Documentation typos for Tripal tutorials

docs/dev_guide/chado.rst

@@ -222,8 +222,8 @@ To check the existence of a specific table and column, you can use the following
 
       [ do your query, etc. here ]
 
-    } else { [warn the admin using tripal_repot_error()] }
-  } else { [warn the admin using tripal_repot_error()] }
+    } else { [warn the admin using tripal_report_error()] }
+  } else { [warn the admin using tripal_report_error()] }
 
 Checking the Schema Version
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/dev_guide/custom_data_loader.rst

@@ -331,7 +331,7 @@ To import data into Chado we will use the Tripal API. After splitting each line
     // We want to provide a progress report to the end-user so that they:
     // 1) Recognize that the loader is not hung if running a large file, but is
     //    executing
-    // 2) Provides some indicatation for how long the file will take to load.
+    // 2) Provides some indication for how long the file will take to load.
     //
     // Here we'll get the size of the file and tell the TripalImporter how
     // many "items" we have to process (in this case bytes of the file).
@@ -369,7 +369,7 @@ To import data into Chado we will use the Tripal API. After splitting each line
 
       // Using the name of the feature from the file, see if we can find a
       // record in the feature table of Chado that matches.  Note: in reality
-      // the feature table of Chado has a unique contraint on the uniquename,
+      // the feature table of Chado has a unique constraint on the uniquename,
       // organism_id and type_id columns of the feature table.  So, to ensure
       // we find a single record ideally we should include the organism_id and
       // type_id in our filter and that would require more widgets on our form!
@@ -450,7 +450,7 @@ In the code above we consider a byte as an item, and when all bytes from a file
 
 Testing Importers
 ------------------
-Unit Testing is a critically important component of any software project. You should always strive to write tests for your software.  Tripal provides unit testing using the ``phpunit`` testing framework. The Tripal Test Suite provides a strategy for adding tests for your new Importer.  It will automatically set up and bootstrap Drupal and Tripal for your testing environment, as well as provide database transactions for your tests, and factories to quickly generate data.  We will use the Tripal Test Suite to provide unit testing for our ``ExampelImporter``.
+Unit Testing is a critically important component of any software project. You should always strive to write tests for your software.  Tripal provides unit testing using the ``phpunit`` testing framework. The Tripal Test Suite provides a strategy for adding tests for your new Importer.  It will automatically set up and bootstrap Drupal and Tripal for your testing environment, as well as provide database transactions for your tests, and factories to quickly generate data.  We will use the Tripal Test Suite to provide unit testing for our ``ExampleImporter``.
 
 .. note::
   Before continuing, please install and configure Tripal Test Suite.

docs/dev_guide/custom_field.rst

@@ -5,7 +5,7 @@ The most common way that new content will be added to an existing site is by cre
 
 By default Tripal v3 provides many fields for display of Chado data. However, you may find that these fields do not display data as you want, or you want to display data that the current fields do not already provide. This section of the Handbook describes how to create new fields that are integrated into the display, search and exchange abilities of both Drupal and Tripal.
 
-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 someitmes 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:
+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:
 
 
 +----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -13,7 +13,7 @@ If you are already familiar with Drupal fields you may be aware of the API funct
 +----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | 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 submittor functions. |
+| 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.                                                                                                                           |
 +----------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

docs/dev_guide/custom_field/ajax_custom_formatter.rst

@@ -36,7 +36,7 @@ The selector has specified that wrapper, and the AJAX callback function ``exampl
       $selected = isset($form_state['values']['featuremap_select']);
     }
 
-    // We need to provide a container for Dupal AJAX to replace.
+    // We need to provide a container for Drupal AJAX to replace.
     // Here we use a fieldset with a set ID which we can refer to below.
     $form['rendered_maps'] = [
       '#type' => 'fieldset',

docs/dev_guide/custom_field/create_instance.rst

@@ -2,14 +2,14 @@ Attach Fields to Content Types
 ==============================
 In summary, creation of a new field requires creation of three classes that inherit from the ``TripalField``, ``TripalFieldWidget`` and ``TripalFieldFormatter`` base classes.  If the fields are created correctly and placed in the ``includes/TripalFields`` directory of your module then Tripal will automatically find them.  However, the field is not yet attached to any content type. They must be attached.  Fields can be attached programmatically or via the online Drupal interface by a site admin. 
 
