Moved drupal_home page to inside the Install Tripal folder

docs/user_guide.rst

@@ -8,7 +8,6 @@ User's Guide
    :glob:
 
    user_guide/what_is_tripal
-   user_guide/drupal_home
    user_guide/install_tripal
    user_guide/drupal_overview
    user_guide/example_genomics

docs/user_guide/bulk_loader.rst

@@ -3,7 +3,7 @@ Bulk Loader
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`./install_tripal/drupal_home`
 
 The bulk loader is a tool that Tripal provides for loading of data contained in tab delimited files. Tripal supports loading of files in standard formats (e.g. ``FASTA``, ``GFF``, ``OBO``), but Chado can support a variety of different biological data types and there are often no community standard file formats for loading these data. For example, there is no file format for importing genotype and phenotype data. Those data can be stored in the feature, stock and natural diversity tables of Chado. The Bulk Loader was introduced in Tripal v1.1 and provides a web interface for building custom data loader. In short, the site developer creates the bulk loader "template". This template can then be used and re-used for any tab delimited file that follows the format described by the template. Additionally, bulk loading templates can be exported allowing Tripal sites to share loaders with one another.  Loading templates that have been shared are available on the Tripal website here: http://tripal.info/extensions/bulk-loader-templates.
 

docs/user_guide/drupal_home.rst

@@ -1,13 +0,0 @@
-DRUPAL_HOME Variable
-====================
-An important convention in this document is the use of the ``$DRUPAL_HOME`` environment variable.  If you are new to UNIX/Linux you can learn about environment variables `here <https://www.tutorialspoint.com/unix/unix-environment.htm>`_.  Drupal is a necessary depenency of Tripal.  The setup and installation sections describe how to install Drupal.  If you follow the instructions exactly as described in this User's Guide you will install Drupal into ``/var/www/html``. However, some may desire to install Drupal elsewhere.  To ensure that all command-line examples in this guide can be cut-and-pasted you **must** set the ``$DRUPAL_HOME`` variable.  You can set the variable in the following way:
-
-  .. code-block:: bash
-
-    DRUPAL_HOME=/var/www/html
-    
-Be sure to change the path ``/var/www/html`` to the location where you have installed Drupal.  If you have never installed Drupal and you intend on following this guide step-by-step then use the command-line above to get started.
-
-.. note::
-
-  You will have to set the ``$DRUPAL_HOME`` environment variable anytime you open a new terminal window.

docs/user_guide/example_genomics/pub_import.rst

@@ -2,7 +2,7 @@ Importing Publications
 ======================
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../install_tripal/drupal_home`
   
 Tripal provides an interface for automatically and manually adding publications.
 

docs/user_guide/install_tripal.rst

@@ -8,6 +8,7 @@ Install Tripal
    :glob:
 
    ./install_tripal/pre_planning
+   ./install_tripal/drupal_home
    ./install_tripal/server_setup
    ./install_tripal/drush_installation
    ./install_tripal/rapid_install

docs/user_guide/install_tripal/automating_job_execution.rst

@@ -3,7 +3,7 @@ Automating Job Execution
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`./drupal_home`
 
 The Drupal cron is used to automatically execute necessary Drupal housekeeping tasks on a regular interval.  You should *always* setup the Drupal cron to ensure your site checks for updates and security issues.  To do this, we want to integrate Drupal cron with the UNIX cron facility.  The UNIX cron will automatically execute commands on set regular intervals.  First, we must get the appropriate URL for the cron by navigating to **Configuration → Cron**. On this page you will see a link that we will use for cron:
 

docs/user_guide/install_tripal/manual_install/install_drupal.rst

@@ -35,7 +35,7 @@ Software Installation
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
 
 
 Before we can install Drupal we must ensure that that we are allowed to add files into the root directory.  Select a user account that will be the owner of all web files and change the owner of the ``$DRUPAL_HOME`` directory to that user:

docs/user_guide/install_tripal/manual_install/install_prereqs.rst

@@ -3,7 +3,7 @@ Tripal Prerequisites
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
 
