Merge pull request #1176 from dsenalik/tripaltypos20210312

Tripal typos 20210312

docs/dev_guide/custom_field.rst

@@ -8,21 +8,21 @@ By default Tripal v3 provides many fields for display of Chado data. However, yo
 If you are already familiar with Drupal fields you may be aware of the API functions and hooks that Drupal provides.  However, for the quantity of fields needed to support biological data, the Drupal API hooks quickly become overwhelming.  Additionally, documentation for fields in the Drupal API can sometimes be difficult to discover when first working with fields.   Therefore, Tripal provides several new PHP classes to simplify creation of fields and to consolidate all functionality into one easy to find set of files.  To develop new fields you should be somewhat familiar working with PHP's Object-Oriented Classes. The new classes provided by Tripal are these:
 
 
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Class Name           | Description                                                                                                                                                                                                               |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| TripalField          | The TripalField class provides the basic information about a new field. It provides loaders for extracting data from the database and functions for querying data managed by the field.                                   |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| TripalFieldWidget    | The TripalFieldWidget class provides the necessary form elements when editing and Entity to allow the end-user to edit the value of the field (if desired). It provides the necessary validators and submitter functions. |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| TripalFieldFormatter | The TripalFieldFormatter class provides the visualization of the field when viewed on the page.                                                                                                                           |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ChadoField           | The ChadoField class extends the TripalField class and provides the necessary settings to allow the field to map entities to data in Chado                                                                                |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ChadoFieldWidget     | Extends the TripalFieldWidget class but currently provides no additional functionality. Use this class when working with Chado data to ensure future backwards compatibility.                                             |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ChadoFieldFormatter  | Extends the TriplFieldFormatter class but currently provides no additional functionality. Use this class when working with Chado data to ensure future backwards compatibility.                                           |
-+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Class Name           | Description                                                                                                                                                                                                              |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| TripalField          | The TripalField class provides the basic information about a new field. It provides loaders for extracting data from the database and functions for querying data managed by the field.                                  |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| TripalFieldWidget    | The TripalFieldWidget class provides the necessary form elements when editing an Entity to allow the end-user to edit the value of the field (if desired). It provides the necessary validators and submitter functions. |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| TripalFieldFormatter | The TripalFieldFormatter class provides the visualization of the field when viewed on the page.                                                                                                                          |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ChadoField           | The ChadoField class extends the TripalField class and provides the necessary settings to allow the field to map entities to data in Chado                                                                               |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ChadoFieldWidget     | Extends the TripalFieldWidget class but currently provides no additional functionality. Use this class when working with Chado data to ensure future backwards compatibility.                                            |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ChadoFieldFormatter  | Extends the TriplFieldFormatter class but currently provides no additional functionality. Use this class when working with Chado data to ensure future backwards compatibility.                                          |
++----------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 
 

docs/user_guide/example_genomics/organisms.rst

@@ -44,7 +44,7 @@ Tripal makes it easy to import additional information about any organisms within
 
 .. image:: organisms.taxonomy_loader.png
 
-Click the checbox beside the 'Import taxonomy for existing species' and click Submit.  Now run the submitted job:
+Click the checkbox beside the 'Import taxonomy for existing species' and click Submit.  Now run the submitted job:
 
 ::
 

legacy/tripal_feature/includes/tripal_feature.delete.inc

@@ -24,7 +24,7 @@ function tripal_feature_delete_form() {
   $form['is_unique'] = [
     '#title' => t('Names are Unique Names'),
     '#type' => 'checkbox',
-    '#description' => t('Select this checbox if the names listed in the feature
+    '#description' => t('Select this checkbox if the names listed in the feature
       names box above are the unique name of the feature rather than the human readable names.'),
   ];
   $cv = tripal_get_cv(['name' => 'sequence']);

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -219,7 +219,7 @@ function chado_get_cvterm($identifiers, $options = []) {
     ];
     $result = chado_select_record('cvtermsynonym', ['cvterm_id'], $values, $options);
 
-    // if the synonym doens't exist or more than one record is returned then
+    // if the synonym doesn't exist or more than one record is returned then
     // return false.
     if (count($result) == 0) {
       return FALSE;

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

@@ -1,7 +1,7 @@
 <?php
 /**
  * @file
- * Provides API functions specificially for managing feature
+ * Provides API functions specifically for managing feature
  * records in Chado.
  */
 
