From 1a7966513c3ed817b89d5890f67b1b1b1a6228c6 Mon Sep 17 00:00:00 2001
From: CLARVIE <clarvie-edouard.yetikoua@sparna.fr>
Date: Mon, 6 Nov 2017 11:59:00 +0100
Subject: [PATCH 1/3] show or hide deprecated concepts

---
 controller/RestController.php  |  3 ++-
 model/GlobalConfig.php         |  2 +-
 model/Model.php                |  5 ++--
 model/Vocabulary.php           |  8 ++++++-
 model/sparql/GenericSparql.php | 42 ++++++++++++++++++++++------------
 5 files changed, 41 insertions(+), 19 deletions(-)

diff --git a/controller/RestController.php b/controller/RestController.php
index 0e22e6fab..4edaf720d 100644
--- a/controller/RestController.php
+++ b/controller/RestController.php
@@ -791,7 +791,8 @@ public function groups($request)
      */
     public function groupMembers($request)
     {
-        $children = $request->getVocab()->listConceptGroupContents($request->getUri(), $request->getLang());
+        $showDeprecated=$request->getVocab()->showDeprecated();
+        $children = $request->getVocab()->listConceptGroupContents($request->getUri(), $request->getLang(),$showDeprecated);
         if (empty($children)) {
             return $this->returnError('404', 'Not Found', "Could not find group <{$request->getUri()}>");
         }
diff --git a/model/GlobalConfig.php b/model/GlobalConfig.php
index 4080e94fe..0cfc1b8c2 100644
--- a/model/GlobalConfig.php
+++ b/model/GlobalConfig.php
@@ -119,7 +119,7 @@ public function getSearchResultsSize()
      */
     public function getTemplateCache() 
     {
-        return $this->getConstant('TEMPLATE_CACHE', '/tmp/skosmos-template-cache');
+        return $this->getConstant('TEMPLATE_CACHE', 'tmp/cache/skosmos-template-cache');
     }
     
     /**
diff --git a/model/Model.php b/model/Model.php
index 90d7b0353..1103864b4 100644
--- a/model/Model.php
+++ b/model/Model.php
@@ -297,16 +297,17 @@ public function searchConcepts($params)
         }
 
         $vocabs = $params->getVocabs();
-
+        $showDeprecated=false;
         if (sizeof($vocabs) === 1) { // search within vocabulary
             $voc = $vocabs[0];
             $sparql = $voc->getSparql();
+            $showDeprecated=$voc->showDeprecated();
         } else { // multi-vocabulary or global search
             $voc = null;
             $sparql = $this->getDefaultSparql();
         }
 
-        $results = $sparql->queryConcepts($vocabs, $params->getAdditionalFields(), $params->getUnique(), $params);
+        $results = $sparql->queryConcepts($vocabs, $params->getAdditionalFields(), $params->getUnique(), $params,$showDeprecated);
         if ($params->getRest() && $results && $params->getSearchLimit() !== 0) {
           $results = array_slice($results, $params->getOffset(), $params->getSearchLimit());
         }
diff --git a/model/Vocabulary.php b/model/Vocabulary.php
index f4a9ceac3..ae6575c6a 100644
--- a/model/Vocabulary.php
+++ b/model/Vocabulary.php
@@ -48,6 +48,12 @@ public function getGraph()
 
         return $graph;
     }
+    
+    public  function showDeprecated(){
+        $showDeprecated=false;
+        $showDeprecated= $this->resource->get('skosmos:showDeprecated');
+        return $showDeprecated;
+    }
 
     /**
      * Get the SPARQL implementation for this vocabulary
@@ -482,7 +488,7 @@ public function getAlphabet($clang)
      */
     public function searchConceptsAlphabetical($letter, $limit = null, $offset = null, $clang = null)
     {
-        return $this->getSparql()->queryConceptsAlphabetical($letter, $clang, $limit, $offset, $this->config->getIndexClasses());
+        return $this->getSparql()->queryConceptsAlphabetical($letter, $clang, $limit, $offset, $this->config->getIndexClasses(),$this->showDeprecated());
     }
 
