src/hg/instinct/bioInt2/bioController.c 1.7
1.7 2009/03/24 05:21:54 jsanborn
updated
Index: src/hg/instinct/bioInt2/bioController.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioController.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/instinct/bioInt2/bioController.c 24 Mar 2009 03:07:55 -0000 1.6
+++ src/hg/instinct/bioInt2/bioController.c 24 Mar 2009 05:21:54 -0000 1.7
@@ -18,10 +18,10 @@
{
errAbort(
"bioController - controller for bioIntegrator pipeline\n"
"usage:\n"
- " bioIntegrator datasets\n"
- " -datasets = comma-separated list of datasets\n"
+ " bioController cohort_id\n"
+ " -cohort_id = number of cohort in cohorts table"
);
}
#define BIOINT_DB "bioInt"
@@ -88,24 +88,25 @@
boolean analysesExists(struct sqlConnection *biConn, struct analyses *an)
{
char query[256];
safef(query, sizeof(query),
- "select * from analyses where id = %d "
+ "select * from %s where id = %d "
"and cohort_id = %d "
"and module_id = %d "
"and result_table = \"%s\" "
"and input_tables = \"%s\" ",
- an->id, an->cohort_id, an->module_id, an->result_table, an->input_tables);
+ AN_TABLE, an->id, an->cohort_id, an->module_id,
+ an->result_table, an->input_tables);
return sqlExists(biConn, query);
}
boolean analysesWithResultTableExists(struct sqlConnection *biConn, char *result_table)
{
char query[256];
safef(query, sizeof(query),
- "select * from analyses where result_table = \"%s\" ",
- result_table);
+ "select * from %s where result_table = \"%s\" ",
+ AN_TABLE, result_table);
return sqlExists(biConn, query);
}
@@ -113,10 +114,10 @@
{
struct hash *hash = hashNew(0);
char query[256];
safef(query, sizeof(query),
- "select * from analysisParams where analysis_id = %d",
- an->id);
+ "select * from %s where analysis_id = %d",
+ AP_TABLE, an->id);
struct analysisParams *ap, *apList = analysisParamsLoadByQuery(biConn, query);
for (ap = apList; ap; ap = ap->next)
hashAdd(hash, ap->name, ap->val);
@@ -139,9 +140,9 @@
ap->analysis_id = an->id;
ap->name = cloneString(name);
ap->val = cloneString(val);
- analysisParamsSaveToDbEscaped(biConn, ap, "analysisParams", 50);
+ analysisParamsSaveToDbEscaped(biConn, ap, AP_TABLE, 50);
analysisParamsFree(&ap);
}
}
@@ -150,10 +151,10 @@
boolean matchingParams(struct sqlConnection *biConn, int analysis_id, struct hash *params)
{
char query[256];
safef(query, sizeof(query),
- "select * from analysisParams where analysis_id = %d",
- analysis_id);
+ "select * from %s where analysis_id = %d",
+ AP_TABLE, analysis_id);
struct analysisParams *ap, *apList = analysisParamsLoadByQuery(biConn, query);
if (!apList) // no analysis params for this id
@@ -232,9 +233,9 @@
foundName = TRUE;
break;
}
- int id = findIdInTable(biConn, "analyses", "id", "result_table", name);
+ int id = findIdInTable(biConn, AN_TABLE, "id", "result_table", name);
if (matchingParams(biConn, id, params))
{
foundName = TRUE;
break;
@@ -260,9 +261,9 @@
return NULL;
/* Get unique name or name already in database for exact matching analysis */
char *result_table = createAnalysesResultTableName(biConn, cohort_id, am, input_tables, params);
-int id = findIdInTable(biConn, "analyses", "id", "result_table", result_table);
+int id = findIdInTable(biConn, AN_TABLE, "id", "result_table", result_table);
struct analyses *an;
AllocVar(an);
an->id = id;
@@ -272,9 +273,9 @@
an->input_tables = cloneString(input_tables);
if (!analysesExists(biConn, an))
