Merge pull request #637 from tripal/633_drupal_home_env

633 implement drupal home env in install documentation

docs/user_guide.rst

@@ -1,5 +1,5 @@
 User's Guide
-==============
+============
 
 
 .. toctree::

docs/user_guide/bulk_loader.rst

@@ -1,7 +1,10 @@
-
 Bulk Loader
 ===========
 
+.. note::
+
+  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.
 
 The following commands can be executed to install the Tripal Bulk Loader using Drush:
@@ -20,7 +23,7 @@ To demonstrate use of the Bulk Loader, a brief example that imports a list of or
 
 .. code-block bash
 
-  cd /var/www/html/sites/default/files
+  cd $DRUPAL_HOME/sites/default/files
   wget http://tripal.info/sites/default/files/book_pages/Fragaria_0.txt
 
 
@@ -244,10 +247,14 @@ Provide the following values:
 
 * Job Name: Import of Fragaria species
 * Template: NCBI Taxonomy Importer (taxid, genus species).
-* Data File: /var/www/html/sites/default/files/Fragaria_0.txt
+* Data File: [DRUPAL_HOME]/sites/default/files/Fragaria_0.txt
 * Keep track of inserted IDs: No
 * File has a header: No
 
+.. note::
+
+  Be sure to change the [DRUPAL_HOME] token to where Drupal is installed.
+
 Click **Save**. The page then appears as follows:
 
 .. image:: ./bulk_loader.9.png
@@ -261,7 +268,7 @@ Now that we have created a job, we can submit it for execution by clicking the *
 .. code-block:: shell
 
   cd /var/www
-  drush trp-run-jobs --username=admin --root=/var/www/html
+  drush trp-run-jobs --username=admin --root=$DRUPAL_HOME
 
 After execution of the job you should see similar output to the terminal window:
 

docs/user_guide/example_genomics/pub_import.rst

@@ -1,5 +1,9 @@
 Importing Publications
 ======================
+.. note::
+
+  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.
 
 Manually Adding a Publication
@@ -81,7 +85,7 @@ Next, there are two ways to import these publications. The first it to manually
 
 ::
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   drush trp-import-pubs --username=administrator
 
 You should see output to the terminal that begins like this:
@@ -105,7 +109,7 @@ Some things to know about the publication importer:
 
   ::
 
-    cd /var/www/html
+    cd $DRUPAL_HOME
     drush trp-run-jobs --user=administrator
 
 The second way to import publications is to add an entry to the UNIX cron. We did this previously for the Tripal Jobs management system when we first installed Tripal. We will add another entry for importing publications. But first, now that we have imported all of the relevant pubs, we need to return to the importers list at **Tripal → Data Loaders → Chado Publication Importers** and disable the first importer we created. We do not want to run that importer again, as we've already imported all historical publications on record at PubMed. Click the edit button next to the importer named Pubs for Citrus sinensis, click the disable checkbox and then save the template. The template should now be disabled.
@@ -120,11 +124,12 @@ Now add the following line to the bottom of the crontab:
 
 ::
 
-  30 8 1,15 * *  su - www-data -c '/usr/local/drush/drush -r /var/www/html -l http://[site url] trp-import-pubs --report=[your email] > /dev/null'
+  30 8 1,15 * *  su - www-data -c '/usr/local/drush/drush -r [DRUPAL_HOME] -l http://[site url] trp-import-pubs --report=[your email] > /dev/null'
 
 Where
 
 - [site url] is the full URL of your site
 - [your email] is the email address of the user that should receive an email containing a list of publications that were imported. You can separate multiple email addresses with a comma.
+- [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.

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

@@ -1,6 +1,10 @@
 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`
+
 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:
 
 .. image:: automating_job_execution.cron.png
@@ -36,9 +40,9 @@ Any job that is added to the Job's system can be run manually on the command lin
 
 .. code-block:: bash
 
-  drush trp-run-jobs --username=administrator --root=/var/www/html
+  drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
-Remember to change the username from **administrator** to the name of the administrator on your site and change **/var/www/html** to the location where your site installed on the server.
+Remember to change the username from **administrator** to the name of the administrator on your site.
 