     /**
diff --git a/model/sparql/GenericSparql.php b/model/sparql/GenericSparql.php
index 7663bc7b2..b18d766a1 100644
--- a/model/sparql/GenericSparql.php
+++ b/model/sparql/GenericSparql.php
@@ -925,7 +925,7 @@ protected function generateConceptSearchQueryInner($term, $lang, $searchLang, $p
      * @param ConceptSearchParameters $params 
      * @return string sparql query
      */
-    protected function generateConceptSearchQuery($fields, $unique, $params) {
+    protected function generateConceptSearchQuery($fields, $unique, $params, $showDeprecated) {
         $vocabs = $params->getVocabs();
         $gcl = $this->graphClause;
         $fcl = empty($vocabs) ? '' : $this->generateFromClause($vocabs);
@@ -941,7 +941,11 @@ protected function generateConceptSearchQuery($fields, $unique, $params) {
                 $schemecond .= "?s skos:inScheme <$scheme> . ";
             }
         }
-
+        $filterDeprecated="";
+        //show or hide deprecated concepts
+        if($showDeprecated==false){
+            $filterDeprecated="FILTER NOT EXISTS { ?s owl:deprecated true }";
+        }
         // extra conditions for parent and group, if specified
         $parentcond = ($params->getParentLimit()) ? "?s skos:broader+ <" . $params->getParentLimit() . "> ." : "";
         $groupcond = ($params->getGroupLimit()) ? "<" . $params->getGroupLimit() . "> skos:member ?s ." : "";
@@ -989,7 +993,7 @@ protected function generateConceptSearchQuery($fields, $unique, $params) {
    ?s a ?type .
    $extrafields $schemecond
   }
-  FILTER NOT EXISTS { ?s owl:deprecated true }
+  $filterDeprecated
  }
  $filterGraph
 }
@@ -1109,8 +1113,8 @@ private function transformConceptSearchResults($results, $vocabs, $fields) {
      * @param ConceptSearchParameters $params 
      * @return array query result object
      */
-    public function queryConcepts($vocabs, $fields = null, $unique = false, $params) {
-        $query = $this->generateConceptSearchQuery($fields, $unique, $params);
+    public function queryConcepts($vocabs, $fields = null, $unique = false, $params, $showDeprecated) {
+        $query = $this->generateConceptSearchQuery($fields, $unique, $params,$showDeprecated);
         $results = $this->query($query);
         return $this->transformConceptSearchResults($results, $vocabs, $fields);
     }
@@ -1155,7 +1159,7 @@ private function formatFilterConditions($letter, $lang) {
      * @param array|null $classes
      * @return string sparql query
      */
-    protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes) {
+    protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes, $showDeprecated) {
         $fcl = $this->generateFromClause();
         $classes = ($classes) ? $classes : array('http://www.w3.org/2004/02/skos/core#Concept');
         $values = $this->formatValues('?type', $classes, 'uri');
@@ -1163,7 +1167,10 @@ protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset
         $conditions = $this->formatFilterConditions($letter, $lang);
         $filtercondLabel = $conditions['filterpref'];
         $filtercondALabel = $conditions['filteralt'];
-
+        $filterDeprecated="";
+        if($showDeprecated==false){
+            $filterDeprecated="FILTER NOT EXISTS { ?s owl:deprecated true }";
