Merge branch 'develop'

application/config/config.php.example

@@ -133,7 +133,7 @@ $config['modules'] = array
          MODPATH.'sref_channel_islands',  // Jersey and Guernsey grid notations
          MODPATH.'sref_utm',              // UTM grid notation
          MODPATH.'demo',                  // Demo and test pages
-         MODPATH.'data_cleaner'           // automatic record checks
+         MODPATH.'data_cleaner',           // automatic record checks
          MODPATH.'cache_builder',         // build a cache for performance reporting
          MODPATH.'spatial_index_builder', // index of location occurrence overlaps
 //         ,MODPATH.'summary_builder'       // build a cache for improving the performance of reporting summary data

application/config/version.php

@@ -31,7 +31,7 @@
  *
  * @var string
  */
-$config['version'] = '1.57.0';
+$config['version'] = '1.58.0';
 /**
  * Version release date.
  *

application/controllers/licence.php

@@ -14,18 +14,13 @@
  * 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 Core
- * @subpackage Controllers
  * @author Indicia Team
  * @license http://www.gnu.org/licenses/gpl.html GPL
  * @link https://github.com/Indicia-Team/warehouse
  */
 
 /**
  * Controller providing CRUD access to the licences list.
- *
- * @package Core
- * @subpackage Controllers
  */
 class Licence_Controller extends Gridview_Base_Controller {
 
@@ -41,7 +36,10 @@ public function __construct() {
   }
 
   /**
-   * You can only access the list of licences if at least an editor of one website.
+   * Check if page access authorised.
+   *
+   * You can only access the list of licences if at least an editor of one
+   * website.
    */
   protected function page_authorised() {
     return $this->auth->logged_in('CoreAdmin') || $this->auth->has_any_website_access('editor');
@@ -50,9 +48,9 @@ protected function page_authorised() {
   /**
    * Returns model values ready to load onto a form.
    *
-   * Returns an array of all values from this model and its super models ready to be
-   * loaded into a form. For this controller, we need to also need to flash a warning
-   * about editing existing licence records.
+   * Returns an array of all values from this model and its super models ready
+   * to be loaded into a form. For this controller, we need to also need to
+   * flash a warning about editing existing licence records.
    */
   protected function getModelValues() {
     $r = parent::getModelValues();

application/libraries/ATTR_ORM.php

@@ -55,6 +55,8 @@ public function validate(Validation $array, $save = FALSE) {
         'description',
         'source_id',
         'caption_i18n',
+        'term_name',
+        'term_identifier',
       )
     );
     $array->add_rules('caption', 'required');

application/views/custom_attribute/custom_attribute_edit.php

@@ -68,6 +68,34 @@
         'helpText' => $helpText,
       ]);
     }
+    if (array_key_exists('term_name', $this->model->as_array())) {
+      $helpText = <<<TXT
+If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise provide
+a brief alphanumeric only (with no spaces) version of the attribute name to give it a unique identifier within the
+context of the survey dataset to make it easier to refer to in configuration.
+TXT;
+      echo data_entry_helper::text_input([
+        'fieldname' => "$model->object_name:term_name",
+        'label' => 'Term name',
+        'default' => html::initial_value($values, "$model->object_name:term_name"),
+        'disabled' => $disabled_input === 'YES' ? 'disabled' : '',
+        'helpText' => $helpText,
+      ]);
+    }
+    if (array_key_exists('term_identifier', $this->model->as_array())) {
+      $helpText = <<<TXT
+If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, typically
+the URL to the term definition.
+TXT;
+      echo data_entry_helper::text_input([
+        'fieldname' => "$model->object_name:term_identifier",
+        'label' => 'Term identifier',
+        'default' => html::initial_value($values, "$model->object_name:term_identifier"),
+        'disabled' => $disabled_input === 'YES' ? 'disabled' : '',
+        'helpText' => $helpText,
+        'class' => 'control-width-6',
+      ]);
+    }
     if (array_key_exists('description', $this->model->as_array())) {
       echo data_entry_helper::textarea([
         'fieldname' => "$model->object_name:description",

modules/indicia_setup/db/version_1_58_0/201803261544_attr_dwc.sql

@@ -0,0 +1,76 @@
+ALTER TABLE survey_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN survey_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN survey_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE sample_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN sample_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN sample_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE occurrence_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN occurrence_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN occurrence_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE location_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN location_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN location_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE taxa_taxon_list_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN taxa_taxon_list_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN taxa_taxon_list_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE termlists_term_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN termlists_term_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN termlists_term_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';
+
+ALTER TABLE person_attributes
+   ADD COLUMN term_name character varying,
+   ADD COLUMN term_identifier character varying;
+COMMENT ON COLUMN person_attributes.term_name
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term name. Otherwise '
+  'provide a brief alphanumeric only (with no spaces) version of the attribute name  to give it a unique identifier '
+  'within the context of the survey dataset to make it easier to refer to in configuration.';
+COMMENT ON COLUMN person_attributes.term_identifier
+  IS 'If the attribute is linked to a standardised glossary such as Darwin Core then provide the term identifier, '
+  'typically the URL to the term definition.';

modules/indicia_setup/db/version_1_56_0/201802190926_attr_caption_i18n_views.sql → modules/indicia_setup/db/version_1_58_0/201803262026_attr_dwc_views.sql