-The hook_bundle_field_info() function
+The hook_bundle_fields_info() function
 -------------------------------------
- The three TripalField classes simply define how the field will function, but Drupal does not yet know about the field.  The ``hook_bundle_field_info`` function tells Drupal about your field. It must be implemented in a custom Drupal module, and provides an array that tells Drupal about the fields and the classes to use for the field.  Suppose we were creating a field named ``obi__genus`` which displays the Genus for a species and we have a custom module named ``tripal_org2``.  The hook function would be named ``tripal_org2_bundle_field_info()``:
+ The three TripalField classes simply define how the field will function, but Drupal does not yet know about the field.  The ``hook_bundle_fields_info`` function tells Drupal about your field. It must be implemented in a custom Drupal module, and provides an array that tells Drupal about the fields and the classes to use for the field.  Suppose we were creating a field named ``obi__genus`` which displays the Genus for a species and we have a custom module named ``tripal_org2``.  The hook function would be named ``tripal_org2_bundle_fields_info()``:
 
 .. code-block:: php
   :linenos:
 
-  function tripal_org2_bundle_field_info($entity_type, $bundle) {
+  function tripal_org2_bundle_fields_info($entity_type, $bundle) {
     $info = [];
     
     // Make sure this bundle is an organism (OBI:0100026) then we'll attach our 
@@ -38,11 +38,11 @@ This function receives as its second argument the ``$bundle`` object. This is th
 
 The settings indicate the field name, the field type, the cardinality (how many values are allowed), any default settings and the storage type.  Because we expect our data to come from Chado we set the ``field_chado_storage`` as the type.  The ``locked`` setting is set to FALSE indicating that Drupal will allow the field to be deleted if the site developer desires.
 
-When the site administrator navigates to **Administer > Structure > Tripal Content Types**, clicks on a content type, and then the **manage fields** tab, a link appears at the top titled **Checkfor new fields**.  When that link is clicked, this hook function is called.
+When the site administrator navigates to **Administer > Structure > Tripal Content Types**, clicks on a content type, and then the **manage fields** tab, a link appears at the top titled **Check for new fields**.  When that link is clicked, this hook function is called.
 
 Programmatically Attaching Fields
 ---------------------------------
-You probably want to programmatically attach fields to content types if your have existing data that you know should be made available. For example, an organism always has a genus and only one genus.  If we have a field that displays the genus for an organism then we will want it automatically attached on installation of our module.  We can do this programmatically using two hook functions: ``hook_bundle_field_info()`` and ``hook_bundle_instance_info()``.  Both functions are required to attach a field to a content type. 
+You probably want to programmatically attach fields to content types if your have existing data that you know should be made available. For example, an organism always has a genus and only one genus.  If we have a field that displays the genus for an organism then we will want it automatically attached on installation of our module.  We can do this programmatically using two hook functions: ``hook_bundle_fields_info()`` and ``hook_bundle_instance_info()``.  Both functions are required to attach a field to a content type. 
 
 The hook_bundle_instance_info() function.
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -106,11 +106,11 @@ Unique to this info array are the settings related to Chado.  Because we expect
  - ``auto_attach``:  set this to TRUE if you want the field to automatically be added to an entity when it is generated for viewing.  Set it to FALSE to allow the field to be added via AJAX. For fields that require time to load setting to FALSE is preferred. 
  