+        }
         $query = <<<EOQ
 SELECT DISTINCT ?s ?label ?alabel $fcl
 WHERE {
@@ -1187,7 +1194,7 @@ protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset
     }
   }
   ?s a ?type .
-  FILTER NOT EXISTS { ?s owl:deprecated true }
+  $filterDeprecated
   $values
 }
 ORDER BY LCASE(IF(BOUND(?alabel), STR(?alabel), STR(?label))) $limitandoffset
@@ -1236,9 +1243,10 @@ private function transformAlphabeticalListResults($results) {
      * @param integer $limit limits the amount of results
      * @param integer $offset offsets the result set
      * @param array $classes
+     * @param boolean $showDeprecated
      */
-    public function queryConceptsAlphabetical($letter, $lang, $limit = null, $offset = null, $classes = null) {
-        $query = $this->generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes);
+    public function queryConceptsAlphabetical($letter, $lang, $limit = null, $offset = null, $classes = null,$showDeprecated) {
+        $query = $this->generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes,$showDeprecated);
         $results = $this->query($query);
         return $this->transformAlphabeticalListResults($results);
     }
@@ -1945,16 +1953,21 @@ public function listConceptGroups($groupClass, $lang) {
      * @param string $groupClass URI of concept group class
      * @param string $group URI of the concept group instance
      * @param string $lang language of labels to return
+     * @param boolean $showDeprecated
      * @return string sparql query
      */
-    private function generateConceptGroupContentsQuery($groupClass, $group, $lang) {
+    private function generateConceptGroupContentsQuery($groupClass, $group, $lang, $showDeprecated) {
         $fcl = $this->generateFromClause();
+        $filterDeprecated="";
+        if($showDeprecated==false){
+            $filterDeprecated="FILTER NOT EXISTS { ?conc owl:deprecated true }";
+        }
         $query = <<<EOQ
 SELECT ?conc ?super ?label ?members ?type ?notation $fcl
 WHERE {
  <$group> a <$groupClass> .
  { <$group> skos:member ?conc . } UNION { ?conc isothes:superGroup <$group> }
- FILTER NOT EXISTS { ?conc owl:deprecated true }
+$filterDeprecated
  ?conc a ?type .
  OPTIONAL { ?conc skos:prefLabel ?label .
   FILTER (langMatches(lang(?label), '$lang'))
@@ -2014,10 +2027,11 @@ private function transformConceptGroupContentsResults($result, $lang) {
      * @param string $groupClass URI of concept group class
      * @param string $group URI of the concept group instance
      * @param string $lang language of labels to return
+     * @param boolean $showDeprecated
      * @return array Result array with concept URI as key and concept label as value
      */
-    public function listConceptGroupContents($groupClass, $group, $lang) {
-        $query = $this->generateConceptGroupContentsQuery($groupClass, $group, $lang);
+    public function listConceptGroupContents($groupClass, $group, $lang,$showDeprecated) {
+        $query = $this->generateConceptGroupContentsQuery($groupClass, $group, $lang,$showDeprecated);
         $result = $this->query($query);
         return $this->transformConceptGroupContentsResults($result, $lang);
     }