@@ -9,7 +9,7 @@
  * @defgroup tripal_organism_api Chado Organism
  * @ingroup tripal_chado_api
  * @{
- * Provides API functions specificially for managing organism
+ * Provides API functions specifically for managing organism
  * records in Chado.
  * @}
  */

tripal_chado/api/modules/tripal_chado.phylotree.api.inc

@@ -181,7 +181,7 @@ function chado_validate_phylotree($val_type, &$options, &$errors, &$warnings) {
   }
 
   // A Dbxref is required by the phylotree module, but if the
-  // tree was generated in-house and the site admin doens't want to
+  // tree was generated in-house and the site admin doesn't want to
   // assign a local dbxref then we will set it to the null db
   // and the local:null dbxref.
   if (array_key_exists('dbxref', $options)) {
@@ -683,7 +683,7 @@ function chado_phylogeny_import_tree(&$tree, $phylotree, $options, $vocab = [],
       if ($tree['is_internal']) {
         $values['type_id'] = $vocab['internal']->cvterm_id;
         $values['parent_phylonode_id'] = $parent['phylonode_id'];
-        // TOOD: a feature may be associated here but it is recommended that it
+        // TODO: a feature may be associated here but it is recommended that it
         // be a feature of type SO:match and should represent the alignment of
         // all features beneath it.
       }
@@ -897,7 +897,7 @@ function chado_phylogeny_import_tree_file($file_name, $format, $options = [], $j
       module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.phylotree_newick');
       $tree = tripal_phylogeny_parse_newick_file($file_name);
 
-      // Assign the right and left indecies to the tree ndoes.
+      // Assign the right and left indices to the tree nodes.
       chado_assign_phylogeny_tree_indices($tree);
     }
     // Iterate through the tree nodes and add them to Chado in accordance

tripal_chado/api/modules/tripal_chado.pub.api.inc

@@ -362,7 +362,7 @@ function chado_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE,
   // the terminal
   $message_type = 'pub_import';
   $message_opts = [
-    'watchdog' == FALSE,
+    'watchdog' => FALSE,
     'print' => TRUE,
   ];
 
@@ -498,7 +498,7 @@ function chado_execute_pub_importer($import_id, $publish = TRUE,
   // the terminal
   $message_type = 'pub_import';
   $message_opts = [
-    'watchdog' == FALSE,
+    'watchdog' => FALSE,
     'job' => $job,
     'print' => TRUE,
   ];
@@ -664,7 +664,7 @@ function chado_reimport_publications($do_contact = FALSE, $dbxref = NULL,
   // the terminal
   $message_type = 'pub_import';
   $message_opts = [
-    'watchdog' == FALSE,
+    'watchdog' => FALSE,
     'print' => TRUE,
   ];
 

tripal_chado/api/tripal_chado.api.inc

@@ -58,7 +58,7 @@ function chado_publish_records($values, $job = NULL) {
   // the terminal
   $message_type = 'publish_records';
   $message_opts = [
-    'watchdog' == FALSE,
+    'watchdog' => FALSE,
     'job' => $job,
     'print' => TRUE,
   ];

tripal_chado/api/tripal_chado.variables.api.inc

@@ -490,7 +490,7 @@ function chado_generate_var($table, $values, $base_options = []) {
  * extremely long, such as text fields are automatically excluded to prevent
  * long page loads.  Linking tables that have a many-to-one relationship with
  * the record are also excluded.  This function allows for custom expansion
- * of the record created by chado_generate_var() by specifyin the field and
+ * of the record created by chado_generate_var() by specifying the field and
  * tables that should be added.
  *
  * Example Usage:

tripal_chado/includes/TripalFields/chado_linker__prop/chado_linker__prop_widget.inc

@@ -143,7 +143,7 @@ class chado_linker__prop_widget extends ChadoFieldWidget {
     $value = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__value'];
     $form_state['values'][$field_name]['und'][$delta]['value'] = $value;
 
-    // A value of zero gets set to empty when sbumitted and some prop
+    // A value of zero gets set to empty when submitted and some prop
     // tables don't have a default value set (e.g. pubprop).
     if (!$form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__rank']) {
       $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__rank'] = 0;

tripal_chado/includes/TripalFields/so__transcript/so__transcript.inc

@@ -201,7 +201,7 @@ class so__transcript extends ChadoField {
       '#default_value' => $settings['transcript_fields'],
     ];
 