 .. note::
-  A base table is one that contains the primary records to which ancilliary data (e.g. properties, cross references, CV terms, publications, contacts, etc) are associated via linker tables. For example some base tables include: ``feature``, ``organism``, ``stock``, ``library``, etc.).  The ``base_table`` and ``chado_table`` will always be the same when you are mapping a field to data in a column in a base table. If your field maps data to a "linker" table where ancilliary data is stored then the ``chado_table`` will be the linker table.
+  A base table is one that contains the primary records to which ancillary data (e.g. properties, cross references, CV terms, publications, contacts, etc) are associated via linker tables. For example some base tables include: ``feature``, ``organism``, ``stock``, ``library``, etc.).  The ``base_table`` and ``chado_table`` will always be the same when you are mapping a field to data in a column in a base table. If your field maps data to a "linker" table where ancillary data is stored then the ``chado_table`` will be the linker table.
 
-Notice as well that the ``display`` and ``widget`` sections list the name of our TripalEntityWidget and TripalEntityFormatter calsses respectively.  This tells drupal to use our widget and formatter classes by default.
+Notice as well that the ``display`` and ``widget`` sections list the name of our TripalEntityWidget and TripalEntityFormatter classes respectively.  This tells drupal to use our widget and formatter classes by default.
 
-When the site administrator navigates to **Administer > Structure > Tripal Content Types**, clicks on a content type, and then the **manage fields** tab, a link appears at the top titled **Checkfor new fields**.  When that link is clicked, this hook function is called.  
+When the site administrator navigates to **Administer > Structure > Tripal Content Types**, clicks on a content type, and then the **manage fields** tab, a link appears at the top titled **Check for new fields**.  When that link is clicked, this hook function is called.  
 
 .. note::
 
@@ -118,21 +118,21 @@ When the site administrator navigates to **Administer > Structure > Tripal Conte
   
 Allowing Manual Attachment of Fields
 ------------------------------------
-Not all fields are created equal.  Some field can be added by the site developer to a bundle and some cannot.  When the ``TripalField`` class is implemented for a class the ``$no_ui`` parameter is set to indicate if a field can be added via the web interface or not.  See the :doc:`manual_field_creation` page for more details. But in short the following setting does not allow a field to be added using the web interface
+Not all fields are created equal.  Some fields can be added by the site developer to a bundle and some cannot.  When the ``TripalField`` class is implemented for a class the ``$no_ui`` parameter is set to indicate if a field can be added via the web interface or not.  See the :doc:`manual_field_creation` page for more details. But in short the following setting does not allow a field to be added using the web interface
 
 .. code-block::  php
 
- public static $no_ui = FALSE;
+ public static $no_ui = TRUE;
  
 The following setting will allow the field to be added:
 
 .. code-block::  php
 
- public static $no_ui = TRUE;
+ public static $no_ui = FALSE;
 
-Next, we must let Drupal know that our field exists.  We do this by adding an entry to the ``$info`` array of in the ``hook_bundle_field_info()`` function described above.  This lets Drupal know about our field. However, because we are not programmatically creating an instance of the field on a content type, but allowing the user to create them we do not need to implement the ``hook_bundle_instance_info()`` function. Instead, we must implement the ``hook_bundle_create_user_field()``.  This function is called when the user attempts to add our new field to a bundle.  One field that comes with Tripal is the ``chado_linker__prop`` field.  Most Chado base tables have an associated property table (e.g. ``organismprop``, ``featureprop``, ``stockprop``, etc). By default, the ``tripal_chado`` module automatically adds this field to all bundles that have existing properties. It adds a new instance for every property type.  However, new properties can be added to bundle, and the site admin may want to add those properties via the user interface rather. Therefore, this field has the ``$no_ui`` set to TRUE and uses the  ``hook_bundle_create_user_field()`` to create the new field instance for the user.
+Next, we must let Drupal know that our field exists.  We do this by adding an entry to the ``$info`` array of in the ``hook_bundle_fields_info()`` function described above.  This lets Drupal know about our field. However, because we are not programmatically creating an instance of the field on a content type, but allowing the user to create them we do not need to implement the ``hook_bundle_instance_info()`` function. Instead, we must implement ``hook_bundle_create_user_field()``.  This function is called when the user attempts to add our new field to a bundle.  One field that comes with Tripal is the ``chado_linker__prop`` field.  Most Chado base tables have an associated property table (e.g. ``organismprop``, ``featureprop``, ``stockprop``, etc). By default, the ``tripal_chado`` module automatically adds this field to all bundles that have existing properties. It adds a new instance for every property type.  However, new properties can be added to bundle, and the site admin may want to add those properties via the user interface rather. Therefore, this field has the ``$no_ui`` set to TRUE and uses the  ``hook_bundle_create_user_field()`` to create the new field instance for the user.
 
