src/hg/instinct/bioInt2/bioIntUI.c 1.14
1.14 2009/04/07 19:01:01 jsanborn
changed way codes were sent
Index: src/hg/instinct/bioInt2/bioIntUI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntUI.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/hg/instinct/bioInt2/bioIntUI.c 7 Apr 2009 03:41:09 -0000 1.13
+++ src/hg/instinct/bioInt2/bioIntUI.c 7 Apr 2009 19:01:01 -0000 1.14
@@ -1,837 +1,958 @@
/* 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 tissues *getTissuesById(struct sqlConnection *conn,
int id)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where id = %d",
TI_TABLE, id);
return tissuesLoadByQuery(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);
}
struct pathways *getPathwayByName(struct sqlConnection *conn, char *name)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where name = \"%s\" ",
PA_TABLE, name);
return pathwaysLoadByQuery(conn, query);
}
void setAnalysisFeatureDesc(struct sqlConnection *conn, struct json *js,
struct analysisFeatures *af)
{
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);
}
void setAnalysisFeatureLink(struct sqlConnection *conn, struct json *js,
struct analysisFeatures *af)
{
char *name, *source;
name = getFieldFromKgXref(conn, af->feature_name, "kgId");
if (name)
source = "UCSC";
else
{
struct pathways *pa = getPathwayByName(conn, af->feature_name);
if (!pa)
return;
name = pa->name;
source = pa->source;
}
jsonAddString(js, "name", name);
jsonAddString(js, "source", source);
}
/****** 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 getCohorts()
{
char query[256];
safef(query, sizeof(query),
"select * from %s;", CO_TABLE);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct cohorts *co, *coList = cohortsLoadByQuery(conn, query);
struct json *js = newJson();
struct json *cohort, *cohorts = jsonAddContainerList(js, "cohorts");
cohort = cohorts;
for (co = coList; co; co = co->next)
{
jsonAddInt(cohort, "cohort_id", co->id);
jsonAddString(cohort, "name", co->name);
struct datasets *da, *daList = getDatasetsByCohortId(conn, co->id);
struct tissues *ti = getTissuesById(conn, daList->tissue_id);
jsonAddString(cohort, "tissue", ti->name);
tissuesFree(&ti);
struct json *dataset, *datasets = jsonAddContainerList(cohort, "datasets");
dataset = datasets;
for (da = daList; da; da = da->next)
{
jsonAddString(dataset, "name", da->name);
jsonAddInt(dataset, "num_samples", da->num_samples);
if (da->next)
dataset = jsonAddContainerToList(&datasets);
}
if (co->next)
cohort = jsonAddContainerToList(&cohorts);
}
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
struct searchResults {
struct searchResults *next;
char *name;
char *source;
int length;
};
int searchResultsCmp(const void *va, const void *vb)
/* Compare function to sort array of ints. */
{
const struct searchResults *a = *((struct searchResults **)va);
const struct searchResults *b = *((struct searchResults **)vb);
int diff = a->length - b->length;
if (diff < 0)
return -1;
else if (diff > 0)
return 1;
else
return 0;
}
struct searchResults *searchForFeatures(struct sqlConnection *conn, int cohort_id,
struct datasets *daList, char *feature_name)
{
int maxResponse = 5;
/* Check analysis features */
char query[256];
safef(query, sizeof(query),
"select feature_name from %s where feature_name like \"%%%s%%\" "
"order by length(feature_name);",
AF_TABLE, feature_name);
int count = 0;
struct searchResults *sp, *spList = NULL;
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
AllocVar(sp);
sp->name = cloneString(name);
sp->source = cloneString("gene/geneset");
sp->length = strlen(sp->name);
slAddHead(&spList, sp);
if (count > maxResponse)
break;
count++;
}
sqlFreeResult(&sr);
/* Check clinical features */
struct datasets *da;
struct dyString *dy = dyStringNew(100);
dyStringPrintf(dy,
"select DISTINCT %s.name from %s join %s on %s.sample_id = %s.id ",
FE_TABLE, CD_TABLE, SA_TABLE, CD_TABLE, SA_TABLE);
dyStringPrintf(dy,
"join %s on %s.id = %s.feature_id ",
FE_TABLE, FE_TABLE, CD_TABLE);
dyStringPrintf(dy,
"where %s.name like \"%%%s%%\" and %s.dataset_id in (",
FE_TABLE, feature_name, SA_TABLE);
for (da = daList; da; da = da->next)
{