 
 Tripal v3.x requires several Drupal modules. These include  `Entity <https://www.drupal.org/project/entity>`_,  `Views <https://www.drupal.org/project/views>`_, `CTools <https://www.drupal.org/project/ctools>`_, `Display Suite <https://www.drupal.org/project/ds>`_, `Field Group <https://www.drupal.org/project/field_group>`_, `Field Group Table <https://www.drupal.org/project/field_group_table>`_, `Field Formatter Class <https://www.drupal.org/project/field_formatter_class>`_ and `Field Formatter Settings <https://www.drupal.org/project/field_formatter_settings>`_ modules.   Modules can be installed using the graphical Drupal website by clicking on the Modules link in the top adminstrative menu bar.  Instructions for instaling Modules via the web-interface can be found here:  https://www.drupal.org/documentation/install/modules-themes/modules-7. However, Drush can be quicker for module installation. The following instructions will show how to install a module using the Drush command-line tool.

docs/user_guide/install_tripal/manual_install/install_tripal.rst

@@ -3,7 +3,7 @@ Tripal Installation
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
 
 
 Before installation of Tripal, you must first have a working Drupal installation.  Please see the previous section of this tutorial for step-by-step examples for server setup and Drupal installation instructions.  After installation of Tripal, you may install any Tripal extension modules you may want.

docs/user_guide/install_tripal/rapid_install.rst

@@ -3,7 +3,7 @@ Installation Method #1: Rapid Installation
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`./drupal_home`
 
 
 Before installing via the rapid installation process please ensure drush is installed, and the server is setup.   Rapid Installation works with Tripal v3.0-rc2 (release candidate 2) and later.  If you are using a previous version of Tripal, please proceed to the step-by-step instructions.

docs/user_guide/job_management.rst

@@ -3,7 +3,7 @@ Job Management (Tripal Daemon)
 
 .. note::
 
-  Remember you must set the $DRUPAL_HOME environment variable to cut-and-paste the commands below. See see :doc:`drupal_home`
+  Remember you must set the $DRUPAL_HOME environment variable to cut-and-paste the commands below. See see :doc:`./install_tripal/drupal_home`
 
 
 The Tripal Daemon module is meant to provide a simple means of creating a robust command-line-driven, fully bootstrapped PHP Daemon. It uses the PHP-Daemon (https://github.com/shaneharter/PHP-Daemon) Library to create the Daemon (via the Libraries API) in order to not re-invent the wheel. It allows you to execute Jobs submitted to Tripal without using cron.  It provides a faster user experience for running jobs.  Prior to Tripal v3, the Tripal Daemon module was an extension module. It was integrated into the core Tripal pacakge.

docs/user_guide/mviews.rst

@@ -3,7 +3,7 @@ Materialized Views
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`./install_tripal/drupal_home`
 
 Chado is efficient as a data warehouse but queries can become slow depending on the type of query. To help simplify and speed up these queries, materialized views can be employed. For a materialized view, a new database table is created and then populated with the results of a pre-defined SQL query. This allows you to execute a much simpler and faster query on the materialized view when producing user pages. A side effect, however is redundant data, with the materialized view becoming stale if not updated regularly.
 

docs/user_guide/web_services.rst

@@ -3,7 +3,7 @@ Web Services
 
 .. note::
 
-  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`drupal_home`
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`./install_tripal/drupal_home`
 
 Overview
 --------

tripal_chado/api/tripal_chado.variables.api.inc

@@ -314,6 +314,7 @@ function chado_generate_var($table, $values, $base_options = array()) {
       // check if the current table maps to a node type-------------------------
       // If this table is connected to a node there will be a chado_tablename 
       // table in drupal.
+      $base_tables = chado_get_base_tables();
       if (module_exists('tripal_core') and db_table_exists('chado_' . $table)) {
         // That has a foreign key to this one ($table_desc['primary key'][0]
         // and to the node table (nid).