Merge branch '7.x-3.x' into 35-multiple_jbrowses_41organism

README.md

@@ -1,9 +1,9 @@
 # Tripal JBrowse Integration
 
-This package of modules integrates [GMOD JBrowse](https://jbrowse.org/) into your [Tripal](http://tripal.info/) site providing 
- - Tripal page integration via **Tripal JBrowse Page** and 
- - a user interface for JBrowse instance creation and management via **Tripal JBrowse Management**. 
- 
+This package of modules integrates [GMOD JBrowse](https://jbrowse.org/) into your [Tripal](http://tripal.info/) site providing
+ - Tripal page integration via **Tripal JBrowse Page** and
+ - a user interface for JBrowse instance creation and management via **Tripal JBrowse Management**.
+
  This powerful combination allows you to provide seamless genome browsing to your users in an administrator-friendly manner.
 
 ## Quick Start
@@ -29,4 +29,4 @@ This module is open-source and licensed under GPLv3. [Read full license](LICENSE
 - Joe West (@jwest60)
 - Other contributors (https://github.com/tripal/tripal_jbrowse/graphs/contributors)
 
-*Copyright 2018 University of Saskatchewan and University of Tennessee Knoxville.* 
+*Copyright 2018 University of Saskatchewan and University of Tennessee Knoxville.*

docs/guide/install.rst

@@ -8,3 +8,4 @@ Installation
    install/dependencies
    install/jbrowse_mgmt
    install/instance_page
+   install/migrate

docs/guide/install/instance_page.rst

@@ -3,12 +3,5 @@
 
 This module is available for download from github.com/tripal/tripal_jbrowse.
 
-1. Download and upack the module into ``[DRUPAL ROOT]/sites/all/modules`` where ``DRUPAL_ROOT`` is the path to your Drupal site.
-2. Navigate to ``https://yourdrupalsite.com/admin/modules`` or click **Administration Toolbar > Modules**
-3. Scroll to **Tripal Extensions**, click the checkbox beside "Tripal JBrowse Integration", and click the "Save Configuration" button at the bottom of the page.
-
-.. image:: ../../assets/tripal_jbrowse.1.install.png
-
-.. note::
-
-   This module is dependent upon the **Link** module. It is not mentioned above in the install instructions since you should already have installed it when installing Tripal.
+1. First install :doc:`Tripal JBrowse Management <jbrowse_mgmt>`
+2. Run ``drush en -y tripal_jbrowse_page`` or enable through the modules page

docs/guide/install/jbrowse_mgmt/configuration.rst

@@ -2,7 +2,8 @@ Configuration
 ===============
 
 In order for the module to function properly, you need to first configure it.
-Please visit ``http://YOUR_SITE/admin/tripal_jbrowse/configure`` (replace YOUR_SITE with your domain)
-and fill out the form. You will need to know information about your JBrowse information.
+
+1. Visit your site through the browser and navigate to Administration » Tripal » Extensions » Tripal JBrowse Management » Settings.
+2. Fill out the configuration form and click "Save Settings". **You will need to know information about your JBrowse instance.**
 
 .. image:: ../../../assets/settings_page.png

docs/guide/install/jbrowse_mgmt/install.rst

@@ -2,8 +2,8 @@ Installation
 ==============
 
 1. Download the module to your Drupal modules folder
-2. Run drush en -y hardwoods_jbrowse or enable through the modules page
-3. Visit the configuration page at /admin/hardwoods_jbrowse/configure
+2. Run ``drush en -y tripal_jbrowse_mgmt`` or enable through the modules page
+3. Visit the configuration page at Administration » Tripal » Extensions » Tripal JBrowse Management » Settings
 
 .. note::
 

