src/hg/instinct/bioInt2/bioIntUI.c 1.3
1.3 2009/03/29 01:40:43 jsanborn
added to UI code
Index: src/hg/instinct/bioInt2/bioIntUI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntUI.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/instinct/bioInt2/bioIntUI.c 27 Mar 2009 21:56:27 -0000 1.2
+++ src/hg/instinct/bioInt2/bioIntUI.c 29 Mar 2009 01:40:43 -0000 1.3
@@ -40,45 +40,26 @@
" bioIntUI\n"
);
}
-/* get a list of the current analyses */
-void getAnalyses()
+/****** BEGIN HELPER FUNCTIONS *******/
+
+struct analyses *getAnalysesById(struct sqlConnection *conn, int analysis_id)
{
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));
+ "select * from %s where id = %d;",
+ AN_TABLE, analysis_id);
-hFreeConn(&conn);
+return analysesLoadByQuery(conn, query);
}
-struct analyses *getAnalysesById(struct sqlConnection *conn, int analysis_id)
+struct analyses *getAnalysesByCohortId(struct sqlConnection *conn, int cohort_id)
{
char query[256];
safef(query, sizeof(query),
- "select * from %s where id = %d;",
- AN_TABLE, analysis_id);
+ "select * from %s where cohort_id = %d;",
+ AN_TABLE, cohort_id);
return analysesLoadByQuery(conn, query);
}
@@ -126,14 +107,69 @@
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);
+}
+
+
+/****** 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 analysis_id = cartUsualInt(cart, bioIntAnalysisId, -1);
-if (analysis_id == -1)
- analysis_id = 0; // hard code for first analysis during testing!
+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)
@@ -152,21 +188,26 @@
hFreeConn(&conn);
errAbort("Could not find analysisFeature in db");
}
-struct analyses *an = getAnalysesById(conn, analysis_id);
-if (!an)
+struct analyses *an, *anList = getAnalysesByCohortId(conn, cohort_id);
+if (!anList)
{
hFreeConn(&conn);
- errAbort("No analysis with id = %d.\n", analysis_id);
+ errAbort("No analyses with cohort_id = %d.\n", cohort_id);
}
char query[512];
-safef(query, sizeof(query),
- "select %s.name, %s.val from %s join %s on %s.sample_id = %s.id "
+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();
struct sqlResult *sr = sqlGetResult(conn, query);
char **row = NULL;
@@ -182,26 +223,65 @@
hFreeConn(&conn);
}
-
-struct datasets *getDatasetsByCohortId(struct sqlConnection *conn, int cohort_id)
+void getClinicalFeatures()
{
-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);
+int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
+if (cohort_id == -1)
+ cohort_id = 1; // hard code for first analysis during testing!
-return datasetsLoadByQuery(conn, query);
-}
+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 = 0; // hard code for first analysis during testing!
+ 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)
@@ -260,8 +340,104 @@
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 = jsonAddContainerList(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 = jsonAddContainerList(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. */
{
@@ -275,8 +451,12 @@
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);