Merge branch 'develop'

Indicia-Team · Jan 11, 2024 · dc7467b · dc7467b
2 parents bdaaacc + 00f9880
commit dc7467b
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Showing 23 changed files with 2,102 additions and 358 deletions.
diff --git a/ElasticsearchProxyHelper.php b/ElasticsearchProxyHelper.php
diff --git a/ElasticsearchReportHelper.php b/ElasticsearchReportHelper.php
@@ -92,6 +92,10 @@ class ElasticsearchReportHelper {
       'caption' => 'Submitted on',
       'description' => 'Date the record was submitted.',
     ],
+    'metadata.licence_code' => [
+      'caption' => 'Licence',
+      'description' => 'Code for the licence that applies to the record.',
+    ],
     'metadata.website.id' => [
       'caption' => 'Website ID',
       'description' => 'Unique ID of the website the record was submitted from.',
@@ -686,6 +690,7 @@ public static function groupIntegration(array $options) {
     if (empty($group_id) && $options['missingGroupIdBehaviour'] !== 'showAll') {
       hostsite_show_message(lang::get('The link you have followed is invalid.'), 'warning', TRUE);
       hostsite_goto_page('<front>');
+      return '';
     }
     require_once 'prebuilt_forms/includes/groups.php';
     $member = group_authorise_group_id($group_id, $options['readAuth']);
@@ -708,6 +713,7 @@ public static function groupIntegration(array $options) {
         if (!count($groups)) {
           hostsite_show_message(lang::get('The link you have followed is invalid.'), 'warning', TRUE);
           hostsite_goto_page('<front>');
+          return '';
         }
         $group = $groups[0];
         if ($options['showGroupSummary']) {
@@ -1141,7 +1147,7 @@ public static function filterSummary(array $options) {
 
     helper_base::$late_javascript .= <<<JS
 $('#es-filter-summary').idcFilterSummary('populate');
-$('.es-filter-param, .user-filter, .permissions-filter, .standalone-quality-filter select').change(function () {
+$('.es-filter-param, .user-filter, .permissions-filter, .standalone-quality-filter select,.standalone-media-filter select').change(function () {
     // Update any summary output
     $('#es-filter-summary').idcFilterSummary('populate');
 });
@@ -1151,6 +1157,25 @@ public static function filterSummary(array $options) {
     return self::getControlContainer('filterSummary', $options, json_encode([]), $html);
   }
 
+  /**
+   * Output a selector for presence of media.
+   *
+   * Mirrors the 'quality - records and photos' drop-down in standardParams
+   * control.
+   *
+   * @return string
+   *   Select HTML.
+   *
+   * @link https://indicia-docs.readthedocs.io/en/latest/site-building/iform/helpers/elasticsearch-report-helper.html#elasticsearchreporthelper-mediafilter
+   */
+  public static function mediaFilter(array $options) {
+    require_once 'prebuilt_forms/includes/report_filters.php';
+    $options = array_merge([
+      'standalone' => TRUE,
+    ], $options);
+    return media_filter_control($options['readAuth'], $options);
+  }
+
   /**
    * Output a selector for record status.
    *
@@ -1166,9 +1191,9 @@ public static function statusFilters(array $options) {
     $options = array_merge([
       'sharing' => 'reporting',
       'elasticsearch' => TRUE,
+      'standalone' => TRUE,
     ], $options);
-
-    return status_control($options['readAuth'], $options);
+    return status_filter_control($options['readAuth'], $options);
   }
 
   /**
@@ -2418,7 +2443,10 @@ private static function convertValueToFilterList($report, array $params, $output
     // Build a hidden input which causes filtering to this list.
     $keys = [];
     foreach ($listEntries as $row) {
-      $keys[] = $row[$outputField];
+      if ($row[$outputField]) {
+        // Don't want nulls as they break ES terms filters.
+        $keys[] = $row[$outputField];
+      }
     }
     return str_replace('"', '&quot;', json_encode($keys));
   }