dyStringPrintf(dy, "%d", da->id);
if (da->next)
dyStringPrintf(dy, ",");
}
dyStringPrintf(dy, ") order by length(%s.name)", FE_TABLE);
char *cquery = dyStringCannibalize(&dy);
count = 0;
sr = sqlGetResult(conn, cquery);
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
AllocVar(sp);
sp->name = cloneString(name);
sp->source = cloneString("clinical");
sp->length = strlen(sp->name);
slAddHead(&spList, sp);
if (count < maxResponse)
break;
count++;
}
sqlFreeResult(&sr);
slSort(&spList, searchResultsCmp);
return spList;
}
void sendNoMatch(struct json *js)
{
return;
}
void sendAmbiguities(struct json *js, struct searchResults *spList)
{
struct searchResults *sp;
for (sp = spList; sp; sp = sp->next)
jsonAddString(js, sp->name, sp->source);
}
void sendAnalysisFeatureData(struct sqlConnection *conn, struct json *js,
int cohort_id, char *feature_name)
{
struct analysisFeatures *af = getAnalysisFeaturesByName(conn, feature_name);
if (!af)
{
hFreeConn(&conn);
errAbort("Could not find analysisFeature named in %s in db", feature_name);
}
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;
}
setAnalysisFeatureDesc(conn, js, af);
setAnalysisFeatureLink(conn, js, af); // e.g. '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(data, name, val);
}
sqlFreeResult(&sr);
}
struct samples *getOverlappingSamples(struct sqlConnection *conn,
struct datasets *daList)
{
struct dyString *dy = dyStringNew(100);
int count = 1;
dyStringPrintf(dy, "select * from %s as t%d ", SA_TABLE, count);
count++;
struct datasets *da = daList->next;
for (da = daList; da; da = da->next)
{
dyStringPrintf(dy,
"join %s as t%d on t1.id = t%d.id ",
SA_TABLE, count, count);
count++;
}
count = 1;
dyStringPrintf(dy, "where ");
for (da = daList; da; da = da->next)
{
dyStringPrintf(dy, "t%d.dataset_id=%d ", count, da->id);
if (da->next)
dyStringPrintf(dy, "and ");
count++;
}
char *query = dyStringCannibalize(&dy);
return samplesLoadByQuery(conn, query);
}
void sendClinicalData(struct sqlConnection *conn, struct json *js,
int cohort_id, char *feature_name, struct datasets *daList)
{
struct features *fe = getFeaturesByName(conn, feature_name);
if (!fe)
{
hFreeConn(&conn);
errAbort("Could not find clinical feature in db");
}
struct samples *sa, *samples = getOverlappingSamples(conn, daList);
struct dyString *dy = dyStringNew(100);
dyStringPrintf(dy,
"select DISTINCT %s.name, %s.val, %s.code from %s "
"join %s on %s.sample_id = %s.id "
"where %s.feature_id = %d and %s.id in (",
SA_TABLE, CD_TABLE, CD_TABLE, CD_TABLE, SA_TABLE, CD_TABLE, SA_TABLE,
CD_TABLE, fe->id, SA_TABLE);
for (sa = samples; sa; sa = sa->next)
{
dyStringPrintf(dy, "%d", sa->id);
if (sa->next)
dyStringPrintf(dy, ",");
}
dyStringPrintf(dy, ")");
char *query = dyStringCannibalize(&dy);
jsonAddString(js, "description", fe->longLabel);
jsonAddString(js, "name", fe->name);
jsonAddString(js, "source", "N/A");
+struct slDouble *sd;
+struct hash *codeHash = hashNew(0);
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]);
char *code = row[2];
- if (sameString(code, "(null)")) // eventually need to fix this.
jsonAddDouble(data, name, val);
- else
- jsonAddString(data, name, code);
+ if (!sameString(code, "(null)")) // eventually need to fix this.
+ {
+ if (hashLookup(codeHash, code))
+ continue;
+ sd = slDoubleNew(val);
+ hashAdd(codeHash, code, sd);
+ }
+ }
+if (hashNumEntries(codeHash) == 0)
+ return;
+
+struct json *codes = jsonAddContainer(js, "codes");
+struct hashEl *el, *elList = hashElListHash(codeHash);
+for (el = elList; el != NULL; el = el->next)
+ {
+ char *name = el->name;
+ sd = el->val;
+
+ jsonAddDouble(codes, name, sd->val);
}
+hashElFreeList(&elList);
}
void sendUniqueMatch(struct sqlConnection *conn, struct json *js,
int cohort_id, char *feature_name, char *source,
struct datasets *daList)
{
if (sameString(source, "gene/geneset"))
sendAnalysisFeatureData(conn, js, cohort_id, feature_name);
else if (sameString(source, "clinical"))
sendClinicalData(conn, js, cohort_id, feature_name, daList);
}
void getFeatureData()
{
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 2; // hard code for first analysis during testing!