From 967381d68e08daf9fd4a441fba8eb14a63a58e87 Mon Sep 17 00:00:00 2001
From: CLARVIE <clarvie-edouard.yetikoua@sparna.fr>
Date: Mon, 6 Nov 2017 15:46:57 +0100
Subject: [PATCH 2/3] show or hide deprecated concepts include unit tests

---
 controller/RestController.php   |  3 +--
 model/GlobalConfig.php          |  2 +-
 model/Model.php                 |  3 ++-
 model/Vocabulary.php            | 11 +++--------
 model/VocabularyConfig.php      |  9 +++++++++
 model/sparql/GenericSparql.php  | 29 ++++++++++++++++-------------
 model/sparql/JenaTextSparql.php | 10 ++++++++--
 tests/GenericSparqlTest.php     | 33 ++++++++++++++++++++++++++++++++-
 tests/ModelTest.php             | 13 +++++++++++++
 tests/VocabularyConfigTest.php  |  8 ++++++++
 tests/VocabularyTest.php        | 19 +++++++++++++++++++
 tests/testvocabularies.ttl      | 15 +++++++++++++++
 12 files changed, 127 insertions(+), 28 deletions(-)

diff --git a/controller/RestController.php b/controller/RestController.php
index 4edaf720d..0e22e6fab 100644
--- a/controller/RestController.php
+++ b/controller/RestController.php
@@ -791,8 +791,7 @@ public function groups($request)
      */
     public function groupMembers($request)
     {
-        $showDeprecated=$request->getVocab()->showDeprecated();
-        $children = $request->getVocab()->listConceptGroupContents($request->getUri(), $request->getLang(),$showDeprecated);
+        $children = $request->getVocab()->listConceptGroupContents($request->getUri(), $request->getLang());
         if (empty($children)) {
             return $this->returnError('404', 'Not Found', "Could not find group <{$request->getUri()}>");
         }
diff --git a/model/GlobalConfig.php b/model/GlobalConfig.php
index 0cfc1b8c2..4080e94fe 100644
--- a/model/GlobalConfig.php
+++ b/model/GlobalConfig.php
@@ -119,7 +119,7 @@ public function getSearchResultsSize()
      */
     public function getTemplateCache() 
     {
-        return $this->getConstant('TEMPLATE_CACHE', 'tmp/cache/skosmos-template-cache');
+        return $this->getConstant('TEMPLATE_CACHE', '/tmp/skosmos-template-cache');
     }
     
     /**
diff --git a/model/Model.php b/model/Model.php
index 1103864b4..2452b2109 100644
--- a/model/Model.php
+++ b/model/Model.php
@@ -301,10 +301,11 @@ public function searchConcepts($params)
         if (sizeof($vocabs) === 1) { // search within vocabulary
             $voc = $vocabs[0];
             $sparql = $voc->getSparql();
-            $showDeprecated=$voc->showDeprecated();
+            $showDeprecated=$voc->getConfig()->getShowDeprecated();
         } else { // multi-vocabulary or global search
             $voc = null;
             $sparql = $this->getDefaultSparql();
+            // @TODO : in a global search showDeprecated will always be false and cannot be set globally
         }
 
         $results = $sparql->queryConcepts($vocabs, $params->getAdditionalFields(), $params->getUnique(), $params,$showDeprecated);
diff --git a/model/Vocabulary.php b/model/Vocabulary.php
index ae6575c6a..194a0f64d 100644
--- a/model/Vocabulary.php
+++ b/model/Vocabulary.php
@@ -48,12 +48,6 @@ public function getGraph()
 
         return $graph;
     }
-    
-    public  function showDeprecated(){
-        $showDeprecated=false;
-        $showDeprecated= $this->resource->get('skosmos:showDeprecated');
-        return $showDeprecated;
-    }
 
     /**
      * Get the SPARQL implementation for this vocabulary
@@ -439,7 +433,7 @@ public function listConceptGroupContents($glname, $clang)
         }
         // no group class defined, so empty result
         $group = $this->getConceptURI($glname);
-        $contents = $this->getSparql()->listConceptGroupContents($gclass, $group, $clang);
+        $contents = $this->getSparql()->listConceptGroupContents($gclass, $group, $clang, $this->config->getShowDeprecated());
         foreach ($contents as $uri => $label) {
             $ret[$uri] = $label;
         }
@@ -488,7 +482,7 @@ public function getAlphabet($clang)
      */
     public function searchConceptsAlphabetical($letter, $limit = null, $offset = null, $clang = null)
     {
-        return $this->getSparql()->queryConceptsAlphabetical($letter, $clang, $limit, $offset, $this->config->getIndexClasses(),$this->showDeprecated());
+        return $this->getSparql()->queryConceptsAlphabetical($letter, $clang, $limit, $offset, $this->config->getIndexClasses(),$this->config->getShowDeprecated());
     }
 
     /**
@@ -615,4 +609,5 @@ public function getShortName() {
     public function getId() {
       return $this->config->getId();
     }
+    
 }
diff --git a/model/VocabularyConfig.php b/model/VocabularyConfig.php
index c619734bf..5df0fcd36 100644
--- a/model/VocabularyConfig.php
+++ b/model/VocabularyConfig.php
@@ -405,6 +405,15 @@ public function showAlphabeticalIndex()
     {
         return $this->getBoolean('skosmos:showAlphabeticalIndex', true);
     }
+    
+    /**
+     * Returns a boolean value set in the vocabularies.ttl config.
+     * @return boolean
+     */
+    public function getShowDeprecated()
+    {
+        return $this->getBoolean('skosmos:showDeprecated', false);
+    }
 