diff --git a/data_entry_helper.php b/data_entry_helper.php
@@ -5846,7 +5846,6 @@ public static function multiple_places_species_checklist($options) {
         'Incorrect configuration - multiple_places_species_checklist requires a @include_sref_handler_jsspatialSystem option.',
         $indicia_templates['messageBox']
       );
-      return;
     }
     // The ID must be done here so it can be accessed by both the species grid and the buttons.
     $code = rand(0, 1000);
@@ -5864,6 +5863,7 @@ public static function multiple_places_species_checklist($options) {
     self::includeSrefHandlerJs([$options['spatialSystem'] => '']);
     $r = '';
     if (isset($options['sample_method_id'])) {
+      require_once 'prebuilt_forms/includes/form_generation.php';
       $sampleAttrs = self::getMultiplePlacesSpeciesChecklistSubsampleAttrs($options);
       foreach ($sampleAttrs as &$attr) {
         $attr['fieldname'] = "sc:n::$attr[fieldname]";

diff --git a/helper_base.php b/helper_base.php
@@ -836,6 +836,7 @@ public static function getTranslations(array $strings) {
    *   * brc_charts
    *   * bigr
    *   * d3
+   *   * html2canvas
    */
   public static function add_resource($resource) {
     // Ensure indiciaFns is always the first resource added.
@@ -1280,6 +1281,27 @@ public static function get_resources() {
             'https://unpkg.com/[email protected]/dist/bigr.min.umd.js',
           ],
         ],
+        'html2canvas' => [
+          'javascript' => [
+            'https://cdnjs.cloudflare.com/ajax/libs/html2canvas/1.4.1/html2canvas.min.js',
+           ],
+        ],
+        'brc_atlas_e' => [
+          'deps' => [
+            'd3_v7',
+          ],
+          'stylesheets' => [
+            'https://cdn.jsdelivr.net/gh/biologicalrecordscentre/[email protected]/dist/brcatlas_e.umd.css',
+          ],
+          'javascript' => [
+            'https://cdn.jsdelivr.net/gh/biologicalrecordscentre/[email protected]/dist/brcatlas_e.umd.min.js',
+          ],
+        ],
+        'd3_v7' => [
+          'javascript' => [
+            'https://d3js.org/d3.v7.min.js',
+          ],
+        ],
       ];
     }
     return self::$resource_list;
@@ -2367,6 +2389,7 @@ public static function getIndiciaData() {
       'buttonDefaultClass' => $indicia_templates['buttonDefaultClass'],
       'buttonHighlightedClass' => $indicia_templates['buttonHighlightedClass'],
       'buttonSmallClass' => 'btn-xs',
+      'jQueryValidateErrorClass' => $indicia_templates['error_class'],
     ];
     self::$indiciaData['formControlClass'] = $indicia_templates['formControlClass'];
     self::$indiciaData['inlineErrorClass'] = $indicia_templates['error_class'];
@@ -3271,12 +3294,6 @@ private static function apply_error_template($error, $fieldname) {
    *   * **report** - Path to the report file to use when loading data from a
    *     report, e.g. "library/occurrences/explore_list", excluding the .xml
    *     extension.
-   *   * **orderby** - Optional. For a non-default sort order, provide the
-   *     field name to sort by. Can be comma separated to sort by several
-   *     fields in descending order of precedence.
-   *   * **sortdir** - Optional. Specify ASC or DESC to define ascending or
-   *     descending sort order respectively. Can be comma separated if several
-   *     sort fields are specified in the orderby parameter.
    *   * **extraParams** - Array of extra URL parameters to send with the web
    *     service request. Should include key value pairs for the field filters
    *     (for table data) or report parameters (for the report data) as well as

