src/hg/instinct/bioInt2/bioIntUI.c 1.17
1.17 2009/04/27 06:15:48 jsanborn
updated lots of stuff, will break older implementation of database
Index: src/hg/instinct/bioInt2/bioIntUI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntUI.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 1000000 -r1.16 -r1.17
--- src/hg/instinct/bioInt2/bioIntUI.c 16 Apr 2009 19:53:55 -0000 1.16
+++ src/hg/instinct/bioInt2/bioIntUI.c 27 Apr 2009 06:15:48 -0000 1.17
@@ -1,976 +1,974 @@
/* 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)
+struct genesets *getGenesetByName(struct sqlConnection *conn, char *name)
{
char query[256];
safef(query, sizeof(query),
"select * from %s where name = \"%s\" ",
- PA_TABLE, name);
+ GE_TABLE, name);
-return pathwaysLoadByQuery(conn, query);
+return genesetsLoadByQuery(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");
+name = getFieldFromKgXref(conn, af->feature_name, "geneSymbol");
if (name)
source = "UCSC";
else
{
- struct pathways *pa = getPathwayByName(conn, af->feature_name);
- if (!pa)
+ struct genesets *gs = getGenesetByName(conn, af->feature_name);
+ if (!gs)
return;
- name = pa->name;
- source = pa->source;
+ name = gs->name;
+ source = gs->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;
+ char *type;
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%%\" "
+ "select feature_name,type 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];
+ char *type = row[1];
AllocVar(sp);
sp->name = cloneString(name);
- sp->source = cloneString("gene/geneset");
+ sp->type = cloneString(type);
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->type = 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);
+ jsonAddString(js, sp->name, sp->type);
}
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 "
+ "select DISTINCT %s.name, %s.conf 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.
{
jsonAddString(data, name, code);
if (hashLookup(codeHash, code))
continue;
sd = slDoubleNew(val);
hashAdd(codeHash, code, sd);
}
else
jsonAddDouble(data, name, val);
}
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_names, char *sources,
struct datasets *daList)
{
struct slName *s, *sList = slNameListFromComma(sources);
struct slName *f, *fList = slNameListFromComma(feature_names);
if (slCount(sList) != slCount(fList))
errAbort("source list length not equal to feature list length\n");
for (s = sList, f = fList; s && f; s = s->next, f = f->next)
{
struct json *container = jsonAddContainer(js, f->name);
- if (sameString(s->name, "gene/geneset"))
+ if (sameString(s->name, "gene") || sameString(s->name, "geneset"))
sendAnalysisFeatureData(conn, container, cohort_id, f->name);
else if (sameString(s->name, "clinical"))
sendClinicalData(conn, container, cohort_id, f->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);
}
void expandFeature()
{
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=getGenesInGeneset\n", bioIntFeatureName);
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 analyses *an, *anList = getAnalysesByCohortId(conn, cohort_id);
if (!anList)
{
hFreeConn(&conn);
errAbort("No analyses with cohort_id = %d.\n", cohort_id);
}
char tmpQ[512];
for (an = anList; an; an = an->next)
{
safef(tmpQ, sizeof(tmpQ),
"select * from %s where feature_id = %d;",
an->result_table, af->id);
if (sqlExists(conn, tmpQ))
break;
}
if (!an)
{
hFreeConn(&conn);
errAbort("No analysis feature with id=%d in any analysis table in cohort with id = %d",
af->id, cohort_id);
}
// input_tables may have comma-separated list of raw datasets
// we don't want to expand into those yet.
char *input_tables = an->input_tables;
-
if (!sqlTableExists(conn, input_tables))
{
hFreeConn(&conn);
errAbort("Table does not exist, %s.\n", input_tables);
}
-/***
-select DISTINCT analysisFeatures.id from pathways join pathwayGenes on pathways.id=pathwayGenes.id join geneLookup on geneLookup.id=pathwayGenes.gene_id join kgXref on kgXref.kgID=geneLookup.kgId join analysisFeatures on analysisFeatures.feature_name=kgXref.geneSymbol where pathways.id=123;
-***/
uglyTime(NULL);
struct dyString *dy = newDyString(100);
dyStringPrintf(dy,
- "select DISTINCT %s.id from %s join %s on %s.id=%s.id "
- "join %s on %s.id=%s.gene_id join %s on %s.kgID=%s.kgId "
- "join %s on %s.feature_name=%s.geneSymbol where %s.name=\"%s\";",
- AF_TABLE, PA_TABLE, PG_TABLE, PA_TABLE, PG_TABLE,
- GL_TABLE, GL_TABLE, PG_TABLE, KX_TABLE, KX_TABLE, GL_TABLE,
- AF_TABLE, AF_TABLE, KX_TABLE, PA_TABLE, af->feature_name);
+ "select DISTINCT gene_id from %s where id = %d",
+ GG_TABLE, af->id);
char *query = dyStringCannibalize(&dy);
struct slInt *si, *siList = sqlQuickNumList(conn, query);
dy = newDyString(100);
dyStringPrintf(dy,
- "select %s.feature_name from %s join %s on feature_id=%s.id where feature_id in (",
- AF_TABLE, input_tables, AF_TABLE, AF_TABLE);
+ "select feature_name, type, sum(abs(conf)) as s from %s "
+ "join %s on feature_id=id where feature_id in (",
+ AF_TABLE, input_tables);
for (si = siList; si; si = si->next)
{
dyStringPrintf(dy, "%d", si->val);
if (si->next)
dyStringPrintf(dy, ",");
}
dyStringPrintf(dy,
- ") group by feature_id order by sum(abs(val)) DESC limit %d;",
+ ") group by feature_id order by s DESC limit %d;",
takeTop);
query = dyStringCannibalize(&dy);
-struct slName *sl, *fList = sqlQuickList(conn, query);
-struct slName *sList = NULL;
-// Only dealing with gene/genesets now
-for (sl = fList; sl; sl = sl->next)
- slNameAddHead(&sList, "gene/geneset");
+struct slName *fList = NULL, *tList = NULL;
+struct sqlResult *sr = sqlGetResult(conn, query);
+char **row = NULL;
+while ((row = sqlNextRow(sr)) != NULL)
+ {
+ char *name = row[0];
+ char *type = row[1];
+ slNameAddHead(&fList, name);
+ slNameAddHead(&tList, type);
+ }
+slReverse(&fList);
+slReverse(&tList);
char *feature_names = slNameListToString(fList, ',');
-char *sources = slNameListToString(sList, ',');
+char *types = slNameListToString(tList, ',');
struct json *js = newJson();
-sendUniqueMatch(conn, js, cohort_id, feature_names, sources, NULL);
+sendUniqueMatch(conn, js, cohort_id, feature_names, types, NULL);
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, "expandFeature"))
expandFeature();
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;
}