fix bug with apostrophes in the search terms

ncats · Mar 31, 2021 · d611ccf · d611ccf
1 parent c036516
commit d611ccf
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Showing 6 changed files with 7 additions and 7 deletions.
diff --git a/src/TCRD.js b/src/TCRD.js
@@ -866,7 +866,7 @@ and f.itype = ?`, [filter.order]));
             for (var i in args.filter.facets) {
                 let f = args.filter.facets[i];
                 if ('type' == f.facet) {
-                    q.whereRaw(`ppitypes REGEXP '${f.values.join("|")}'`);
+                    q.whereRaw(`ppitypes REGEXP "${f.values.join('|')}"`);
                 } else {
                     q = q.whereIn(f.facet, f.values);
                 }

diff --git a/src/models/FieldInfo.ts b/src/models/FieldInfo.ts
@@ -138,7 +138,7 @@ export class FieldInfo {
             }
         } else {
             if (this.valuesDelimited) {
-                query.where(this.parent.database.raw(`${this.select} REGEXP '${this.allowedValues.join('|')}'`));
+                query.where(this.parent.database.raw(`${this.select} REGEXP "${this.allowedValues.join('|')}"`));
             } else {
                 query.whereIn(this.parent.database.raw(this.select), this.allowedValues);
             }

diff --git a/src/models/disease/diseaseList.ts b/src/models/disease/diseaseList.ts
@@ -18,7 +18,7 @@ export class DiseaseList extends DataModelList {
     static getDescendentsQuery(knex: any, diseaseName: string) {
         let finderQuery = knex("ncats_do")
             .min({lft: 'lft', rght: 'rght'})
-            .whereRaw(`name = "?"`, diseaseName);
+            .whereRaw(`name = ?`, diseaseName);
         let query = knex({lst: 'ncats_do', finder: finderQuery})
             .select('lst.name')
             .where('finder.lft', '<=', knex.raw('lst.lft'))
@@ -110,7 +110,7 @@ export class DiseaseList extends DataModelList {
     getAssociatedTargetQuery(): any {
         return this.database({ncats_disease: 'ncats_disease', ncats_d2da: 'ncats_d2da', disease: 'disease', protein: 'protein'})
             .distinct({name: this.keyString()}).count('* as associationCount')
-            .whereRaw(this.database.raw(`match(uniprot,sym,stringid) against('${this.associatedTarget}' in boolean mode)`))
+            .whereRaw(this.database.raw(`match(uniprot,sym,stringid) against("${this.associatedTarget}" in boolean mode)`))
             .andWhere('ncats_disease.id', this.database.raw('ncats_d2da.ncats_disease_id'))
             .andWhere('ncats_d2da.disease_assoc_id', this.database.raw('disease.id'))
             .andWhere('disease.protein_id', this.database.raw(`protein.id`))

diff --git a/src/models/ligand/ligandList.ts b/src/models/ligand/ligandList.ts
@@ -58,7 +58,7 @@ export class LigandList extends DataModelList {
                     protein: "protein"
                 })
                     .distinct("ncats_ligands.identifier")
-                    .whereRaw(this.database.raw(`match(uniprot,sym,stringid) against('${this.associatedTarget}' in boolean mode)`))
+                    .whereRaw(this.database.raw(`match(uniprot,sym,stringid) against("${this.associatedTarget}" in boolean mode)`))
                     .andWhere(this.database.raw(`ncats_ligands.id = ncats_ligand_activity.ncats_ligand_id`))
                     .andWhere(this.database.raw(`ncats_ligand_activity.target_id = t2tc.target_id`))
                     .andWhere(this.database.raw(`t2tc.protein_id = protein.id`)).as('assocTarget');

diff --git a/src/resolvers.js b/src/resolvers.js
@@ -1544,7 +1544,7 @@ const resolvers = {
                     reference: 'reference',
                     pubs: 'pubmed_ids'
                 })
-                .whereRaw(`ncats_ligands.identifier = '${ligand.ligid}'`)
+                .whereRaw(`ncats_ligands.identifier = "${ligand.ligid}"`)
                 .andWhere(dataSources.tcrd.db.raw(`ncats_ligand_activity.ncats_ligand_id = ncats_ligands.id`));
             if (dataSources.associatedTargetTCRDID) {
                 query.andWhere(dataSources.tcrd.db.raw(`ncats_ligand_activity.target_id = ${dataSources.associatedTargetTCRDID}`));

diff --git a/src/target_search.js b/src/target_search.js
@@ -2,7 +2,7 @@
 
 module.exports.getProteinListFromPPI = function(ppiTarget, confidence) {
     let proteinIDquery = this.db("protein")
-        .select("id").whereRaw(this.db.raw(`match(uniprot,sym,stringid) against('${ppiTarget}' in boolean mode)`));
+        .select("id").whereRaw(this.db.raw(`match(uniprot,sym,stringid) against("${ppiTarget}" in boolean mode)`));
     let ppiListQuery = this.db("ncats_ppi")
         .select(this.db.raw('distinct other_id as protein_id'))
         .whereIn('protein_id', proteinIDquery)