docs/guide/install/migrate.rst

@@ -0,0 +1,33 @@
+Tripal JBrowse Nodes Migration
+================================
+
+The old method of Tripal JBrowse page integration using nodes has been **deprecated**. If you are still using this method of integration, administrators will see a warning directing you here.
+
+The new method of page integration using the Tripal JBrowse Management module to register instances with your Tripal site. The following steps will help you register your existing JBrowse instances with Tripal JBrowse Management in order to take advantage of the new page integration.
+
+1. Enable Tripal JBrowse Management as you would any other Drupal/Tripal module. This can be done using ``drush pm-enable tripal_jbrowse_mgmt``.
+2. Download JBrowse and install a single instance in a web-accessible location. We recommend ``DRUPAL_ROOT/tools/jbrowse``.
+3. Create symbolic links to each of your existing instances where the name of the link matches the organism it is for: ``genus_species__common_name``.
+
+.. code::
+
+  cd DRUPAL_ROOT/tools/jbrowse
+  mkdir data
+  cd data
+  ln -s path/to/existing/instance/data/directory genus_species__common_name
+
+4. Navigate to Administration » Tripal » Extensions » Tripal JBrowse and click on "Settings". Fill out the paths for your new single JBrowse instance.
+
++------------------------------------+---------------------------------------+
+| Data Directory                     | DRUPAL_ROOT/tools/jbrowse/data        |
++------------------------------------+---------------------------------------+
+| Data Path                          | ./tools/jbrowse/data                  |
++------------------------------------+---------------------------------------+
+| Path to JBrowse's Index File       | ./tools/jbrowse                       |
++------------------------------------+---------------------------------------+
+| Path to JBrowse's bin Directory    | DRUPAL_ROOT/tools/jbrowse/bin         |
++------------------------------------+---------------------------------------+
+
+5. Navigate to Administration » Tripal » Extensions » Tripal JBrowse and click on "Register Existing Instance". Fill in the details for each of your existing instances.
+6. Enable the new Tripal JBrowse Page Integration module and dynamic pages will now be available for each of your newly registered instances. This can be done using ``drush pm-enable tripal_jbrowse_page``.
+7. Delete your existing Tripal JBrowse Instance nodes under Admin » Content and disable the old module using ``drush pm-disable tripal_jbrowse``.

docs/guide/jbrowse_mgmt/instances.rst

@@ -4,7 +4,7 @@ Managing Instances
 Listing and Creating Instances
 ------------------------------
 
-To list all instances, visit ``/admin/tripal_jbrowse``.
+To list all instances, visit Administration » Tripal » Extensions » Tripal JBrowse Management.
 
 .. image:: ../../assets/instances.png
 
@@ -12,10 +12,29 @@ To list all instances, visit ``/admin/tripal_jbrowse``.
 Creating Instances
 ------------------
 
-As highlighted on the screenshot above, you can create new instances by clicking the "Add New Instance" link.
+As highlighted on the screenshot above, you can create new instances by clicking the "Create New Instance" link. This will create a new data directory based on the organism choosen. All instances created will use the same JBrowse installation, which makes it easier to update JBrowse.
+
+Registering Existing Instances
+--------------------------------
+
+You can also register existing JBrowse instances with this module. To do so
+1. Create a symbolic link in your configured data directory where the name of the link matches the organism it is for: ``genus_species__common_name``.
+2. Click on "Register Existing Instance" as highlighted on the screenshot above.
+3. Fill out the form to describe the existing JBrowse instance.
+
+.. note::
+
+  If you would like to move an existing instance to the JBrowse managed by this module permanently then copy the data directory rather then creating a symbolic link.
 
 Deleting Instances
 ------------------
 
 To delete an instance, you must first visit the instances list page and clicking the delete instance link.
-Note that the actual files for the instance are not deleted. You will need to delete all files manually.
+
+.. warning::
+
+  The actual files for the instance are not deleted. You will need to delete all files manually.
+
+.. note::
+
+  If you accidentally delete an instance, you can use the "Register Existing Instance" process to re-register it with the system. All previously created tracks will no longer be able to be managed but you will be able to add new tracks, etc.

docs/guide/jbrowse_mgmt/tracks.rst

@@ -4,7 +4,7 @@ Managing Tracks
 Creating and Deleting Tracks
 ----------------------------
 
-To create a new track, you need visit the instances list page and click Manage Tracks.
+To create a new track, you need visit the instances list page (Administration » Tripal » Extensions » Tripal JBrowse Management) and click Manage Tracks.
 
 .. image:: ../../assets/manage_tracks.png
 
@@ -19,7 +19,6 @@ The manage tracks link, will lead to a page where you can create and delete trac
 Editing Tracks
 --------------
 
-This modules allows you to configure a track after it has been created. This provides a way to
-add the track to a category, change the colors and type of the track amongst other configuration options.
+This modules allows you to configure a track after it has been created. This provides a way to add the track to a category, change the colors and type of the track amongst other configuration options.
 
