EnsPGvdatabaseadaptor ensGvdatabaseadaptorNewIni(EnsPDatabaseadaptor dba)
{
EnsPGvdatabaseadaptor gvdba = NULL;
if (!dba)
return NULL;
if (ensDatabaseadaptorGetGroup(dba) !=
ensEDatabaseadaptorGroupGeneticVariation)
return NULL;
AJNEW0(gvdba);
gvdba->Adaptor = dba;
gvdba->Failedvariations = ajFalse;
return gvdba;
}
int main(int argc, char** argv)
{
AjPFile outf = NULL;
AjPFile cachef = NULL;
AjIList iterator = NULL;
AjPList aliases = NULL;
AjPList dbas = NULL;
AjPList species = NULL;
AjPStr alias = NULL;
AjPStr dbname = NULL;
AjPStr spname = NULL;
AjPStr svrname = NULL;
AjPStr svrurl = NULL;
AjPStr dbcurl = NULL;
AjPTime svrtime = NULL;
EnsEDatabaseadaptorGroup dbag = ensEDatabaseadaptorGroupNULL;
EnsPDatabaseadaptor dba = NULL;
EnsPDatabaseconnection dbc = NULL;
embInit("cacheensembl", argc, argv);
ensInit();
svrname = ajAcdGetString("servername");
outf = ajAcdGetOutfile("outfile");
cachef = ajAcdGetOutfile("cachefile");
dbcurl = ajStrNew();
svrurl = ajStrNew();
dbname = ajStrNew();
ajNamSvrGetUrl(svrname, &svrurl);
if(!svrurl)
ajFatal("Could not resolve server name '%S'.", svrname);
dbc = ensDatabaseconnectionNewUrl(svrurl);
ensRegistryLoadDatabaseconnection(dbc);
ensDatabaseconnectionDel(&dbc);
/* Write the server file header. */
svrtime = ajTimeNewTodayFmt("cachefile");
ajFmtPrintF(cachef, "# %S %D\n", ajFileGetNameS(cachef), svrtime);
ajTimeDel(&svrtime);
ajFmtPrintF(cachef,
"# Automatically generated by cacheensembl "
"for server '%S'.\n\n",
svrname);
/*
** Get all Ensembl Database Adaptor objects and write them as
** EMBOSS Database definitions.
*/
aliases = ajListstrNew();
dbas = ajListNew();
species = ajListstrNew();
ensRegistryRetrieveAllSpecies(species);
while(ajListstrPop(species, &spname))
{
ensRegistryGetAllDatabaseadaptors(ensEDatabaseadaptorGroupNULL,
spname,
dbas);
while(ajListPop(dbas, (void**) &dba))
{
dbag = ensDatabaseadaptorGetGroup(dba);
if(dbag == ensEDatabaseadaptorGroupNULL)
{
ajDebug("cacheensembl main got unexpected "
"Ensembl Database Adaptor Group %d.\n",
dbag);
continue;
}
ajStrAssignS(&dbname, ensDatabaseadaptorGetSpecies(dba));
if(dbag != ensEDatabaseadaptorGroupCore)
{
ajStrAppendC(&dbname, "_");
ajStrAppendC(&dbname, ensDatabaseadaptorGroupToChar(dbag));
}
dbc = ensDatabaseadaptorGetDatabaseconnection(dba);
ensDatabaseconnectionFetchUrl(dbc, &dbcurl);
if(outf)
ajFmtPrintF(outf, "%S\n", dbname);
ajFmtPrintF(cachef, "DBNAME %S [\n", dbname);
ajFmtPrintF(cachef, " release: \"%s\"\n", ensSoftwareGetVersion());
ajFmtPrintF(cachef, " server: \"%S\"\n", svrname);
ajFmtPrintF(cachef, " url: \"%S\"\n", dbcurl);
ajFmtPrintF(cachef, "]\n");
ajFmtPrintF(cachef, "\n");
if(dbag != ensEDatabaseadaptorGroupCore)
continue;
ensRegistryAliasFetchAllbySpecies(
ensDatabaseadaptorGetSpecies(dba),
aliases);
/*
** Format all aliases to lower case,
** sort them alphabetically and remove duplicates.
*/
iterator = ajListIterNew(aliases);
while(!ajListIterDone(iterator))
{
alias = ajListstrIterGet(iterator);
ajStrFmtLower(&alias);
}
ajListIterDel(&iterator);
ajListSortUnique(aliases,
cacheensembl_stringcompare,
cacheensembl_stringdelete);
alias = NULL;
if(ajListGetLength(aliases) > 0)
{
while(ajListstrPop(aliases, &alias))
{
/*
** Reject any aliases with other than alpha-numeric
** characters like white space.
*/
if(ajStrIsAlnum(alias))
ajFmtPrintF(cachef,
"ALIAS %S %S\n",
alias,
ensDatabaseadaptorGetSpecies(dba));
ajStrDel(&alias);
}
ajFmtPrintF(cachef, "\n");
}
/* Ensembl Database Adaptor objects *must not* be deleted. */
}
ajStrDel(&spname);
}
ajListstrFree(&aliases);
ajListFree(&dbas);
ajStrDel(&dbcurl);
ajStrDel(&svrurl);
ajStrDel(&dbname);
ajStrDel(&svrname);
ajFileClose(&outf);
ajFileClose(&cachef);
embExit();
return EXIT_SUCCESS;
}
