aba8125cb532df17beb7c7c9bc8467a43d09e3d6
braney
Wed Feb 10 13:39:27 2016 -0800
changes to allow for GenBank metadata to be held in a common table. #16809
diff --git src/hg/hgc/mgcClick.c src/hg/hgc/mgcClick.c
index 6a9f3d5..c716f22 100644
--- src/hg/hgc/mgcClick.c
+++ src/hg/hgc/mgcClick.c
@@ -1,59 +1,60 @@
/* mgcClick - click handling for MGC and ORFEome related tracks */
/* Copyright (C) 2013 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#include "common.h"
#include "hgc.h"
#include "mgcClick.h"
#include "ccdsClick.h"
#include "ccdsGeneMap.h"
#include "gbMiscDiff.h"
#include "web.h"
#include "genbank.h"
#include "htmshell.h"
#include "genePred.h"
#include "geneSimilarities.h"
+#include "genbank.h"
static char *findRefSeqSummary(struct sqlConnection *conn,
struct geneSimilarities *refSeqs,
char **sumAccv)
/* Given similar refseq genes, find the first one with a RefSeq
* summary and return that summary, or NULL if not found. Also returns
* accv of matched */
{
char buf[GENBANK_ACC_BUFSZ];
struct geneSim *rs;
for (rs = refSeqs->genes; rs != NULL; rs = rs->next)
{
char *sum = getRefSeqSummary(conn, genbankDropVer(buf, rs->gene->name));
if (sum != NULL)
{
*sumAccv = cloneString(rs->gene->name);
return sum;
}
}
*sumAccv = NULL;
return NULL;
}
static char *getAccVersion(struct sqlConnection *conn, char *acc)
/* given a accession, get acc.ver */
{
char query[256], accver[64];
-sqlSafef(query, sizeof(query), "SELECT version FROM gbCdnaInfo WHERE acc=\"%s\"", acc);
+sqlSafef(query, sizeof(query), "SELECT version FROM %s WHERE acc=\"%s\"", gbCdnaInfoTable, acc);
safef(accver, sizeof(accver), "%s.%d", acc, sqlNeedQuickNum(conn, query));
return cloneString(accver);
}
struct mgcDb
/* information about an MGC databases */
{
char *name; /* collection name */
char *title; /* collection title */
char *organism; /* organism name for URL, case-sensitive */
char *server; /* MGC server */
};
static struct mgcDb getMgcDb()
/* get the mgc database info for the current host */
@@ -173,54 +174,54 @@
boolean inMBLabValidDb = FALSE;
struct sqlConnection *fconn = sqlMayConnect("hgFixed");
if ((fconn != NULL) && sqlTableExists(fconn, "mgcMBLabValid"))
{
char query[64], buf[32];
sqlSafef(query, sizeof(query), "select acc from mgcMBLabValid where acc=\"%s\"",
acc);
if (sqlQuickQuery(fconn, query, buf, sizeof(buf)) != NULL)
inMBLabValidDb = TRUE;
sqlDisconnect(&fconn);
}
return inMBLabValidDb;
}
static void cdnaInfoLoad(struct cloneInfo *ci, struct sqlConnection *conn)
-/* Loading clone information from gbCdnaInfo relational tables. */
+/* Loading clone information from gbCdnaInfoTable relational tables. */
{
-// data from gbCdnaInfo and friends
+// data from gbCdnaInfoTable and friends
char query[1024];
sqlSafef(query, sizeof(query),
"select "
- "description.name, organism.name, tissue.name, library.name,"
- "development.name, geneName.name, productName.name, mrnaClone.name,"
- "cds.name,keyword.name,gbCdnaInfo.moddate,gbCdnaInfo.version,"
- "gbCdnaInfo.gi"
+ "des.name, o.name, t.name, l.name,"
+ "dev.name, gene.name, p.name, m.name,"
+ "c.name,k.name,g.moddate,g.version,"
+ "g.gi"
" from "
- "gbCdnaInfo,description,organism,tissue,library,development,"
- "geneName,productName,mrnaClone,cds,keyword"
+ "%s g,%s des,%s o,%s t,%s l,%s dev,"
+ "%s gene,%s p,%s m,%s c,%s k"
" where "
"(acc = \"%s\") and"
- "(description = description.id) and (organism = organism.id) and"
- "(tissue = tissue.id) and (library = library.id) and"
- "(development = development.id) and (geneName = geneName.id) and"
- "(productName = productName.id) and (mrnaClone = mrnaClone.id) and"
- "(cds = cds.id) and (keyword = keyword.id)", ci->acc);
+ "(description = des.id) and (organism = o.id) and"
+ "(tissue = t.id) and (library = l.id) and"
+ "(development = dev.id) and (geneName = gene.id) and"
+ "(productName = p.id) and (mrnaClone = m.id) and"
+ "(cds = c.id) and (keyword = k.id)", gbCdnaInfoTable, descriptionTable, organismTable, tissueTable, libraryTable, developmentTable,geneNameTable, productNameTable, mrnaCloneTable, cdsTable, keywordTable, ci->acc);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = sqlNextRow(sr);
if (row == NULL)
- errAbort("can't find %s in gbCdnaInfo", ci->acc);
+ errAbort("can't find %s in %s", ci->acc, gbCdnaInfoTable);
int i = 0;
ci->desc = cloneString(row[i++]);
ci->organism = cloneString(row[i++]);
ci->tissue = cloneString(row[i++]);
ci->library = cloneString(row[i++]);
ci->development = cloneString(row[i++]);
ci->geneName = cloneString(row[i++]);
ci->productName = cloneString(row[i++]);
ci->clone = cloneString(row[i++]);
ci->cds = cloneString(row[i++]);
ci->keyword = cloneString(row[i++]);
ci->moddate = cloneString(row[i++]);
ci->version = sqlUnsigned(row[i++]);
ci->gi = sqlUnsigned(row[i++]);
sqlFreeResult(&sr);
@@ -560,33 +561,33 @@
webPrintLinkTableNewRow();
webPrintIntCell(gmd->mrnaStart);
webPrintIntCell(gmd->mrnaEnd);
if (miscDiffFlds & gbMiscDiffGene)
webPrintLinkCell(gmd->gene);
if (miscDiffFlds & gbMiscDiffReplace)
webPrintLinkCell(gmd->replacement);
if (miscDiffFlds & gbMiscDiffNotes)
webPrintLinkCell(gmd->notes);
}
static void prMiscDiffs(struct sqlConnection *conn, char *acc)
/* print any gbMiscDiff rows for the accession */
{
struct gbMiscDiff *gmds = NULL, *gmd;
-if (sqlTableExists(conn, "gbMiscDiff"))
+if (sqlTableExists(conn, gbMiscDiffTable))
gmds = sqlQueryObjs(conn, (sqlLoadFunc)gbMiscDiffLoad, sqlQueryMulti,
- "select * from gbMiscDiff where acc=\"%s\"", acc);
+ "select * from %s where acc=\"%s\"", gbMiscDiffTable, acc);
webNewSection("NCBI Clone Validation");
if (gmds != NULL)
{
unsigned miscDiffFlds = getMiscDiffFields(gmds);
webPrintLinkTableStart();
prMiscDiffHdr(miscDiffFlds);
for (gmd = gmds; gmd != NULL; gmd = gmd->next)
prMiscDiff(gmd, miscDiffFlds);
webPrintLinkTableEnd();
}
else
printf("<EM>No clone discrepancies annotated</EM><BR><BR>\n");
}
static void prMethodsLink(struct sqlConnection *conn, char *track)