 To edit a track, simply click the manage track button on the "manage tracks" page as shown on the screenshot above.

docs/index.rst

@@ -9,8 +9,8 @@ Tripal JBrowse
 
 This package of modules integrates `GMOD JBrowse <https://jbrowse.org/>`_ into your `Tripal <http://tripal.info/>`_ site providing
 
-   - Tripal page integration via **Tripal JBrowse** and
-   - a user interface for JBrowse instance creation and management via **Tripal JBrowse Management**.
+  1. A user interface for JBrowse instance creation and management via **Tripal JBrowse Management**
+  2. Drupal menu links and pages with embedded JBrowse instances via  **Tripal-JBrowse Page Integration**
 
  This powerful combination allows you to provide seamless genome browsing to your users in an administrator-friendly manner.
 

tripal_jbrowse/tripal_jbrowse.info

@@ -1,6 +1,6 @@
 name = JBrowse Nodes DEPRECATED
 description = Creates nodes embedding JBrowse instances.
 core = 7.x
-package = Tripal Extensions
+package = Tripal Extensions: JBrowse Integration
 
 dependencies[] = tripal

tripal_jbrowse/tripal_jbrowse.module

@@ -4,6 +4,19 @@
  * Core functions of this module.
  */
 
+/**
+ * Implements hook_init().
+ */
+function tripal_jbrowse_init() {
+  global $user;
+
+  // Only show message to administrators.
+  if (in_array('admin', $user->roles)) {
+    $msg = t('We have detected that you still have Tripal JBrowse Nodes installed. This module is DEPRECATED! Please follow the migration instructions <a href="@url">here</a>.', ['@url' => 'https://tripal-jbrowse.readthedocs.io/en/latest/guide/install/migrate.html']);
+    drupal_set_message($msg, 'warning');
+  }
+}
+
 /**
  * Implements hook_theme().
  */
@@ -19,4 +32,4 @@ function tripal_jbrowse_theme($existing, $type, $theme, $path) {
   );
 
   return $items;
-}
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.api.inc

@@ -493,12 +493,17 @@ function tripal_jbrowse_mgmt_build_http_query($instance) {
 function tripal_jbrowse_mgmt_get_json($instance) {
   $path = tripal_jbrowse_mgmt_get_track_list_file_path($instance);
 
-  $contents = file_get_contents($path);
-  if (!$contents) {
-    throw new Exception('Unable to find ' . $path . ' file');
-  }
+  if (file_exists($path)) {
+    $contents = file_get_contents($path);
+    if (!$contents) {
+      throw new Exception('Unable to find ' . $path . ' file');
+    }
 
-  return json_decode($contents, TRUE);
+    return json_decode($contents, TRUE);
+  }
+  else {
+    return [];
+  }
 }
 
 /**

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_add.form.inc

@@ -19,21 +19,6 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
     return $form;
   }
 
-  // Check to see if this is an edit form.
-  $edit_form = FALSE;
-  if (isset($form_state['build_info']['args'][0]) AND is_numeric($form_state['build_info']['args'][0])) {
-    $instance_id = $form_state['build_info']['args'][0];
-    $result = tripal_jbrowse_mgmt_get_instances(['id' => $instance_id]);
-    if (!empty($result)) {
-      $instance = $result[0];
-      $edit_form = TRUE;
-    }
-    else {
-      drupal_set_message('Unable to access the instance you would like to edit.', 'error');
-      return $form;
-    }
-  }
-
   $organisms = tripal_jbrowse_mgmt_get_organisms_list();
   $mapped_organisms = [];
   foreach ($organisms as $organism) {
@@ -44,12 +29,10 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
 
   $form_description = 'Create a new JBrowse instance for a given organism. Submitting this form
   creates all the necessary files for a new JBrowse instance.';
-  if ($edit_form) {
-    $form_description = 'Edit details regarding the current JBrowse instance.';
-  }
   $form['description_of_form'] = [
     '#type' => 'item',
     '#markup' => t($form_description),
+    '#weight' => -10,
   ];
 
   $form['organism'] = [
@@ -58,7 +41,7 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
     '#type' => 'select',
     '#options' => $mapped_organisms,
     '#required' => TRUE,
-    '#default_value' => ($edit_form) ? $instance->organism_id : NULL,
+    '#weight' => -8,
   ];
 
