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add hard threshold for GWAS quick search, fix GWAS performance for postgres #154

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add hard threshold for GWAS quick search, fix GWAS performance for postgres #154

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2 changes: 1 addition & 1 deletion ...lugin/grails-app/controllers/com/recomdata/grails/plugin/gwas/GwasSearchController.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,7 @@ class GwasSearchController {
def columnNames = []

def wasShortcut = false
if (!regions && !geneNames && !transcriptGeneNames && analysisIds.size() == 1 && sortField.equals('null') && !cutoff && !search && max > 0) {
if (!regions && !geneNames && !transcriptGeneNames && analysisIds.size() == 1 && sortField.equals('null') && !cutoff && !search && max > 0 && offset < 500) {
println("Triggering shortcut query")
wasShortcut = true
//If displaying no regions and only one analysis, run the alternative query and pull back the rows for the limits
Expand Down
158 changes: 132 additions & 26 deletions ...as-plugin/grails-app/services/com/recomdata/grails/plugin/gwas/RegionSearchService.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ package com.recomdata.grails.plugin.gwas

import de.DeSNPInfo;
import grails.transaction.Transactional
import java.sql.Connection

@Transactional
class RegionSearchService {
Expand Down Expand Up @@ -74,8 +75,9 @@ class RegionSearchService {
def analysisNameSqlQuery = """
SELECT DATA.bio_assay_analysis_id as id, DATA.analysis_name as name
FROM BIOMART.bio_assay_analysis DATA WHERE 1=1
"""
//Query with mad Oracle pagination
"""

//Query in Oracle SQL - GWAS
def gwasSqlQuery = """
SELECT a.*
FROM (SELECT _analysisSelect_ info.chrom AS chrom,
Expand All @@ -91,7 +93,22 @@ class RegionSearchService {
_leftJoinOrNot_ JOIN deapp.de_rc_snp_info info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""
//changed query

//Query in Postgres SQL - GWAS
def gwasPostgresSqlQuery = """
SELECT _analysisSelect_ info.chrom AS chrom,
info.pos AS pos, info.gene_name AS rsgene,
DATA.rs_id AS rsid, DATA.p_value AS pvalue, DATA.p_value_char AS pvalue_char,
DATA.log_p_value AS logpvalue, DATA.ext_data AS extdata,
info.exon_intron as intronexon, info.recombination_rate as recombinationrate, info.regulome_score as regulome,
DATA.beta as beta, DATA.standard_error as standard_error, DATA.EFFECT_ALLELE as effect_allele, DATA.OTHER_ALLELE as other_allele, info.strand as strand
FROM biomart.bio_assay_analysis_gwas DATA
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_rc_snp_info info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""

//Query in Oracle SQL - GWAS HG19
def gwasHg19SqlQuery = """
SELECT a.*
FROM (SELECT _analysisSelect_ info.chrom AS chrom,
Expand All @@ -106,8 +123,23 @@ class RegionSearchService {
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and ( _regionlist_ )
WHERE 1=1

"""
"""

//Query in Postgres SQL - GWAS HG19
def gwasHg19PostgresSqlQuery = """
SELECT _analysisSelect_ info.chrom AS chrom,
info.pos AS pos, info.rsgene AS rsgene,
DATA.rs_id AS rsid, DATA.p_value AS pvalue, DATA.p_value_char AS pvalue_char,
DATA.log_p_value AS logpvalue, DATA.ext_data AS extdata,
info.exon_intron as intronexon, info.recombination_rate as recombinationrate, info.regulome_score as regulome,
DATA.beta as beta, DATA.standard_error as standard_error, DATA.EFFECT_ALLELE as effect_allele, DATA.OTHER_ALLELE as other_allele, info.strand as strand
FROM biomart.bio_assay_analysis_gwas DATA
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and ( _regionlist_ )
WHERE 1=1
"""

//Query in Oracle SQL - EQTL
def eqtlSqlQuery = """
SELECT a.*
FROM (SELECT _analysisSelect_ info.chrom AS chrom,
Expand All @@ -123,6 +155,20 @@ class RegionSearchService {
WHERE 1=1
"""

