Merge branch 'dsenalik-agl_restoration' into 7.x-3.x

docs/user_guide/example_genomics/pub_import.rst

@@ -135,3 +135,48 @@ Where
 - [DRUPAL_HOME] is the directory where Drupal is installed
 
 The cron entry above will launch the importer at 8:30am on the first and fifteenth days of the month. We will run this importer twice a month in the event it fails to run (e.g. server is down) at least one time during the month.
+
+
+Import from the USDA National Agricultural Library
+--------------------------------------------------
+The instructions for the Tripal publication importer described previously use the the NCBI PubMed database. However, you can also import publications from the USDA National Agriculture Library (AGRICOLA). However, to use this repository a few software dependences are required.  These include:
+
+- The `YAZ library <https://www.indexdata.com/resources/software/yaz/>`_
+- `PHP support for YAZ <https://www.php.net/manual/en/book.yaz.php>`_  
+
+The following instructions are to install the necessary dependencies on an Ubuntu 18.04 LTS.   
+
+First install yaz, the yaz development library and the php development library:
+
+.. code-block:: bash
+ 
+  sudo apt-get install yaz libyaz5-dev php-dev
+
+
+Next update the PECL tool and install the PHP yaz library:
+
+
+.. code-block:: bash
+  
+  sudo pecl channel-update pecl.php.net
+  sudo pecl install yaz
+  
+Next, edit the `php.ini` files.  On Ubuntu 18.04 there are two PHP files:
+
+- `/etc/php/7.2/cli/php.ini`
+- `/etc/php/7.2/apache2/php.ini`
+
+Add the following line to each file:
+
+::
+
+  extension=yaz.so
+
+Finally, restart the web server so that it picks up the changes to the `php.ini` file.
+
+.. code-block:: bash
+  
+  sudo service apache2 restart
+
+You can now import publications from Agricola using the same interface as with PubMed.
+

tripal_chado/includes/loaders/tripal_chado.pub_importers.inc

@@ -82,7 +82,7 @@ function tripal_pub_importers_list() {
       <li>Create a new importer by clicking the 'New Importer' link above, and after saving it should appear in the list below.  Click the
           link labeled 'Import Pubs' to schedule a job to import the publications</li>
       <li>The first method only performs the import once.  However, you can schedule the
-          importer to run peridically by adding a cron job. </li> 
+          importer to run peridically by adding a cron job. </li>
      </ol><br>");
 
   $form = drupal_get_form('tripal_pub_importer_ncbi_api_key_form');
@@ -134,7 +134,7 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
   }
 
   if(!extension_loaded ('yaz')){
-    drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Pub Module help page'), 'admin/tripal/legacy/tripal_pub/help') . ' for assistance.  If you do not want to use AGL you can ignore this warning.', 'warning');
+    drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Users Guide for Instructions'), 'https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/pub_import.html#import-from-the-usda-national-agricultural-library') . ' for assistance.  If you do not want to use AGL you can ignore this warning.', 'warning');
   }
 
   // generate the search form
@@ -478,7 +478,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
  * @ingroup tripal_pub
  */
 function tripal_pub_importer_ncbi_api_key_form($form, $form_state) {
-  $description = t('Tripal imports publications using NCBI\'s ') 
+  $description = t('Tripal imports publications using NCBI\'s ')
     . l('EUtils API', 'https://www.ncbi.nlm.nih.gov/books/NBK25500/')
     . t(', which limits users and programs to a maximum of 3 requests per second without an API key. '
         . 'However, NCBI allows users and programs to an increased maximum of 10 requests per second if '
@@ -1116,7 +1116,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   $pub_id = 0;
 
   // These are options for the tripal_report_error function. We do not
-  // want to log messages to the watchdog except for errors and to the job and 
+  // want to log messages to the watchdog except for errors and to the job and
   // to the terminal
   $message_type = 'pub_import';
   $message_opts = [
@@ -1134,7 +1134,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     return FALSE;
   }
 
-  // Before proceeding check to see if the publication already exists. If there 
+  // Before proceeding check to see if the publication already exists. If there
   // is only one match and the $update_if_exists is NOT set then return FALSE.
   $pub_ids = chado_publication_exists($pub_details);
 
@@ -1152,7 +1152,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     return FALSE;
   }
 
-  // If we have more than one matching pub then return an error as we don't 
+  // If we have more than one matching pub then return an error as we don't
   // know which to update even if update_if_exists is set to TRUE.
   if (count($pub_ids) > 1) {
     tripal_report_error($message_type, TRIPAL_NOTICE,
@@ -1203,7 +1203,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     return FALSE;
   }
 
-  // The series name field in the pub table is only 255 characters, so we 
+  // The series name field in the pub table is only 255 characters, so we
   // should trim just in case.
   $series_name = '';
   if (array_key_exists('Series_Name', $pub_details)) {
@@ -1257,8 +1257,8 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     }
   }
 
-  // Before we add any new properties we need to remove those that are there 
-  // if this is an update.  The only thing we don't want to remove are the 
+  // Before we add any new properties we need to remove those that are there
+  // if this is an update.  The only thing we don't want to remove are the
   // 'Publication Dbxref'.
   if ($update_if_exists) {
     $sql = "
@@ -1277,7 +1277,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   // Iterate through the properties and add them.
   foreach ($pub_details as $key => $value) {
 
-    // The pub_details may have the raw search data (e.g. in XML from PubMed. 
+    // The pub_details may have the raw search data (e.g. in XML from PubMed.
     // We'll irgnore this for now.
     if ($key == 'raw') {
       continue;