   $form['analysis'] = [
@@ -72,13 +55,14 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
     '#title' => t('Description'),
     '#description' => t('Optional description for the instance.'),
     '#type' => 'textarea',
-    '#default_value' => ($edit_form) ? $instance->description : NULL,
+    '#weight' => -7,
   ];
 
   $form['data'] = [
     '#type' => 'fieldset',
     '#title' => t('Reference Sequence File'),
     '#collabsible' => FALSE,
+    '#weight' => 0
   ];
 
   $form['data']['data_desc'] = [
@@ -92,7 +76,6 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
   $form['data']['ref_seq_file'] = [
     '#type' => 'file',
     '#title' => t('Reference Sequence FASTA File'),
-    '#disabled' => ($edit_form) ? TRUE : FALSE,
   ];
 
   $form['data']['ref_seq_path'] = [
@@ -101,7 +84,6 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
     '#description' => t(
       'This path will be ignored if a file is provided above. Ex: sites/default/files/file.fasta or /data/file.fasta'
     ),
-    '#disabled' => ($edit_form) ? TRUE : FALSE,
   ];
 
   $form['page'] = [
@@ -144,7 +126,6 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
       position 0, starting position of the gene, to a certain end point.</p>\r\n
       <pre>     ctgA</pre>\r\n<p>Displays an arbitrary region from the ctgA
       reference.</p>",
-    '#default_value' => ($edit_form) ? tripal_jbrowse_mgmt_get_instance_property($instance_id, 'start-loc') : NULL,
   ];
 
   $form['page']['start-tracks'] = [
@@ -155,16 +136,12 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
       each of which should correspond to the \"label\" element of the track
       information dictionaries that are currently viewed in the viewing field.</p>\r\n
       <pre>     DNA,knownGene,ccdsGene,snp131,pgWatson,simpleRepeat</pre>",
-    '#default_value' => ($edit_form) ? tripal_jbrowse_mgmt_get_instance_property($instance_id, 'start-tracks') : NULL,
   ];
 
-  $button = 'Create New Instance';
-  if ($edit_form) {
-    $button = 'Save Changes';
-  }
   $form['submit'] = [
     '#type' => 'submit',
-    '#value' => $button,
+    '#value' => 'Create New Instance',
+    '#weight' => 10,
   ];
 
   return $form;
@@ -187,36 +164,36 @@ function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
     $edit_form = TRUE;
   }
 
-  if (!$edit_form) {
-    $file = $_FILES['files']['tmp_name']['ref_seq_file'];
-    $local_file = isset($values['ref_seq_path']) ? $values['ref_seq_path'] : NULL;
 
-    if (empty($file) && empty($local_file)) {
-      form_set_error(
-        'ref_seq_file',
-        'Please provide a local file path or upload a new file.'
-      );
+  $file = $_FILES['files']['tmp_name']['ref_seq_file'];
+  $local_file = isset($values['ref_seq_path']) ? $values['ref_seq_path'] : NULL;
+
+  if (empty($file) && empty($local_file)) {
+    form_set_error(
+      'ref_seq_file',
+      'Please provide a local file path or upload a new file.'
+    );
+  }
+  elseif (empty($file) && !empty($local_file)) {
+    if (!file_exists($local_file)) {
+      form_set_error('ref_seq_path', 'The file path provided does not exist.');
     }
-    elseif (empty($file) && !empty($local_file)) {
-      if (!file_exists($local_file)) {
-        form_set_error('ref_seq_path', 'The file path provided does not exist.');
-      }
+  }
+  else {
+    $uploaded = tripal_jbrowse_mgmt_upload_file('ref_seq_file');
+    if (!$uploaded) {
+      form_set_error('ref_seq_file', 'Unable to upload file');
     }
     else {
-      $uploaded = tripal_jbrowse_mgmt_upload_file('ref_seq_file');
-      if (!$uploaded) {
-        form_set_error('ref_seq_file', 'Unable to upload file');
-      }
-      else {
-        $uploaded = tripal_jbrowse_mgmt_move_file($uploaded);
-        $form_state['values']['uploaded_file'] = $uploaded;
-      }
+      $uploaded = tripal_jbrowse_mgmt_move_file($uploaded);
+      $form_state['values']['uploaded_file'] = $uploaded;
     }
   }
 
