tripal_sra.module

<?php
/**
 * @file
 * Basic functionality for the tripal analysis expression module.
 */

/**
 * @defgroup tripal_analysis_expression Tripal Analysis Expression
 * @ingroup tripal_modules *** is this right?
 * @{
 * Integrates the several tables from the Chado Mage module with
 * the Analysis module.
 * @}
 */
require_once "api/tripal_sra.api.inc";
require_once "includes/tripal_sra.chado.node.inc";

// change keyword biomaterial to biosample for: 
//   1: not conflict with tripal_analysis_expression
//   2: consistant with SRA database
require_once "api/tripal_bioproject.api.inc";
require_once "includes/tripal_biosample.chado_node.inc";
require_once "includes/tripal_biosample.admin.inc";
require_once "includes/tripal_biosample_loader.inc";

// node bioproject 
require_once "includes/tripal_bioproject.chado_node.inc";
require_once "includes/tripal_bioproject.admin.inc";

// node experiment
require_once "includes/tripal_experiment.chado_node.inc";
require_once "includes/tripal_experiment.admin.inc";
require_once "includes/tripal_experiment_loader.inc";
// theme preprocessing
require_once "theme/tripal_sra.theme.inc";

/**
 * Implements hook_help().
 *
 * Display help and module information.
 *
 * @ingroup tripal_analysis_expression
 */
function tripal_sra_help($path, $arg) {
  switch ($path) {

    // Both of the following cases should display the below HTML.
    case 'admin/tripal/extension/tripal_analysis_expression/help' :
    case 'admin/help#tripal_analysis_expression' : {
      $ret_val = '<h3>' . t('Module Content Types') . '</h3>';
      $ret_val .= '<p>' . t('The expression module allows the user to load and display expression information.') . '</p>';
      $ret_val .= "<b>" . t("Analysis: Expression") . "</b> - " . t("This analysis: expression content type") . " ";
      $ret_val .= t("provides the ability") . " ";
      $ret_val .= t("to describe either microarray expression data or next generation sequencing") . " ";
      $ret_val .= t("expression data (such as data obtained from RNASeq). The analysis: expression content") . " ";
      $ret_val .= t("type also provides a") . " ";
      $ret_val .= t("form to load expression data associated with the analysis.") . "<br>";
      $ret_val .= l(t("Analysis: Expression Administrative Pages"), "admin/tripal/extension/tripal_analysis_expression/content_types/analysis_expression");
      $ret_val .= "<br>" . l(t("Create Analysis: Expression"), "node/add/chado-analysis-expression");
      $ret_val .= "<br>" . l(t("Analysis: Expression Help"), "admin/tripal/extension/tripal_analysis_expression/content_types/analysis_expression/help");
      $ret_val .= "<br><br><b>" . t("Biomaterial") . "</b> - " . t("The biomaterial content type") . " ";
      $ret_val .= t("represents the Chado biomaterial table. The Chado biomaterial table is a member") . " ";
      $ret_val .= t("of the Chado MAGE module. The biomaterial content type is similar to the") . " ";
      $ret_val .= l(t("BioSample"), "http://www.ncbi.nlm.nih.gov/books/NBK169436/") . " ";
      $ret_val .= t("content type provided by NCBI. See the biomaterial description at the") . " ";
      $ret_val .= l(t("GMOD wiki."), "http://gmod.org/wiki/Chado_Mage_Module#Table:_biomaterial") . "<br>";
      $ret_val .= l(t("Biomaterial Administrative Pages"), "admin/tripal/extension/tripal_analysis_expression/content_types/biomaterial");
      $ret_val .= "<br>" . l(t("Create Biomaterial"), "node/add/chado-biomaterial");
      $ret_val .= "<br>" . l(t("Biomaterial Help"), "admin/tripal/extension/tripal_analysis_expression/content_types/biomaterial/help");
      $ret_val .= "<br><br><b>" . t("Array Design") . "</b> - " . t("The array design content type") . " ";
      $ret_val .= t("represents the Chado arraydesign table. This table is only used when describing") . " ";
      $ret_val .= t("the experimental design of data collected from a microarray expression experiment.") . " ";
      $ret_val .= t("See the arraydesign description at the");
      $ret_val .= l(t(" GMOD wiki."), "http://gmod.org/wiki/Chado_Mage_Module#Table:_arraydesign") . "<br>";
      $ret_val .= l(t("Array Design Administrative Pages"), "admin/tripal/extension/tripal_analysis_expression/content_types/arraydesign");
      $ret_val .= "<br>" . l(t("Create Array Design"), "node/add/chado-arraydesign");
      $ret_val .= "<br>" . l(t("Array Design Help"), "admin/tripal/extension/tripal_analysis_expression/content_types/arraydesign/help");
      $ret_val .= "<br><br><b>" . t("Protocol") . "</b> -" . t(" The protocol content type represents") . " ";
      $ret_val .= t("the Chado protocol table. This table is used to describe the protocol, software,") . " ";
      $ret_val .= t("and hardware used in different steps of the experiment. See the protocol description at the") . " ";
      $ret_val .= l(t("GMOD wiki."), "http://gmod.org/wiki/Chado_Tables#Table:_protocol") . "<br>";
      $ret_val .= l(t("Protocol Administrative Pages"), "admin/tripal/extension/tripal_analysis_expression/content_types/protocol");
      $ret_val .= "<br>" . l(t("Create Protocol"), "node/add/chado-protocol") . "<br>";
      $ret_val .= l(t("Protocol Help"), "admin/tripal/extension/tripal_analysis_expression/content_types/protocol/help");
      $ret_val .= '<h3>' . t('Module Data Loaders') . '</h3>';
      $ret_val .= "<p>" . t("This module provides several data loaders.") . '</p>';
      $ret_val .= "<b>" . l(t("Biomaterial Loader"), "admin/tripal/extension/tripal_analysis_expression/biomaterial_loader");
      $ret_val .= "</b> - " . t("The biomaterial loader has the ability to load ");
      $ret_val .= l(t("BioSample"), "http://www.ncbi.nlm.nih.gov/biosample/") . t(" data downloaded from NCBI in an xml format. ");
      $ret_val .= t("The biomaterial loader can also load data from a CSV or TSV file formatted as a ");
      $ret_val .= l(t("BioSample submission template"), "https://submit.ncbi.nlm.nih.gov/biosample/template/") . t(".");
      $ret_val .= "<br><br><b>" . l(t("Expression Loader"), "node/add/chado-analysis-expression") . "</b> - ";
      $ret_val .= t("The expression loader is associated with the Analysis: Expression ");
      $ret_val .= t("content type. To load expression data, create an Analysis: Expression and configure the expression loading job ");
      $ret_val .= t("in the Analysis: Expression form. Expression data may be loaded from two types of tab separted formats, ");
      $ret_val .= t("a matrix file or a column file.") . "<br><br>";

