Merge branch 'hotfix-elastic'

Indicia-Team · Jan 9, 2019 · 996f4bc · 996f4bc
2 parents a3904de + 07bf124
commit 996f4bc
Show file tree

Hide file tree

Showing 9 changed files with 38 additions and 43 deletions.
diff --git a/application/controllers/scheduled_tasks.php b/application/controllers/scheduled_tasks.php
@@ -797,7 +797,6 @@ private function loadOccurrencesDelta($plugin, $timestamp, $currentTime) {
     when o.created_on>'$timestamp' then o.created_on
     else greatest(o.updated_on, s.updated_on, sp.updated_on)
   end as timestamp,
-  w.verification_checks_enabled,
   lower(coalesce(onf.attr_stage, onf.attr_sex_stage)) as stage
 into temporary occdelta
 from occlist ol
@@ -806,7 +805,6 @@ private function loadOccurrencesDelta($plugin, $timestamp, $currentTime) {
 join cache_occurrences_nonfunctional onf on onf.id=co.id
 join samples s on s.id=o.sample_id and s.deleted=false
 left join samples sp on sp.id=s.parent_id and sp.deleted=false
-join websites w on w.id=o.website_id and w.deleted=false;
 
 create index ix_occdelta_taxa_taxon_list_id on occdelta(taxa_taxon_list_id);
 create index ix_occdelta_taxa_taxon_list_external_key on occdelta(taxa_taxon_list_external_key);

diff --git a/modules/data_cleaner/controllers/services/data_cleaner.php b/modules/data_cleaner/controllers/services/data_cleaner.php
@@ -13,8 +13,7 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see http://www.gnu.org/licenses/gpl.html.
  *
- * @package Services
- * @author  Indicia Team
+ * @author Indicia Team
  * @license http://www.gnu.org/licenses/gpl.html GPL 3.0
  * @link  http://code.google.com/p/indicia/
  */
@@ -71,15 +70,14 @@ public function verify() {
 LIMIT 0;
 SQL
 );
-      // Ensure the verify service always performs checks
-      $db->query("ALTER TABLE occdelta ADD COLUMN verification_checks_enabled boolean NOT NULL DEFAULT true;");
       try {
         $this->prepareOccdelta($db, $sample, $occurrences);
         $r = $this->runRules($db);
         $db->query('drop table occdelta');
         $this->content_type = 'Content-Type: application/json';
         $this->response = json_encode($r);
-      } catch (Exception $e) {
+      }
+      catch (Exception $e) {
         $db->query('drop table occdelta');
         $this->response = "Query failed";
         error_logger::log_error('Error occurred calling verification rule service', $e);
@@ -118,8 +116,8 @@ private function prepareOccdelta($db, $sample, $occurrences) {
       $date_start = $vd[0];
       $date_end = $vd[1];
       $date_type = $vd[2];
-      $db->query("insert into occdelta (website_id, survey_id, date_start, date_end, date_type, public_geom, taxa_taxon_list_id)
-          values ($website_id, $survey_id, '$date_start', '$date_end', '$date_type',  st_geomfromtext('$geom', $srid), $taxa_taxon_list_id);");
+      $db->query("insert into occdelta (website_id, survey_id, date_start, date_end, date_type, public_geom, taxa_taxon_list_id, verification_checks_enabled)
+          values ($website_id, $survey_id, '$date_start', '$date_end', '$date_type',  st_geomfromtext('$geom', $srid), $taxa_taxon_list_id, 't');");
     }
     // patch in some extra details about the taxon required for each cache entry
     $db->query("update occdelta o set taxon_meaning_id=ttl.taxon_meaning_id, taxa_taxon_list_external_key=ttl.external_key ".

diff --git a/modules/data_cleaner/tests/services/data_cleanerTest.php b/modules/data_cleaner/tests/services/data_cleanerTest.php
@@ -14,11 +14,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see http://www.gnu.org/licenses/gpl.html.
  *
- * @package  Services
- * @subpackage Data
- * @author  Indicia Team
- * @license  http://www.gnu.org/licenses/gpl.html GPL
- * @link   http://code.google.com/p/indicia/
+ * @author Indicia Team
+ * @license http://www.gnu.org/licenses/gpl.html GPL
+ * @link https://github.com/indicia-team/warehouse/
  */
 