diff --git a/import_helper_2.php b/import_helper_2.php
@@ -128,6 +128,7 @@ public static function importer($options) {
     self::$indiciaData['importChunkUrl'] = $options['importChunkUrl'];
     self::$indiciaData['getErrorFileUrl'] = $options['getErrorFileUrl'];
     self::$indiciaData['write'] = $options['writeAuth'];
+    self::$indiciaData['advancedFields'] = $options['advancedFields'];
     $nextImportStep = empty($_POST['next-import-step']) ? 'fileSelectForm' : $_POST['next-import-step'];
     self::$indiciaData['step'] = $nextImportStep;
     switch ($nextImportStep) {
@@ -779,10 +780,13 @@ private static function mappingsForm(array $options) {
     $lang = [
       'columnInImportFile' => lang::get('Column in import file'),
       'destinationDatabaseField' => lang::get('Destination database field'),
+      'display' => lang::get('Display'),
       'instructions' => lang::get($options['mappingsFormIntro']),
       'next' => lang::get('Next step'),
       'requiredFields' => lang::get('Required fields'),
       'requiredFieldsInstructions' => lang::get($options['requiredFieldsIntro']),
+      'standardFieldsOnly' => lang::get('standard fields'),
+      'standardAndAdvancedFields' => lang::get('standard and advanced fields'),
       'title' => lang::get('Map import columns to destination database fields'),
     ];
     self::addLanguageStringsToJs('import_helper_2', [
@@ -843,6 +847,11 @@ private static function mappingsForm(array $options) {
     return <<<HTML
 <h3>$lang[title]</h3>
 <p>$lang[instructions]</p>
+<div class="inline field-type-selector">
+  <span>$lang[display]</span>
+  <label class="radio-inline auto"><input type="radio" name="field-type-toggle" value="standard" checked> $lang[standardFieldsOnly]</label>
+  <label class="radio-inline auto"><input type="radio" name="field-type-toggle" value="advanced"> $lang[standardAndAdvancedFields]</label>
+</div>
 <form method="POST">
   <div class="row">
     <div class="col-md-8">
@@ -908,42 +917,74 @@ private static function getAvailableDbFieldsAsOptions(array $options, array $ava
         $shortGroupLabels[$optGroup] = lang::get("optionGroup-$fieldParts[0]-shortLabel");
       }
       // Find variants of field names for auto matching.
+      $alts = [];
       switch ($field) {
+        case 'occurrence:comment':
+          $alts = ['comment', 'comments', 'notes'];
+          break;
+
+        case 'occurrence:external_key':
+          $alts = ['recordkey', 'ref', 'referenceno', 'referencenumber'];
+          break;
+
+        case 'occurrence:fk_taxa_taxon_list':
+          $alts = ['commonname', 'scientificname', 'species', 'speciesname', 'taxon', 'taxonname', 'vernacular'];
+          break;
+
+        case 'occurrence:fk_taxa_taxon_list:search_code':
+          $alts = ['searchcode','tvk','taxonversionkey'];
+          break;
+
         case 'sample:date':
-          $alt = ' data-alt="eventdate"';
+          $alts = ['eventdate'];
           break;
 
         case 'sample:entered_sref':
-          $alt = ' data-alt="gridref,gridreference,spatialref,spatialreference,mapref,mapreference"';
+          $alts = ['gridref', 'gridreference', 'spatialref', 'spatialreference', 'mapref', 'mapreference', 'coords', 'coordinates'];
           break;
 
         case 'sample:location_name':
-          $alt = ' data-alt="location,site,sitename"';
+          $alts = ['location', 'site', 'sitename'];
           break;
 
         case 'sample:recorder_names':
-          $alt = ' data-alt="recorder,recordername,recordernames"';
-          break;
-
-        case 'occurrence:fk_taxa_taxon_list':
-          $alt = ' data-alt="species,speciesname,taxon,taxonname,scientificname"';
+          $alts = ['recorder', 'recordername', 'recordernames'];
           break;
 
         default:
           $alt = '';
       }
-      // Also use caption to pick up custom attributes.
-      if (substr($field, 3, 5) === 'Attr:') {
-        switch (preg_replace('/[^a-z]/', '', strtolower($caption))) {
-          case 'recorder':
-          case 'recordername':
-          case 'recordernames':
-            $alt = ' data-alt="recorder,recordername,recordernames"';
-            break;
+      // Matching variations for some potential custom attribute captions.
+      if (preg_match('/(.+) \(.+\)/', $caption, $matches)) {
+        // Strip anything in brackets from caption we are checking.
+        $captionSimplified = preg_replace('/[^a-z]/', '', strtolower($matches[1]));
+      }
+      else {
+        $captionSimplified = preg_replace('/[^a-z]/', '', strtolower($caption));
+      }
+      $customAttrVariations = [
+        ['abundance', 'count', 'qty', 'quantity'],
+        ['vc', 'vicecounty', 'vicecountynumber'],
+        ['recorder', 'recordername', 'recordernames', 'recorders'],
+        ['determinedby', 'determiner', 'identifiedby', 'identifier'],
+        ['lifestage','stage'],
+      ];
+      foreach ($customAttrVariations as $variationSet) {
+        if (in_array(strtolower($captionSimplified), $variationSet)) {
+          unset($variationSet[array_search($captionSimplified, $variationSet)]);
+          $alts = array_merge($alts, $variationSet);
         }
       }
-      $translatedCaption = lang::get($caption);
-      $colsByGroup[$optGroup][$translatedCaption] = "<option value=\"$field\" data-untranslated=\"$caption\"$alt>$translatedCaption</option>";
+      // Build the data attribute.
+      $alt = empty($alts) ? '' : ' data-alt="' . implode(',', $alts) . '"';
+      // Translation can be a precise term keyed by the field name, or a loose
+      // term keyed off the caption.
+      $translatedCaption = lang::get($field);
+      if ($translatedCaption === $field) {
+        $translatedCaption = lang::get($caption);
+      }
+      $advanced = in_array($field, $options['advancedFields']) ? ' class="advanced" ' : '';
+      $colsByGroup[$optGroup][$translatedCaption] = "<option value=\"$field\"$advanced data-untranslated=\"$caption\"$alt>$translatedCaption</option>";
     }
     $optGroupHtmlList = ["<option value=\"\">- $lang[notImported] -</option>"];
     foreach ($colsByGroup as $thisColOptionGroup => $optionsList) {
@@ -1589,6 +1630,7 @@ private static function clearTemplateCache(array $options) {
       'extraParams' => $options['readAuth'] + [
         'entity' => $options['entity'],
         'created_by_id' => hostsite_get_user_field('indicia_user_id'),
+        'orderby' => 'title',
       ],
     ]);
   }

