Merge pull request #225 from abretaud/typos

Fix minor typos

tripal/api/tripal.entities.api.inc

@@ -1048,7 +1048,7 @@ function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL)
 
     if (property_exists($entity, $field_name)) {
       // Note: there is a memory leak in field_get_items() so we can't use it
-      // here or bulk publising will slowly erode memory.
+      // here or bulk publishing will slowly erode memory.
       //$field_value = field_get_items('TripalEntity', $entity, $field_name);
       if (array_key_exists(0, $entity->{$field_name}['und'])) {
         $value = $entity->{$field_name}['und'][0]['value'];
@@ -1286,4 +1286,4 @@ function tripal_insert_entity($bundle_name, $values){
 function tripal_update_entity($bundle_name, $values) {
 
 
-}
+}

tripal/includes/TripalFields/TripalField.inc

@@ -474,7 +474,7 @@ class TripalField {
    *   An array of the following format:
    *     $entity->{$field_name}['und'][0]['value'] = $value;
    *   where:
-   *     - $entity is the enity object to which this field is attached.
+   *     - $entity is the entity object to which this field is attached.
    *     - $field_name is the name of this field
    *     - 'und' is the language code (in this case 'und' == undefined)
    *     - 0 is the cardinality.  Increment by 1 when more than one item is
@@ -549,7 +549,7 @@ class TripalField {
         'elements' => array(
           'rdfs:label' => array(
             'searchable' => TRUE,
-            'name' => 'scientfic_name',
+            'name' => 'scientific_name',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
           ),

tripal/includes/tripal.importer.inc

@@ -191,7 +191,7 @@ function tripal_get_importer_form_submit($form, &$form_state) {
   }
   try {
 
-    // Now allow the loader to do it's own submit if needed.
+    // Now allow the loader to do its own submit if needed.
     $importer = new $class();
     $importer->formSubmit($form, $form_state);
     // If the formSubmit made changes to the $form_state we need to update the
@@ -213,4 +213,4 @@ function tripal_get_importer_form_submit($form, &$form_state) {
   catch (Exception $e) {
     drupal_set_message('Cannot submit import: ' . $e->getMessage(), 'error');
   }
-}
+}

tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc

@@ -194,7 +194,7 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
       $tables[$record_array['table']] = $record_array['table'];
     }
 
-    // iterate through each of the fiels for the current record and
+    // iterate through each of the fields for the current record and
     // set the default_data array
     foreach ($record_array['fields'] as $field_index => $field_array) {
 

tripal_chado/api/modules/tripal_chado.organism.api.inc

@@ -154,7 +154,7 @@ function tripal_get_organism_scientific_name($organism) {
     }
 
     if ($rank) {
-      $rank = tripal_abbreviate_infraspeicifc_rank($rank);
+      $rank = tripal_abbreviate_infraspecific_rank($rank);
       $name .= ' ' . $rank . ' ' . $organism->infraspecific_name;
     }
     else if ($organism->infraspecific_name) {
@@ -313,7 +313,7 @@ function tripal_autocomplete_organism($text) {
  * @return
  *   The proper abbreviation for the rank.
  */
-function tripal_abbreviate_infraspeicifc_rank($rank) {
+function tripal_abbreviate_infraspecific_rank($rank) {
   $abb = '';
   switch($rank) {
     case 'no_rank':
@@ -344,4 +344,4 @@ function tripal_abbreviate_infraspeicifc_rank($rank) {
       $abb = $rank;
   }
   return $abb;
-}
+}

tripal_chado/api/tripal_chado.api.inc

@@ -180,9 +180,9 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
       "If the load fails or is terminated prematurely then the entire set of \n" .
       "is rolled back with no changes to the database\n\n";
 
+  $i = 0;
   printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, 0, number_format(memory_get_usage()));
   try {
-    $i = 0;
     while($record = $records->fetchObject()) {
 
       // update the job status every interval
@@ -199,8 +199,8 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
       $entity = $ec->create(array(
         'bundle' => $bundle_name,
         'term_id' => $bundle->term_id,
-        // Add in the Chaod details for when the hook_entity_create()
-        // is called and our tripal_cahdo_entity_create() implementation
+        // Add in the Chado details for when the hook_entity_create()
+        // is called and our tripal_chado_entity_create() implementation
         // can deal with it.
         'chado_record' => chado_generate_var($table, array($pkey_field => $record_id)),
         'chado_record_id' => $record_id,

tripal_chado/api/tripal_chado.entity.api.inc

@@ -3,7 +3,7 @@
  * Retreive the entity_id assigned to a given record_id and bundle.
  *
  * @param $bundle
- *   A bundle object (as retreieved from tripal_load_bundle_entity().
+ *   A bundle object (as retrieved from tripal_load_bundle_entity().
  * @param $record_id
  *   The ID of the record in the Chado table. The record must belong to
  *   the table to which the bundle is associated in chado.

tripal_chado/includes/TripalFields/ChadoField.inc

@@ -8,7 +8,7 @@ class ChadoField extends TripalField {
   // The default description for this field.
   public static $default_description = 'The generic base class for all Chado fields. Replace this text as appropriate for the child implementation.';
 