//Query in Postgres SQL - EQTL
def eqtlPostgresSqlQuery = """
SELECT _analysisSelect_ info.chrom AS chrom,
info.pos AS pos, info.gene_name AS rsgene,
DATA.rs_id AS rsid, DATA.p_value AS pvalue, DATA.p_value_char AS pvalue_char,
DATA.log_p_value AS logpvalue, DATA.ext_data AS extdata, DATA.gene as gene,
info.exon_intron as intronexon, info.recombination_rate as recombinationrate, info.regulome_score as regulome, info.strand as strand,
FROM biomart.bio_assay_analysis_eqtl DATA
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_rc_snp_info info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""

//Query in Oracle SQL - EQTL HG19
def eqtlHg19SqlQuery = """
SELECT a.*
FROM (SELECT _analysisSelect_ info.chrom AS chrom,
Expand All @@ -136,7 +182,20 @@ class RegionSearchService {
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""
"""

//Query in Postgres SQL - EQTL HG19
def eqtlHg19PostgresSqlQuery = """
SELECT _analysisSelect_ info.chrom AS chrom,
info.pos AS pos, info.rsgene AS rsgene,
DATA.rs_id AS rsid, DATA.p_value AS pvalue, DATA.p_value_char AS pvalue_char,
DATA.log_p_value AS logpvalue, DATA.ext_data AS extdata, DATA.gene as gene,
info.exon_intron as intronexon, info.recombination_rate as recombinationrate, info.regulome_score as regulome, info.strand as strand,
FROM biomart.bio_assay_analysis_eqtl DATA
_analysisJoin_
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""

def gwasSqlCountQuery = """
SELECT COUNT(*) AS TOTAL FROM biomart.Bio_Assay_Analysis_Gwas data
Expand All @@ -148,17 +207,20 @@ class RegionSearchService {
SELECT COUNT(*) AS TOTAL FROM biomart.Bio_Assay_Analysis_Gwas data
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""
"""

def eqtlSqlCountQuery = """
SELECT COUNT(*) AS TOTAL FROM biomart.Bio_Assay_Analysis_Eqtl data
_leftJoinOrNot_ JOIN deapp.de_rc_snp_info info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""

def eqtlHg19SqlCountQuery = """
SELECT COUNT(*) AS TOTAL FROM biomart.Bio_Assay_Analysis_Eqtl data
_leftJoinOrNot_ JOIN deapp.de_snp_info_hg19_mv info ON DATA.rs_id = info.rs_id and (_regionlist_)
WHERE 1=1
"""
"""

def getGeneLimits(Long searchId, String ver, Long flankingRegion) {
//Create objects we use to form JDBC connection.
def con, stmt, rs = null;
Expand Down Expand Up @@ -260,6 +322,10 @@ class RegionSearchService {

def con, stmt, rs = null;
con = dataSource.getConnection()

// Getting the DB type
def dbType = con.getMetaData().getDatabaseProductName()

StringBuilder queryCriteria = new StringBuilder();
def analysisQuery
def countQuery
Expand All @@ -285,10 +351,23 @@ class RegionSearchService {
}

if (type.equals("gwas")) {
analysisQuery = gwasSqlQuery

// Insert branching logic on dbType
if (dbType.equals('PostgreSQL')) {
analysisQuery = gwasPostgresSqlQuery
} else {
analysisQuery = gwasSqlQuery
}

countQuery = gwasSqlCountQuery

if(hg19only){ // for hg19, special query
analysisQuery = gwasHg19SqlQuery;

if (dbType.equals('PostgreSQL')) {
analysisQuery = gwasHg19PostgresSqlQuery
} else {
analysisQuery = gwasHg19SqlQuery
}
countQuery = gwasHg19SqlCountQuery
}
if (!search && !ranges && !geneNames && !transcriptGeneNames ){
Expand All @@ -301,10 +380,23 @@ class RegionSearchService {
}
}
else if (type.equals("eqtl")) {
analysisQuery = eqtlSqlQuery

