Merge pull request #1125 from michizhou/michizhou-patch-1

Resolve cases and typos in documentation guides

docs/dev_guide/custom_field/custom_widget.rst

@@ -135,7 +135,7 @@ But what do you do if the record you want to link to via foreign key constraint
       // Set all chado fields to their values.
     }
     // Otherwise, maybe we are creating the entity...
-    // The storage API should handle this case and automagically add the key in // once the chado record is created... so all we need to do is set the
+    // The storage API should handle this case and automatically add the key in // once the chado record is created... so all we need to do is set the
     // other columns.
     elseif ($subject_name && $object_id && $type_id) {
       $form_state['values'][$field_name][$langcode][$delta]['value'] = 'value must be set but is not used';

docs/dev_guide/custom_field/select_vocab_terms.rst

@@ -27,7 +27,7 @@ Consider the term for `organism <http://www.ebi.ac.uk/ols/ontologies/obi/terms?i
 
 .. figure:: select_vocab_terms.1.organism.png
 
-Notice how the teal box (the **short name**) is OBI, and the orange box contains the **full accession**, OBI:0100026 which includes but the **short name** and the unique term **accession** value.  Unfortunately, the OLS does not indicate the **namespace** terms.   So, as a rule we will use the short name converted to lower case.  Before using this term in a Tripal Bundle or Field you may need to insert this term into Chado.  You can do so in your custom module cude using the **tripal_insert_cvterm** function. The following provides a demonstration:
+Notice how the teal box (the **short name**) is OBI, and the orange box contains the **full accession**, OBI:0100026 which includes but the **short name** and the unique term **accession** value.  Unfortunately, the OLS does not indicate the **namespace** terms.   So, as a rule we will use the short name converted to lower case.  Before using this term in a Tripal Bundle or Field you may need to insert this term into Chado.  You can do so in your custom module code using the **tripal_insert_cvterm** function. The following provides a demonstration:
 
 .. code-block:: php
 
@@ -104,7 +104,7 @@ Some ontologies are b into sub-ontologies. This includes the Gene Ontology (GO).
 .. figure:: select_vocab_terms.3.go.png
 
 
-Case 4: Ontologies with muliptle short names
+Case 4: Ontologies with multiple short names
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The EDAM ontology builds its term accessions using different short names instead of the ontology. Consider the EDAM term for `Sequence <http://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2044>`_. The teal box is EDAM, the orange box is data:2044, and there is no **namespace**.

docs/dev_guide/custom_web_services.rst

@@ -10,7 +10,7 @@ New in Tripal v3 are `RESTful web services <https://en.wikipedia.org/wiki/Repres
 
 Tripal v3 has been redesigned from Tripal v2 to be fully organized around controlled vocabularies.  All data made available via Tripal is expected to be described by the terms of a controlled vocabulary or ontology.  For example, all content types in Tripal are assigned a controlled vocabulary term that describes what the content is.  Additionally, each field of data attached to a content type also is described using a controlled vocabulary term.  If a field provides more than just a single data value (i.e. it provides a list or nested structured array of data of key/value pairs) then each of the keys for those pairs must also be a controlled vocabulary term.  This requirement allows Tripal to fully describe the data it houses to any other Tripal site and any other script or service that can read the web services.  As long as the client application understands the vocabulary term it will understand the meaning of the data.  Using controlled vocabulary terms to describe all data allows a Tripal site to participate in the `Semantic Web <https://en.wikipedia.org/wiki/Semantic_Web>`_. 
 
-Finally, the Tripal RESTful services are meant to be discoverable.  In some cases, when a web services is designed, the only way to understand the structure of it and the operations that it provides are for a programmer to read online documentation for the service before she can write the client application.  However, to better support automatic data discovery without human intervention by a client the Tripal web services have been designed to be discoverable.  To this end, Tripal uses the  `Hyrda Core Vocabulary <https://www.hydra-cg.com/spec/latest/core/>`_ specification.  It fully describes all of the services, their operations, and the resulting value.  A client application that understands the Hydra language can therefore learn  to use the web service without human intervention.  However, in practice, its a good idea to continue to provide online documentation for humans.  And this User's Guide :doc:`provides those instructions </user_guide/web_services>` for the default Tripal content service.  
+Finally, the Tripal RESTful services are meant to be discoverable.  In some cases, when a web services is designed, the only way to understand the structure of it and the operations that it provides are for a programmer to read online documentation for the service before she can write the client application.  However, to better support automatic data discovery without human intervention by a client the Tripal web services have been designed to be discoverable.  To this end, Tripal uses the  `Hydra Core Vocabulary <https://www.hydra-cg.com/spec/latest/core/>`_ specification.  It fully describes all of the services, their operations, and the resulting value.  A client application that understands the Hydra language can therefore learn  to use the web service without human intervention.  However, in practice, its a good idea to continue to provide online documentation for humans.  And this User's Guide :doc:`provides those instructions </user_guide/web_services>` for the default Tripal content service.  
 