 Option #2: Additional Cron Entry
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -53,7 +57,7 @@ Add this line to the crontab:
 
 .. code-block:: bash
 
-  0,5,10,15,20,25,30,35,40,45,50,55 * * * * drush trp-run-jobs --username=administrator --root=/var/www/html
+  0,5,10,15,20,25,30,35,40,45,50,55 * * * * drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
 Here, job execution will occur every 5 minutes.
 

docs/user_guide/install_tripal/manual_install/install_drupal.rst

@@ -33,29 +33,32 @@ We no longer need to be the postgres user so exit
 Software Installation
 ---------------------
 
-We want to install Drupal into our web document root (/var/www/html).   Before we can install Drupal we must ensure that that we are allowed to add files into the /var/www/html directory.  Select a user account that will be the owner of all web files and change the owner of the /var/www/html directory to that user:
+.. note::
+
+  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:
 
 .. code-block:: bash
 
-  sudo chown -R [user] /var/www/html
+
+  sudo chown -R [user] $DRUPAL_HOME
 
 Substitute [user] for the name of the user that will own the web files.
 
 
 .. note::
 
-  The apache web server runs as the user 'www-data'.  For security reasons you should chose a user other than 'www-data' to be the owner of the /var/www/html directory.
+  The apache web server runs as the user 'www-data'.  For security reasons you should chose a user other than 'www-data' to be the owner of the Drupal root directory.
 
-Tripal 3.x requires version 7.x of Drupal. Drupal can be freely downloaded from the http://www.drupal.org website. At the writing of this Tutorial the most recent version of Drupal 7 is version 7.59. The software can be downloaded manually from the Drupal website through a web browser or we can use the 'wget' command to retrieve it:
+Tripal 3.x requires version 7.x of Drupal. Drupal can be freely downloaded from the http://www.drupal.org website. At the writing of this Tutorial the most recent version of Drupal 7 is version 7.59. The software can be downloaded manually from the Drupal website through a web browser or we can use the ``wget`` command to retrieve it:
 
 .. code-block:: bash
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   wget http://ftp.drupal.org/files/projects/drupal-7.59.tar.gz
 
-.. note::
-
-  If you are using older version of Ubuntu the web root directory may be /var/www rather than /var/www/html and you may need to change the path accordingly.
 
 Next, we want to install Drupal. We will use the tar command to uncompress the software:
 
@@ -78,11 +81,11 @@ If an index.html file is present (as is the case with Ubuntu installations) you
 
 .. note::
 
-  It is extremely important the the hidden file .htaccess is also moved (note the second 'mv' command above. Check to make sure this file is there
+  It is extremely important the the hidden file ``.htaccess`` is also moved (note the second ``mv`` command above. Check to make sure this file is there:
 
-.. code-block:: bash
+  .. code-block:: bash
 
-  ls -l .htaccess
+    ls -l .htaccess
 
 Configuration File
 ------------------
@@ -93,15 +96,15 @@ First navigate to the location where the configuration file should go:
 
 .. code-block:: bash
 
-  cd /var/www/html/sites/default/
+  cd $DRUPAL_HOME/sites/default/
 
-Next, copy the example configuration that already exists in the directory to be our actual configuration file by renaming it to settings.php.
+Next, copy the example configuration that already exists in the directory to be our actual configuration file by renaming it to ``settings.php``.
 
 .. code-block:: bash
 
   cp default.settings.php settings.php
 
-Now, we need to edit the configuration file to tell Drupal how to connect to our database server. To do this we'll use an easy to use text editor gedit
+Now, we need to edit the configuration file to tell Drupal how to connect to our database server. To do this we'll use an easy to use text editor **gedit**.
 
