src/hg/instinct/bioInt2/bioIntUI.c 1.5
1.5 2009/03/31 01:06:15 jsanborn
added description field
Index: src/hg/instinct/bioInt2/bioIntUI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntUI.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/instinct/bioInt2/bioIntUI.c 29 Mar 2009 03:31:05 -0000 1.4
+++ src/hg/instinct/bioInt2/bioIntUI.c 31 Mar 2009 01:06:15 -0000 1.5
@@ -1,492 +1,519 @@
/* bioIntUI */
#include "common.h"
#include "bed.h"
#include "cart.h"
#include "linefile.h"
#include "customTrack.h"
#include "genoLay.h"
#include "hash.h"
#include "hCommon.h"
#include "hdb.h"
#include "hPrint.h"
#include "htmshell.h"
#include "hui.h"
#include "trackLayout.h"
#include "web.h"
#include "microarray.h"
#include "ra.h"
#include "hgStatsLib.h"
#include "featuresLib.h"
#include "json.h"
#include "bioIntDb.h"
#include "bioIntDriver.h"
#include "bioIntUI.h"
static char const rcsid[] = "$Id$";
/* ---- Global variables. ---- */
struct cart *cart; /* This holds cgi and other variables between clicks. */
struct hash *oldVars; /* Old cart hash. */
char *db = "bioInt";
char *localDb = "localDb";
void usage()
/* Explain usage and exit. */
{
errAbort(
"bioIntUI\n"
"usage:\n"
" bioIntUI\n"
);
}
/****** BEGIN HELPER FUNCTIONS *******/
struct analyses *getAnalysesById(struct sqlConnection *conn, int analysis_id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where id = %d;",
AN_TABLE, analysis_id);
return analysesLoadByQuery(conn, query);
}
struct analyses *getAnalysesByCohortId(struct sqlConnection *conn, int cohort_id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where cohort_id = %d;",
AN_TABLE, cohort_id);
return analysesLoadByQuery(conn, query);
}
struct analysisFeatures *getAnalysisFeaturesByName(struct sqlConnection *conn,
char *name)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where feature_name = \"%s\"",
AF_TABLE, name);
return analysisFeaturesLoadByQuery(conn, query);
}
struct analysisFeatures *getAnalysisFeaturesById(struct sqlConnection *conn,
int id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where id = %d",
AF_TABLE, id);
return analysisFeaturesLoadByQuery(conn, query);
}
struct features *getFeaturesByName(struct sqlConnection *conn,
char *name)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where name = \"%s\"",
FE_TABLE, name);
return featuresLoadByQuery(conn, query);
}
struct features *getFeaturesById(struct sqlConnection *conn,
int id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where id = %d",
FE_TABLE, id);
return featuresLoadByQuery(conn, query);
}
struct datasets *getDatasetsByCohortId(struct sqlConnection *conn, int cohort_id)
{
char query[256];
safef(query, sizeof(query),
"select %s.* from %s join %s on %s.id = %s.dataset_id "
"where %s.cohort_id = %d",
DA_TABLE, DA_TABLE, DC_TABLE, DA_TABLE, DC_TABLE, DC_TABLE, cohort_id);
return datasetsLoadByQuery(conn, query);
}
struct cohortCorr *getCohortCorrByCohortId(struct sqlConnection *conn, int cohort_id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where cohort_id = %d",
CC_TABLE, cohort_id);
return cohortCorrLoadByQuery(conn, query);
}
+char *getFieldFromKgXref(struct sqlConnection *conn, char *geneSymbol,
+ char *field)
+{
+char query[256];
+safef(query, sizeof(query),
+ "select %s from %s where geneSymbol = \"%s\" ",
+ field, KX_TABLE, geneSymbol);
+
+return sqlQuickString(conn, query);
+}
/****** END HELPER FUNCTIONS *******/
/* get a list of the current analyses */
void getAnalyses()
{
char query[256];
safef(query, sizeof(query),
"select * from analyses;");
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct analyses *an, *anList = analysesLoadByQuery(conn, query);
struct json *js = newJson();
struct json *analysis, *analyses = jsonAddContainerList(js, "analyses");
analysis = analyses;
for (an = anList; an; an = an->next)
{
jsonAddInt(analysis, "id", an->id);
jsonAddInt(analysis, "cohort_id", an->cohort_id);
jsonAddInt(analysis, "module_id", an->module_id);
jsonAddString(analysis, "result_table", an->result_table);
jsonAddString(analysis, "input_tables", an->input_tables);
if (an->next)
analysis = jsonAddContainerToList(&analyses);
}
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
void getFeatureData()
{
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 1; // hard code for first analysis during testing!
