Merge branch 'gitlab/f.guitton'

grails-app/services/PlinkService.groovy

@@ -67,7 +67,7 @@ class PlinkService {
 						select a.platform_name, a.trial_name 
 						from DE_SUBJECT_SNP_DATASET a
 						INNER JOIN de_subject_sample_mapping c on c.omic_patient_id=a.patient_num
-						INNER JOIN (SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = ? AND patient_num IN 
+						INNER JOIN (SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = CAST(? AS numeric) AND patient_num IN
 						            (SELECT patient_num FROM patient_dimension WHERE sourcesystem_cd NOT LIKE '%:S:%')) b on c.patient_id=b.patient_num
 						where rownum=1 
 						and a.platform_name is not null

grails-app/services/PostgresI2b2HelperService.groovy

@@ -301,7 +301,7 @@ class PostgresI2b2HelperService {
 
 		String sqlt="SELECT NVAL_NUM FROM OBSERVATION_FACT f WHERE CONCEPT_CD = '" +
 				concept_cd + "' AND PATIENT_NUM IN (select distinct patient_num " +
-				"from qt_patient_set_collection where result_instance_id = " + result_instance_id + ")";
+				"from qt_patient_set_collection where result_instance_id = CAST(" + result_instance_id + " AS numeric))";
 
 		log.debug("executing query: sqlt=" + sqlt);
 		try {
@@ -904,10 +904,10 @@ class PostgresI2b2HelperService {
 						from qt_patient_set_collection q
 						inner join patient_trial p
 						on q.patient_num=p.patient_num
-						where q.result_instance_id=""";
+						where q.result_instance_id=CAST(""";
 
-		String sqlTemplate2 = """ or result_instance_id=""";
-		String sqlTemplate3 = """) and x.parent_cd=""";
+		String sqlTemplate2 = """ AS numeric) or result_instance_id=CAST(""";
+		String sqlTemplate3 = """ AS numeric)) and x.parent_cd=""";
 
 
 

grails-app/services/com/recomdata/transmart/data/export/AdditionalDataService.groovy

@@ -44,7 +44,7 @@ class AdditionalDataService {
 				  select distinct s.sample_cd from de_subject_sample_mapping s
 				  where s.trial_name in ${studies} and patient_id in (
 					SELECT DISTINCT sc.patient_num FROM qt_patient_set_collection sc, patient_dimension pd
-					WHERE sc.result_instance_id = ? AND sc.patient_num = pd.patient_num
+					WHERE sc.result_instance_id = CAST(? AS numeric) AND sc.patient_num = pd.patient_num
 				  ) and s.sample_cd is not null and b.file_name like s.sample_cd||'%'
 				)
 				"""

grails-app/services/com/recomdata/transmart/data/export/ClinicalDataService.groovy

@@ -113,7 +113,7 @@ class ClinicalDataService {
 				sqlQuery <<= "LEFT JOIN DEAPP.DE_SUBJECT_SAMPLE_MAPPING ssm ON ssm.PATIENT_ID = ofa.PATIENT_NUM  "
 			}
 
-			sqlQuery <<= "WHERE qt.RESULT_INSTANCE_ID = ? AND ofa.MODIFIER_CD = ?"
+			sqlQuery <<= "WHERE qt.RESULT_INSTANCE_ID = CAST(? AS numeric) AND ofa.MODIFIER_CD = ?"
 
 			if (!retrievalTypeMRNAExists && parFilterHighLevelConcepts) {
 				sqlQuery <<= " AND cd.concept_cd NOT IN (SELECT DISTINCT NVL(sample_type_cd,'-1') as gene_expr_concept"
@@ -432,7 +432,7 @@ class ClinicalDataService {
 		queryToReturn <<= "INNER JOIN DE_XTRIAL_CHILD_MAP XMAP ON XMAP.CONCEPT_CD = ofa.CONCEPT_CD "
 		queryToReturn <<= "INNER JOIN CONCEPT_DIMENSION C1 ON C1.CONCEPT_CD = XMAP.CONCEPT_CD "
 		queryToReturn <<= "INNER JOIN CONCEPT_DIMENSION C2 ON C2.CONCEPT_CD = XMAP.PARENT_CD "
-		queryToReturn <<= "WHERE	qt.RESULT_INSTANCE_ID = ? "
+		queryToReturn <<= "WHERE	qt.RESULT_INSTANCE_ID = CAST(? AS numeric) "
 		queryToReturn <<= "AND		ofa.MODIFIER_CD = ? "
 		queryToReturn <<= "AND		ofa.CONCEPT_CD IN "
 		queryToReturn <<= "( "

grails-app/services/com/recomdata/transmart/data/export/DataCountService.groovy

@@ -47,7 +47,7 @@ class DataCountService {
 		StringBuilder subjectsFromBothSubsetsQuery = new StringBuilder()
 		StringBuilder gseaQuery = new StringBuilder()
 