 .. code-block:: bash
 
@@ -127,17 +130,19 @@ and then insert the following array just after the above line:
   );
 
 Replace the text '********' with your database password for the user 'drupal' created previously.  Save the configuration file and close the editor.
-Files directory creation
 
-Finally, we need to create the directory where Drupal will have write-access to add files.  By default, Drupal expects to have write permission in the /var/www/html/sites/default/files directory.  Therefore, we will set group ownership of the directory to the group used by the Apache web server.  This will be the user that Drupal uses to write files.
+Files Directory Creation
+--------------------------
+
+Finally, we need to create the directory where Drupal will have write-access to add files.  By default, Drupal expects to have write permission in the ``$DRUPAL_HOME/sites/default/files`` directory.  Therefore, we will set group ownership of the directory to the group used by the Apache web server.  This will be the user that Drupal uses to write files.
 
 .. code-block:: bash
 
-  mkdir -p /var/www/html/sites/default/files
-  sudo chgrp [group] /var/www/html/sites/default/files
-  sudo chmod g+rw /var/www/html/sites/default/files
+  mkdir -p $DRUPAL_HOME/sites/default/files
+  sudo chgrp [group] $DRUPAL_HOME/sites/default/files
+  sudo chmod g+rw $DRUPAL_HOME/sites/default/files
 
-Substitute [group] for the name of the web server's group.  In Ubuntu this is www-data in CentOS this is apache.The above commands creates the directory, sets the group ownership for group. and gives read/write permissions to the group on the directory.
+Substitute [group] for the name of the web server's group.  In Ubuntu this is www-data in CentOS this is apache. The above commands creates the directory, sets the group ownership for group, and gives read/write permissions to the group on the directory.
 
 Web-based Steps
 ---------------

docs/user_guide/install_tripal/manual_install/install_prereqs.rst

@@ -1,13 +1,18 @@
 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`
+
+
 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.
 
 First, install the Entity module.  We will download the current version using the drush command. On the command-line, execute the following:
 
 .. code-block:: bash
 
-  cd /var/www/html/sites/all/modules
+  cd $DRUPAL_HOME/sites/all/modules
   drush pm-download entity
 
 Typically for all module installation we should check the README for additional installation instructions. Next, enable the module using a drush command:
@@ -23,14 +28,14 @@ For basic Tripal functionality you must also enable the Views and CTools modules
   drush pm-download views ctools
   drush pm-enable views views_ui ctools
 
-Finally, Tripal works best when it can provide default display layouts.   To support default layouts you must also enable the remainig dependencies:
+Finally, Tripal works best when it can provide default display layouts.   To support default layouts you must also enable the remaining dependencies:
 
 .. code-block:: bash
 
   drush pm-download ds field_group field_group_table field_formatter_class field_formatter_settings
   drush pm-enable ds field_group field_group_table field_formatter_class field_formatter_settings
 
-Optionally, you can install the ckeditor module.  This module provides a nice WYSIWYG editor that allows you to edit text on your site using a graphical editor. Otherwise, if you need images or formatting (e.g. underline, bold, headers) you would be required to write HTML.   It is recommended that this module be installed to improve the user experience:
+Optionally, you can install the ckeditor module.  This module provides a nice WYSIWYG editor that allows you to edit text on your site using a graphical editor. Otherwise, if you need images or formatting (e.g. underline, bold, headers) you would be required to write HTML.  It is recommended that this module be installed to improve the user experience:
 
 .. code-block:: bash
 

docs/user_guide/install_tripal/manual_install/install_tripal.rst

@@ -1,6 +1,11 @@
 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`
+
+
 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.
 