-  // A list of global settings. These can be accessed witihn the
+  // A list of global settings. These can be accessed within the
   // globalSettingsForm.  When the globalSettingsForm is submitted then
   // Drupal will automatically change these settings for all fields.
   // Once instances exist for a field type then these settings cannot be

tripal_chado/includes/TripalFields/obi__organism/obi__organism.inc

@@ -126,7 +126,7 @@ class obi__organism extends ChadoField {
         $genus_term => $organism->genus,
         $species_term => $organism->species,
       );
-      // The infraspecific fiels were introdcued in Chado v1.3.
+      // The infraspecific fields were introduced in Chado v1.3.
       if (property_exists($organism, 'infraspecific_name')) {
         $entity->{$field_name}['und'][0]['value'][$infraspecific_type_term] = NULL;
         $entity->{$field_name}['und'][0]['value'][$infraspecific_name_term] = $organism->infraspecific_name;

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon.inc

@@ -85,7 +85,7 @@ class taxrank__infraspecific_taxon extends ChadoField {
             'name' => 'infraspecific_name',
             'sortable' => TRUE,
             'searchable' => TRUE,
-            'label' => 'Infrasepcies Name',
+            'label' => 'Infraspecies Name',
             'help' => 'The infraspecific name of the organism below the rank of species.',
             'type' => 'xs:string',
             'readonly' => FALSE,
@@ -192,4 +192,4 @@ class taxrank__infraspecific_taxon extends ChadoField {
       $entity->{$field_name}['und'][0]['chado-organism__type_id'] = $record->type_id->cvterm_id;
     }
   }
-}
+}

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon_widget.inc

@@ -32,7 +32,7 @@ class taxrank__infraspecific_taxon_widget extends ChadoFieldWidget {
     if (array_key_exists('values', $form_state) and
         array_key_exists($field_name, $form_state['values'])) {
       $type_id = $form_state['values'][$field_name][$langcode][$delta]['infraname']['specific_epithet'];
-      $infra_name = $form_state['values'][$field_name][$langcode][$delta]['infraname']['infrapsecific_epithet'];
+      $infra_name = $form_state['values'][$field_name][$langcode][$delta]['infraname']['infraspecific_epithet'];
     }
 
     $widget['value'] = array(
@@ -52,7 +52,7 @@ class taxrank__infraspecific_taxon_widget extends ChadoFieldWidget {
     $terms = tripal_get_cvterm_select_options($cv->cv_id);
 
     // Unfortunately the taxonomic_rank vocabulary is not properly organized
-    // such that we an only include terms below 'species'. Therefore we will
+    // such that we only include terms below 'species'. Therefore we will
     // just list them here and hope we haven't missed one.
     $valid_terms = array('cultivar', 'subspecies', 'varietas', 'subvariety', 'forma', 'subforma');
     $options = array();
@@ -77,9 +77,9 @@ class taxrank__infraspecific_taxon_widget extends ChadoFieldWidget {
       '#options' => $options,
       '#default_value' => $type_id,
     );
-    $widget['infraname']['infrapsecific_epithet'] = array(
+    $widget['infraname']['infraspecific_epithet'] = array(
       '#type' => 'textfield',
-      '#title' => 'Infrapsecific Epithet',
+      '#title' => 'Infraspecific Epithet',
       '#description' => 'The name below species.',
       '#default_value' => $infra_name,
       '#required' => $element['#required'],
@@ -95,7 +95,7 @@ class taxrank__infraspecific_taxon_widget extends ChadoFieldWidget {
     $field_column = $this->instance['settings']['chado_column'];
 
     $type_id = $form_state['values'][$field_name]['und'][0]['infraname']['specific_epithet'];
-    $infra_name = $form_state['values'][$field_name]['und'][0]['infraname']['infrapsecific_epithet'];
+    $infra_name = $form_state['values'][$field_name]['und'][0]['infraname']['infraspecific_epithet'];
 
     if ($infra_name and $type_id) {
       $form_state['values'][$field_name]['und'][0]['value'] = $infra_name;

tripal_chado/includes/TripalImporter/TaxonomyImporter.inc

@@ -131,7 +131,7 @@ class TaxonomyImporter extends TripalImporter {
     );
     $form['taxonomy_ids'] = array(
       '#type' => 'textarea',
-      '#title' => 'Taxonomy IDa',
+      '#title' => 'Taxonomy ID',
       '#description' => t('Please provide a list of NCBI taxonomy IDs separated
         by spaces, tabs or new lines.
         The information about these organisms will be downloaded and new organism
@@ -141,7 +141,7 @@ class TaxonomyImporter extends TripalImporter {
     $form['import_existing'] = array(
       '#type' => 'checkbox',
       '#title' => 'Import details for existing species.',
-      '#description' =>  t('The NCBI Taxonmic Importer examines the organisms
+      '#description' =>  t('The NCBI Taxonomic Importer examines the organisms
         currently present in the database and queries NCBI for the
         taxonomic details.  If the importer is able to match the
         genus and species with NCBI the species details will be imported,
@@ -600,7 +600,7 @@ class TaxonomyImporter extends TripalImporter {
       ));
 