   //  if selected organism already exist, analysis_id is required
   //  also make sure organism+analysis does not exist
   $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]);
+<<<<<<< HEAD
   if (empty($values['analysis'])) {
     if (!empty($instances)){
       form_set_error(
@@ -224,6 +201,13 @@ function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
         'A JBrowse instance for the selected organism already exists. Please choose one analysis for this instance.'
       );
     }
+=======
+  if (!empty($instances)) {
+    form_set_error(
+      'organism',
+      'A JBrowse instance for the selected organism already exists. You can edit the instance from the instances page.'
+    );
+>>>>>>> 7.x-3.x
   }
   else{
     $values_analysis_id = tripal_jbrowse_mgmt_get_analysis_id_from_string($values['analysis']);
@@ -265,40 +249,50 @@ function tripal_jbrowse_mgmt_add_form_submit($form, &$form_state) {
   $analysis_id = array_pop($match_analysis[0]);
   $description = isset($values['description']) ? $values['description'] : '';
 
-  // Check if this is an add or edit form.
-  $edit_form = FALSE;
-  if (isset($form_state['build_info']['args'][0]) AND is_numeric($form_state['build_info']['args'][0])) {
-    $instance_id = $form_state['build_info']['args'][0];
-    $edit_form = TRUE;
+  if (empty($values['uploaded_file'])) {
+    $file = $values['ref_seq_path'];
+  }
+  else {
+    $file = $values['uploaded_file'];
   }
 
-  if ($edit_form) {
-
-    $organism = db_select('chado.organism', 'CO')
-      ->fields('CO')
-      ->condition('organism_id', $organism_id)
-      ->execute()
-      ->fetchObject();
-
-    $title = tripal_jbrowse_mgmt_construct_organism_name($organism);
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism_id)
+    ->execute()
+    ->fetchObject();
 
-    $data = [
+  $instance_id = tripal_jbrowse_mgmt_create_instance(
+    [
       'organism_id' => $organism_id,
+<<<<<<< HEAD
       'analysis_id' => $analysis_id,
       'title' => $title,
+=======
+      'title' => tripal_jbrowse_mgmt_construct_organism_name($organism),
+>>>>>>> 7.x-3.x
       'description' => $description,
-    ];
-    $success = tripal_jbrowse_mgmt_update_instance($instance_id, $data);
+      'created_at' => time(),
+      'file' => $file,
+    ]
+  );
 
-    if ($success) {
-      drupal_set_message("Successfully updated $title JBrowse instance.");
-      $form_state['redirect'] = 'admin/tripal/extension/tripal_jbrowse/management/instances';
-    }
-    else {
-      drupal_set_message('Failed to update the current instance!', 'error');
-    }
+  if ($instance_id) {
+    drupal_set_message('Instance created successfully!');
+    $name = 'Create JBrowse instance for ';
+    $name .= tripal_jbrowse_mgmt_construct_organism_name($organism);
+
+    tripal_add_job(
+      $name,
+      'tripal_jbrowse_mgmt',
+      'tripal_jbrowse_mgmt_create_instance_files',
+      [$instance_id],
+      $user->uid
+    );
+    $form_state['redirect'] = "admin/tripal/extension/tripal_jbrowse/management/instances/$instance_id";
   }
   else {
+<<<<<<< HEAD
     if (empty($values['uploaded_file'])) {
       $file = $values['ref_seq_path'];
     }
@@ -340,6 +334,10 @@ function tripal_jbrowse_mgmt_add_form_submit($form, &$form_state) {
     else {
       drupal_set_message('Failed to create instance!', 'error');
     }
+=======
+    drupal_set_message('Failed to create instance!', 'error');
+    return;
+>>>>>>> 7.x-3.x
   }
 
   // Now save the instance properties.