 Download Tripal
@@ -24,15 +29,15 @@ A bug exists in Drupal related to the bytea data type in PostgreSQL. At the writ
 
 .. code-block:: bash
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   wget --no-check-certificate https://drupal.org/files/drupal.pgsql-bytea.27.patch
   patch -p1 < drupal.pgsql-bytea.27.patch
 
-There is also a bug in the Drupal Views 3.0 code that prevents Tripal's administrative and search data views from functioning. The patch is provided within the tripal_veiws module. To apply the patch execute the following:
+There is also a bug in the Drupal Views 3.0 code that prevents Tripal's administrative and search data views from functioning. The patch is provided within the tripal_views module. To apply the patch execute the following:
 
 .. code-block:: bash
 
-  cd /var/www/html/sites/all/modules/views
+  cd $DRUPAL_HOME/sites/all/modules/views
   patch -p1 < ../tripal/tripal_chado_views/views-sql-compliant-three-tier-naming-1971160-30.patch
 
 Install Tripal
@@ -74,7 +79,7 @@ Jobs in the queue can be executed using drush to manually launch the job:
 
 .. code-block:: bash
 
-  drush trp-run-jobs --username=administrator --root=/var/www/html
+  drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
 As the installation of Chado proceeds, we should see output on the terminal console indicating the progress of the installation.  You should see output similar to the following:
 
@@ -108,7 +113,7 @@ To prepare the site click the button Prepare this site.   A new job is added to
 
 .. code-block:: bash
 
-  drush trp-run-jobs --username=administrator --root=/var/www/html
+  drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
 
 .. note::
 
@@ -125,4 +130,4 @@ Preparing Chado and Drupal in a previous step resulted in the automatic creation
 
 .. image:: install_tripal.install7.png
 
-Review these permissions and set them according to how you want content to be managed.   Typically, the administrator user receives all permissions, and anonymous and authenticated users receive 'View' permissions for all content types.  If you desire to create other types of users, Drupal allows you to do this by creating new types of roles.  For example, if you know that some users will be responsible for curating content, then you may add a curator role by clicking the Roles link in the top right corner of this permissions page.  After the new role is created you can return to the permission page to set the permissions accordingly.
+Review these permissions and set them according to how you want content to be managed.  Typically, the administrator user receives all permissions, and anonymous and authenticated users receive 'View' permissions for all content types.  If you desire to create other types of users, Drupal allows you to do this by creating new types of roles.  For example, if you know that some users will be responsible for curating content, then you may add a curator role by clicking the **Roles** link in the top right corner of this permissions page.  After the new role is created you can return to the permission page to set the permissions accordingly.

docs/user_guide/install_tripal/rapid_install.rst

@@ -1,8 +1,15 @@
 Installation Method #1: Rapid Installation
 ==========================================
 
-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.
+.. note::
+
+  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.
+
 Database Setup
+---------------
 
 Before we can install Tripal we must have a database ready for it.  In the server setup instructions were provided to set up a PostgreSQL database server. Now, we need to create the Drupal database. To do so we must first become the PostgreSQL user.
 
@@ -10,7 +17,7 @@ Before we can install Tripal we must have a database ready for it.  In the serve
 
   sudo su - postgres
 
-Next, create the new 'drupal' user account. This account will not be a "superuser' nor allowed to create new roles, but should be allowed to create a database.
+Next, create the new 'drupal' user account. This account will not be a "superuser" nor allowed to create new roles, but should be allowed to create a database.
 
 .. code-block:: bash
 
@@ -31,17 +38,17 @@ We no longer need to be the postgres user so exit
 Tripal Installation
 -------------------
 
-Navigate to the directory you want to create the website. For this example it will be /var/www/html (the typical home location for Ubuntu and CentOS)
+Navigate to your Drupal install directory.
 
 .. code-block:: bash
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
 
 .. note::
 
   Make sure you have write permissions within this directory.
 
-Clone the tripal_install project using the git command and move the contents up one level into the web document directory:
+Clone the tripal_install project using the ``git`` command and move the contents up one level into the web document directory:
 
 .. code-block:: bash
 
@@ -70,7 +77,7 @@ From this point onward, you will be asked a series of questions in the terminal
      Administrator password: P@55w0rd
   Is this information correct? (y/n): y
 
