src/hg/instinct/bioInt2/bioIntDriver.c 1.2
1.2 2009/03/24 05:21:54 jsanborn
updated
Index: src/hg/instinct/bioInt2/bioIntDriver.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntDriver.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/instinct/bioInt2/bioIntDriver.c 20 Mar 2009 06:06:31 -0000 1.1
+++ src/hg/instinct/bioInt2/bioIntDriver.c 24 Mar 2009 05:21:54 -0000 1.2
@@ -92,10 +92,10 @@
{
struct datasets *da = bi->dataset;
char query[128];
safef(query, sizeof(query),
- "select * from samples where dataset_id = %d order by id;",
- da->id);
+ "select * from %s where dataset_id = %d order by id;",
+ SA_TABLE, da->id);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
@@ -115,9 +115,9 @@
struct slName *sl;
struct datasets *da = bi->dataset;
struct dyString *dy = newDyString(100);
-dyStringPrintf(dy, "select * from samples where name in (");
+dyStringPrintf(dy, "select * from %s where name in (", SA_TABLE);
for (sl = sampleList; sl; sl = sl->next)
{
dyStringPrintf(dy, "'%s'", sl->name);
if (sl->next)
@@ -147,13 +147,14 @@
struct datasets *da = bi->dataset;
struct dyString *dy = newDyString(100);
dyStringPrintf(dy,
- "select * from samples "
- "join clinicalData on samples.id = clinicalData.sample_id "
- "join features on clinicalData.feature_id = features.id "
- "where samples.dataset_id = %d ",
- da->id);
+ "select * from %s "
+ "join %s on %s.id = %s.sample_id "
+ "join %s on %s.feature_id = %s.id "
+ "where %s.dataset_id = %d ",
+ SA_TABLE, CD_TABLE, SA_TABLE, CD_TABLE, FE_TABLE,
+ CD_TABLE, FE_TABLE, SA_TABLE, da->id);
struct slName *sl, *fv, *slList = NULL;
for (fv = featureValList; fv; fv = fv->next)
{
@@ -171,16 +172,16 @@
char *operation = sl->name;
sl = sl->next;
char *val = sl->name;
- dyStringPrintf(dy, " and features.name = '%s'", name);
- dyStringPrintf(dy, " and clinicalData.val %s %s", operation, val);
+ dyStringPrintf(dy, " and %s.name = '%s'", FE_TABLE, name);
+ dyStringPrintf(dy, " and %s.val %s %s", CD_TABLE, operation, val);
slNameFreeList(&slList);
slList = NULL;
}
-dyStringPrintf(dy, " order by samples.id;");
+dyStringPrintf(dy, " order by %s.id;", SA_TABLE);
char *query = dyStringCannibalize(&dy);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
@@ -204,13 +205,14 @@
struct datasets *da = bi->dataset;
struct dyString *dy = newDyString(100);
dyStringPrintf(dy,
- "select * from samples "
- "join clinicalData on samples.id = clinicalData.sample_id "
- "join features on clinicalData.feature_id = features.id "
- "where samples.dataset_id = %d and (",
- da->id);
+ "select * from %s "
+ "join %s on %s.id = %s.sample_id "
+ "join %s on %s.feature_id = %s.id "
+ "where %s.dataset_id = %d and (",
+ SA_TABLE, CD_TABLE, SA_TABLE, CD_TABLE, FE_TABLE,
+ CD_TABLE, FE_TABLE, SA_TABLE, da->id);
struct slName *sl, *fc, *slList = NULL;
for (fc = featureCodeList; fc; fc = fc->next)
{
@@ -228,21 +230,21 @@
char *operation = sl->name;
sl = sl->next;
char *code = sl->name;
- dyStringPrintf(dy, " (features.name = '%s'", name);
+ dyStringPrintf(dy, " (%s.name = '%s'", FE_TABLE, name);
if (sameString(code, "NULL"))