@@ -5,6 +5,8 @@ CREATE OR REPLACE VIEW list_survey_attributes AS
   SELECT a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type,
@@ -41,6 +43,8 @@ CREATE OR REPLACE VIEW list_sample_attributes AS
   SELECT a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type,
@@ -80,6 +84,8 @@ CREATE OR REPLACE VIEW list_occurrence_attributes AS
     a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type, ct.control AS control_type,
@@ -117,6 +123,8 @@ CREATE OR REPLACE VIEW list_location_attributes AS
     a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type, ct.control AS control_type,
@@ -154,6 +162,8 @@ CREATE OR REPLACE VIEW list_taxa_taxon_list_attributes AS
   SELECT a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type,
@@ -189,6 +199,8 @@ CREATE OR REPLACE VIEW list_termlists_term_attributes AS
   SELECT a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type,
@@ -227,6 +239,8 @@ CREATE OR REPLACE VIEW list_person_attributes AS
  SELECT a.id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     fsb2.name AS outer_structure_block,
     fsb.name AS inner_structure_block,
     a.data_type,
@@ -266,6 +280,8 @@ CREATE OR REPLACE VIEW list_survey_attribute_values AS
     a.id AS survey_attribute_id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -319,6 +335,8 @@ CREATE OR REPLACE VIEW list_sample_attribute_values AS
     a.id AS sample_attribute_id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -373,6 +391,8 @@ CREATE OR REPLACE VIEW list_occurrence_attribute_values AS
     a.id AS occurrence_attribute_id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -429,6 +449,8 @@ CREATE OR REPLACE VIEW list_location_attribute_values AS
     a.id AS location_attribute_id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -484,6 +506,8 @@ CREATE OR REPLACE VIEW list_taxa_taxon_list_attribute_values AS
     a.id AS taxa_taxon_list_attribute_id,
     a.caption,
     a.caption_i18n::text,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -510,6 +534,8 @@ UNION
     a.id AS taxa_taxon_list_attribute_id,
     a.caption,
     a.caption_i18n::text,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -566,6 +592,8 @@ CREATE OR REPLACE VIEW list_termlists_term_attribute_values AS
     a.id AS termlists_term_attribute_id,
     a.caption,
     a.caption_i18n,
+    a.term_name,
+    a.term_identifier,
     CASE a.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar
@@ -620,6 +648,8 @@ CREATE OR REPLACE VIEW list_person_attribute_values AS
     pa.id AS person_attribute_id,
     pa.caption,
     pa.caption_i18n,
+    pa.term_name,
+    pa.term_identifier,
     CASE pa.data_type
       WHEN 'T'::bpchar THEN 'Text'::bpchar
       WHEN 'L'::bpchar THEN 'Lookup List'::bpchar

modules/indicia_svc_data/controllers/services/data.php

@@ -839,7 +839,7 @@ private function decodeArrayParameter($value) {
     $decoded = json_decode($value);
     // Strings which contain commas but not valid JSON are almost certainly mistakes.
     if ($decoded === null && strpos($value, ',') !== false) {
-      ValidationError('Validation error', 2003, 'Invalid format for array parameter.');
+      throw new ValidationError('Validation error', 2003, 'Invalid format for array parameter.');
     }
     return $decoded === null ? $value : $decoded;
   }

reports/library/occurrences/filterable_dwc_nbn_occurrences.xml

@@ -9,14 +9,27 @@
     FROM cache_occurrences_functional o
     JOIN cache_occurrences_nonfunctional onf ON onf.id=o.id
     JOIN cache_taxa_taxon_lists cttl ON cttl.id=o.taxa_taxon_list_id
-    JOIN cache_taxon_searchterms cts ON cts.taxa_taxon_list_id=o.taxa_taxon_list_id AND cts.name_type='A'
+    JOIN cache_taxon_searchterms cts ON cts.taxa_taxon_list_id=o.taxa_taxon_list_id AND cts.simplified=false
     JOIN cache_samples_nonfunctional snf ON snf.id=o.sample_id
+    LEFT JOIN (sample_attribute_values vdatasetID
+      JOIN sample_attributes adatasetID ON adatasetID.id=vdatasetID.sample_attribute_id AND adatasetID.term_name='datasetID'
+    ) ON vdatasetID.sample_id=o.sample_id AND vdatasetID.deleted=false
     #agreements_join#
     #joins#
     WHERE #sharing_filter#
     #idlist#
   </query>
   <params>
+    <param name="dataset_name"
+           display="Dataset name"
+           datatype="string"
+           default="Indicia"
+           description="Name of the dataset to populate into Dwc datasetName." />
+    <param name="rights_holder"
+           display="Rights holder"
+           datatype="string"
+           default="Not set"
+           description="A person or organisation owning or managing rights over the resource." />
     <param name="smpattrs"
            display="Sample attribute list"
            datatype="smpattrs"
@@ -112,10 +125,9 @@ END"
           datatype="text"
           term="http://purl.org/dc/terms/license" />
     <column name="rightsHolder"
-          sql="null::text"
+          sql="'#rights_holder#'"
           datatype="text"
           term="http://purl.org/dc/terms/rightsHolder" />
-    <!-- check since using output_sref, this is not relevant? -->
     <column name="coordinateUncertaintyInMeters"
           sql="CASE
   WHEN o.sensitive=true OR snf.privacy_precision IS NOT NULL OR snf.entered_sref_system NOT SIMILAR TO '[0-9]+' THEN
@@ -146,9 +158,17 @@ END"
           datatype="integer"
           term="http://rs.tdwg.org/dwc/terms/decimaLongitude" />
     <column name="datasetName"
-          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"
+          sql="'#dataset_name#'"
           datatype="text"
           term="http://rs.tdwg.org/dwc/terms/datasetName" />
+    <column name="datasetID"
+          sql="vdatasetID.text_value"
+          datatype="text"
+          term="http://rs.tdwg.org/dwc/terms/datasetID" />
+    <column name="collectionCode"
+          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"
+          datatype="text"
+          term="http://rs.tdwg.org/dwc/terms/collectionCode" />
     <column name="locality"
           sql="o.location_name"
           datatype="text"