-The following code is a snippet from the ``tripal_chado_bundle_create_user_field`` function of the ``tripal_chado`` module. Note that it uses the ``field_create_field`` function and the ``field_create_instance`` functions directly.  The arrays passed to these functions are identical to the ``$info`` arrays of both the ``hook_bundle_field_info`` and ``hook_bundle_instance_info`` functions described above.
+The following code is a snippet from the ``tripal_chado_bundle_create_user_field`` function of the ``tripal_chado`` module. Note that it uses the ``field_create_field`` function and the ``field_create_instance`` functions directly.  The arrays passed to these functions are identical to the ``$info`` arrays of both the ``hook_bundle_fields_info`` and ``hook_bundle_instance_info`` functions described above.
 
 .. code-block:: php
   :linenos:
@@ -218,6 +218,6 @@ The following code is a snippet from the ``tripal_chado_bundle_create_user_field
 
 .. note::
   
-  It is possible to have a field that is both programmtically attached to some content types but is also allowed to be attached to another content type by the site admin using the web interface. To do this, programmatically add the field to the content types using the ``hook_bundle_instance_info`` function and also implement the ``hook_bundle_create_user_field`` function to support manual adding.
+  It is possible to have a field that is both programmatically attached to some content types but is also allowed to be attached to another content type by the site admin using the web interface. To do this, programmatically add the field to the content types using the ``hook_bundle_instance_info`` function and also implement the ``hook_bundle_create_user_field`` function to support manual adding.
   
  

docs/dev_guide/custom_field/custom_formatter.rst

@@ -64,11 +64,11 @@ You may recall that the ``$items`` array structure is the same as that created b
 
 Because our organisms are also published entities we want to link to their respective pages each time an organism is displayed.  Because the ``value`` array has an element named ``entity`` we know that this item is published.  Lines 5-6 of the ``view()`` function shown above use this information to create a clickable link to the organism page.   Finally, the ``$element`` argument is set to provide content of type ``markup``.  This ``$element`` array is a `Drupal renderable array <https://www.drupal.org/docs/7/api/render-arrays/render-arrays-overview>`_.
 
-Lastly, notice the element named ``chado-feature__organsim_id``.  This element is at the same level as the ``value`` element.  This data is meant to be used internally by the field. It maps this fields values to the appropriate table in Chado where the data is stored.  
+Lastly, notice the element named ``chado-feature__organism_id``.  This element is at the same level as the ``value`` element.  This data is meant to be used internally by the field. It maps this fields values to the appropriate table in Chado where the data is stored.  
 
 .. warning:: 
 
-  You should never show the user any data that is outside of ``value`` element.  Remember that your field can be shown by other viewers, including web services.  By ensuring that data in the ``value`` element is mean to be displayed we ensure that information on the web page, web services, or any othe future form of display is always consistent.
+  You should never show the user any data that is outside of ``value`` element.  Remember that your field can be shown by other viewers, including web services.  By ensuring that data in the ``value`` element is mean to be displayed we ensure that information on the web page, web services, or any other future form of display is always consistent.
 