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_edit.form.inc

@@ -0,0 +1,126 @@
+<?php
+/**
+ * @file
+ * Instance Edit Form.
+ */
+
+/**
+ *
+ */
+function tripal_jbrowse_mgmt_edit_form($form, &$form_state) {
+
+  $instance_id = $form_state['build_info']['args'][0];
+  $result = tripal_jbrowse_mgmt_get_instances(['id' => $instance_id]);
+  if (!empty($result)) {
+    $instance = $result[0];
+    $edit_form = TRUE;
+  }
+  else {
+    drupal_set_message('Unable to access the instance you would like to edit.', 'error');
+    return $form;
+  }
+
+  // This is essentiall the add form with defaults.
+  // We use a second function here for cleaner validation and submit.
+  require_once 'tripal_jbrowse_mgmt_add.form.inc';
+  $form = tripal_jbrowse_mgmt_add_form($form, $form_state);
+
+  $form['description_of_form']['#markup'] = t('Edit details regarding the current JBrowse instance.');
+
+  // Set Default Values.
+  $form['organism']['#default_value'] = $instance->organism_id;
+  $form['description']['#default_value'] = $instance->description;
+  $form['page']['start-loc']['#default_value'] = tripal_jbrowse_mgmt_get_instance_property($instance_id, 'start-loc');
+  $form['page']['start-tracks']['#default_value'] = tripal_jbrowse_mgmt_get_instance_property($instance_id, 'start-tracks');
+
+  // Remove the file upload.
+  unset($form['data']);
+
+  // Change the submit button.
+  $form['submit']['#value'] = 'Save Changes';
+
+  return $form;
+}
+
+/**
+ * Validate the form.
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_edit_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $organism = isset($values['organism']) ? $values['organism'] : NULL;
+
+  $instance_id = $form_state['build_info']['args'][0];
+  $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]);
+  if (!empty($instances)) {
+    if ($instances[0]->id != $instance_id) {
+      form_set_error(
+        'organism',
+        'A JBrowse instance for the selected organism already exists. You can edit the instance from the instances page.'
+      );
+    }
+  }
+
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism)
+    ->execute()
+    ->fetchObject();
+
+  if (empty($organism)) {
+    form_set_error('organism', 'Invalid organism selected ' . $organism);
+  }
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_edit_form_submit($form, &$form_state) {
+  global $user;
+
+  $values = $form_state['values'];
+  $organism_id = $values['organism'];
+  $description = isset($values['description']) ? $values['description'] : '';
+
+  // Check if this is an add or edit form.
+  $edit_form = FALSE;
+  if (isset($form_state['build_info']['args'][0]) AND is_numeric($form_state['build_info']['args'][0])) {
+    $instance_id = $form_state['build_info']['args'][0];
+    $edit_form = TRUE;
+  }
+
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism_id)
+    ->execute()
+    ->fetchObject();
+
+  $title = tripal_jbrowse_mgmt_construct_organism_name($organism);
+
+  $data = [
+    'organism_id' => $organism_id,
+    'title' => $title,
+    'description' => $description,
+  ];
+  $success = tripal_jbrowse_mgmt_update_instance($instance_id, $data);
+
+  if ($success) {
+    drupal_set_message("Successfully updated $title JBrowse instance.");
+    $form_state['redirect'] = 'admin/tripal/extension/tripal_jbrowse/management/instances';
+  }
+  else {
+    drupal_set_message('Failed to update the current instance!', 'error');
+    return FALSE;
+  }
+
+  // Now save the instance properties.
+  tripal_jbrowse_mgmt_save_instance_properties(
+    $instance_id,
+    $form_state['values']['page']
+  );
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_instance.page.inc

@@ -56,6 +56,7 @@ function tripal_jbrowse_mgmt_instance_page($instance_id) {
     ),
   ];
 
+  // First get tracks added by this module.
   $tracks = tripal_jbrowse_mgmt_get_tracks($instance, ['is_deleted' => 0]);
 
   $content['tracks_title'] = [
@@ -63,31 +64,61 @@ function tripal_jbrowse_mgmt_instance_page($instance_id) {
     '#markup' => '<h4>Tracks</h4>',
   ];
 