     /**
      * Returns the vocabulary dc:type value(s) with their labels and uris, if set in the vocabulary configuration.
diff --git a/model/sparql/GenericSparql.php b/model/sparql/GenericSparql.php
index b18d766a1..49e4254ba 100644
--- a/model/sparql/GenericSparql.php
+++ b/model/sparql/GenericSparql.php
@@ -922,10 +922,11 @@ protected function generateConceptSearchQueryInner($term, $lang, $searchLang, $p
      * Query for concepts using a search term.
      * @param array|null $fields extra fields to include in the result (array of strings). (default: null = none)
      * @param boolean $unique restrict results to unique concepts (default: false)
+     * @param boolean $showDeprecated whether to include deprecated concepts in search results (default: false)
      * @param ConceptSearchParameters $params 
      * @return string sparql query
      */
-    protected function generateConceptSearchQuery($fields, $unique, $params, $showDeprecated) {
+    protected function generateConceptSearchQuery($fields, $unique, $params, $showDeprecated = false) {
         $vocabs = $params->getVocabs();
         $gcl = $this->graphClause;
         $fcl = empty($vocabs) ? '' : $this->generateFromClause($vocabs);
@@ -943,7 +944,7 @@ protected function generateConceptSearchQuery($fields, $unique, $params, $showDe
         }
         $filterDeprecated="";
         //show or hide deprecated concepts
-        if($showDeprecated==false){
+        if(!$showDeprecated){
             $filterDeprecated="FILTER NOT EXISTS { ?s owl:deprecated true }";
         }
         // extra conditions for parent and group, if specified
@@ -1110,10 +1111,11 @@ private function transformConceptSearchResults($results, $vocabs, $fields) {
      * @param array $vocabs array of Vocabulary objects to search; empty for global search
      * @param array $fields extra fields to include in the result (array of strings). (default: null = none)
      * @param boolean $unique restrict results to unique concepts (default: false)
+     * @param boolean $showDeprecated whether to include deprecated concepts in the result (default: false)
      * @param ConceptSearchParameters $params 
      * @return array query result object
      */
-    public function queryConcepts($vocabs, $fields = null, $unique = false, $params, $showDeprecated) {
+    public function queryConcepts($vocabs, $fields = null, $unique = false, $params, $showDeprecated = false) {
         $query = $this->generateConceptSearchQuery($fields, $unique, $params,$showDeprecated);
         $results = $this->query($query);
         return $this->transformConceptSearchResults($results, $vocabs, $fields);
@@ -1157,9 +1159,10 @@ private function formatFilterConditions($letter, $lang) {
      * @param integer $limit limits the amount of results
      * @param integer $offset offsets the result set
      * @param array|null $classes
+     * @param boolean $showDeprecated whether to include deprecated concepts in the result (default: false)
      * @return string sparql query
      */
-    protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes, $showDeprecated) {
+    protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes, $showDeprecated = false) {
         $fcl = $this->generateFromClause();
         $classes = ($classes) ? $classes : array('http://www.w3.org/2004/02/skos/core#Concept');
         $values = $this->formatValues('?type', $classes, 'uri');
@@ -1168,7 +1171,7 @@ protected function generateAlphabeticalListQuery($letter, $lang, $limit, $offset
         $filtercondLabel = $conditions['filterpref'];
         $filtercondALabel = $conditions['filteralt'];