 In summary, the following should be observed when processing the ``$items`` array for viewing:
 
@@ -81,11 +81,11 @@ In summary, the following should be observed when processing the ``$items`` arra
 
 .. warning::
 
-  You should never have SQL statements or any API calls that retrieve data in the foramter ``view()`` function. The formatter should strictly format data for viewing.
+  You should never have SQL statements or any API calls that retrieve data in the formatter ``view()`` function. The formatter should strictly format data for viewing.
   
 Creating Pagers
 ~~~~~~~~~~~~~~~
-The example shown in the previous section was for a field that will always only contain a single element.  However some fields may contain a large number of elements.  Consider an mRNA and it's relationships to subfeatures: exons, 5' UTRs, 3'UTRs, CDS, etc.).  A large mRNA can have many relationships.  Alternatively, consider the case where a genentic map content type may have a field that lists all of the markers on the map.  Such a list could become extremely long on the page.  In these cases it may be best to only list a few items at a time and to provide a pager to let the user cycle through the items.  An example of a pager added to the bottom of relationships is shown in the example below.
+The example shown in the previous section was for a field that will always only contain a single element.  However some fields may contain a large number of elements.  Consider an mRNA and it's relationships to subfeatures: exons, 5' UTRs, 3'UTRs, CDS, etc.).  A large mRNA can have many relationships.  Alternatively, consider the case where a genetic map content type may have a field that lists all of the markers on the map.  Such a list could become extremely long on the page.  In these cases it may be best to only list a few items at a time and to provide a pager to let the user cycle through the items.  An example of a pager added to the bottom of relationships is shown in the example below.
 
 .. image:: custom_formatter.pager.1.png
 
@@ -132,7 +132,7 @@ Now that we have a pager, it has been setup for AJAX and we know the current pag
     
 The settingsForm() Function.
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Sometimes you may want to provide some control to the site developer for the formatter.  For example, the ``sbo__relationship_formater`` allows the site developer to customize the title that appears above the table that houses relationships and the text the appears if there are no relationships.  By default the title is "Relationships" and the empty text indicates there are no relationships. Both are a bit too generic.  The ``settingsForm()`` function allows you to provide a Drupal form for the field that appears on the **Administer > Strucutre > Tripal Content Types** on any content type's **manage display** page:
+Sometimes you may want to provide some control to the site developer for the formatter.  For example, the ``sbo__relationship_formatter`` allows the site developer to customize the title that appears above the table that houses relationships and the text the appears if there are no relationships.  By default the title is "Relationships" and the empty text indicates there are no relationships. Both are a bit too generic.  The ``settingsForm()`` function allows you to provide a Drupal form for the field that appears on the **Administer > Structure > Tripal Content Types** on any content type's **manage display** page:
 
 .. image:: custom_formatter.settings.1.png
 

docs/dev_guide/custom_field/custom_widget.rst

@@ -108,7 +108,7 @@ For our ``obi__organism`` example, the drop-down returns the chado organism_id o
     }
   }
 
-But what do you do if the record you want to link to via foreign key constraint doesn't yet exist? Luckily the Chado Storage API has a solution for this as well. Consider the example of the ``sbo__relationship_widget``. When this widget is on the create form for a given content type, we will first need to create the base record before we can create a relationship to it. This is done by setting the values you do know (e.g. ``chado-feature__type_id`` and ``chado-feature__object_id``) but nnot setting the column mapping to the base record. The Chado Storage API will then fill it in automatically once the base record is created.
+But what do you do if the record you want to link to via foreign key constraint doesn't yet exist? Luckily the Chado Storage API has a solution for this as well. Consider the example of the ``sbo__relationship_widget``. When this widget is on the create form for a given content type, we will first need to create the base record before we can create a relationship to it. This is done by setting the values you do know (e.g. ``chado-feature__type_id`` and ``chado-feature__object_id``) but not setting the column mapping to the base record. The Chado Storage API will then fill it in automatically once the base record is created.
 
