Merge pull request #1705 from SynBioHub/fixAdvSearch

Fix issue with advanced search with unique predicates

Author: cjmyers

lib/search.js

@@ -136,7 +136,10 @@ search.lucene = function lucene (value) {
     for (i = 0; i < values.length - 1; i++) {
       var query = values[i].split('=')
       if (query[0].indexOf(':') > -1) {
-        criteriaStr += '   ?subject ' + query[0] + ' ' + query[1] + ' . '
+        let predicate = query[0].startsWith('http') ? '<' + query[0] + '>' : query[0]
+        let object = query[1].startsWith('http') ? '<' + query[1] + '>' : query[1]
+        criteriaStr += '   ?subject ' + predicate + ' ' + object + ' . '
+        console.log('criteriaStr=' + criteriaStr)
       } else if (query[0] === 'objectType') {
         if (query[1].includes(':')) {
           criteriaStr += '   ?subject a ' + query[1] + ' . '

lib/views/advancedSearch.js

@@ -129,13 +129,19 @@ function advancedSearchForm (req, res, locals, errors) {
 
 function getQuery (searchPred, searchObj, filterObj, criteriaStr, queryStr, list) {
   if (searchPred !== 'No Filter' && (searchObj || (filterObj && filterObj !== 'No Filter'))) {
+    if (searchPred.toString().startsWith('http')) {
+      searchPred = '<' + searchPred + '>'
+    }
     var predStr = searchPred
     if (!searchPred.toString().startsWith('sbol2:')) {
       predStr = searchPred.replace('sbol2:', '')
     }
     if (searchPred === 'a') {
       predStr = 'objectType'
     }
+    if (searchPred.toString().startsWith('http')) {
+      searchPred = '<' + searchPred + '>'
+    }
     var objStr
     if (searchObj) {
       objStr = namespace.longName(searchObj)
@@ -315,11 +321,21 @@ function getUriList (req, graphUri) {
     }
   }
 
+  function fixPred (a) {
+    let short = namespace.shortName(a)
+    // TODO: a better check for URI would be good
+    if (a === short && a.startsWith('http')) {
+      return '<' + a + '>'
+    } else {
+      return short
+    }
+  }
+
   return Promise.all([
 
     new Promise((resolve, reject) => {
       if (req.body.searchPred1 && req.body.searchPred1 !== 'No Filter') {
-        templateParams.predicate = req.body.searchPred1.includes(':') ? req.body.searchPred1 : 'sbol2:' + req.body.searchPred1
+        templateParams.predicate = fixPred(req.body.searchPred1)
         var objectQuery1 = loadTemplate('sparql/searchObj.sparql', templateParams)
         console.debug(objectQuery1)
         sparql.queryJson(objectQuery1, graphUri).then((object1List) => {
@@ -338,7 +354,7 @@ function getUriList (req, graphUri) {
 
     new Promise((resolve, reject) => {
       if (req.body.searchPred2 && req.body.searchPred2 !== 'No Filter') {
-        templateParams.predicate = req.body.searchPred2.includes(':') ? req.body.searchPred2 : 'sbol2:' + req.body.searchPred2
+        templateParams.predicate = fixPred(req.body.searchPred2)
         var objectQuery2 = loadTemplate('sparql/searchObj.sparql', templateParams)
         console.debug(objectQuery2)
         sparql.queryJson(objectQuery2, graphUri).then((object2List) => {
@@ -357,7 +373,7 @@ function getUriList (req, graphUri) {
 
     new Promise((resolve, reject) => {
       if (req.body.searchPred3 && req.body.searchPred3 !== 'No Filter') {
-        templateParams.predicate = req.body.searchPred3.includes(':') ? req.body.searchPred3 : 'sbol3:' + req.body.searchPred3
+        templateParams.predicate = fixPred(req.body.searchPred3)
         var objectQuery3 = loadTemplate('sparql/searchObj.sparql', templateParams)
         console.debug(objectQuery3)
         sparql.queryJson(objectQuery3, graphUri).then((object3List) => {
@@ -376,7 +392,7 @@ function getUriList (req, graphUri) {
 
     new Promise((resolve, reject) => {
       if (req.body.searchPred4 && req.body.searchPred4 !== 'No Filter') {
-        templateParams.predicate = req.body.searchPred4.includes(':') ? req.body.searchPred4 : 'sbol4:' + req.body.searchPred4
+        templateParams.predicate = fixPred(req.body.searchPred4)
         var objectQuery4 = loadTemplate('sparql/searchObj.sparql', templateParams)
         console.debug(objectQuery4)
         sparql.queryJson(objectQuery4, graphUri).then((object4List) => {
@@ -395,7 +411,7 @@ function getUriList (req, graphUri) {
 
     new Promise((resolve, reject) => {
       if (req.body.searchPred5 && req.body.searchPred5 !== 'No Filter') {
-        templateParams.predicate = req.body.searchPred5.includes(':') ? req.body.searchPred5 : 'sbol5:' + req.body.searchPred5
+        templateParams.predicate = fixPred(req.body.searchPred5)
         var objectQuery5 = loadTemplate('sparql/searchObj.sparql', templateParams)
         console.debug(objectQuery5)
         sparql.queryJson(objectQuery5, graphUri).then((object5List) => {

sparql/search.sparql

@@ -11,6 +11,10 @@ PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
+PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
+PREFIX so: <http://identifiers.org/so/>
+PREFIX bench: <http://wiki.synbiohub.org/wiki/Terms/benchling#>
+PREFIX genbank: <http://www.ncbi.nlm.nih.gov/genbank#>
 
 SELECT DISTINCT
     ?subject

sparql/searchCount.sparql

@@ -11,6 +11,10 @@ PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
+PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
+PREFIX so: <http://identifiers.org/so/>
+PREFIX bench: <http://wiki.synbiohub.org/wiki/Terms/benchling#>
+PREFIX genbank: <http://www.ncbi.nlm.nih.gov/genbank#>
 
 select (sum(?tempcount) as ?count) WHERE {
 {

sparql/searchObj.sparql

@@ -11,6 +11,10 @@ PREFIX cello: <http://cellocad.org/Terms/cello#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX purl: <http://purl.obolibrary.org/obo/>
+PREFIX biopax: <http://www.biopax.org/release/biopax-level3.owl#>
+PREFIX so: <http://identifiers.org/so/>
+PREFIX bench: <http://wiki.synbiohub.org/wiki/Terms/benchling#>
+PREFIX genbank: <http://www.ncbi.nlm.nih.gov/genbank#>
 
 SELECT DISTINCT
     ?object