-		subjectsQuery.append("SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = ?")
+		subjectsQuery.append("SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = CAST(? AS numeric)")
 		.append(" AND patient_num IN (select patient_num from patient_dimension where sourcesystem_cd not like '%:S:%')")
 		subjectsFromBothSubsetsQuery.append("SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id IN (")
 		.append(resultInstanceIds).append(')')

grails-app/services/com/recomdata/transmart/data/export/I2b2ExportHelperService.groovy

@@ -31,7 +31,7 @@ def  findStudyAccessions( result_instance_ids){
 		def rids = []
 		for(r in result_instance_ids){
 			if(r?.trim()?.length()>0 ){
-				rids.add(r);
+				rids.add('CAST('+ r + ' AS numeric)');
 			}
 		}
 

grails-app/services/com/recomdata/transmart/data/export/MetadataService.groovy

@@ -215,7 +215,7 @@ class MetadataService {
 				  select distinct s.sample_cd from de_subject_sample_mapping s
 				  where s.trial_name = ? and patient_id in (
 					SELECT DISTINCT sc.patient_num FROM qt_patient_set_collection sc, patient_dimension pd
-					WHERE sc.result_instance_id = ? AND sc.patient_num = pd.patient_num
+					WHERE sc.result_instance_id = CAST(? AS numeric) AND sc.patient_num = pd.patient_num
 				  ) and s.sample_cd is not null and b.file_name like s.sample_cd||'%'
 				)
 			"""

grails-app/services/com/recomdata/transmart/data/export/PostgresClinicalDataService.groovy

@@ -113,7 +113,7 @@ class PostgresClinicalDataService {
 				sqlQuery <<= "LEFT JOIN DE_SUBJECT_SAMPLE_MAPPING ssm ON ssm.PATIENT_ID = ofa.PATIENT_NUM  "
 			}
 
-			sqlQuery <<= "WHERE qt.RESULT_INSTANCE_ID = ? AND ofa.MODIFIER_CD = ?"
+			sqlQuery <<= "WHERE qt.RESULT_INSTANCE_ID = CAST(? AS numeric) AND ofa.MODIFIER_CD = ?"
 
 			if (!retrievalTypeMRNAExists && parFilterHighLevelConcepts) {
 				sqlQuery <<= " AND cd.concept_cd NOT IN (SELECT DISTINCT coalesce(sample_type_cd,'-1') as gene_expr_concept"
@@ -436,7 +436,7 @@ class PostgresClinicalDataService {
 		queryToReturn <<= "INNER JOIN DE_XTRIAL_CHILD_MAP XMAP ON XMAP.CONCEPT_CD = ofa.CONCEPT_CD "
 		queryToReturn <<= "INNER JOIN CONCEPT_DIMENSION C1 ON C1.CONCEPT_CD = XMAP.CONCEPT_CD "
 		queryToReturn <<= "INNER JOIN CONCEPT_DIMENSION C2 ON C2.CONCEPT_CD = XMAP.PARENT_CD "
-		queryToReturn <<= "WHERE	qt.RESULT_INSTANCE_ID = ? "
+		queryToReturn <<= "WHERE	qt.RESULT_INSTANCE_ID = CAST(? AS numeric) "
 		queryToReturn <<= "AND		ofa.MODIFIER_CD = ? "
 		queryToReturn <<= "AND		ofa.CONCEPT_CD IN "
 		queryToReturn <<= "( "

grails-app/services/com/recomdata/transmart/data/export/PostgresDataCountService.groovy

@@ -48,7 +48,7 @@ class PostgresDataCountService {
 		StringBuilder gseaQuery = new StringBuilder()
 
 		subjectsQuery.append("select omic_patient_id from de_subject_sample_mapping where patient_id in ")
-		subjectsQuery.append("(SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = ?")
+		subjectsQuery.append("(SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = CAST(? AS numeric)")
 		.append(" AND patient_num IN (select patient_num from patient_dimension where sourcesystem_cd not like '%:S:%'))")
 
 		subjectsFromBothSubsetsQuery.append("SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id IN (")

grails-app/services/com/recomdata/transmart/data/export/PostgresExportService.groovy