 .. code-block:: php
 
@@ -150,4 +150,4 @@ But what do you do if the record you want to link to via foreign key constraint
 
 Drupal typically does not provide a submit hook for fields because, as mentioned above, saving should be done by the storage backend. However, the TripalField provides a ``TripalFieldWidget::submit()`` to allow for behind-the-scenes actions to occur. This function should never be used for updates, deletes or inserts for the Chado table associated with the field as these actions should be handled by the storage backend.
 
-However, it is permissible to perform inserts, updates or deletions within Chado using this function.  Those operations can be performed if needed but on other tables not directly associated with the field. An example is the ``chado.feature_synonym`` table.  The ``chado_linker__synonym`` field allows the user to provide a brand new synonynm and it must add it to the chado.synonym table prior to the record in the chado.feature_synonym table.
+However, it is permissible to perform inserts, updates or deletions within Chado using this function.  Those operations can be performed if needed but on other tables not directly associated with the field. An example is the ``chado.feature_synonym`` table.  The ``chado_linker__synonym`` field allows the user to provide a brand new synonym and it must add it to the chado.synonym table prior to the record in the chado.feature_synonym table.

docs/dev_guide/custom_field/manual_field_creation.rst

@@ -68,7 +68,7 @@ As described in the section titled Tripal Data Structures, fields that are attac
   // term_name, term_vocab, term_accession and term_fixed keys as these are
   // required for all TripalFields.
   public static $default_instance_settings  = array(
-    // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
+    // The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
     'term_vocabulary' => 'OBI',
     // The name of the term.
     'term_name' => 'organism',
@@ -156,7 +156,7 @@ Because this is a ChadoField and the TripalChado module supports this field and
 
     $record = $entity->chado_record;
 
-Having the record helps tremendously.  Our **obi__organism** field is meant to be attached to genomic feature content types (e.g. genes, mRNA, etc.), germplasm, etc.  Therefore, the entity will be a record of one of those types. In the case of a genomic feature, these come from the **feature** table of Chado.  In the case of a germplam, these records come from the **stock** table of Chado.  Both of these records have an **organism_id** field which is a foreign key to the organism table where we find out details about the organism.
+Having the record helps tremendously.  Our **obi__organism** field is meant to be attached to genomic feature content types (e.g. genes, mRNA, etc.), germplasm, etc.  Therefore, the entity will be a record of one of those types. In the case of a genomic feature, these come from the **feature** table of Chado.  In the case of germplasm, these records come from the **stock** table of Chado.  Both of these records have an **organism_id** field which is a foreign key to the organism table where we find out details about the organism.
 
 Before we set the values for our field, we need a little bit more information.  Remember that all field instances have settings?   The Tripal Chado module also populates for us the name of the Chado table and the column that this field maps to.  Our obi__organism field can be used for multiple Bundles.  A gene bundle would map to the **feature** table of Chado and a germplasm Bundle would map to the **stock** table.  We need to know what table and column this field is mapping to:  We can get that from the instance object of the class and its settings:
 
@@ -186,7 +186,7 @@ Now, let's plan how we want our values to appear in our field.  The organism rec
     $infraspecific_type_term = tripal_get_chado_semweb_term('organism', 'type_id');
 
 
-Notice that for our organism fields we can easily get the ontology terms for them using the API function **tripal_get_chado_semweb_term**.  You will also notice a **label_term** variable.  Sometimes a user may want to see the full name of the organism and not pieces of it in various elements.  Therefore, we will provide a label in our list of values that will concatenate the full organism name.  This field is not in our organism table so we hard-code the term 'rdfs:lable' which is a term from the Resource Data Framework Schema vocabulary that defines a label.