diff --git a/lang/default.php b/lang/default.php
@@ -63,7 +63,8 @@
   // Default labels for various database fields.
   'occurrence:taxa_taxon_list_id' => 'Species',
   'sample:date' => 'Date',
-  'sample:entered_sref' => 'Spatial Reference',
+  'sample:entered_sref' => 'Spatial reference',
+  'sample:entered_sref_system' => 'Spatial reference system',
 
   // Spatial reference systems.
   'sref:OSGB' => 'British National Grid',
@@ -98,6 +99,13 @@
   'Click to Filter Occ_id' => 'Select records by record ID',
   'Click to Filter Quality' => 'Select records based on quality criteria such as verification status or presence of photos',
   'Click to Filter Source' => 'Select records based on source website, survey or input form',
+
+  // Data cleaner rules.
+  'ancillary_species failed' => 'Rarity check failed',
+  'identification_difficulty failed' => 'ID difficulty check failed',
+  'period failed' => 'Year range check failed',
+  'period_within_year failed' => 'Date range check failed',
+  'without_polygon failed' => 'Distribution check failed',
 ];
 
 // Some bigger bits of text better handled with HEREDOC.

diff --git a/lang/import_helper_2.php b/lang/import_helper_2.php
@@ -31,7 +31,13 @@
 TXT;
 
 $default_terms['import2mappingsFormIntro'] = <<<TXT
-Select which database field each of your import file's columns should be mapped to. Any columns in your file that do not have matches can be set to "- not imported -".
+Select which database field each of your import file's columns should be mapped to. Any columns in
+your file that do not need to be imported, or that have no matches, should be set to
+“- not imported -“.<br><br>
+By default this page shows all the “standard” attributes that will be sufficient for typical
+biological record formats. If needed you can add “advanced”  attributes to the list - these provide
+additional options but are not always straightforward to use.
+
 TXT;
 
 $default_terms['import2lookupMatchingFormIntro'] = <<<TXT
@@ -82,8 +88,14 @@
 $default_terms['optionGroup-sample-shortLabel'] = 'Sample';
 $default_terms['optionGroup-sample_medium-shortLabel'] = 'Sample media';
 $default_terms['optionGroup-smpAttr-shortLabel'] = 'Sample attributes';
+// Improved field name captions.
+$default_terms['occurrence:comment'] = 'Occurrence comment';
+$default_terms['occurrence:external_key'] = 'External record ID';
+$default_terms['location:external_key'] = 'External location ID';
+$default_terms['sample:comment'] = 'Sample comment';
+$default_terms['sample:external_key'] = 'External sample ID';
+$default_terms['sample:record_status'] = 'Sample verification status';
 
 $default_terms['Deleted'] = 'Deleted (for existing records)';
-$default_terms['External key'] = 'External key (your reference)';
 $default_terms['Id'] = 'ID (primary key for existing records)';
-$default_terms['Taxa taxon list (lookup in database)'] = 'Species or taxon name';
+$default_terms['Taxa taxon list (lookup)'] = 'Species or taxon name';