEN];
struct hash *cvHash;

if (argc != 4)
    usage();
char *database = argv[1];
char *metaDbName = argv[2];
char *cvRaPath = argv[3];
tdbList = hTrackDb(database);
struct sqlConnection *conn = hAllocConn(database);

grps = hLoadGrps(database);
for (grp = grps; grp != NULL; grp = grp->next)
    hashAdd(grpHash, grp->name, grp->label);

safecpy(filePath, sizeof(filePath), cvRaPath );
if(!fileExists(filePath))
    errAbort("Error: can't locate cv.ra; %s doesn't exist\n", filePath);
cvHash = raReadAll(filePath, "term");

for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
    printTrack(conn, tdb, NULL, grpHash, cvHash, tdbHash, metaDbName);

return 0;
}