@@ -74,9 +74,9 @@ class PostgresExportService {
 		def rID1 = RequestValidator.nullCheck(params.result_instance_id1)
 		def rID2 = RequestValidator.nullCheck(params.result_instance_id2)
 		def rIDs = null
-		if (rID1 && rID1?.trim() != '' && rID2 && rID2?.trim() != '') rIDs = rID1 + ',' + rID2
-		else if (rID1 && rID1?.trim() != '') rIDs = rID1
-		else if (rID2 && rID2?.trim() != '') rIDs = rID2
+		if (rID1 && rID1?.trim() != '' && rID2 && rID2?.trim() != '') rIDs = 'CAST(' + rID1 + ' AS numeric), CAST(' + rID2 + 'AS numeric)'
+		else if (rID1 && rID1?.trim() != '') rIDs = 'CAST(' + rID1 + ' AS numeric)'
+		else if (rID2 && rID2?.trim() != '') rIDs = 'CAST(' + rID2 + ' AS numeric)'
 
 		def subsetLen = (rID1 && rID2) ? 2 : (rID1 || rID2) ? 1 : 0
 		log.debug('rID1 :: ' + rID1 + ' :: rID2 :: ' + rID2)

grails-app/services/com/recomdata/transmart/data/export/PostgresGeneExpressionDataService.groovy

@@ -118,7 +118,7 @@ class PostgresGeneExpressionDataService {
 			ssm.GPL_ID
 		FROM
 		de_subject_sample_mapping ssm
-		INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id = ? AND ssm.patient_id = sc.patient_num
+		INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id = CAST(? AS numeric) AND ssm.patient_id = sc.patient_num
 
 		""");
 		sQuery.append(" WHERE ssm.trial_name = '").append(study).append("' ")
@@ -184,7 +184,7 @@ class PostgresGeneExpressionDataService {
 	   FROM de_subject_microarray_data a
 			   INNER JOIN de_mrna_annotation b ON a.probeset_id = b.probeset_id
 			   INNER JOIN de_subject_sample_mapping ssm ON ssm.assay_id = A.assay_id
-			   INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id = ? AND ssm.PATIENT_ID = sc.patient_num
+			   INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id = CAST(? AS numeric) AND ssm.PATIENT_ID = sc.patient_num
 	   		   INNER JOIN PATIENT_DIMENSION pd on ssm.patient_id = pd.patient_num
 	   """)
 
@@ -302,7 +302,7 @@ class PostgresGeneExpressionDataService {
 		assayS.append("""	SELECT DISTINCT s.assay_id 
 							FROM 	de_subject_sample_mapping s,
 									qt_patient_set_collection qt 
-							WHERE qt.patient_num = s.patient_id AND qt.result_instance_id = ? """);
+							WHERE qt.patient_num = s.patient_id AND qt.result_instance_id = CAST(? AS numeric) """);
 
 
 		//If we have a sample type, append it to the query.
@@ -879,11 +879,11 @@ class PostgresGeneExpressionDataService {
 							SELECT DISTINCT ssm.patient_id FROM de_subject_sample_mapping ssm 
 							INNER JOIN (SELECT DISTINCT patient_num 
 							            FROM qt_patient_set_collection
-							            WHERE result_instance_id = ?
+							            WHERE result_instance_id = CAST(? AS numeric)
 							            INTERSECT
 							            SELECT DISTINCT patient_num 
 							            FROM qt_patient_set_collection
-							            WHERE result_instance_id = ?) sc ON ssm.patient_id = sc.patient_num
+							            WHERE result_instance_id = CAST(? AS numeric)) sc ON ssm.patient_id = sc.patient_num
 							"""
 			groovy.sql.Sql sql = new groovy.sql.Sql(dataSource)
 			def queryParams = []
@@ -1056,7 +1056,7 @@ class PostgresGeneExpressionDataService {
 	   def str = new StringBuffer()
 	   def mapValues = resultInstanceIdMap.values()
 	   mapValues.each { val ->
-		   if (val && ((String)val)?.trim() != '') str.append(val).append(',')
+		   if (val && ((String)val)?.trim() != '') str.append('CAST(').append(val).append(' AS numeric),')
 	   }
 	   str.delete(str.length()-1, str.length())
 

grails-app/services/com/recomdata/transmart/data/export/PostgresSnpDataService.groovy