+Notice that for our organism fields we can easily get the ontology terms for them using the API function **tripal_get_chado_semweb_term**.  You will also notice a **label_term** variable.  Sometimes a user may want to see the full name of the organism and not pieces of it in various elements.  Therefore, we will provide a label in our list of values that will concatenate the full organism name.  This field is not in our organism table so we hard-code the term 'rdfs:label' which is a term from the Resource Data Framework Schema vocabulary that defines a label.
 
 Next, let's initialize our field's value to be empty.  When setting a field value we must do so in the entity object that got passed into our load function.  The entity is an object and it stores values using the names of the fields.  The following code sets an empty record for our field:
 
@@ -392,9 +392,9 @@ The code above generates and returns an associative array that provides metadata
       'type' => 'xs:complexType',
       'elements' => array(
 
-Notice the value for $field_term variable was easily obtained by calling the $this->getFieldTermID function and all of the terms for the elements were obtained using the chado_get_semweb_term function which maps table columns in the Chado database schema to ontology terms.  The operations key indicates which search filter operations are supported for the field as a whole.  For this example these include 'eq' (for equals), 'contains' and 'starts' (for starts with).   The field is sortable and searchable so those values are set to TRUE.   Later, we weill learn how to implement the sorting, searching and filtering that the field will support.  For now we know we want them so we set the values accordingly.  Additionally, the field allows updating so 'readonly' is set to FALSE.   By convention, the 'type' of a field follows the XML data types for simple types (https://www.w3schools.com/xml/schema_simple.asp) and Complex types (https://www.w3schools.com/xml/schema_complex.asp) that have multiple elements.  Because our obi__organism field has subelements  and is not a single value, the field type is 'xs:complexType'.
+Notice the value for $field_term variable was easily obtained by calling the $this->getFieldTermID function and all of the terms for the elements were obtained using the chado_get_semweb_term function which maps table columns in the Chado database schema to ontology terms.  The operations key indicates which search filter operations are supported for the field as a whole.  For this example these include 'eq' (for equals), 'contains' and 'starts' (for starts with).   The field is sortable and searchable so those values are set to TRUE.   Later, we will learn how to implement the sorting, searching and filtering that the field will support.  For now we know we want them so we set the values accordingly.  Additionally, the field allows updating so 'readonly' is set to FALSE.   By convention, the 'type' of a field follows the XML data types for simple types (https://www.w3schools.com/xml/schema_simple.asp) and Complex types (https://www.w3schools.com/xml/schema_complex.asp) that have multiple elements.  Because our obi__organism field has subelements  and is not a single value, the field type is 'xs:complexType'.
 
-The array keys just mentioned fully describe our field to Drupal and Tripal.  Next we will define the sub elements in the same way, and these go in the 'elements' key.  First, we will describe the label.  Our obi__oranganism field provides a handly label element that concatenates the genus, species and infraspecific name into one simple string.  Therefore, we need to describe this element in the same way we described the field itself.  In the code below that the key is set to 'rdfs:label' (which is the controlled vocabulary term for a label) and that the child keys are the same as for the field.
+The array keys just mentioned fully describe our field to Drupal and Tripal.  Next we will define the sub elements in the same way, and these go in the 'elements' key.  First, we will describe the label.  Our obi__organism field provides a handy label element that concatenates the genus, species and infraspecific name into one simple string.  Therefore, we need to describe this element in the same way we described the field itself.  In the code below that the key is set to 'rdfs:label' (which is the controlled vocabulary term for a label) and that the child keys are the same as for the field.
 
 .. code-block:: php
 

docs/dev_guide/custom_web_services.rst

@@ -141,7 +141,7 @@ Notice currently all this function does is call the parent getDocumentation func
 