- dyStringPrintf(dy, " and clinicalData.code is NULL)");
+ dyStringPrintf(dy, " and %s.code is NULL)", CD_TABLE);
else
- dyStringPrintf(dy, " and clinicalData.code %s '%s')", operation, code);
+ dyStringPrintf(dy, " and %s.code %s '%s')", CD_TABLE, operation, code);
slNameFreeList(&slList);
slList = NULL;
if (fc->next)
dyStringPrintf(dy, " or");
}
-dyStringPrintf(dy, ") order by samples.id;");
+dyStringPrintf(dy, ") order by %s.id;", SA_TABLE);
char *query = dyStringCannibalize(&dy);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
@@ -311,12 +313,15 @@
struct dyString *dy = newDyString(100);
dyStringPrintf(dy,
"select %s.* from %s join %s on %s.probe_id = %s.id "
- "join pathwayGenes on pathwayGenes.gene_id = %s.gene_id "
- "join pathways on pathways.id = pathwayGenes.id "
- "where pathways.name in (",
- pInfo, pInfo, p2g, p2g, pInfo, p2g);
+ "join %s on %s.gene_id = %s.gene_id "
+ "join %s on %s.id = %s.id "
+ "where %s.name in (",
+ pInfo, pInfo, p2g, p2g, pInfo,
+ PG_TABLE, PG_TABLE, p2g,
+ PA_TABLE, PA_TABLE, PG_TABLE,
+ PA_TABLE);
for (sl = pathwayList; sl; sl = sl->next)
{
dyStringPrintf(dy, "'%s'", sl->name);
@@ -351,10 +356,11 @@
struct dyString *dy = newDyString(100);
dyStringPrintf(dy,
"select * from %s join %s on %s.probe_id = %s.id "
- "join geneLookup on geneLookup.id = %s.gene_id where kgId in (",
- pInfo, p2g, p2g, pInfo, p2g);
+ "join %s on %s.id = %s.gene_id where kgId in (",
+ pInfo, p2g, p2g, pInfo,
+ GL_TABLE, GL_TABLE, p2g);
for (sl = geneList; sl; sl = sl->next)
{
dyStringPrintf(dy, "'%s'", sl->name);
@@ -909,10 +915,10 @@
struct datasets *da = bi->dataset;
char query[128];
safef(query, sizeof(query),
- "select * from dataTypes where id = %d",
- da->type_id);
+ "select * from %s where id = %d",
+ DT_TABLE, da->type_id);
struct dataTypes *dt = dataTypesLoadByQuery(conn, query);
if (!dt)
errAbort("Datatype with id = %d not found in database", da->type_id);
@@ -951,10 +957,10 @@
/* Make sure only one dataset is loaded (hence 'limit 1') */
char query[256];
safef(query, sizeof(query),
- "select * from datasets where data_table = '%s' limit 1;",
- bi->name);
+ "select * from %s where data_table = '%s' limit 1;",
+ DA_TABLE, bi->name);
bi->dataset = datasetsLoadByQuery(conn, query);
if (!bi->dataset)
errAbort("No datasets named %s found in database.", bi->name);
@@ -1087,12 +1093,14 @@
char query[1024];
safef(query, sizeof(query),
"select DISTINCT kgXref.geneSymbol, %s.name from %s "
"join %s on %s.id = %s.probe_id "
- "join geneLookup on geneLookup.id = %s.gene_id "
- "join kgXref on kgXref.kgId = geneLookup.kgId;",
- da->probe_table, da->probe_table, da->probe_to_gene_table,
- da->probe_table, da->probe_to_gene_table, da->probe_to_gene_table);
+ "join %s on %s.id = %s.gene_id "
+ "join kgXref on kgXref.kgId = %s.kgId;",
+ da->probe_table, da->probe_table,
+ da->probe_to_gene_table, da->probe_table, da->probe_to_gene_table,
+ GL_TABLE, GL_TABLE, da->probe_to_gene_table,
+ GL_TABLE);
struct sqlResult *sr = sqlGetResult(biConn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)