@@ -83,7 +83,7 @@ class PostgresSnpDataService {
 						WHERE platform = 'SNP' and patient_id in (
 							SELECT DISTINCT patient_num 
 							FROM qt_patient_set_collection 
-							WHERE result_instance_id = ?)
+							WHERE result_instance_id = CAST(? AS numeric))
 					"""
 		def patientDataMap = [:]
 		sql.eachRow(query, [resultInstanceId]) { row ->
@@ -194,7 +194,7 @@ class PostgresSnpDataService {
 		INNER JOIN de_subject_sample_mapping dssm on ssd.patient_num=dssm.omic_patient_id
 		WHERE dssm.patient_id IN (SELECT DISTINCT patient_num
 							FROM qt_patient_set_collection 
-							WHERE result_instance_id = ?)"""
+							WHERE result_instance_id = CAST(? AS numeric))"""
 
 		def firstRow = sql.firstRow(platformQuery, [resultInstanceId])
 		def platformName = firstRow.title
@@ -419,7 +419,7 @@ class PostgresSnpDataService {
 			FROM bio_content b
 			WHERE b.study_name in ${studies}
 			AND b.file_name IN (SELECT DISTINCT sg.gsm_num FROM de_snp_calls_by_gsm sg WHERE sg.patient_num IN (
-			    SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = ?
+			    SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = CAST(? AS numeric)
 					 AND patient_num IN (SELECT patient_num FROM patient_dimension WHERE sourcesystem_cd NOT LIKE '%:S:%')))
 		"""
 
@@ -473,7 +473,7 @@ class PostgresSnpDataService {
 		//This from statement needs to be in all selects.
 		sTables.append(""" 	FROM DE_SUBJECT_SAMPLE_MAPPING DSM
 							INNER JOIN patient_dimension PD ON DSM.patient_id = PD.patient_num 
-							INNER JOIN qt_patient_set_collection qt ON qt.result_instance_id = ? AND qt.PATIENT_NUM = DSM.PATIENT_ID
+							INNER JOIN qt_patient_set_collection qt ON qt.result_instance_id = CAST(? AS numeric) AND qt.PATIENT_NUM = DSM.PATIENT_ID
 							LEFT JOIN DE_SNP_CALLS_BY_GSM SNP_GENO ON DSM.OMIC_PATIENT_ID = SNP_GENO.PATIENT_NUM AND DSM.SAMPLE_CD = SNP_GENO.GSM_NUM
 							LEFT JOIN DE_SNP_COPY_NUMBER SNP_COPY ON DSM.OMIC_PATIENT_ID = SNP_COPY.PATIENT_NUM AND SNP_GENO.snp_name = SNP_COPY.snp_name
 							INNER JOIN DE_SNP_GENE_MAP D2 ON D2.SNP_NAME = SNP_GENO.SNP_NAME

grails-app/services/com/recomdata/transmart/data/export/SnpDataService.groovy

@@ -83,7 +83,7 @@ class SnpDataService {
 						WHERE platform = 'SNP' and patient_id in (
 							SELECT DISTINCT patient_num 
 							FROM qt_patient_set_collection 
-							WHERE result_instance_id = ?)
+							WHERE result_instance_id = CAST(? AS numeric))
 					"""
 		def patientDataMap = [:]
 		sql.eachRow(query, [resultInstanceId]) { row ->
@@ -194,7 +194,7 @@ class SnpDataService {
 		INNER JOIN de_subject_sample_mapping dssm on ssd.patient_num=dssm.omic_patient_id
 		WHERE dssm.patient_id IN (SELECT DISTINCT patient_num
 							FROM qt_patient_set_collection 
-							WHERE result_instance_id = ?)"""
+							WHERE result_instance_id = CAST(? AS numeric))"""
 
 		def firstRow = sql.firstRow(platformQuery, [resultInstanceId])
 		def platformName = firstRow.title
@@ -419,7 +419,7 @@ class SnpDataService {
 			FROM bio_content b
 			WHERE b.study_name in ${studies}
 			AND b.file_name IN (SELECT DISTINCT sg.gsm_num FROM de_snp_calls_by_gsm sg WHERE sg.patient_num IN (
-			    SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = ?
+			    SELECT DISTINCT patient_num FROM qt_patient_set_collection WHERE result_instance_id = CAST(? AS numeric)
 					 AND patient_num IN (SELECT patient_num FROM patient_dimension WHERE sourcesystem_cd NOT LIKE '%:S:%')))
 		"""
 
