Merge pull request #64 from KeithKelleher/master

TIGA, UNIIs, TCRD upgrade

pharos_database_transforms/README.md

@@ -33,14 +33,17 @@ Here's what that looks like for our AWS server
     USER = 'ncats'
     PWORD = '<set password, don't commit it to a repo!>'
     ```
-4. Run the pharos specific transformations
-    * Run these python files at the terminal, they will use credentials from credentials.py to update the database
+4. Run the pharos specific transformations 
+    * all of these have been moved to pharos-etl repo, go there to do the knex migrations
+    The only one here that you might want to do is the lychi one if the drug tables have changed
+    * ~~Run these python files at the terminal, they will use credentials from credentials.py to update the database~~
 
-    * First
+    * ~~First~~
         * create indices and columns necessary for pharos
         ```
       python executeSQLfile.py tcrd-create-indexes.sql
         ```
+    
     * Second
         * Populate lychi_h4 keys for all ligands and drugs
             * write smiles to files
@@ -67,7 +70,7 @@ Here's what that looks like for our AWS server
             python lychi-set.py
             ```
             
-    * Later
+    * ~~Later~~
         * create and populate the table that hold the lists of IDG targets
         ```
         python executeSQLfile.py tcrd-create-idg-lists.sql
@@ -98,7 +101,7 @@ Here's what that looks like for our AWS server
         ```
         python tcrd-create-generif-pubmed-map.py
         ```
-    * Later still
+    * ~~Later still~~
         * create mapping between data sources and all the targets, diseases, and ligands we have data from there for
         ```
         python tcrd-create-datasource-table.py

src/TCRD.js

@@ -470,6 +470,11 @@ OR b.id = (SELECT protein_id FROM xref where xtype = 'Ensembl' and value = ? lim
 and b.geneid=?`, [args.geneid]));
         }
 
+        if (args.protein_id) {
+            return this.db.select(this.db.raw(TARGET_SQL + `
+and b.id=?`, [args.protein_id]));
+        }
+
         return this.db.select(this.db.raw(TARGET_SQL + `
 and a.id = ?`, [args.tcrdid]));
     }
@@ -973,7 +978,7 @@ and b.target_id = ?`, [target.tcrdid]));
         }
 
         let q = this.db.select(this.db.raw(p + ` as name,
-avg(a.attr_cdf) as value
+avg(a.attr_cdf) as value, group_concat(distinct concat(b.name,'!',b.url) order by b.name separator '|') as sources
 from hgram_cdf a, gene_attribute_type b, t2tc c
 where a.protein_id = c.protein_id
 and c.target_id = ?
@@ -1724,7 +1729,8 @@ a.*,b.parent_id from do a, do_parent b where a.doid = b.doid`));
     getDTO(args) {
         let matches = [];
         if (args.dtoid) {
-            let n = this.dto[args.dtoid];
+            const dtoFormat = args.dtoid.replace('_',':');
+            let n = this.dto[dtoFormat];
             while (n) {
                 matches.push(n);
                 n = n.parent;
@@ -1751,7 +1757,7 @@ and b.target_id = ?`, [target.tcrdid]));
 
     getTINXForTarget(target, args) {
         let q = this.db.select(this.db.raw(`
-a.*,b.doid, b.score as novelty, a.id as tinxid
+a.*, b.doid, b.score as novelty
 from tinx_importance a, tinx_disease b, t2tc c`));
 
         let sort = true;
@@ -1763,7 +1769,7 @@ match(b.name,b.summary) against(? in boolean mode)`, [t]));
                 sort = false;
             }
         }
-        q = q.andWhere(this.db.raw(`a.disease_id = b.id
+        q = q.andWhere(this.db.raw(`a.doid = b.doid
 and a.protein_id = c.protein_id
 and c.target_id = ?`, [target.tcrdid]));
 

src/__tests__/targetQueries/comprehensive.test.js

@@ -225,8 +225,8 @@ describe('all the queries should be consistent with each other', function () {
     });
 
     test('Similarity query', () => {
-        const fullList = new TargetList(tcrd, {top:1000000, filter: {similarity: "(Q6P1J9, GWAS)"}});
-        const filteredList = new TargetList(tcrd, {filter: {similarity: "(Q6P1J9, GWAS)", facets: [{facet: "Target Development Level", values: ["Tclin"]}]}});
+        const fullList = new TargetList(tcrd, {top:1000000, filter: {similarity: "(DRD2, GWAS)"}});
+        const filteredList = new TargetList(tcrd, {filter: {similarity: "(DRD2, GWAS)", facets: [{facet: "Target Development Level", values: ["Tclin"]}]}});
 