 /**
@@ -174,25 +172,25 @@ public function testPeriodWithinYearFail() {
    * data_cleaner_period_within_year module must be enabled.
    */
   public function testPeriodWithinYearPass() {
-    $response = data_entry_helper::http_post($this->request, array(
-      'sample'=>json_encode(array(
-        'sample:survey_id'=>1,
-        'sample:date'=>'12/08/2012',
-        'sample:entered_sref'=>'SU1234',
-        'sample:entered_sref_system'=>'osgb'
-      )),
-      'occurrences'=>json_encode(array(
-        array(
-          'occurrence:taxa_taxon_list_id'=>1
-        ))
-      ),
-      'rule_types'=>json_encode(array('PeriodWithinYear'))
-    ));
-    $errors = json_decode($response['output'], true);
+    $response = data_entry_helper::http_post($this->request, [
+      'sample' => json_encode([
+        'sample:survey_id' => 1,
+        'sample:date' => '12/08/2012',
+        'sample:entered_sref' => 'SU1234',
+        'sample:entered_sref_system' => 'osgb',
+      ]),
+      'occurrences' => json_encode([
+        [
+          'occurrence:taxa_taxon_list_id' => 1,
+        ],
+      ]),
+      'rule_types' => json_encode(['PeriodWithinYear']),
+    ]);
+    $errors = json_decode($response['output'], TRUE);
 
     $this->assertTrue($response['result'], 'Invalid response');
     $this->assertInternalType('array', $errors, 'Errors list not returned');
     $this->assertCount(0, $errors, 'Errors contanied in list');
   }
 
-}
+}
diff --git a/modules/indicia_svc_data/controllers/services/data.php b/modules/indicia_svc_data/controllers/services/data.php
@@ -1046,7 +1046,7 @@ protected function build_query_results($count=false)
       // we have a filter on website_id to apply
       if ($this->website_id) {
         // check if a request for shared data is being made. Also check this is valid to prevent injection.
-        if (isset($_REQUEST['sharing']) && preg_match('/[reporting|peer_review|verification|data_flow|moderation|editing]/', $_REQUEST['sharing'])) {
+        if (isset($_REQUEST['sharing']) && preg_match('/(reporting|peer_review|verification|data_flow|moderation|editing)/', $_REQUEST['sharing'])) {
           // request specifies the sharing mode (i.e. the task being performed, such as verification, moderation). So
           // we can use this to work out access to other website data.
           $this->db->join('index_websites_website_agreements as iwwa', array(

diff --git a/modules/indicia_svc_security/tests/controllers/services/user_identifierTest.php b/modules/indicia_svc_security/tests/controllers/services/user_identifierTest.php
@@ -27,6 +27,7 @@ public function getDataSet() {
             'updated_by_id' => 1,
             'url' => 'http://www.indicia.org.uk',
             'password' => 'password',
+            'verification_checks_enabled' => 'f',
           ),
         ),
         'surveys' => array(

diff --git a/...currence_associations/reports/library/occurrence_associations/filterable_explore_list.xml b/...currence_associations/reports/library/occurrence_associations/filterable_explore_list.xml
@@ -8,7 +8,6 @@
   JOIN cache_occurrences_nonfunctional onf on onf.id=o.id
   JOIN cache_samples_nonfunctional snf on snf.id=o.sample_id
   JOIN cache_taxa_taxon_lists cttl on cttl.id=o.taxa_taxon_list_id
-  JOIN websites w on w.id=o.website_id and w.deleted=false
   #agreements_join#
   #joins#
   WHERE #sharing_filter#
@@ -26,7 +25,7 @@
     <column name='occurrence_id' display='ID' sql='o.id' datatype="integer"
             template='&lt;span class="status-icon status-{record_status} release-{release_status} substatus-{record_substatus} query-{query} certainty-{certainty}" title="{status_hint}"&gt;&lt;/span&gt;&lt;span class="record-id"&gt;{occurrence_id}&lt;/span&gt;'  />
     <column name='source' display='Source' datatype="text"
-            sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = w.title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
+            sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = snf.website_title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
     <column name='source_id' display='Source ID' datatype="text" visible="false"
             sql="o.website_id::varchar || '|' || o.survey_id::varchar"
             template="&lt;span title=&quot;{source}&quot;&gt;{source_id}&lt;/span&gt;" />
@@ -86,8 +85,8 @@
     <column name='input_form' visible="false" sql="case when o.input_form is null then '#default_input_form#' else o.input_form end" datatype="text" />
     <column name='pass' visible='false' sql="CASE
       WHEN o.data_cleaner_result='t' THEN '&lt;div class=&quot;pass-icon&quot; title=&quot;Passes all auto-checks.&quot;&gt;&lt;/div&gt;'
-      WHEN true and w.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
-      WHEN w.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
+      WHEN true and o.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
+      WHEN o.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
     END" />
     <column name='fails' display='Auto check' template="{pass}{fails}"
             sql="case when o.data_cleaner_result='f' then

diff --git a/modules/phpUnit/config/core_fixture.yaml b/modules/phpUnit/config/core_fixture.yaml
@@ -12,6 +12,7 @@ websites:
     updated_by_id: 1
     url: "http://www.indicia.org.uk"
     password: "password"
+    verification_checks_enabled: "true"
 
 
 surveys:
@@ -606,6 +607,7 @@ cache_occurrences_functional:
     map_sq_1km_id: 1
     map_sq_2km_id: 1
     map_sq_10km_id: 1
+    verification_checks_enabled: "true"
   -
     id: 2
     sample_id: 1
@@ -629,6 +631,7 @@ cache_occurrences_functional:
     map_sq_1km_id: 1
     map_sq_2km_id: 1
     map_sq_10km_id: 1
+    verification_checks_enabled: "true"
 