         $filterDeprecated="";
-        if($showDeprecated==false){
+        if(!$showDeprecated){
             $filterDeprecated="FILTER NOT EXISTS { ?s owl:deprecated true }";
         }
         $query = <<<EOQ
@@ -1243,9 +1246,9 @@ private function transformAlphabeticalListResults($results) {
      * @param integer $limit limits the amount of results
      * @param integer $offset offsets the result set
      * @param array $classes
-     * @param boolean $showDeprecated
+     * @param boolean $showDeprecated whether to include deprecated concepts in the result (default: false)
      */
-    public function queryConceptsAlphabetical($letter, $lang, $limit = null, $offset = null, $classes = null,$showDeprecated) {
+    public function queryConceptsAlphabetical($letter, $lang, $limit = null, $offset = null, $classes = null,$showDeprecated = false) {
         $query = $this->generateAlphabeticalListQuery($letter, $lang, $limit, $offset, $classes,$showDeprecated);
         $results = $this->query($query);
         return $this->transformAlphabeticalListResults($results);
@@ -1953,14 +1956,14 @@ public function listConceptGroups($groupClass, $lang) {
      * @param string $groupClass URI of concept group class
      * @param string $group URI of the concept group instance
      * @param string $lang language of labels to return
-     * @param boolean $showDeprecated
+     * @param boolean $showDeprecated whether to include deprecated in the result
      * @return string sparql query
      */
-    private function generateConceptGroupContentsQuery($groupClass, $group, $lang, $showDeprecated) {
+    private function generateConceptGroupContentsQuery($groupClass, $group, $lang, $showDeprecated = false) {
         $fcl = $this->generateFromClause();
         $filterDeprecated="";
-        if($showDeprecated==false){
-            $filterDeprecated="FILTER NOT EXISTS { ?conc owl:deprecated true }";
+        if(!$showDeprecated){
+            $filterDeprecated="  FILTER NOT EXISTS { ?conc owl:deprecated true }";
         }
         $query = <<<EOQ
 SELECT ?conc ?super ?label ?members ?type ?notation $fcl
@@ -2027,10 +2030,10 @@ private function transformConceptGroupContentsResults($result, $lang) {
      * @param string $groupClass URI of concept group class
      * @param string $group URI of the concept group instance
      * @param string $lang language of labels to return
-     * @param boolean $showDeprecated
+     * @param boolean $showDeprecated whether to include deprecated concepts in search results
      * @return array Result array with concept URI as key and concept label as value
      */
-    public function listConceptGroupContents($groupClass, $group, $lang,$showDeprecated) {
+    public function listConceptGroupContents($groupClass, $group, $lang,$showDeprecated = false) {
         $query = $this->generateConceptGroupContentsQuery($groupClass, $group, $lang,$showDeprecated);
         $result = $this->query($query);
         return $this->transformConceptGroupContentsResults($result, $lang);
diff --git a/model/sparql/JenaTextSparql.php b/model/sparql/JenaTextSparql.php
index 7d60e8db8..613a636d7 100644
--- a/model/sparql/JenaTextSparql.php
+++ b/model/sparql/JenaTextSparql.php
@@ -80,10 +80,11 @@ protected function generateConceptSearchQueryCondition($term, $searchLang)
      * @param integer $limit limits the amount of results
      * @param integer $offset offsets the result set
      * @param array|null $classes
+     * @param boolean $showDeprecated whether to include deprecated concepts in the result (default: false)
      * @return string sparql query
      */
 