{
- analysesSaveToDbEscaped(biConn, an, "analyses", 20);
+ analysesSaveToDbEscaped(biConn, an, AN_TABLE, 20);
storeAnalysisParams(biConn, an, params);
}
return an;
@@ -283,11 +284,11 @@
struct datasets *datasetsInCohort(struct sqlConnection *biConn, int cohort_id)
{
char query[256];
safef(query, sizeof(query),
- "select * from datasets join datasetCohort on datasets.id = datasetCohort.dataset_id "
- "where datasetCohort.cohort_id = %d;",
- cohort_id);
+ "select * from %s join %s on %s.id = %s.dataset_id "
+ "where %s.cohort_id = %d;",
+ DA_TABLE, DC_TABLE, DA_TABLE, DC_TABLE, DC_TABLE, cohort_id);
return datasetsLoadByQuery(biConn, query);
}
@@ -295,10 +296,10 @@
char *field, char *val)
{
char query[128];
safef(query, sizeof(query),
- "select * from analysisModules where %s = \"%s\" ",
- field, val);
+ "select * from %s where %s = \"%s\" ",
+ AM_TABLE, field, val);
return analysisModulesLoadByQuery(biConn, query);
}
@@ -309,10 +310,10 @@
return;
char query[128];
safef(query, sizeof(query),
- "select * from analysisModules where id = %d",
- module_id);
+ "select * from %s where id = %d",
+ AM_TABLE, module_id);
struct analysisModules *am = analysisModulesLoadByQuery(biConn, query);
if (!am)
errAbort("No module with id = %d", module_id);
@@ -340,10 +341,10 @@
struct biAnalysis *ba, *baList = NULL;
char query[128];
safef(query, sizeof(query),
- "select * from analyses where cohort_id = %d",
- cohort_id);
+ "select * from %s where cohort_id = %d",
+ AN_TABLE, cohort_id);
struct analyses *an, *anList = analysesLoadByQuery(biConn, query);
if (!anList)
@@ -370,21 +371,23 @@
boolean cohortExists(struct sqlConnection *biConn, int cohort_id)
{
char query[128];
-safef(query, sizeof(query), "select * from cohorts where id = %d", cohort_id);
+safef(query, sizeof(query),
+ "select * from %s where id = %d",
+ CO_TABLE, cohort_id);
return sqlExists(biConn, query);
}
boolean analysisModuleExists(struct sqlConnection *biConn, struct analysisModules *am)
{
char query[128];
safef(query, sizeof(query),
- "select * from analysisModules where id = %d "
+ "select * from %s where id = %d "
"and name = \"%s\" "
"and type = \"%s\" ",
- am->id, am->name, am->type);
+ AM_TABLE, am->id, am->name, am->type);
return sqlExists(biConn, query);
}
@@ -393,12 +396,12 @@
struct analysisModules *am;
AllocVar(am);
am->name = cloneString(name);
am->type = cloneString(type);
-am->id = findIdInTable(biConn, "analysisModules", "id", "name", am->name);
+am->id = findIdInTable(biConn, AM_TABLE, "id", "name", am->name);
if (!analysisModuleExists(biConn, am))
- analysisModulesSaveToDb(biConn, am, "analysisModules", 10);
+ analysisModulesSaveToDb(biConn, am, AM_TABLE, 10);
analysisModulesFree(&am);
}
@@ -454,16 +457,16 @@
void prepareDatabase(struct sqlConnection *biConn)
{
-if (!sqlTableExists(biConn, "analyses"))
- createAnalysesTable(biConn, "analyses");
+if (!sqlTableExists(biConn, AN_TABLE))
+ createAnalysesTable(biConn, AN_TABLE);
-if (!sqlTableExists(biConn, "analysisParams"))
- createAnalysisParamsTable(biConn, "analysisParams");
+if (!sqlTableExists(biConn, AP_TABLE))
+ createAnalysisParamsTable(biConn, AP_TABLE);
-if (!sqlTableExists(biConn, "analysisModules"))
- createAnalysisModulesTable(biConn, "analysisModules");
+if (!sqlTableExists(biConn, AM_TABLE))
+ createAnalysisModulesTable(biConn, AM_TABLE);
setupAnalysisModules(biConn);
}