Merge branch 'develop'

.travis.yml

@@ -70,8 +70,9 @@ before_script:
   - .travis/postgres_setup.sh
   # Enable the phpunit module in config.php (meaning initialise() is not tested)
   - cp application/config/config.php.travis application/config/config.php
-  # Provide a config file for the rest_api and request_logging modules
+  # Provide a config file for the rest_api, spatial_index_builder and request_logging modules
   - cp modules/rest_api/config/rest.php.travis  modules/rest_api/config/rest.php
+  - cp modules/spatial_index_builder/config/spatial_index_builder.php.travis  modules/spatial_index_builder/config/spatial_index_builder.php
   - cp modules/request_logging/config/request_logging.example.php modules/request_logging/config/request_logging.php
   # Downgrade to PHPUnit 5.7
   - wget https://phar.phpunit.de/phpunit-5.7.phar

application/config/sref_notations.php

@@ -35,6 +35,8 @@
   '3109' => 'ETRS89 / Jersey Transverse Mercator',
   '23030' => 'ED50 / UTM zone 30N',
   '29902' => 'TM65 / Irish Grid',
+  '3006' => 'SWEREF99 TM / Swedish Transverse Mercator',
+  '3021' => 'RT90 2.5 gon v / Swedish Grid',
 ];
 
 // Set the internally stored geoms to use spherical mercator projection.
@@ -45,6 +47,8 @@
   '4326' => 5,
   '4277' => 5,
   '2169' => 0,
+  '3006' => 0,
+  '3021' => 0,
 ];
 
 // provide a list of systems which translate x,y format into a proper Lat/Long format, and the default ouput format

application/config/version.php

@@ -29,14 +29,14 @@
  *
  * @var string
  */
-$config['version'] = '3.0.1';
+$config['version'] = '3.1.0';
 
 /**
  * Version release date.
  *
  * @var string
  */
-$config['release_date'] = '2019-12-10';
+$config['release_date'] = '2020-01-15';
 
 /**
  * Link to the code repository downloads page.

application/helpers/spatial_ref.php

@@ -27,38 +27,41 @@ class spatial_ref {
   /**
    * Retrieves the metadata for all the supported spatial reference systems.
    *
-   * @param boolean $refresh Set to true to force a full refresh, otherwise the result is cached.
+   * @param bool $refresh
+   *   Set to true to force a full refresh, otherwise the result is cached.
    */
-  public static function system_metadata($refresh=false) {
+  public static function system_metadata($refresh = FALSE) {
     $cacheId = 'spatial-ref-systems';
     if ($refresh) {
       $cache = Cache::instance();
       $cache->delete($cacheId);
-      self::$system_metadata=false;
+      self::$system_metadata = FALSE;
     }
-    if (self::$system_metadata === false) {
+    if (self::$system_metadata === FALSE) {
       $latlong_systems = Kohana::config('sref_notations.lat_long_systems');
       $cache = Cache::instance();
       if ($cached = $cache->get($cacheId)) {
         self::$system_metadata = $cached;
-      } else {
+      }
+      else {
         self::$system_metadata = array();
         // fetch any systems that are just declared as srids, with no notation module required
         foreach (Kohana::config('sref_notations.sref_notations') as $code => $title) {
           self::$system_metadata["EPSG:$code"] = array(
             'title' => $title,
             'srid' => $code,
-            // make a small assumption here, that a non-lat long system is going to be an x y grid of metres.
-            'treat_srid_as_x_y_metres' => !isset($latlong_systems[$code])
+            // make a small assumption here, that a non-lat long system is
+            // going to be an x y grid of metres.
+            'treat_srid_as_x_y_metres' => !isset($latlong_systems[$code]),
           );
         }
-        // Now look for any modules which extend the sref systems available
+        // Now look for any modules which extend the sref systems available.
         foreach (Kohana::config('config.modules') as $path) {
           $plugin = basename($path);
           if (file_exists("$path/plugins/$plugin.php")) {
-            require_once("$path/plugins/$plugin.php");
-            if (function_exists($plugin.'_sref_systems')) {
-              $metadata = call_user_func($plugin.'_sref_systems');
+            require_once "$path/plugins/$plugin.php";
+            if (function_exists($plugin . '_sref_systems')) {
+              $metadata = call_user_func($plugin . '_sref_systems');
               self::$system_metadata = array_merge(self::$system_metadata, $metadata);
             }
           }

application/models/location.php

@@ -238,19 +238,23 @@ public function calcCentroid($boundary, $system = '4326') {
   }
 
   private static function getConvertedOptionValue($first, $second) {
-    return str_replace(array(',', ':'), array('&#44', '&#56'), $first) .
+    return str_replace(array(',', ':'), array('&#44', '&#58'), $first) .
             ":" .
-            str_replace(array(',', ':'), array('&#44', '&#56'), $second);
+            str_replace(array(',', ':'), array('&#44', '&#58'), $second);
   }
 