if (dbType.equals('PostgreSQL')) {
analysisQuery = eqtlPostgresSqlQuery
} else {
analysisQuery = eqtlSqlQuery
}

countQuery = eqtlSqlCountQuery

if(hg19only){
analysisQuery = eqtlHg19SqlQuery

if (dbType.equals('PostgreSQL')) {
analysisQuery = eqtlHg19PostgresSqlQuery
} else {
analysisQuery = eqtlHg19SqlQuery
}

countQuery = eqtlHg19SqlCountQuery
}
if (!search && !ranges && !geneNames && !transcriptGeneNames ){
Expand Down Expand Up @@ -429,7 +521,12 @@ class RegionSearchService {
}else{
queryCriteria.append(" OR info.gene_name LIKE '%${search}%'");
}
queryCriteria.append(" OR info.pos LIKE '%${search}%'")

if (dbType.equals('PostgreSQL')) {
queryCriteria.append(" OR cast(info.pos as character(50)) LIKE '%${search}%'")
} else {
queryCriteria.append(" OR info.pos LIKE '%${search}%'")
}
queryCriteria.append(" OR info.chrom LIKE '%${search}%'")
if (type.equals("eqtl")) {
queryCriteria.append(" OR data.gene LIKE '%${search}%'")
Expand Down Expand Up @@ -463,32 +560,41 @@ class RegionSearchService {

def results = []
def total = 0
def finalQuery
try {
// analysis name query
def nameQuery = analysisNameQuery + analysisQCriteria.toString();
def nameQuery = analysisNameQuery + analysisQCriteria.toString()
stmt = con.prepareStatement(nameQuery)

rs = stmt.executeQuery();
rs = stmt.executeQuery()
while (rs.next()) {
analysisNameMap.put(rs.getLong("id"), rs.getString("name"));
analysisNameMap.put(rs.getLong("id"), rs.getString("name"))
}

//println(analysisNameMap)
// data query
def finalQuery = analysisQuery + queryCriteria.toString() + "\n) a";
if (limit > 0) {
finalQuery += " where a.row_nbr between ${offset + 1} and ${offset + limit}";
// Modifying the final DB query based on DB type
if (dbType.equals('PostgreSQL')) {
finalQuery = analysisQuery + queryCriteria.toString() + "\n "

if (limit > 0) {
finalQuery += " order by data.rs_id asc offset " + offset + " limit " + limit
}
} else {
finalQuery = analysisQuery + queryCriteria.toString() + "\n) a"

if (limit > 0) {
finalQuery += " where a.row_nbr between ${offset + 1} and ${offset + limit}"
}
}

stmt = con.prepareStatement(finalQuery);
stmt = con.prepareStatement(finalQuery)

//stmt.setString(1, sortField)
if (cutoff) {
stmt.setDouble(1, cutoff);
stmt.setDouble(1, cutoff)
}
log.debug("Executing: " + finalQuery)

rs = stmt.executeQuery();
rs = stmt.executeQuery()
while (rs.next()) {
if ((type.equals("gwas"))) {
results.push([rs.getString("rsid"), rs.getString("pvalue_char"), rs.getDouble("logpvalue"), rs.getString("extdata"), analysisNameMap.get(rs.getLong("analysis_id")), rs.getString("rsgene"), rs.getString("chrom"), rs.getLong("pos"), rs.getString("intronexon"), rs.getString("recombinationrate"), rs.getString("regulome"), rs.getString("beta"), rs.getString("standard_error"), rs.getString("effect_allele"), rs.getString("other_allele"), rs.getString("strand")]);
Expand Down Expand Up @@ -547,6 +653,7 @@ class RegionSearchService {

def con, stmt, rs = null;
con = dataSource.getConnection()

StringBuilder queryCriteria = new StringBuilder();
def quickQuery

Expand Down Expand Up @@ -588,5 +695,4 @@ class RegionSearchService {
return [results: results]

}

}
}