 cache_occurrences_nonfunctional:
   -

diff --git a/modules/verifier_notifications/reports/library/occdelta_overdue/filterable_explore_list.xml b/modules/verifier_notifications/reports/library/occdelta_overdue/filterable_explore_list.xml
@@ -10,7 +10,6 @@
   JOIN cache_occurrences_nonfunctional onf on onf.id=o.id
   JOIN cache_samples_nonfunctional snf on snf.id=o.sample_id
   JOIN cache_taxa_taxon_lists cttl on cttl.id=o.taxa_taxon_list_id
-  JOIN websites w on w.id=o.website_id and w.deleted=false
   LEFT JOIN index_websites_website_agreements canEdit on canEdit.from_website_id=o.website_id
     and canEdit.to_website_id in (#website_ids#) and canEdit.provide_for_editing=true
   #agreements_join#
@@ -35,7 +34,7 @@
     <column name='occurrence_id' display='ID' sql='o.id' datatype="integer"
         template='&lt;span class="status-icon status-{record_status} release-{release_status} substatus-{record_substatus} query-{query} certainty-{certainty}" title="{status_hint}"&gt;&lt;/span&gt;&lt;span class="record-id"&gt;{occurrence_id}&lt;/span&gt;'  />
     <column name='source' display='Source' datatype="text"
-        sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = w.title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
+        sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = snf.website_title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
     <column name='source_id' display='Source ID' datatype="text" visible="false"
             sql="o.website_id::varchar || '|' || o.survey_id::varchar"
             template="&lt;span title=&quot;{source}&quot;&gt;{source_id}&lt;/span&gt;" />
@@ -74,8 +73,8 @@
 end" datatype="text" />
     <column name='pass' visible='false' sql="CASE
       WHEN o.data_cleaner_result='t' THEN '&lt;div class=&quot;pass-icon&quot; title=&quot;Passes all auto-checks.&quot;&gt;&lt;/div&gt;'
-      WHEN true and w.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
-      WHEN w.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
+      WHEN true and o.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
+      WHEN o.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
     END" />
     <column name='fails' display='Auto check' template="{pass}{fails}"
         sql="case when o.data_cleaner_result='f' then

diff --git a/modules/workflow/reports/library/occurrences/filterable_explore_list_workflow.xml b/modules/workflow/reports/library/occurrences/filterable_explore_list_workflow.xml
@@ -11,7 +11,6 @@
   JOIN cache_samples_nonfunctional snf on snf.id=o.sample_id
   JOIN samples s on s.id=o.sample_id and s.deleted=false
   JOIN cache_taxa_taxon_lists cttl on cttl.id=o.taxa_taxon_list_id
-  JOIN websites w on w.id=o.website_id and w.deleted=false
   LEFT JOIN index_websites_website_agreements canEdit on canEdit.from_website_id=o.website_id
     and canEdit.to_website_id in (#website_ids#) and canEdit.provide_for_editing=true
   JOIN workflow_metadata wm ON wm.key='taxa_taxon_list_external_key'
@@ -62,7 +61,7 @@
         &lt;input type='hidden' class='external_key' value='{external_key}' /&gt;" />
     <column name="external_key" display="External key" sql="cttl.external_key" datatype="text" visible="false" />
     <column name="source" display="Source" datatype="text"
-        sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = w.title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
+        sql="snf.website_title || ' | ' || case when substring(snf.survey_title from 1 for length(snf.website_title)) = snf.website_title then trim(substring(snf.survey_title from length(snf.website_title)+1)) else snf.survey_title end" />
     <column name="source_id" display="Source ID" datatype="text" visible="false"
             sql="o.website_id::varchar || '|' || o.survey_id::varchar"
             template="&lt;span title=&quot;{source}&quot;&gt;{source_id}&lt;/span&gt;" />
@@ -100,8 +99,8 @@
 end" datatype="text" />
     <column name='pass' visible='false' sql="CASE
       WHEN o.data_cleaner_result='t' THEN '&lt;div class=&quot;pass-icon&quot; title=&quot;Passes all auto-checks.&quot;&gt;&lt;/div&gt;'
-      WHEN true and w.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
-      WHEN w.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
+      WHEN true and o.verification_checks_enabled='f' THEN '&lt;div class=&quot;auto-check-disabled-icon&quot; title=&quot;Auto-check disabled.&quot;&gt;-&lt;/div&gt;'
+      WHEN o.verification_checks_enabled='t' AND o.data_cleaner_result IS NULL THEN '&lt;div class=&quot;pending-icon&quot; title=&quot;Pending auto-check.&quot;&gt;...&lt;/div&gt;'
     END" />
     <column name="fails" display="Auto check" template="{pass}{fails}"
         sql="case when o.data_cleaner_result='f' then