   /**
-   * Define a form that is used to capture a set of predetermined values that apply to every record during an import.
+   * Defines inputs required for values that apply to all imported records.
+   *
+   * Define a form that is used to capture a set of predetermined values that
+   * apply to every record during an import.
    */
-  public function fixed_values_form() {
-    $srefs = array();
-    $systems = spatial_ref::system_metadata();
-    foreach ($systems as $code => $metadata)
-        $srefs[] = self::getConvertedOptionValue($code, $metadata['title']);
+  public function fixedValuesForm() {
+    $srefs = [];
+    $systems = spatial_ref::system_list();
+    foreach ($systems as $code => $title) {
+      $srefs[] = self::getConvertedOptionValue($code, $title);
+    }
 
     $location_types = array(":Defined in file");
     $parent_location_types = array(":No filter");
@@ -265,28 +269,28 @@ public function fixed_values_form() {
         'display' => 'Website',
         'description' => 'Select the website to import records into.',
         'datatype' => 'lookup',
-        'population_call' => 'direct:website:id:title'
+        'population_call' => 'direct:website:id:title',
       ),
       'location:centroid_sref_system' => array(
         'display' => 'Spatial Ref. System',
         'description' => 'Select the spatial reference system used in this import file. Note, if you have a file with a mix of spatial reference systems then you need a ' .
             'column in the import file which is mapped to the Location Spatial Reference System field containing the spatial reference system code.',
         'datatype' => 'lookup',
-        'lookup_values'=>implode(',', $srefs)
+        'lookup_values' => implode(',', $srefs),
       ),
       'location:location_type_id' => array(
         'display' => 'Location Type',
         'description' => 'Select the Location Type for all locations in this import file. Note, if you have a file with a mix of location type then you need a ' .
                          'column in the import file which is mapped to the Location Type field.',
         'datatype' => 'lookup',
-        'lookup_values' => implode(',', $location_types)
+        'lookup_values' => implode(',', $location_types),
       ),
       'fkFilter:location:location_type_id' => array(
         'display' => 'Parent Location Type',
         'description' => 'If this import file includes locations which reference parent locations records, you can restrict the type of parent locations looked ' .
                          'up by setting this location type. It is not currently possible to use a column in the file to do this on a location by location basis.',
         'datatype' => 'lookup',
-        'lookup_values' => implode(',', $parent_location_types)
+        'lookup_values' => implode(',', $parent_location_types),
       ),
     );
   }

application/models/occurrence.php

@@ -570,32 +570,32 @@ private function _check_module_active($module) {
    *   * **occurrence_associations** - Set to 't' to enable occurrence associations options. The
    *     relevant warehouse module must also be enabled.
    */
-  public function fixed_values_form($options = array()) {
+  public function fixedValuesForm($options = array()) {
     $srefs = array();
     $systems = spatial_ref::system_list();
     foreach ($systems as $code => $title) {
-      $srefs[] = str_replace(array(',', ':'), array('&#44', '&#56'), $code) .
+      $srefs[] = str_replace(array(',', ':'), array('&#44', '&#58'), $code) .
             ":" .
-            str_replace(array(',', ':'), array('&#44', '&#56'), $title);
+            str_replace(array(',', ':'), array('&#44', '&#58'), $title);
     }
 
     $sample_methods = array(":Defined in file");
     $parent_sample_methods = array(":No filter");
     $terms = $this->db->select('id, term')->from('list_termlists_terms')->where('termlist_external_key', 'indicia:sample_methods')->orderby('term', 'asc')->get()->result();
     foreach ($terms as $term) {
-      $sample_method = str_replace(array(',', ':'), array('&#44', '&#56'), $term->id) .
+      $sample_method = str_replace(array(',', ':'), array('&#44', '&#58'), $term->id) .
         ":" .
-        str_replace(array(',', ':'), array('&#44', '&#56'), $term->term);
+        str_replace(array(',', ':'), array('&#44', '&#58'), $term->term);
       $sample_methods[] = $sample_method;
       $parent_sample_methods[] = $sample_method;
     }
 