         const fullCountQuery = fullList.getCountQuery();
         const fullListQuery = fullList.getListQuery();

src/db_credentials.js

@@ -3,9 +3,9 @@
 //
 const cred = {
     DBHOST: 'tcrd.ncats.io',
-    DBNAME: 'tcrd684',
-    CONFIGDB: 'pharos_config_prod',
+    DBNAME: 'tcrd6110',
     USER: 'tcrd',
-    PWORD: ''
+    PWORD: '',
+    CONFIGDB: 'pharos_config_prod',
 };
 module.exports.cred = cred;

src/models/DataModelList.ts

@@ -157,7 +157,7 @@ export abstract class DataModelList implements IBuildable {
         return query;
     };
 
-    getListQuery() {
+    getListQuery(innerJoinAll: boolean = false) {
         let dataFields: FieldInfo[];
         if (this.fields && this.fields.length > 0) {
             dataFields = this.GetDataFields('list');
@@ -172,7 +172,7 @@ export abstract class DataModelList implements IBuildable {
 
         const queryDefinition = QueryDefinition.GenerateQueryDefinition(this, dataFields);
 
-        const query = queryDefinition.generateBaseQuery(false);
+        const query = queryDefinition.generateBaseQuery(innerJoinAll);
 
         this.addFacetConstraints(query, this.filteringFacets);
         this.addModelSpecificFiltering(query, true, this.dataFields.map(f => f.table));

src/models/databaseTable.ts

@@ -77,7 +77,8 @@ export class DatabaseTable {
             ["protein-target", ["t2tc"]],
             ["protein-ncats_idg_list_type", ["ncats_idg_list"]],
             ["protein-ncats_ligands", ["ncats_ligand_activity", "target", "t2tc"]],
-            ["protein-ncats_ligand_activity", ["target", "t2tc"]]
+            ["protein-ncats_ligand_activity", ["target", "t2tc"]],
+            ["protein-drgc_resource", ["target", "t2tc"]]
         ]);
 
     static getRequiredLinks(table1: string, table2: string): string[] | undefined {

src/models/disease/diseaseList.ts

@@ -41,7 +41,7 @@ export class DiseaseList extends DataModelList {
                 importance:knex.raw('(tinx_importance.score)')
             })
             .join(doidList.as('idList'), 'idList.did', 'tinx_disease.doid')
-            .where(knex.raw('tinx_importance.disease_id = tinx_disease.id'))
+            .where(knex.raw('tinx_importance.doid = tinx_disease.doid'))
             .andWhere(knex.raw('tinx_importance.protein_id = t2tc.protein_id'))
             .andWhere(knex.raw('tinx_importance.protein_id = tinx_novelty.protein_id'))
             .andWhere(knex.raw('t2tc.target_id = target.id'));

src/models/queryDefinition.ts

@@ -144,7 +144,7 @@ export class QueryDefinition {
         return dataTable.tableName === this.buildable.rootTable && dataTable.alias === this.buildable.rootTable;
     }
 
-    generateBaseQuery(forFacet: boolean){
+    generateBaseQuery(innerJoinAll: boolean){
         const buildableObj = this.buildable;
         let rootTableObject = this.getRootTable();
         if (rootTableObject == undefined) {
@@ -161,7 +161,7 @@ export class QueryDefinition {
                 return;
             }
             let joinFunction = 'leftJoin';
-            if(forFacet || this.buildable.tableNeedsInnerJoin(dataTable)){
+            if(innerJoinAll || this.buildable.tableNeedsInnerJoin(dataTable)){
                 joinFunction = 'join';
             }
             let leftTable = rootTableObject;

src/models/target/targetDetails.ts

@@ -61,4 +61,17 @@ export class TargetDetails{
             .orderBy(['startResidue', 'endResidue']);
         return query;
     }
+
+    static LD2JSON(ldObject: any){
+        const jsonObject: any = {};
+        for (const prop in ldObject) {
+            if (ldObject[prop]['@value']) {
+                jsonObject[prop] = ldObject[prop]['@value'];
+            }
+            else if (ldObject[prop]['rdfs:label']) {
+                jsonObject[prop] = ldObject[prop]['rdfs:label'];
+            }
+        }
+        return jsonObject;
+    }
 }