-  if (empty($tracks)) {
-    $content['no_tracks'] = [
-      '#type' => 'item',
-      '#markup' => 'No tracks found for this instance. Please use the add tracks link above to add new tracks.',
-    ];
+  $managed_tracks = [];
+  $rows = [];
+
+  if (!empty($tracks)) {
+    foreach ($tracks as $track) {
+
+      // Keep track of managed tracks so they are not duplicated later.
+      $managed_tracks[] = $track->label;
+
+      // Add the current tracks to the table.
+      $rows[] = [
+        $track->label,
+        $track->track_type,
+        $track->file_type,
+        $track->user->name,
+        date('m/d/Y', $track->created_at),
+        l('Manage Track', 'admin/tripal/extension/tripal_jbrowse/management/tracks/' . $track->id),
+        l(
+          'Delete Track',
+          'admin/tripal/extension/tripal_jbrowse/management/tracks/' . $track->id . '/delete'
+        ),
+      ];
+    }
   }
-  else {
-    $rows = array_map(
-      function ($track) {
-        return [
-          $track->label,
-          $track->track_type,
-          $track->file_type,
-          $track->user->name,
-          date('m/d/Y', $track->created_at),
-          l('Manage Track', 'admin/tripal/extension/tripal_jbrowse/management/tracks/' . $track->id),
-          l(
-            'Delete Track',
-            'admin/tripal/extension/tripal_jbrowse/management/tracks/' . $track->id . '/delete'
-          ),
-        ];
-      },
-      $tracks
-    );
 
+  // Second grab all tracks from the JSON.
+  $trackList = tripal_jbrowse_mgmt_get_json($instance);
+  if (!empty($trackList) and isset($trackList['tracks'])) {
+
+    foreach ($trackList['tracks'] as $track) {
+
+      // Make sure we only get the readable component for the type.
+      $path_type = explode('/', $track['type']);
+      $type = end($path_type);
+
+      // Make sure this is not a managed track.
+      if (in_array($track['key'], $managed_tracks)) {
+        continue;
+      }
+
+      // Now compile our row.
+      $rows[] = [
+        $track['key'],
+        $type,
+        '',
+        '',
+        '',
+        '',
+        '',
+      ];
+    }
+  }
+
+  // Finally, if there are tracks, show them in a table.
+  if (!empty($rows)) {
     $content['tracks_table'] = [
       '#type' => 'markup',
       '#markup' => theme(
@@ -107,6 +138,13 @@ function tripal_jbrowse_mgmt_instance_page($instance_id) {
       ),
     ];
   }
+  // Otherwise, prompt people to add tracks!
+  else {
+    $content['no_tracks'] = [
+      '#type' => 'item',
+      '#markup' => 'No tracks found for this instance. Please use the add tracks link above to add new tracks.',
+    ];
+  }
 
   return $content;
 }

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_register.form.inc

@@ -0,0 +1,117 @@
+<?php
+/**
+ * @file
+ * Instance Register Form.
+ */
+
+/**
+ *
+ */
+function tripal_jbrowse_mgmt_register_form($form, &$form_state) {
+
+  // This is essentiall the add form without create JBrowse functionality.
+  // We use a second function here for cleaner validation and submit.
+  require_once 'tripal_jbrowse_mgmt_add.form.inc';
+  $form = tripal_jbrowse_mgmt_add_form($form, $form_state);
+
+  $settings = tripal_jbrowse_mgmt_get_settings();
+  $path = $settings['data_dir'] . '/genus_species/data/';
+
+  $msg = '<p>Register an already existing JBrowse instance to be managed by this module.</p>'
+  . '<div class="messages warning">It is expected that the data directory for the existing JBrowse instance is <code>@path</code> where <code>genus_species</code> matches what you select for the organism. If this is not the location of your JBrowse, you should create a symbolic link between the current instance location and the expected one mentioned above.</div>';
+  $form['description_of_form']['#markup'] = t($msg, ['@path' => $path]);
+
+  // Remove the file upload.
+  unset($form['data']);
+
+  // Change the submit button.
+  $form['submit']['#value'] = 'Register Instance';
+
+  return $form;
+}
+
+/**
+ * Validate the form.
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_register_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $organism = isset($values['organism']) ? $values['organism'] : NULL;
+
+  // Check an instance does not already exist.
+  $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]);
+  if (!empty($instances)) {
+    form_set_error(
+      'organism',
+      'A JBrowse instance for the selected organism already exists. You can edit the instance from the instances page.'
+    );
+  }
+
+  // Check that the organism does exist.
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism)
+    ->execute()
+    ->fetchObject();
+
+  if (empty($organism)) {
+    form_set_error('organism', 'Invalid organism selected ' . $organism);
+  }
+
+  // Check that the directory we assume contains the instance does exist.
+  $title = tripal_jbrowse_mgmt_construct_organism_name($organism);
+  $settings = tripal_jbrowse_mgmt_get_settings();
+  $path = $settings['data_dir'];
+  $path .= '/' . tripal_jbrowse_mgmt_make_slug($title);
+  $path .= '/data/trackList.json';
+  if (!file_exists($path)) {
+    form_set_error('organism', "We expect there is already an existing instane at the following path: $path");
+  }
+}
+
+/**
+ * @param $form
+ * @param $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_register_form_submit($form, &$form_state) {
+  global $user;
+
+  $values = $form_state['values'];
+  $organism_id = $values['organism'];
+  $description = isset($values['description']) ? $values['description'] : '';
+
+  $organism = db_select('chado.organism', 'CO')
+    ->fields('CO')
+    ->condition('organism_id', $organism_id)
+    ->execute()
+    ->fetchObject();
+
+  $instance_id = tripal_jbrowse_mgmt_create_instance(
+    [
+      'organism_id' => $organism_id,
+      'title' => tripal_jbrowse_mgmt_construct_organism_name($organism),
+      'description' => $description,
+      'created_at' => time(),
+      'file' => '',
+    ]
+  );
+
+  if ($instance_id) {
+    drupal_set_message('Instance registered successfully!');
+    $form_state['redirect'] = "admin/tripal/extension/tripal_jbrowse/management/instances/$instance_id";
+  }
+  else {
+    drupal_set_message('Failed to create instance!', 'error');
+    return;
+  }
+
+  // Now save the instance properties.
+  tripal_jbrowse_mgmt_save_instance_properties(
+    $instance_id,
+    $form_state['values']['page']
+  );
+}