-    public function generateAlphabeticalListQuery($letter, $lang, $limit = null, $offset = null, $classes = null)
+    public function generateAlphabeticalListQuery($letter, $lang, $limit = null, $offset = null, $classes = null, $showDeprecated = false)
     {
         if ($letter == '*' || $letter == '0-9' || $letter == '!*') {
             // text index cannot support special character queries, use the generic implementation for these
@@ -100,6 +101,11 @@ public function generateAlphabeticalListQuery($letter, $lang, $limit = null, $of
         $textcondPref = $this->createTextQueryCondition($letter . '*', 'skos:prefLabel', $lang);
         $textcondAlt = $this->createTextQueryCondition($letter . '*', 'skos:altLabel', $lang);
 
+        $filterDeprecated="";
+        if(!$showDeprecated){
+            $filterDeprecated="FILTER NOT EXISTS { ?s owl:deprecated true }";
+        }
+        
         $query = <<<EOQ
 SELECT DISTINCT ?s ?label ?alabel
 WHERE {
@@ -122,7 +128,7 @@ public function generateAlphabeticalListQuery($letter, $lang, $limit = null, $of
       }
     }
     ?s a ?type .
-    FILTER NOT EXISTS { ?s owl:deprecated true }
+    $filterDeprecated
   } $values
 }
 ORDER BY LCASE(?match) $limitandoffset
diff --git a/tests/GenericSparqlTest.php b/tests/GenericSparqlTest.php
index a9f7503f5..7afc2065e 100644
--- a/tests/GenericSparqlTest.php
+++ b/tests/GenericSparqlTest.php
@@ -820,7 +820,7 @@ public function testListConceptGroups()
    * @covers GenericSparql::generateConceptGroupContentsQuery
    * @covers GenericSparql::transformConceptGroupContentsResults
    */
-  public function testListConceptGroupContentsIncludingDeprecatedConcept()
+  public function testListConceptGroupContentsExcludingDeprecatedConcept()
   {
     $voc = $this->model->getVocabulary('groups');
     $graph = $voc->getGraph();
@@ -829,6 +829,37 @@ public function testListConceptGroupContentsIncludingDeprecatedConcept()
     $this->assertEquals('http://www.skosmos.skos/groups/ta113', $actual[0]['uri']);
     $this->assertEquals(1, sizeof($actual));
   }
+  
+  /**
+   * @covers GenericSparql::listConceptGroupContents
+   * @covers GenericSparql::generateConceptGroupContentsQuery
+   * @covers GenericSparql::transformConceptGroupContentsResults
+   */
+  public function testListConceptGroupContentsIncludingDeprecatedConcept()
+  {
+      $voc = $this->model->getVocabulary('showDeprecated');
+      $graph = $voc->getGraph();
+      $sparql = new GenericSparql('http://localhost:3030/ds/sparql', $graph, $this->model);
+      $actual = $sparql->ListConceptGroupContents('http://www.w3.org/2004/02/skos/core#Collection', 'http://www.skosmos.skos/groups/salt', 'en', $voc->getConfig()->getShowDeprecated());
+      $expected = array (
+          0 => array (
+              'uri' => 'http://www.skosmos.skos/groups/ta113',
+              'isSuper' => false,
+              'hasMembers' => false,
+              'type' => array('skos:Concept'),
+              'prefLabel' => 'Flatfish'
+          ),
+          1 => array (
+              'uri' => 'http://www.skosmos.skos/groups/ta111',
+              'isSuper' => false,
+              'hasMembers' => false,
+              'type' => array('skos:Concept'),
+              'prefLabel' => 'Tuna'
+          )
+      );
+      $this->assertEquals($expected, $actual);
+      $this->assertEquals(2, sizeof($actual));
+  }
 
   /**
    * @covers GenericSparql::queryChangeList
diff --git a/tests/ModelTest.php b/tests/ModelTest.php
index 5c8a6e201..ca347bba6 100644
--- a/tests/ModelTest.php
+++ b/tests/ModelTest.php
@@ -253,6 +253,19 @@ public function testSearchConceptsUnique() {
     $this->assertCount(2, $result);
   }
   
+  /**
+   * @covers Model::searchConcepts
+   */
+  public function testSearchConceptsIncludingDeprecated() {
+      $params = $this->getMockBuilder('ConceptSearchParameters')->disableOriginalConstructor()->getMock();
+      $params->method('getSearchTerm')->will($this->returnValue('Tuna'));
+      $params->method('getVocabIds')->will($this->returnValue('showDeprecated'));
+      $params->method('getVocabs')->will($this->returnValue(array($this->model->getVocabulary('showDeprecated'))));
+      $result = $this->model->searchConcepts($params);
+      $this->assertCount(1, $result);
+      $this->assertEquals('http://www.skosmos.skos/groups/ta111', $result[0]['uri']);
+  }
+  
   /**
    * @covers Model::searchConcepts
    */
diff --git a/tests/VocabularyConfigTest.php b/tests/VocabularyConfigTest.php
index 6ff94dd64..021150d16 100644
--- a/tests/VocabularyConfigTest.php
+++ b/tests/VocabularyConfigTest.php
@@ -346,6 +346,14 @@ public function testGetTypes() {
     $vocab = $this->model->getVocabulary('test');
     $this->assertEquals(array(0 => array('uri' => 'http://publications.europa.eu/resource/authority/dataset-type/ONTOLOGY', 'prefLabel' => 'Ontology')), $vocab->getConfig()->getTypes('en'));
   }
+  
+  /**
+   * @covers VocabularyConfig::showDeprecated
+   */
+  public function testShowDeprecated() {
+      $vocab = $this->model->getVocabulary('showDeprecated');
+      $this->assertEquals(true, $vocab->getConfig()->getShowDeprecated());
+  }
 