-    // Get the content type for the mRNA term (SO:0000234) and it's feilds.
+    // Get the content type for the mRNA term (SO:0000234) and its fields.
     // If it isn't published then don't show the form below.
     $bundle = tripal_load_bundle_entity(['accession' => 'SO:0000234']);
     if (!$bundle) {

tripal_chado/includes/TripalImporter/FASTAImporter.inc

@@ -839,7 +839,7 @@ class FASTAImporter extends TripalImporter {
 
     // add in the analysis link
     if ($analysis_id) {
-      // if the association doens't already exist then add one
+      // if the association doesn't already exist then add one
       $values = [
         'analysis_id' => $analysis_id,
         'feature_id' => $feature->feature_id,

tripal_chado/includes/TripalImporter/OBOImporter.inc

@@ -1431,7 +1431,7 @@ class OBOImporter extends TripalImporter {
       }
     }
 
-    // We have no conflict so it's save to update or insert.
+    // We have no conflict so it's safe to update or insert.
     return FALSE;
   }
 
@@ -1502,7 +1502,7 @@ class OBOImporter extends TripalImporter {
     chado_query($sql, [':cvterm_id' => $cvterm_id]);
 
     // We should never have the problem where we don't have a cvterm_id. The
-    // saveTerm() function should always return on.  But if for some unknown
+    // saveTerm() function should always return one.  But if for some unknown
     // reason we don't have one then fail.
     if (!$cvterm_id) {
       throw new Exception(t('Missing cvterm after saving term: !term',

tripal_chado/includes/TripalImporter/TaxonomyImporter.inc

@@ -491,7 +491,7 @@ class TaxonomyImporter extends TripalImporter {
       ];
       $this->addTaxonomyNode($tree, $node, $lineage_depth);
 
-      // Set the indecies for the tree.
+      // Set the indices for the tree.
       chado_assign_phylogeny_tree_indices($tree);
     }
 
@@ -880,7 +880,7 @@ class TaxonomyImporter extends TripalImporter {
       ];
       $this->addTaxonomyNode($this->tree, $node, $lineage_depth);
 
-      // Set the indecies for the tree.
+      // Set the indices for the tree.
       chado_assign_phylogeny_tree_indices($this->tree);
       return TRUE;
     }

tripal_chado/includes/loaders/tripal_chado.pub_importer_AGL.inc

@@ -708,7 +708,7 @@ function tripal_pub_AGL_parse_pubxml($pub_xml) {
           $author = tripal_pub_remote_search_AGL_get_author($xml, $ind1);
           $pub['Author List'][] = $author;
           break;
-        case '110':  // main entry-corporate nmae
+        case '110':  // main entry-corporate name
           $author = [];
           $codes = tripal_pub_remote_search_AGL_get_subfield($xml);
           foreach ($codes as $code => $value) {

tripal_chado/includes/loaders/tripal_chado.pub_importers.inc

@@ -1004,7 +1004,7 @@ function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE, $job =
   // the terminal
   $message_type = 'pub_import';
   $message_opts = [
-    'watchdog' == TRUE,
+    'watchdog' => FALSE,
     'job' => $job,
     'print' => TRUE,
   ];
@@ -1120,12 +1120,12 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   // to the terminal
   $message_type = 'pub_import';
   $message_opts = [
-    'watchdog' == FALSE,
+    'watchdog' => FALSE,
     'job' => $job,
     'print' => TRUE,
   ];
   $error_opts = [
-    'watchdog' == TRUE,
+    'watchdog' => TRUE,
     'job' => $job,
     'print' => TRUE,
   ];

tripal_chado/includes/tripal_chado.fields.inc

@@ -861,7 +861,7 @@ function tripal_chado_bundle_fields_info_linker(&$info, $details, $entity_type,
 }
 
 /**
- * Impelments hook_create_tripalfield_instance().
+ * Implements hook_create_tripalfield_instance().
  *
  * This is a Tripal defined hook that supports integration with the
  * TripalEntity field.

tripal_chado/includes/tripal_chado.phylotree.inc

@@ -178,7 +178,7 @@ function tripal_phylogeny_ajax_get_tree_json($phylotree_id)
       ];
 
       // If the nodes are taxonomic then set an equal distance
-      if ($phylotree->type_id->name == 'taxonomy' or $phylotree->type_id->name == 'Speces tree') {
+      if ($phylotree->type_id->name == 'taxonomy' or $phylotree->type_id->name == 'Species tree') {
         $node['length'] = 0.001;
       }
 

tripal_chado/tripal_chado.module

@@ -55,7 +55,7 @@ require_once 'api/modules/tripal_chado.module.DEPRECATED.api.inc';
 // REQUIRED INCLUDE FILES
 //
 // These require files implement hooks and therefore must
-// ways be included when the module is interpreted.
+// always be included when the module is interpreted.
 require_once "includes/tripal_chado.entity.inc";
 require_once "includes/tripal_chado.schema.inc";
 require_once "includes/tripal_chado.vocab_storage.inc";