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -97,7 +97,7 @@ function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
   $form['data']['symbolic_link'] = [
     '#type' => 'checkbox',
     '#title' => t('Symbolic Link'),
-    '#description' => t('Create a symbolic link rather than make a copy of the file.'),
+    '#description' => t('Create a symbolic link rather than make a copy of the file. This only applies when a path on the server is supplied.'),
   ];
 
   $form['submit'] = [

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.info

@@ -1,6 +1,7 @@
 name = Tripal JBrowse Management
 description = Create JBrowse instances and manage tracks.
 core = 7.x
+package = Tripal Extensions: JBrowse Integration
 
 dependecies[] = tripal
 ; Not on the drupal repository but a required dependency!

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.module

@@ -46,8 +46,18 @@ function tripal_jbrowse_mgmt_menu() {
     'type' => MENU_LOCAL_TASK,
   ];
 
+  $items['admin/tripal/extension/tripal_jbrowse/management/instances/register'] = [
+    'title' => 'Register Existing Instance',
+    'description' => 'Adds an existing JBrowse to the list of instances managed within Tripal.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_register_form'],
+    'access arguments' => ['administer tripal_jbrowse_mgmt'],
+    'file' => 'includes/tripal_jbrowse_mgmt_register.form.inc',
+    'type' => MENU_LOCAL_ACTION,
+  ];
+
   $items['admin/tripal/extension/tripal_jbrowse/management/instances/add'] = [
-    'title' => 'Add New Instance',
+    'title' => 'Create New Instance',
     'description' => 'List and create JBrowse instances.',
     'page callback' => 'drupal_get_form',
     'page arguments' => ['tripal_jbrowse_mgmt_add_form'],
@@ -70,9 +80,9 @@ function tripal_jbrowse_mgmt_menu() {
     'title' => 'Edit Instance',
     'description' => 'Edit metadata for existing JBrowse instances.',
     'page callback' => 'drupal_get_form',
-    'page arguments' => ['tripal_jbrowse_mgmt_add_form', 6],
+    'page arguments' => ['tripal_jbrowse_mgmt_edit_form', 6],
     'access arguments' => ['administer tripal_jbrowse_mgmt'],
-    'file' => 'includes/tripal_jbrowse_mgmt_add.form.inc',
+    'file' => 'includes/tripal_jbrowse_mgmt_edit.form.inc',
     'type' => MENU_LOCAL_ACTION,
   ];
 

tripal_jbrowse_page/tripal_jbrowse_page.info

@@ -1,7 +1,7 @@
 name = Tripal-JBrowse Page Integration
 description = Integrates JBrowse instances into Tripal Pages.
 core = 7.x
-package = Tripal Extensions
+package = Tripal Extensions: JBrowse Integration
 
 dependencies[] = tripal
 dependencies[] = tripal_jbrowse_mgmt