int feature_id = cartUsualInt(cart, bioIntFeatureId, -1);
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name && feature_id == -1)
errAbort("%s or %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct analysisFeatures *af = NULL;
if (feature_id == -1)
af = getAnalysisFeaturesByName(conn, feature_name);
else
af = getAnalysisFeaturesById(conn, feature_id);
if (!af)
{
hFreeConn(&conn);
errAbort("Could not find analysisFeature in db");
}
struct analyses *an, *anList = getAnalysesByCohortId(conn, cohort_id);
if (!anList)
{
hFreeConn(&conn);
errAbort("No analyses with cohort_id = %d.\n", cohort_id);
}
char query[512];
for (an = anList; an; an = an->next)
{
safef(query, sizeof(query),
"select DISTINCT %s.name, %s.val from %s join %s on %s.sample_id = %s.id "
"where %s.feature_id = %d;",
SA_TABLE, an->result_table, an->result_table, SA_TABLE, an->result_table, SA_TABLE,
an->result_table, af->id);
if (sqlExists(conn, query))
break;
}
struct json *js = newJson();
+
+char *desc = getFieldFromKgXref(conn, af->feature_name, "description");
+if (!desc)
+ desc = cloneString(af->feature_name);
+
+/* String 'isoform xxx' from description... almost all entries have them */
+char *ptr = rStringIn("isoform", desc);
+if (ptr)
+ *ptr = '\0';
+jsonAddString(js, "description", desc);
+
+char *kgId = getFieldFromKgXref(conn, af->feature_name, "kgId");
+if (kgId)
+ jsonAddString(js, "hgg_gene", kgId);
+
+struct json *data = jsonAddContainer(js, "data");
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
double val = atof(row[1]);
- jsonAddDouble(js, name, val);
+ jsonAddDouble(data, name, val);
}
+sqlFreeResult(&sr);
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
void getClinicalFeatures()
{
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 1; // hard code for first analysis during testing!
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct datasets *da, *daList = getDatasetsByCohortId(conn, cohort_id);
if (!daList)
{
hFreeConn(&conn);
errAbort("No datasets matching cohort_id = %d", cohort_id);
}
struct dyString *dy = dyStringNew(100);
dyStringPrintf(dy,
"select DISTINCT %s.* from %s join %s on %s.id = %s.feature_id "
"join %s on %s.sample_id = %s.id where %s.dataset_id in (",
FE_TABLE, FE_TABLE, CD_TABLE, FE_TABLE, CD_TABLE,
SA_TABLE, CD_TABLE, SA_TABLE, SA_TABLE);
for (da = daList; da; da = da->next)
{
dyStringPrintf(dy, "%d", da->id);
if (da->next)
dyStringPrintf(dy, ",");
}
dyStringPrintf(dy, ")");
char *query = dyStringCannibalize(&dy);
struct features *fe, *feList = featuresLoadByQuery(conn, query);
struct json *js = newJson();
struct json *feature, *features = jsonAddContainerList(js, "features");
feature = features;
for (fe = feList; fe; fe = fe->next)
{
jsonAddInt(feature, "id", fe->id);
jsonAddString(feature, "name", fe->name);
jsonAddString(feature, "shortLabel", fe->shortLabel);
jsonAddString(feature, "longLabel", fe->longLabel);
if (fe->next)
feature = jsonAddContainerToList(&features);
}
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
void getClinicalData()
{
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 1; // hard code for first analysis during testing!
int feature_id = cartUsualInt(cart, bioIntFeatureId, -1);
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name && feature_id == -1)
errAbort("%s or %s must be set for mode=getClinicalData\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct features *fe = NULL;
if (feature_id == -1)
fe = getFeaturesByName(conn, feature_name);
else
fe = getFeaturesById(conn, feature_id);
if (!fe)
{
hFreeConn(&conn);
errAbort("Could not find clinical feature in db");
}
struct datasets *da, *daList = getDatasetsByCohortId(conn, cohort_id);
if (!daList)
{
hFreeConn(&conn);
errAbort("No datasets matching cohort_id = %d", cohort_id);
}
struct dyString *dy = dyStringNew(100);
dyStringPrintf(dy,
"select DISTINCT %s.name, %s.val from %s join %s on %s.sample_id = %s.id ",
SA_TABLE, CD_TABLE, CD_TABLE, SA_TABLE, CD_TABLE, SA_TABLE);
dyStringPrintf(dy,
"where %s.feature_id = %d and %s.dataset_id in (",
CD_TABLE, fe->id, SA_TABLE);
for (da = daList; da; da = da->next)
{
dyStringPrintf(dy, "%d", da->id);
if (da->next)
dyStringPrintf(dy, ",");
}
dyStringPrintf(dy, ")");
char *query = dyStringCannibalize(&dy);
struct json *js = newJson();
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
double val = atof(row[1]);
jsonAddDouble(js, name, val);
}
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
void getMostCorrelated()
{
int takeTop = cartUsualInt(cart, bioIntTakeTop, 5);
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 1; // hard code for first analysis during testing!