   /**
    * @covers VocabularyConfig::getTypes
diff --git a/tests/VocabularyTest.php b/tests/VocabularyTest.php
index 9c98303df..cf5eebb2b 100644
--- a/tests/VocabularyTest.php
+++ b/tests/VocabularyTest.php
@@ -240,6 +240,25 @@ public function testSearchConceptsAlphabetical() {
     $this->assertEquals('Grouped fish', $concepts[0]['prefLabel']);
     $this->assertEquals('Guppy', $concepts[1]['prefLabel']);
   }
+  
+  /**
+  * @covers Vocabulary::searchConceptsAlphabetical
+  */
+  public function testSearchConceptsAlphabeticalExcludingDeprecated() {
+      $vocab = $this->model->getVocabulary('groups');
+      $concepts = $vocab->searchConceptsAlphabetical('T', null, null, 'en');
+      $this->assertCount(0, $concepts);
+  }
+  
+  /**
+   * @covers Vocabulary::searchConceptsAlphabetical
+   */
+  public function testSearchConceptsAlphabeticalIncludingDeprecated() {
+      $vocab = $this->model->getVocabulary('showDeprecated');
+      $concepts = $vocab->searchConceptsAlphabetical('T', null, null, 'en');
+      $this->assertCount(1, $concepts);
+      $this->assertEquals('Tuna', $concepts[0]['prefLabel']);
+  }
 
   /**
    * @covers Vocabulary::searchConceptsAlphabetical
diff --git a/tests/testvocabularies.ttl b/tests/testvocabularies.ttl
index 8704c52ca..69ce68b97 100644
--- a/tests/testvocabularies.ttl
+++ b/tests/testvocabularies.ttl
@@ -64,6 +64,21 @@
 	skosmos:indexShowClass meta:TestClass, meta:TestClass2;
 	skosmos:sparqlGraph <http://www.skosmos.skos/groups/> .
 
+
+:showDeprecated a skosmos:Vocabulary, void:Dataset ;
+	dc11:title "Show deprecated test vocabulary"@en ;
+	dc:subject :cat_general ;
+	void:dataDump <http://skosmos.skos/dump/test/groups.ttl>,
+		<http://skosmos.skos/dump/test/groups> ;
+	void:uriSpace "http://www.skosmos.skos/onto/groups/";
+	skosmos:arrayClass isothes:ThesaurusArray ;
+  	skosmos:groupClass skos:Collection ;
+	void:sparqlEndpoint <http://localhost:3030/ds/sparql> ;
+	skosmos:language "fi", "en";
+	skosmos:defaultLanguage "fi";
+	skosmos:showDeprecated "true";
+	skosmos:sparqlGraph <http://www.skosmos.skos/groups/> .
+
 :cycle a skosmos:Vocabulary, void:Dataset ;
 	dc11:title "Cycle test vocabulary"@en ;
 	dc:subject :cat_general ;

From 4318efd381dba49be1220d1455bc27977c3b1970 Mon Sep 17 00:00:00 2001
From: Thomas Francart <thomas.francart@sparna.fr>
Date: Mon, 6 Nov 2017 16:20:46 +0100
Subject: [PATCH 3/3] Fix @covers

---
 tests/VocabularyConfigTest.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/VocabularyConfigTest.php b/tests/VocabularyConfigTest.php
index 021150d16..2d81d9cc4 100644
--- a/tests/VocabularyConfigTest.php
+++ b/tests/VocabularyConfigTest.php
@@ -348,7 +348,7 @@ public function testGetTypes() {
   }
   
   /**
-   * @covers VocabularyConfig::showDeprecated
+   * @covers VocabularyConfig::getShowDeprecated
    */
   public function testShowDeprecated() {
       $vocab = $this->model->getVocabulary('showDeprecated');