/* genark.c was originally generated by the autoSql program, which also 
 * generated genark.h and genark.sql.  This module links the database and
 * the RAM representation of objects. */

#include "common.h"
#include "linefile.h"
#include "dystring.h"
#include "jksql.h"
#include "genark.h"
#include "hgConfig.h"
#include "hdb.h"



char *genarkCommaSepFieldNames = "gcAccession,hubUrl,asmName,scientificName,commonName,taxId";

void genarkStaticLoad(char **row, struct genark *ret)
/* Load a row from genark table into ret.  The contents of ret will
 * be replaced at the next call to this function. */
{

ret->gcAccession = row[0];
ret->hubUrl = row[1];
ret->asmName = row[2];
ret->scientificName = row[3];
ret->commonName = row[4];
ret->taxId = sqlSigned(row[5]);
}

struct genark *genarkLoadByQuery(struct sqlConnection *conn, char *query)
/* Load all genark from table that satisfy the query given.  
 * Where query is of the form 'select * from example where something=something'
 * or 'select example.* from example, anotherTable where example.something = 
 * anotherTable.something'.
 * Dispose of this with genarkFreeList(). */
{
struct genark *list = NULL, *el;
struct sqlResult *sr;
char **row;

sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
    {
    el = genarkLoad(row);
    slAddHead(&list, el);
    }
slReverse(&list);
sqlFreeResult(&sr);
return list;
}

void genarkSaveToDb(struct sqlConnection *conn, struct genark *el, char *tableName, int updateSize)
/* Save genark as a row to the table specified by tableName. 
 * As blob fields may be arbitrary size updateSize specifies the approx size
 * of a string that would contain the entire query. Arrays of native types are
 * converted to comma separated strings and loaded as such, User defined types are
 * inserted as NULL. This function automatically escapes quoted strings for mysql. */
{
struct dyString *update = dyStringNew(updateSize);
sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%d)", 
	tableName,  el->gcAccession,  el->hubUrl,  el->asmName,  el->scientificName,  el->commonName,  el->taxId);
sqlUpdate(conn, update->string);
dyStringFree(&update);
}

struct genark *genarkLoad(char **row)
/* Load a genark from row fetched with select * from genark
 * from database.  Dispose of this with genarkFree(). */
{
struct genark *ret;

AllocVar(ret);
ret->gcAccession = cloneString(row[0]);
ret->hubUrl = cloneString(row[1]);
ret->asmName = cloneString(row[2]);
ret->scientificName = cloneString(row[3]);
ret->commonName = cloneString(row[4]);
ret->taxId = sqlSigned(row[5]);
return ret;
}

struct genark *genarkLoadAll(char *fileName) 
/* Load all genark from a whitespace-separated file.
 * Dispose of this with genarkFreeList(). */
{
struct genark *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[6];

while (lineFileRow(lf, row))
    {
    el = genarkLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct genark *genarkLoadAllByChar(char *fileName, char chopper) 
/* Load all genark from a chopper separated file.
 * Dispose of this with genarkFreeList(). */
{
struct genark *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[6];

while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
    {
    el = genarkLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

struct genark *genarkCommaIn(char **pS, struct genark *ret)
/* Create a genark out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new genark */
{
char *s = *pS;

if (ret == NULL)
    AllocVar(ret);
ret->gcAccession = sqlStringComma(&s);
ret->hubUrl = sqlStringComma(&s);
ret->asmName = sqlStringComma(&s);
ret->scientificName = sqlStringComma(&s);
ret->commonName = sqlStringComma(&s);
ret->taxId = sqlSignedComma(&s);
*pS = s;
return ret;
}

void genarkFree(struct genark **pEl)
/* Free a single dynamically allocated genark such as created
 * with genarkLoad(). */
{
struct genark *el;

if ((el = *pEl) == NULL) return;
freeMem(el->gcAccession);
freeMem(el->hubUrl);
freeMem(el->asmName);
freeMem(el->scientificName);
freeMem(el->commonName);
freez(pEl);
}

void genarkFreeList(struct genark **pList)
/* Free a list of dynamically allocated genark's */
{
struct genark *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    genarkFree(&el);
    }
*pList = NULL;
}

void genarkOutput(struct genark *el, FILE *f, char sep, char lastSep) 
/* Print out genark.  Separate fields with sep. Follow last field with lastSep. */
{
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->gcAccession);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->hubUrl);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->asmName);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->scientificName);
if (sep == ',') fputc('"',f);
fputc(sep,f);
if (sep == ',') fputc('"',f);
fprintf(f, "%s", el->commonName);
if (sep == ',') fputc('"',f);
fputc(sep,f);
fprintf(f, "%d", el->taxId);
fputc(lastSep,f);
}

void genarkJsonOutput(struct genark *el, FILE *f) 
/* Print out genark in JSON format. */
{
fputc('{',f);
fputc('"',f);
fprintf(f,"gcAccession");
fputc('"',f);
fputc(':',f);
fputc('"',f);
fprintf(f, "%s", el->gcAccession);
fputc('"',f);
fputc(',',f);
fputc('"',f);
fprintf(f,"hubUrl");
fputc('"',f);
fputc(':',f);
fputc('"',f);
fprintf(f, "%s", el->hubUrl);
fputc('"',f);
fputc(',',f);
fputc('"',f);
fprintf(f,"asmName");
fputc('"',f);
fputc(':',f);
fputc('"',f);
fprintf(f, "%s", el->asmName);
fputc('"',f);
fputc(',',f);
fputc('"',f);
fprintf(f,"scientificName");
fputc('"',f);
fputc(':',f);
fputc('"',f);
fprintf(f, "%s", el->scientificName);
fputc('"',f);
fputc(',',f);
fputc('"',f);
fprintf(f,"commonName");
fputc('"',f);
fputc(':',f);
fputc('"',f);
fprintf(f, "%s", el->commonName);
fputc('"',f);
fputc(',',f);
fputc('"',f);
fprintf(f,"taxId");
fputc('"',f);
fputc(':',f);
fprintf(f, "%d", el->taxId);
fputc('}',f);
}

/* -------------------------------- End autoSql Generated Code -------------------------------- */

char *genarkUrl(char *accession)
/* Return the URL to the genark assembly with this accession if present,
 * otherwise return NULL
 * */
{
char *genarkPrefix = cfgOption("genarkHubPrefix");

if (genarkPrefix == NULL)
    return NULL;

struct sqlConnection *conn = hConnectCentral();
if (!sqlTableExists(conn, genarkTableName()))
    return NULL;

char *url = NULL;
char query[4096];
char buffer[4096];
sqlSafef(query, sizeof query, "select hubUrl from %s where gcAccession='%s'", genarkTableName(), accession);
if (sqlQuickQuery(conn, query, buffer, sizeof buffer))
    {
    char buffer2[4096];
    safef(buffer2, sizeof buffer2, "%s/%s", genarkPrefix, buffer);

    url = cloneString(buffer2);
    }

hDisconnectCentral(&conn);

return url;
}

static char *_genarkTableName = NULL;

char *genarkTableName()
/* return the genark table name from the environment, 
 * or hg.conf, or use the default.  Cache the result */
{
if (_genarkTableName == NULL)
    _genarkTableName = cfgOptionEnvDefault("HGDB_GENARK_STATUS_TABLE",
	    genarkTableConfVariable, defaultGenarkTableName);

return _genarkTableName;
}