/* feature source = gene,geneset,clinical... */
char *source = cartOptionalString(cart, bioIntSourceName);
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name || !source)
errAbort("%s and %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntSourceName);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct datasets *daList = getDatasetsByCohortId(conn, cohort_id);
if (!daList)
errAbort("No datasets matching cohort_id = %d", cohort_id);
struct json *js = newJson();
sendUniqueMatch(conn, js, cohort_id, feature_name, source, daList);
if (js)
hPrintf("%s\n", js->print(js));
hFreeConn(&conn);
}
void getSuggestions()
{
int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
if (cohort_id == -1)
cohort_id = 2; // hard code for first analysis during testing!
/* feature source = gene,geneset,clinical... */
//char *source = cartOptionalString(cart, bioIntSourceName);
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name)
errAbort("%s or %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct datasets *daList = getDatasetsByCohortId(conn, cohort_id);
if (!daList)
errAbort("No datasets matching cohort_id = %d", cohort_id);
struct json *js = newJson();
if (sameString(feature_name, "")) // blank was sent, return no match
sendNoMatch(js);
else
{
struct searchResults *spList = searchForFeatures(conn, cohort_id, daList, feature_name);
int numMatched = slCount(spList);
if (numMatched == 0)
sendNoMatch(js);
else
sendAmbiguities(js, spList);
}
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 = 2; // 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 = 2; // hard code for first analysis during testing!
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name)
errAbort("%s or %s must be set for mode=getClinicalData\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct features *fe = getFeaturesByName(conn, feature_name);
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 = 2; // hard code for first analysis during testing!
char *feature_name = cartOptionalString(cart, bioIntFeatureName);
if (!feature_name)
errAbort("%s or %s must be set for mode=getMostCorrelated\n", bioIntFeature, bioIntFeatureId);
struct sqlConnection *conn = hAllocConnProfile(localDb, db);
struct analysisFeatures *af = getAnalysisFeaturesByName(conn, feature_name);
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);
}
+boolean runStat(struct analysisVals *avList, double *prob)
+{
+if (!avList)
+ return FALSE;
+
+*prob = slCount(avList);
+return TRUE;
+}
+
+void getMostDiff()
+{
+int takeTop = cartUsualInt(cart, bioIntTakeTop, 5);
+
+int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
+if (cohort_id == -1)
+ cohort_id = 2; // hard code for first analysis during testing!
+
+char *feature_name = cartOptionalString(cart, bioIntFeatureName);
+if (!feature_name)
+ errAbort("%s must be set for mode=getMostDiff\n", bioIntFeatureName);
+
+struct sqlConnection *conn = hAllocConnProfile(localDb, db);
+
+struct analyses *an, *analyses = getAnalysesByCohortId(conn, cohort_id);
+char query[512];
+
+an = analyses;
+safef(query, sizeof(query), "select * from %s order by feature_id", an->result_table);
+
+uglyTime(NULL);
+
+//struct analysisVals *avList = analysisValsLoadByQuery(conn, query);
+struct slPair *sp, *spList = NULL;
+struct slDouble *sd;
+double prob;
+
+struct sqlResult *sr = sqlGetResult(conn, query);
+char **row = NULL;
+struct analysisVals *av, *avList = NULL;
+int currentId = -1;
+
+while ((row = sqlNextRow(sr)) != NULL)
+ {
+ av = analysisValsLoad(row);
+ if (currentId == -1)
+ currentId = av->feature_id;
+
+ if (av->feature_id == currentId)
+ slAddHead(&avList, av);
+ else
+ {
+ prob = -1.0;
+ if (runStat(avList, &prob))
+ {
+ sd = slDoubleNew(prob);
+ AllocVar(sp);
+ sp->name = cloneString("test");
+ sp->val = sd;
+ slAddHead(&spList, sp);
+ }
+ analysisValsFreeList(&avList);
+ avList = NULL;
+ currentId = av->feature_id;
+ slAddHead(&avList, av);
+ }
+ }
+sqlFreeResult(&sr);
+
+prob = -1.0;
+if (runStat(avList, &prob))
+ {
+ sd = slDoubleNew(prob);
+ AllocVar(sp);
+ sp->name = cloneString("test");
+ sp->val = sd;
+ slAddHead(&spList, sp);
+ }
+
+uglyTime("finished");
+analysisValsFreeList(&avList);
+uglyTime("free'd");
+
+int count = 0;
+struct json *js = newJson();
+for (sp = spList; sp; sp = sp->next)
+ {
+ sd = sp->val;
+ jsonAddDouble(js, sp->name, sd->val);
+ if (count > takeTop)
+ break;
+ count++;
+ }
+
+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, "getCohorts"))
getCohorts();
else if (sameString(mode, "getFeatureData"))
getFeatureData();
else if (sameString(mode, "getSuggestions"))
getSuggestions();
else if (sameString(mode, "getClinicalData"))
getClinicalData();
else if (sameString(mode, "getClinicalFeatures"))
getClinicalFeatures();
else if (sameString(mode, "getMostCorrelated"))
getMostCorrelated();
+else if (sameString(mode, "getMostDiff"))
+ getMostDiff();
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;
}