void hgTrackDb(char *org, char *database, char *trackDbName, char *sqlFile, char *hgRoot,
boolean strict)
/* hgTrackDb - Create trackDb table from text files. */
{
struct trackDb *td;
char tab[PATH_LEN];
safef(tab, sizeof(tab), "%s.tab", trackDbName);
struct trackDb *tdbList = buildTrackDb(org, database, hgRoot, strict);
tdbList = flatten(tdbList);
slSort(&tdbList, trackDbCmp);
verbose(1, "Loaded %d track descriptions total\n", slCount(tdbList));
/* Write to tab-separated file; hold off on html, since it must be encoded */
{
verbose(2, "Starting write of tabs to %s\n", tab);
FILE *f = mustOpen(tab, "w");
for (td = tdbList; td != NULL; td = td->next)
{
hVarSubstTrackDb(td, database);
char *hold = td->html;
td->html = "";
subChar(td->type, '\t', ' '); /* Tabs confuse things. */
subChar(td->shortLabel, '\t', ' '); /* Tabs confuse things. */
subChar(td->longLabel, '\t', ' '); /* Tabs confuse things. */
trackDbTabOut(td, f);
td->html = hold;
}
carefulClose(&f);
verbose(2, "Wrote tab representation to %s\n", tab);
}
/* Update database */
{
char *create, *end;
char query[256];
struct sqlConnection *conn = sqlConnect(database);
/* Load in table definition. */
readInGulp(sqlFile, &create, NULL);
create = trimSpaces(create);
create = substituteTrackName(create, trackDbName);
end = create + strlen(create)-1;
if (*end == ';') *end = 0;
sqlRemakeTable(conn, trackDbName, create);
/* Load in regular fields. */
sqlSafef(query, sizeof(query), "load data local infile '%s' into table %s", tab, trackDbName);
verbose(2, "sending mysql \"%s\"\n", query);
sqlUpdate(conn, query);
verbose(2, "done tab file load");
/* Load in html and settings fields. */
for (td = tdbList; td != NULL; td = td->next)
{
if (isEmpty(td->html))
{
if (strict && !trackDbLocalSetting(td, "parent") && !trackDbLocalSetting(td, "superTrack") &&
!sameString(td->track,"cytoBandIdeo"))
{
fprintf(stderr, "Warning: html missing for %s %s %s '%s'\n",org, database, td->track, td->shortLabel);
}
}
else
{
updateBigTextField(conn, trackDbName, "tableName", td->track, "html", td->html);
}
if (td->settingsHash != NULL)
{
char *settings = settingsFromHash(td->settingsHash);
updateBigTextField(conn, trackDbName, "tableName", td->track,
"settings", settings);
if (showSettings)
{
verbose(1, "%s: type='%s';", td->track, td->type);
if (isNotEmpty(settings))
{
char *oneLine = replaceChars(settings, "\n", "; ");
eraseTrailingSpaces(oneLine);
verbose(1, " %s", oneLine);
freeMem(oneLine);
}
verbose(1, "\n");
}
freeMem(settings);
}
}
sqlDisconnect(&conn);
verbose(1, "Loaded database %s\n", database);
}
}
void hgFindSpec(char *org, char *database, char *hgFindSpecName, char *sqlFile,
char *hgRoot, boolean strict)
/* hgFindSpec - Create hgFindSpec table from text files. */
{
struct hash *uniqHash = newHash(8);
struct hash *htmlHash = newHash(8);
struct hgFindSpec *hfsList = NULL, *hfs;
char rootDir[512], orgDir[512], asmDir[512];
char tab[512];
snprintf(tab, sizeof(tab), "%s.tab", hgFindSpecName);
/* Create track list from hgRoot and hgRoot/org and hgRoot/org/assembly
* ra format database. */
sprintf(rootDir, "%s", hgRoot);
sprintf(orgDir, "%s/%s", hgRoot, org);
sprintf(asmDir, "%s/%s/%s", hgRoot, org, database);
layerOn(strict, database, asmDir, uniqHash, htmlHash, FALSE, &hfsList);
layerOn(strict, database, orgDir, uniqHash, htmlHash, FALSE, &hfsList);
layerOn(strict, database, rootDir, uniqHash, htmlHash, TRUE, &hfsList);
slSort(&hfsList, hgFindSpecCmp);
if (verboseLevel() > 0)
printf("Loaded %d search specs total\n", slCount(hfsList));
/* Write to tab-separated file. */
{
FILE *f = mustOpen(tab, "w");
for (hfs = hfsList; hfs != NULL; hfs = hfs->next)
hgFindSpecTabOut(hfs, f);
carefulClose(&f);
}
/* Update database */
{
char *create, *end;
char query[256];
struct sqlConnection *conn = sqlConnect(database);
/* Load in table definition. */
readInGulp(sqlFile, &create, NULL);
create = trimSpaces(create);
create = subTrackName(create, hgFindSpecName);
end = create + strlen(create)-1;
if (*end == ';') *end = 0;
sqlRemakeTable(conn, hgFindSpecName, create);
/* Load in regular fields. */
sqlSafef(query, sizeof query, "load data local infile '%s' into table %s", tab,
hgFindSpecName);
sqlUpdate(conn, query);
/* Load in settings fields. */
for (hfs = hfsList; hfs != NULL; hfs = hfs->next)
{
if (hfs->settingsHash != NULL)
{
char *settings = settingsFromHash(hfs->settingsHash);
updateBigTextField(conn, hgFindSpecName, "searchName",
hfs->searchName,
"searchSettings", settings);
freeMem(settings);
}
}
sqlDisconnect(&conn);
if (verboseLevel() > 0)
printf("Loaded database %s\n", database);
}
}