-Next, you will be asked for the database information: database name, database  username, database  user password, host, and port.  The database name and user should match what you created in the previous section (i.e. database name = 'drupal' and database user = 'drupal').  The 'host' is the name of the server or its IP address, and the port is a numerical value that PostgreSQL uses for communication.  By default PostgreSQL uses the port 5432.  If a mistake is made you can make corrections as shown in the following screenshot:
+Next, you will be asked for the database information: database name, database  username, database  user password, host, and port.  The database name and user should match what you created in the previous section (i.e. database name = 'drupal' and database user = 'drupal').  The 'host' is the name of the server or its IP address, and the port is a numerical value that PostgreSQL uses for communication.  By default PostgreSQL uses the port 5432.  If a mistake is made you can make corrections as shown below:
 
 ::
 

docs/user_guide/install_tripal/upgrade_from_tripal2.rst

@@ -44,7 +44,7 @@ Step 1: Upgrade Tripal
 
     drush pm-disable tripal_core
 
-4.  The Tripal modules must also be downloaded and updated. To do this, delete the old Tripal v2 modules directories, located in ``sites/all/modules`` from your Drupal root:  for example ``/var/www/html/sites/all/modules``(be sure you have a backup before removing). The following command will retrieve the Tripal 3 version:
+4.  The Tripal modules must also be downloaded and updated. To do this, delete the old Tripal v2 modules directories, located in ``sites/all/modules`` from your Drupal root:  for example ``/var/www/html/sites/all/modules`` (be sure you have a backup before removing). The following command will retrieve the Tripal 3 version:
 
   .. code-block:: bash
 
@@ -137,11 +137,11 @@ The process allows you to create Tripal 3 content types exposing the same data a
 
 4. Select the checkbox beside each Tripal v3 type you would like to create. The number of entities/pages that will be created for that content type is shown in brackets beside the name.
 
-5. Then click the "Migrate [Tripal v2 Type]" button. This will submit a Tripal job to create the requested content. Submit this job manually on the command-line as follows:
+5. Then click the "Migrate [Tripal v2 Type]" button. This will submit a Tripal job to create the requested content. Submit this job manually on the command-line as follows (note we ``cd`` to the project root at ``/var/www/html``: please navigate to wherever your site is installed):
 
   .. code-block:: bash
 
-    cd /var/www/html
+    cd $DRUPAL_HOME
     drush trp-run-jobs --user=administrator
 
 6. Now repeat 1-5 for each content type. Since this step simply creates new Tripal v3 content without touching the existing Tripal v2 content, there really is no reason not to migrate all your content types. Especially since the Tripal v3 content remains private and thus hidden from your users.

docs/user_guide/job_management.rst

@@ -1,6 +1,11 @@
 Job Management (Tripal Daemon)
 ==============================
 
+.. note::
+
+  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.
 
 Features
@@ -27,7 +32,7 @@ Next, we need the `PHP-Daemon Library version 2.0 <https://github.com/shaneharte
 
 .. code-block:: shell
 
-  cd /var/www/html/sites/all/libraries
+  cd $DRUPAL_HOME/sites/all/libraries
   wget https://github.com/shaneharter/PHP-Daemon/archive/v2.0.tar.gz
   tar -zxvf v2.0.tar.gz
   mv v2.0.tar.gz PHP-Daemon

docs/user_guide/mviews.rst

@@ -1,6 +1,10 @@
 Materialized Views
 ==================
 
+.. note::
+
+  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.
 
 Tripal provides a mechanism for populating and updating these materialized views. These can be found on the **Tripal → Data Storage → Chado -> Materialized Views** page.
@@ -13,7 +17,7 @@ This will submit jobs to populate the views with data. Now, run the jobs:
 
 .. code-block:: shell
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   drush trp-run-jobs --user=administrator
 
 You can now see that all views are up-to-date on the **Materialized Views Page**. The number of rows in the view table is shown.

docs/user_guide/web_services.rst

@@ -1,6 +1,10 @@
 Web Services
 ============
 
+.. note::
+
+  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
 --------
 
@@ -31,7 +35,7 @@ To enable web services, simply install the ``tripal_ws`` module, either using th
 
 .. code-block:: shell
 
-  cd /var/www/html
+  cd $DRUPAL_HOME
   drush pm-enable tripal_ws
 
 Exploring Web Services

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).