static void recurseThroughIncludes(char *fileName, struct lm *lm,
struct hash *circularHash, struct raLevel *level, struct raFile **pFileList)
/* Recurse through include files. */
{
struct raFile *raFile = raFileRead(fileName, level, lm);
slAddHead(pFileList, raFile);
struct raRecord *r;
for (r = raFile->recordList; r != NULL; r = r->next)
{
struct raTag *tag = r->tagList;
if (sameString(tag->name, "include"))
{
for (; tag != NULL; tag = tag->next)
{
if (!sameString(tag->name, "include"))
recordAbort(r, "Non-include tag %s in an include stanza", tag->name);
char *relPath = tag->val;
char dir[PATH_LEN];
splitPath(fileName, dir, NULL, NULL);
char includeName[PATH_LEN];
safef(includeName, sizeof(includeName), "%s%s", dir, relPath);
if (hashLookup(circularHash, includeName))
recordAbort(r, "Including file %s in an infinite loop", includeName);
recurseThroughIncludes(includeName, lm, circularHash, level, pFileList);
}
}
}
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (optionExists("help"))
{
printHelp();
}
if (argc != 3)
{
usage();
}
outMdb = optionVal("outMdb", outMdb);
onlyCompTdb = optionExists("onlyCompTdb");
release = optionVal("release", release);
releaseNum = optionInt("releaseNum", releaseNum);
char *database = argv[1];
char *composite = argv[2];
char defaultMetaDb[1024];
char defaultDownloadDir[1024];
char tempDownloadDir[1024];
char *src = getSrcDir();
char *org = cloneString(hOrganism(database));
org[0] = tolower(org[0]);
/* If user doesn't provide a metaDB, assume the path using the database and composite */
safef(defaultMetaDb, sizeof(defaultMetaDb), "%s/hg/makeDb/trackDb/%s/%s/metaDb/%s/%s.ra", src, org, database, release, composite);
/* If user doesn't provide a downloadDir, assume the path using the database and composite */
safef(defaultDownloadDir, sizeof(defaultDownloadDir), "/usr/local/apache/htdocs-hgdownload/goldenPath/%s/encodeDCC/%s", database, composite);
safef(tempDownloadDir, sizeof(tempDownloadDir), "/usr/local/apache/htdocs-hgdownload/goldenPath/%s/encodeDCC/%s", database, composite);
if (releaseNum)
safef(defaultDownloadDir, sizeof(defaultDownloadDir), "%s/release%d", tempDownloadDir, releaseNum);
/* If user doesn't provide a trackDB, assume the path using the database and composite */
char defaultTrackDb[1024];
/* Load encode composite-includer trackDb.wgEncode.ra */
char trackDbIncluder[1024];
safef(trackDbIncluder, sizeof(trackDbIncluder), "%s/hg/makeDb/trackDb/%s/%s/%s", src, org, database, "trackDb.wgEncode.ra");
struct raFile *includerFile = raFileRead(trackDbIncluder);
/* Find the correct trackDb.ra for the composite */
int numTagsFound = -1;
char *compositeName = findCompositeRa(includerFile, composite, release, &numTagsFound);
if (!compositeName)
errAbort("unable to find composite .ra for the track in trackDb.wgEncode.ra\n");
// if numTagsFound == 1 then a composite .ra with a single alpha tag exists already,
// so no further work required on trackDb.wgEncode.ra
safef(defaultTrackDb, sizeof(defaultTrackDb), "%s/hg/makeDb/trackDb/%s/%s/%s", src, org, database, compositeName);
verbose(1,"database: %s\ncomposite: %s\nrelease %s\ndefault trackDb: %s\ndefault metaDb: %s\ndefault downloadDir: %s\n",
database, composite, release, defaultTrackDb, defaultMetaDb, defaultDownloadDir);
char *metaDb = optionVal("metaDb",defaultMetaDb);
replaceTildeWithHome(&metaDb);
if (!fileExists(metaDb))
errAbort("metaDb %s does not exist.", metaDb);
char *trackDb = optionVal("trackDb",defaultTrackDb);
replaceTildeWithHome(&trackDb);
if (!fileExists(trackDb))
errAbort("trackDb %s does not exist.", trackDb);
char *downloadDir = optionVal("downloadDir",defaultDownloadDir);
replaceTildeWithHome(&downloadDir);
if (!fileExists(downloadDir))
errAbort("downloadDir %s does not exist.", downloadDir);
printf("metaDb = %s\n trackDb = %s\n downloadDir = %s\n",metaDb,trackDb,downloadDir);
metaCheck(database, composite, metaDb, trackDb, downloadDir);
return 0;
}