     $locationTypes = array(":No filter");
     $terms = $this->db->select('id, term')->from('list_termlists_terms')->where('termlist_external_key', 'indicia:location_types')->orderby('term', 'asc')->get()->result();
     foreach ($terms as $term) {
-      $locationTypes[] = str_replace(array(',', ':'), array('&#44', '&#56'), $term->id) .
+      $locationTypes[] = str_replace(array(',', ':'), array('&#44', '&#58'), $term->id) .
         ":" .
-        str_replace(array(',', ':'), array('&#44', '&#56'), $term->term);
+        str_replace(array(',', ':'), array('&#44', '&#58'), $term->term);
     }
     $retVal = array(
       'website_id' => array(

application/models/sample.php

@@ -346,7 +346,7 @@ public function caption() {
   /**
    * Define a form that is used to capture a set of predetermined values that apply to every record during an import.
    */
-  public function fixed_values_form($options = array()) {
+  public function fixedValuesForm($options = array()) {
     $srefs = array();
     $systems = spatial_ref::system_list();
     foreach ($systems as $code => $title)

application/models/taxa_taxon_list.php

@@ -463,7 +463,7 @@ public function getDefaults() {
    * Define a form that is used to capture a set of predetermined values that
    * apply to every record during an import.
    */
-  public function fixed_values_form() {
+  public function fixedValuesForm() {
     return array(
       'taxa_taxon_list:taxon_list_id' => array(
         'display' => 'Species List',

application/models/termlists_term.php

@@ -325,7 +325,7 @@ public function getDefaults() {
   /**
    * Define a form that is used to capture a set of predetermined values that apply to every record during an import.
    */
-  public function fixed_values_form() {
+  public function fixedValuesForm() {
     return array(
         'termlists_term:termlist_id' => array(
             'display' => 'Termlist',

application/tests/helpers/vague_dateTest.php

@@ -187,6 +187,7 @@ public function testVagueDateToString($from, $to, $type, $expected) {
   public function provideStringToVagueDate() {
     $year = date('Y');
     $lastYear = $year - 1;
+    $lastDayInFeb = date('L') === '1' ? '29' : '28';
     return [
       'Date 1997-08-02' => ['1997-08-02', '1997-08-02', '1997-08-02', 'D'],
       'Date 02/08/1997' => ['02/08/1997', '1997-08-02', '1997-08-02', 'D'],
@@ -269,7 +270,7 @@ public function provideStringToVagueDate() {
       'Season Autumn 92' => ['Autumn 92', '1992-09-01', '1992-11-30', 'P'],
       // Month only and season only years are always for the current year.
       'Month only March' => ['March', "$year-03-01", "$year-03-31", 'M'],
-      'Season only Winter' => ['Winter', "$lastYear-12-01", "$year-02-28", 'S'],
+      'Season only Winter' => ['Winter', "$lastYear-12-01", "$year-02-$lastDayInFeb", 'S'],
       'Season only Spring' => ['Spring', "$year-03-01", "$year-05-31", 'S'],
       'Season only Summer' => ['Summer', "$year-06-01", "$year-08-31", 'S'],
       'Season only Autumn' => ['Autumn', "$year-09-01", "$year-11-30", 'S'],

application/views/templates/template.php

@@ -56,7 +56,6 @@
 );
 echo html::script(
   array(
-    'media/js/json2.js',
     'media/js/jquery.js?v=3.2.1',
     'media/js/jquery.url.js',
     'media/js/fancybox/source/jquery.fancybox.pack.js',