@@ -473,7 +473,7 @@ class SnpDataService {
 		//This from statement needs to be in all selects.
 		sTables.append(""" 	FROM DE_SUBJECT_SAMPLE_MAPPING DSM
 							INNER JOIN patient_dimension PD ON DSM.patient_id = PD.patient_num 
-							INNER JOIN qt_patient_set_collection qt ON qt.result_instance_id = ? AND qt.PATIENT_NUM = DSM.PATIENT_ID
+							INNER JOIN qt_patient_set_collection qt ON qt.result_instance_id = CAST(? AS numeric) AND qt.PATIENT_NUM = DSM.PATIENT_ID
 							INNER JOIN DE_SAMPLE_SNP_DATA SNP ON DSM.SAMPLE_CD = SNP.SAMPLE_ID
 							INNER JOIN DE_SNP_GENE_MAP D2 ON D2.SNP_NAME = SNP.SNP_NAME
 							INNER JOIN bio_marker bm ON bm.PRIMARY_EXTERNAL_ID = to_char(D2.ENTREZ_GENE_ID)

grails-app/services/com/recomdata/transmart/data/export/VcfDataService.groovy

@@ -370,10 +370,10 @@ class VcfDataService {
 """;
 		def param = []
 		if(resultInstanceId1!=null){
-			param.add(resultInstanceId1)
+			param.add('CAST(' + resultInstanceId1 + '? AS numeric)')
 		}
 		if(resultInstanceId2!=null){
-			param.add(resultInstanceId2)
+			param.add('CAST(' + resultInstanceId2 + '? AS numeric)')
 		}
 
 		groovy.sql.Sql sql = new groovy.sql.Sql(dataSource);
@@ -399,7 +399,7 @@ class VcfDataService {
 		def q  =
 """				SELECT distinct a.DATASET_ID, a.SUBJECT_ID, a.POSITION from DE_VARIANT_SUBJECT_IDX a
 		INNER JOIN de_subject_sample_mapping b on a.SUBJECT_ID = b.SUBJECT_ID 
-		INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id in (?) AND b.patient_id = sc.patient_num
+		INNER JOIN qt_patient_set_collection sc ON sc.result_instance_id in (CAST(? AS numeric)) AND b.patient_id = sc.patient_num
  ORDER BY a.POSITION"""
 		groovy.sql.Sql sql = new groovy.sql.Sql(dataSource);
 		def datasetIdxMap =[:]

src/groovy/com/recomdata/gex/GexDao.groovy

@@ -135,7 +135,7 @@ public class GexDao {
 				INNER JOIN search_keyword sk ON sk.bio_data_id = sbm.bio_marker_id
 				INNER JOIN de_subject_sample_mapping ssm ON (ssm.trial_name = A.trial_name AND ssm.assay_id = A.assay_id)
 				INNER JOIN (SELECT DISTINCT sc.patient_num FROM qt_patient_set_collection sc, patient_dimension pd
-		 		WHERE sc.result_instance_id = ? AND pd.sourcesystem_cd NOT LIKE '%:S:%'
+		 		WHERE sc.result_instance_id = CAST(? AS numeric) AND pd.sourcesystem_cd NOT LIKE '%:S:%'
 		 		AND sc.patient_num = pd.patient_num) sub ON ssm.patient_id = sub.patient_num
 				""");
 		//TODO replace study within query as parameter to query
@@ -190,7 +190,7 @@ public class GexDao {
 		//SQL Query string.
 		StringBuilder assayS = new StringBuilder("select distinct s.assay_id  from de_subject_sample_mapping s");
 		assayS.append(", (SELECT DISTINCT sc.patient_num FROM qt_patient_set_collection sc, patient_dimension pd")
-		.append(" WHERE sc.result_instance_id = ? AND pd.sourcesystem_cd NOT LIKE '%:S:%'")
+		.append(" WHERE sc.result_instance_id = CAST(? AS numeric) AND pd.sourcesystem_cd NOT LIKE '%:S:%'")
 		.append(" AND sc.patient_num = pd.patient_num) A where s.patient_id = A.patient_num");
 
 		//If we have a sample type, append it to the query.