 This documentation provides instructions to construct your own custom web services and making that service available through Tripal's existing web service infrastructure.  This will enable your web service to be discoverable and to provide a consistent experience to end-users.  Before proceeding with the following instructions, please review the **Structure of a Web Service Response** section on the User's Guide :doc:`Web Services page </user_guide/web_services>`.
 

docs/dev_guide/exporting_field_settings.rst

@@ -111,7 +111,7 @@ Go to our target site, all we need to do is download and unpack the ``.tar`` fil
 
 The field should now appear when you go to create a new analysis on your target site.  To check for yourself, create a new Analysis with dummy information: you'll be able to upload a file for the new file field.
 
-Unfortunately, the field still gets imported **disabled** due to Tripal preference, so we have to go to the display settings on our target site and enable the tripal pane/field.
+Unfortunately, the field still gets imported **disabled** due to Tripal preference, so we have to go to the display settings on our target site and enable the Tripal pane/field.
 
 
 .. image:: ./exporting_field_settings.6.png

docs/extensions/data_input.rst

@@ -14,7 +14,7 @@ A Drush-based loader for VCF files that follows the genotype storage rules outli
 Mainlab Chado Loader
 ---------------------
 
-MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to Chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a chado schema.
+MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to Chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a Chado schema.
 
 `Documentation <https://gitlab.com/mainlabwsu/mcl/blob/master/README.md>`__
 `Repository <https://gitlab.com/mainlabwsu/mcl>`__

docs/extensions/module_rating.rst

@@ -23,7 +23,7 @@ Silver
 
 - Follows basic Drupal Coding standards; specifically, `code format <https://www.drupal.org/docs/develop/standards/coding-standards>`_ and `API documentation <https://www.drupal.org/docs/develop/standards/api-documentation-and-comment-standards#drupal>`_.
 - Uses Tripal API functions. Specifically, it should use the
-    - Chado Query API for querying chado (if using chado as the storage system). (`API <http://api.tripal.info/api/tripal/tripal_chado%21api%21tripal_chado.query.api.inc/group/tripal_chado_query_api/3.x>`_, :doc:`Tutorial <../dev_guide/chado>`)
+    - Chado Query API for querying Chado (if using Chado as the storage system). (`API <http://api.tripal.info/api/tripal/tripal_chado%21api%21tripal_chado.query.api.inc/group/tripal_chado_query_api/3.x>`_, :doc:`Tutorial <../dev_guide/chado>`)
     - Tripal Jobs API for long running processes. (`API  <http://api.tripal.info/api/tripal/tripal%21api%21tripal.jobs.api.inc/group/tripal_jobs_api/3.x>`_)
     - TripalField class to add data to pages (Tripal3). (:doc:`Tutorial <../dev_guide/custom_field>`)
 - Provides ways to customize the module (e.g. drush options, field/formatter settings, admin UI).

docs/extensions/search.rst

@@ -28,7 +28,7 @@ The Tripal ElasticSearch module allows you to easily manage the indexing and dis
 Tripal MegaSearch
 ---------------------
 
-Tripal MegaSearch is a tool for downloading biological data stored in a Tripal/Chado database. The module was designed to be generic and flexible so it can be used on most Tripal sites. Site administrators may choose from 1) a set of predefined materialized views or 2) chado base tables as the data source to serve data. If neither data source is desired, developers may create their own materialized views and serve them through Tripal MegaSearch via a flexible dynamic query form. This form allows filters to be added dynamically and combined using 'AND/OR' operators. The filters correspond to the underlying data source columns so the user can filter data on each column.
+Tripal MegaSearch is a tool for downloading biological data stored in a Tripal/Chado database. The module was designed to be generic and flexible so it can be used on most Tripal sites. Site administrators may choose from 1) a set of predefined materialized views or 2) Chado base tables as the data source to serve data. If neither data source is desired, developers may create their own materialized views and serve them through Tripal MegaSearch via a flexible dynamic query form. This form allows filters to be added dynamically and combined using 'AND/OR' operators. The filters correspond to the underlying data source columns so the user can filter data on each column.
 
 `Documentation <https://gitlab.com/mainlabwsu/tripal_megasearch/blob/master/README.md>`__
 `Repository <https://gitlab.com/mainlabwsu/tripal_megasearch>`__