int feature_id = cartUsualInt(cart, bioIntFeatureId, -1);
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name && feature_id == -1)
errAbort("%s or %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct analysisFeatures *af = NULL;
if (feature_id == -1)
af = getAnalysisFeaturesByName(conn, feature_name);
else
af = getAnalysisFeaturesById(conn, feature_id);
if (!af)
{
hFreeConn(&conn);
errAbort("Could not find analysisFeature in db");
}
struct cohortCorr *cc = getCohortCorrByCohortId(conn, cohort_id);
if (!cc)
{
hFreeConn(&conn);
errAbort("No cohort correlation table with cohort_id = %d.\n", cohort_id);
}
struct dyString *dy = dyStringNew(100);
dyStringPrintf(dy, "select a1.feature_name, a2.feature_name, %s.val from %s "
"join %s as a1 on %s.feature_id1 = a1.id ",
cc->result_table, cc->result_table, AF_TABLE, cc->result_table);
dyStringPrintf(dy, "join %s as a2 on %s.feature_id2 = a2.id ",
AF_TABLE, cc->result_table);
dyStringPrintf(dy, "where feature_id1 = %d or feature_id2 = %d order by %s.val DESC",
af->id, af->id, cc->result_table);
char *query = dyStringCannibalize(&dy);
struct slPair *sp, *spList = NULL;
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = NULL;
char *name1 = row[0];
char *name2 = row[1];
double val = atof(row[2]);
if (sameString(name1, af->feature_name))
name = name2;
else if (sameString(name2, af->feature_name))
name = name1;
else // doesn't match either, should *never* get here
continue;
AllocVar(sp);
sp->name = cloneString(name);
sp->val = slDoubleNew(val);
slAddHead(&spList, sp);
}
slReverse(&spList);
int count;
struct json *js = newJson();
struct json *corrs = jsonAddContainer(js, "Top Correlated");
for (sp = spList, count = 0; sp && (count < takeTop); sp = sp->next, count++)
{
struct slDouble *sd = sp->val;
if (sd->val < 0.0)
continue;
jsonAddDouble(corrs, sp->name, sd->val);
}
slReverse(&spList);
corrs = jsonAddContainer(js, "Top Anti-Correlated");
for (sp = spList, count = 0; sp && (count < takeTop); sp = sp->next, count++)
{
struct slDouble *sd = sp->val;
if (sd->val > 0.0)
continue;
jsonAddDouble(corrs, sp->name, sd->val);
}
if (js)
hPrintf("%s", js->print(js));
hFreeConn(&conn);
}
void dispatchRoutines()
/* Look at command variables in cart and figure out which
* page to draw. */
{
/* retrieve cart variables, handle various modes */
char *mode = cartOptionalString(cart, bioIntMode);
if (!mode)
errAbort("%s is required.", bioIntMode);
if (sameString(mode, "getAnalyses"))
getAnalyses();
else if (sameString(mode, "getFeatureData"))
getFeatureData();
else if (sameString(mode, "getClinicalData"))
getClinicalData();
else if (sameString(mode, "getClinicalFeatures"))
getClinicalFeatures();
else if (sameString(mode, "getMostCorrelated"))
getMostCorrelated();
else
errAbort("Incorrect mode = %s", mode);
cartRemovePrefix(cart, bioIntPrefix);
}
void hghDoUsualHttp()
/* Wrap html page dispatcher with code that writes out
* HTTP header and write cart back to database. */
{
cartWriteCookie(cart, hUserCookie());
printf("Content-Type:application/x-javascript\r\n\r\n");
/* Dispatch other pages, that actually want to write HTML. */
cartWarnCatcher(dispatchRoutines, cart, jsonEarlyWarningHandler);
cartCheckout(&cart);
}
char *excludeVars[] = {"Submit", "submit", NULL};
int main(int argc, char *argv[])
/* Process command line. */
{
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
oldVars = hashNew(12);
cart = cartForSession(hUserCookie(), excludeVars, oldVars);
hghDoUsualHttp();
return 0;
}