 In the above array, notice the @id is URL that represents a unique identifier for the class.   The @type will always be 'hydra:Class' because we are documenting a resource.  Then there is information about the class defined using the 'hydra:title' and 'hydra:description'.  The 'subclassOf' is always set to 'hydra:Resource'.  Next is the list of supported operations for this resource.  Remember, in our design we only want to support the GET operation for our Jobs service, so just like in the example above, the method we will support is GET.  The key/value pairs for the GET method are described using Hydra terms.  
 
-For our services we need to provide the information to Tripal so that it can generate these Hydra JSON arrays that document our service.  Tripal provides some easy API functions to help with this.  The firt is the **addDoc** member function.  This function will take as input the class details, operations and properties necessary to generate the documentation for our class.  First, lets use this function to document our Jobs Collection resource.  Below is sample code that will do this for us.
+For our services we need to provide the information to Tripal so that it can generate these Hydra JSON arrays that document our service.  Tripal provides some easy API functions to help with this.  The first is the **addDoc** member function.  This function will take as input the class details, operations and properties necessary to generate the documentation for our class.  First, lets use this function to document our Jobs Collection resource.  Below is sample code that will do this for us.
 
 
 .. code-block:: php
@@ -290,7 +290,7 @@ Now, because we have instantiated a TripalWebServiceCollection object it can han
 
         $this->resource->initPager($num_records, $limit, $page);
 
-Lastly, we need to add our "members" of the collection.  These are the jobs from our query.  The following for loop iterates through alll of our jobs and creates new member objects that are added to our collection:
+Lastly, we need to add our "members" of the collection.  These are the jobs from our query.  The following for loop iterates through all of our jobs and creates new member objects that are added to our collection:
 
 .. code-block:: php
 

docs/dev_guide/data_structures.rst

@@ -1,7 +1,7 @@
 Tripal Data Structures
 =======================
 
-This page explains the relationships between Entity types, Bundles (content type), Entities and Fields. These are data structures provided by Drupal that Tripal v3 uses to expose biological content through your Drupal site, and to provide flexibility in site customization.  It is important to understand these terms and their relationships before developing new modules or custom functionlaity.   A quick summary of these Drupal data structures are as follows:
+This page explains the relationships between Entity types, Bundles (content type), Entities and Fields. These are data structures provided by Drupal that Tripal v3 uses to expose biological content through your Drupal site, and to provide flexibility in site customization.  It is important to understand these terms and their relationships before developing new modules or custom functionality.   A quick summary of these Drupal data structures are as follows:
 
 * Entity:  a discrete data record.  Entities are most commonly are seen as "pages" on a Drupal web site.
 * Field:  an "atomic" piece of ancillary data that describes, defines or expands the entity.  Common fields include the name of an entity, a "body" of descriptive text, etc.

docs/dev_guide/exporting_field_settings.rst

@@ -56,7 +56,7 @@ Configuring the bundle fields
 
 To begin, let's quickly configure a bundle.  Navigate to the structure of your site and select Analysis (**Admin ->Structure -> Tripal Content -> Analysis -> Manage Fields**).  Scroll to the bottom and add a new field of type File, with a machine name of ``field_fasta_file‎``, and click **Save**. Be sure to change the **Allowed extensions** parameter to accept ``.fasta``, otherwise, it will only allow `.txt` files to be uploaded.  You may also want to increase the file size limit, as the default 2MB can be too small for many FASTA files.
 
-We now have to pick a CV term for our field.  Because we are providing a FASTA file field, we can use a term such as FASTA `(SWO:0000142 <https://www.ebi.ac.uk/ols/ontologies/ero/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2Fswo%2FSWO_0000142>`_.  Please see  :ref:`adding_a_cvterm` for help loading a term.  Once the term is in our DB, we can assign it to this field.
+We now have to pick a CV term for our field.  Because we are providing a FASTA file field, we can use a term such as FASTA (`SWO:0000142 <https://www.ebi.ac.uk/ols/ontologies/ero/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2Fswo%2FSWO_0000142>`_).  Please see  :ref:`adding_a_cvterm` for help loading a term.  Once the term is in our DB, we can assign it to this field.
 
 
 .. image:: ./exporting_field_settings.1.assign_term.png