modules/attribute_sets/helpers/attribute_sets.php

@@ -435,13 +435,61 @@ private static function deleteAttributesTaxonRestriction($db, $model) {
     and aw.{$entity}_attribute_id=attla.{$entity}_attribute_id
     and aw.deleted=false
   where astr.deleted=false
-  and atr.{$entity}_attributes_website_id=atr.id
+  and atr.{$entity}_attributes_website_id=aw.id
   and atr.restrict_to_taxon_meaning_id=astr.restrict_to_taxon_meaning_id
   and coalesce(atr.restrict_to_stage_term_meaning_id, 0)=coalesce(astr.restrict_to_stage_term_meaning_id, 0)
 );
 SQL;
       $db->query($qry);
     }
+
+    // taxa_taxon_list_attributes do not use a website table so the above SQL does not work
+    // This code is a version of the above code for taxa_tax_list_attributes
+    $ttlQry = <<<SQL
+    update taxa_taxon_list_attribute_taxon_restrictions atr
+    set deleted=true, updated_on=now(), updated_by_id=$userId
+    from attribute_sets_taxon_restrictions astr
+    join attribute_sets_surveys ass
+      on ass.id=astr.attribute_sets_survey_id
+    join attribute_sets aset
+      on aset.id=ass.attribute_set_id
+    join attribute_sets_taxa_taxon_list_attributes asttla
+      on asttla.attribute_set_id=ass.attribute_set_id
+    join taxon_lists_taxa_taxon_list_attributes tlttla
+      on tlttla.taxon_list_id=aset.taxon_list_id
+      and tlttla.taxa_taxon_list_attribute_id=asttla.taxa_taxon_list_attribute_id
+    where (astr.deleted or ass.deleted or aset.deleted or asttla.deleted or tlttla.deleted)
+    and $alias.id=$model->id
+    and atr.taxon_lists_taxa_taxon_list_attribute_id=tlttla.id
+    and atr.restrict_to_taxon_meaning_id=astr.restrict_to_taxon_meaning_id
+    and coalesce(atr.restrict_to_stage_term_meaning_id, 0)=coalesce(astr.restrict_to_stage_term_meaning_id, 0)
+    and atr.deleted=false
+    and atr.id not in (
+      -- Exclude deletions for any restriction that is still valid because of
+      -- another attribute set.
+      select atr.id
+      from taxa_taxon_list_attribute_taxon_restrictions, attribute_sets_taxon_restrictions astr
+      join attribute_sets_surveys ass
+        on ass.id=astr.attribute_sets_survey_id
+        and ass.deleted=false
+      join attribute_sets aset
+        on aset.id=ass.attribute_set_id
+        and aset.deleted=false
+      join attribute_sets_taxa_taxon_list_attributes asttla
+        on asttla.attribute_set_id=ass.attribute_set_id
+        and asttla.deleted=false
+      join taxon_lists_taxa_taxon_list_attributes tlttla
+        on tlttla.taxon_list_id=aset.taxon_list_id
+        and tlttla.taxa_taxon_list_attribute_id=asttla.taxa_taxon_list_attribute_id
+        and tlttla.deleted=false
+      where astr.deleted=false
+      --AVB changed this in original code
+      and atr.taxon_lists_taxa_taxon_list_attribute_id=tlttla.id
+      and atr.restrict_to_taxon_meaning_id=astr.restrict_to_taxon_meaning_id
+      and coalesce(atr.restrict_to_stage_term_meaning_id, 0)=coalesce(astr.restrict_to_stage_term_meaning_id, 0)
+    );
+SQL;
+    $db->query($ttlQry);
   }
 
   /**

modules/auto_verify/config/auto_verify.php.example.php

@@ -1,4 +1,5 @@
 <?php
+
 /**
  * Indicia, the OPAL Online Recording Toolkit.
  *
@@ -13,16 +14,16 @@
  * 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	Species Alerts
- * @subpackage Config
- * @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 http://code.google.com/p/indicia/
  */
 
-$config['auto_accept_occurrences_with_null_id_difficulty']='true';
-// Note that -1 (or less) is unlimited, 0 processes nothing
-$config['max_num_records_to_process_at_once']=0;
-$config['oldest_record_created_date_to_process']='01/01/2000';
-// 1 (or less) is effectively unlimited
-$config['oldest_occurrence_id_to_process']=1;
+$config['auto_accept_occurrences_with_null_id_difficulty'] = 'true';
+
+// Note that -1 (or less) is unlimited, 0 processes nothing.
+$config['max_num_records_to_process_at_once'] = 0;
+$config['oldest_record_created_date_to_process'] = '01/01/2000';
+
+// 1 (or less) is effectively unlimited.
+$config['oldest_occurrence_id_to_process'] = 1;