src/hg/utils/refSeqGet/refSeqVerInfo.c 1.2

Index: src/hg/utils/refSeqGet/refSeqVerInfo.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/refSeqGet/refSeqVerInfo.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/utils/refSeqGet/refSeqVerInfo.c	23 Nov 2009 02:56:20 -0000	1.1
+++ src/hg/utils/refSeqGet/refSeqVerInfo.c	30 Nov 2009 17:54:31 -0000	1.2
@@ -1,152 +1,153 @@
 /* object to track refseqs that are to be retrieved */
 #include "common.h"
 #include "refSeqVerInfo.h"
 #include "linefile.h"
 #include "hash.h"
 #include "jksql.h"
 #include "sqlNum.h"
 
 enum refSeqVerInfoStatus
 /* validation status */
 {
     refSeqVerInfoOk,
     refSeqVerInfoIgnore,  // duplicate, ignore
     refSeqVerInfoError
 };
 
 static struct refSeqVerInfo *refSeqVerInfoNewDb(char **row)
 /* construct a refSeqVerInfo object from a database query */
 {
 struct refSeqVerInfo *rsvi;
 AllocVar(rsvi);
 rsvi->acc = cloneString(row[0]);
 rsvi->ver = sqlSigned(row[1]);
 return rsvi;
 }
 
 struct hash *refSeqVerInfoFromDb(struct sqlConnection *conn, boolean getNM, boolean getNR)
 /* load refSeqVerInfo table for all native refseqs in the database */
 {
 struct hash *refSeqVerInfoTbl = hashNew(18);
 char *restrict = "";
 if (getNM && !getNR)
     restrict = " AND (acc LIKE \"NM%\")";
 else if (!getNM && getNR)
     restrict = " AND (acc LIKE \"NR%\")";
 char query[128];
 safef(query, sizeof(query),
       "SELECT acc, version FROM gbStatus WHERE (srcDb = \"RefSeq\") AND (orgCat = \"native\")%s", restrict);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct refSeqVerInfo *rsvi = refSeqVerInfoNewDb(row);
     hashAdd(refSeqVerInfoTbl, rsvi->acc, rsvi);
     }
 
 sqlFreeResult(&sr);
 return refSeqVerInfoTbl;
 }
 
 static struct refSeqVerInfo *refSeqVerInfoNewFile(char *acc)
 /* construct a refSeqVerInfo object from a file */
 {
 struct refSeqVerInfo *rsvi;
 AllocVar(rsvi);
 char *dot = strchr(acc, '.');
 rsvi->acc = cloneStringZ(acc, ((dot != NULL) ? (dot - acc) : strlen(acc)));
 if (dot != NULL)
     rsvi->requestVer = sqlUnsigned(dot+1);
 return rsvi;
 }
 
 static void prAccReqVer(struct refSeqVerInfo *rsvi, FILE *fh)
 /* print acc + requested version, or just acc if no version */
 {
 fputs(rsvi->acc, fh);
 if (rsvi->requestVer != 0)
     fprintf(fh, ".%d", rsvi->requestVer);
 }
 
 static enum refSeqVerInfoStatus dupCheck(struct hash *refSeqVerInfoTbl, struct refSeqVerInfo *rsvi, struct sqlConnection *conn)
 {
 struct refSeqVerInfo *rsvi0 = hashFindVal(refSeqVerInfoTbl, rsvi->acc);
 if (rsvi0 != NULL)
     {
     if (rsvi0->requestVer == rsvi->requestVer)
         return refSeqVerInfoIgnore;  // already there with the same version, ignore
     else
         {
         fprintf(stderr, "Error: RefSeq %s specified multiple times in accList, once as ", rsvi->acc);
         prAccReqVer(rsvi0, stderr);
         fputs(" and once as ", stderr);
         prAccReqVer(rsvi0, stderr);
         fputc('\n', stderr);
         return refSeqVerInfoError;
         }
     }
 else
     return refSeqVerInfoOk;
 }
 
 int refSeqVerInfoGetVersion(char *acc, struct sqlConnection *conn)
 /* get the version from the database, or zero if accession is not found */
 {
 char query[128];
 safef(query, sizeof(query),
       "SELECT version FROM gbSeq WHERE (acc = \"%s\")", acc);
 return sqlQuickNum(conn, query);
 }
 
 static enum refSeqVerInfoStatus versionGetCheck(struct refSeqVerInfo *rsvi, struct sqlConnection *conn)
 /* get or validate the version from the file against the database */
 {
 int dbVer = refSeqVerInfoGetVersion(rsvi->acc, conn);
 if (dbVer == 0)
     {
     fprintf(stderr, "Error: RefSeq %s not in database\n", rsvi->acc);
     return refSeqVerInfoError;
     }
 if ((rsvi->requestVer != 0) && (dbVer != rsvi->requestVer))
     {
     fprintf(stderr, "Error: RefSeq %s.%d requested in accList, database contains %s.%d \n", rsvi->acc, rsvi->requestVer, rsvi->acc, dbVer);
     return refSeqVerInfoError;
     }
 rsvi->ver = dbVer;
 return refSeqVerInfoOk;
 }
 
 static enum refSeqVerInfoStatus fromFileAdd(struct hash *refSeqVerInfoTbl, struct refSeqVerInfo *rsvi, struct sqlConnection *conn)
 /* add a refseq parsed from a file to the table, validating against database
  * and setting the actually version number. */
 {
 enum refSeqVerInfoStatus stat = dupCheck(refSeqVerInfoTbl, rsvi, conn);
 if (stat != refSeqVerInfoOk)
     return stat;
 stat = versionGetCheck(rsvi, conn);
 if (stat != refSeqVerInfoOk)
     return stat;
 hashAdd(refSeqVerInfoTbl, rsvi->acc, rsvi);
 return refSeqVerInfoOk;
 }
 
 struct hash *refSeqVerInfoFromFile(struct sqlConnection *conn, char *accList)
 /* load refSeqVerInfo table for all native refseqs specified in a file, then validate it against
  * the database. */
 {
 struct hash *refSeqVerInfoTbl = hashNew(18);
 struct lineFile *lf = lineFileOpen(accList, TRUE); 
 int errCnt = 0;
-char **row;
-while (lineFileNextReal(lf, row))
+char *line;
+while (lineFileNextReal(lf, &line))
     {
-    if (fromFileAdd(refSeqVerInfoTbl, refSeqVerInfoNewFile(row[0]), conn) == refSeqVerInfoError)
+    char *acc = trimSpaces(line);
+    if (fromFileAdd(refSeqVerInfoTbl, refSeqVerInfoNewFile(acc), conn) == refSeqVerInfoError)
         errCnt++;
     }
 lineFileClose(&lf);
 if (errCnt > 0)
     errAbort("%d errors detected loading RefSeq accessioned from %s", errCnt, accList);
 return refSeqVerInfoTbl;
 }