       // Remove the rank from the infraspecific name.
-      $abbrev = tripal_abbreviate_infraspeicifc_rank($rank);
+      $abbrev = tripal_abbreviate_infraspecific_rank($rank);
       $infra = preg_replace("/$abbrev/", "", $infra);
       $infra = trim($infra);
 
@@ -914,4 +914,4 @@ class TaxonomyImporter extends TripalImporter {
     );
     chado_insert_record('organism_dbxref', $values);
   }
-}
+}

tripal_chado/includes/tripal_chado.entity.inc

@@ -249,7 +249,7 @@ function tripal_chado_entity_view($entity, $type, $view_mode, $langcode) {
       $enabled_templates = variable_get('tripal_chado_enabled_legacy_templates', array());
       $legacy_template = 'legacy_template--chado_' . $chado_table;
 
-      // If the site admin has indicated that thhis entity type should use
+      // If the site admin has indicated that this entity type should use
       // a legacy tmplate then prepare the entity and content to fake a
       // node.
       if (key_exists($legacy_template, $enabled_templates) && $enabled_templates[$legacy_template]) {

tripal_chado/tripal_chado.module

@@ -1012,7 +1012,7 @@ function tripal_chado_form_field_ui_field_edit_form_alter(&$form, &$form_state,
   // such that record can't be saved in Chado.
 
   // TODO: we shouldn't check for specific field types here
-  // (e.g. chaod_linker_prop). That should be done via the TripalField
+  // (e.g. chado_linker_prop). That should be done via the TripalField
   // functions.
   if ($form['#instance']['entity_type'] == 'TripalEntity') {
     if ($form['#field']['storage']['type'] == 'field_chado_storage' and
@@ -1141,4 +1141,4 @@ function tripal_feature_match_features_page($id) {
   }
 
 
-}
+}

tripal_ws/includes/TripalWebService/TripalEntityService_v0_1.inc

@@ -950,8 +950,8 @@ class TripalEntityService_v0_1 extends TripalWebService {
       'title' => 'Content Collection',
     );
     $vocab = tripal_get_vocabulary_details('hydra');
-    $propeties = array();
-    $propeties[] = array(
+    $properties = array();
+    $properties[] = array(
       'type' => $vocab['sw_url'],
       'title' => 'member',
       'description' => "The list of available content types.",
@@ -959,7 +959,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
       "readonly" => FALSE,
       "writeonly" => FALSE,
     );
-    $propeties[] = array(
+    $properties[] = array(
       "type" => $vocab['sw_url'],
       "title" => "totalItems",
       "description" => "The total number of content types.",
@@ -967,7 +967,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
       "readonly" => FALSE,
       "writeonly" => FALSE
     );
-    $propeties[] = array(
+    $properties[] = array(
       "type" => $vocab['sw_url'],
       "title" => "label",
       "description" => "The type content.",
@@ -983,7 +983,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
       'expects' => NULL,
       'returns' => 'vocab:ContentCollection',
     );
-    $this->addDocClass($details,$operations, $propeties);
+    $this->addDocClass($details,$operations, $properties);
   }
   /**
    * Adds classes for every content type to the documentation for this service.
@@ -1183,8 +1183,8 @@ class TripalEntityService_v0_1 extends TripalWebService {
       'description' => 'A collection (or list) of ' . $bundle->label . ' resources.',
     );
     $vocab = tripal_get_vocabulary_details('hydra');
-    $propeties = array();
-    $propeties[] = array(
+    $properties = array();
+    $properties[] = array(
       'type' => $vocab['sw_url'],
       'title' => 'member',
       'description' => "The list of available " . $bundle->label . '(s).',
@@ -1192,7 +1192,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
       "readonly" => FALSE,
       "writeonly" => FALSE,
     );
-    $propeties[] = array(
+    $properties[] = array(
       "type" => $vocab['sw_url'],
       "title" => "totalItems",
       "description" => "The total number of resources.",
@@ -1200,7 +1200,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
       "readonly" => FALSE,
       "writeonly" => FALSE
     );
-    $propeties[] = array(
+    $properties[] = array(
       "type" => $vocab['sw_url'],
       "title" => "label",
       "description" => "A label or name for the resource.",
@@ -1241,7 +1241,7 @@ class TripalEntityService_v0_1 extends TripalWebService {
 //         ),
 //       );
     }
-    $this->addDocClass($details, $operations, $propeties);
+    $this->addDocClass($details, $operations, $properties);
   }
 
-}
+}

tripal_ws/includes/tripal_ws.field_storage.inc

@@ -7,7 +7,7 @@ function tripal_ws_field_storage_info() {
   return array(
     'field_tripal_ws_storage' => array(
       'label' => t('Tripal Web Services'),
-      'description' => t('Retreives fields data from a remote site using Tripal web services.'),
+      'description' => t('Retrieves fields data from a remote site using Tripal web services.'),
       'settings' => array(),
     ),
   );