      return $ret_val;
      break;
    }
  }
}

/**
 * Implements hook_permission().
 *
 *  Set the permissions types used by the tripal analysis expression module.
 *  Permissions include: access, create, delete, edit, and administer.
 *  Permissions are set for the following content types provided by this module:
 *  Analysis: Expression, Arraydesign, Biomaterial, and Protocol.
 *
 * @ingroup tripal_analysis_expression
 */
//function tripal_sra_permission() {
  /**
  return array(
    'access chado_analysis_expression content' => array(
      'title' => t('View Analysis: Expressions'),
      'description' => t('Allow users to view analysis: expression pages.'),
    ),
    'create chado_analysis_expression content' => array(
      'title' => t('Create Analysis: Expressions'),
      'description' => t('Allow users to create new analysis: expression pages.'),
    ),
    'delete chado_analysis_expression content' => array(
      'title' => t('Delete Analysis: Expressions'),
      'description' => t('Allow users to delete analysis: expression pages.'),
    ),
    'edit chado_analysis_expression content' => array(
      'title' => t('Edit Analysis: Expressions'),
      'description' => t('Allow users to edit analysis: expression pages.'),
    ),
    'administer tripal analysis expression' => array(
      'title' => t('Administer Analysis: Expressions'),
      'description' => t('Allow users to administer all analysis: expressions.'),
    ),
    'access chado_arraydesign content' => array(
      'title' => t('View Arraydesigns'),
      'description' => t('Allow users to view arraydesign pages.'),
    ),
    'create chado_arraydesign content' => array(
      'title' => t('Create Arraydesigns'),
      'description' => t('Allow users to create new arraydesign pages.'),
    ),
    'delete chado_arraydesign content' => array(
      'title' => t('Delete Arraydesigns'),
      'description' => t('Allow users to delete arraydesign pages.'),
    ),
    'edit chado_arraydesign content' => array(
      'title' => t('Edit Arraydesigns'),
      'description' => t('Allow users to edit arraydesign pages.'),
    ),
    'administer tripal arraydesign' => array(
      'title' => t('Administer Arraydesigns'),
      'description' => t('Allow users to administer all arraydesigns.'),
    ),
    'access chado_biomaterial content' => array(
      'title' => t('View Biomaterials'),
      'description' => t('Allow users to view biomaterial pages.'),
    ),
    'create chado_biomaterial content' => array(
      'title' => t('Create Biomaterials'),
      'description' => t('Allow users to create new biomaterial pages.'),
    ),
    'delete chado_biomaterial content' => array(
      'title' => t('Delete Biomaterials'),
      'description' => t('Allow users to delete biomaterial pages.'),
    ),
    'edit chado_biomaterial content' => array(
      'title' => t('Edit Biomaterials'),
      'description' => t('Allow users to edit biomaterial pages.'),
    ),
    'administer tripal biomaterial' => array(
      'title' => t('Administer Biomaterials'),
      'description' => t('Allow users to administer all biomaterials.'),
    ),
    'access chado_protocol content' => array(
      'title' => t('View Protocols'),
      'description' => t('Allow users to view protocol pages.'),
    ),
    'create chado_protocol content' => array(
      'title' => t('Create Protocols'),
      'description' => t('Allow users to create new protocol pages.'),
    ),
    'delete chado_protocol content' => array(
      'title' => t('Delete Protocols'),
      'description' => t('Allow users to delete protocol pages.'),
    ),
    'edit chado_protocol content' => array(
      'title' => t('Edit Protocols'),
      'description' => t('Allow users to edit protocol pages.'),
    ),
    'administer tripal protocol' => array(
      'title' => t('Administer Protocols'),
      'description' => t('Allow users to administer all protocols.'),
    ),
  );
  */
//}

/**
 * Implements hook_menu().
 */
function tripal_sra_menu() {
  $items = array();

  // === main admin page ===.
  $items['admin/tripal/extension/tripal_sra'] = array(
    'title' => 'Tripal SRA',
    'description' => 'A module for management of NGS samples like NCBI SRA.',
    'access arguments' => array('administer site configuration'),
  );

  // === help === 
  $items['admin/tripal/extension/tripal_sra/help'] = array(
    'title' => 'Tripal SRA Help',
    'description' => 'Document for how to use Tripal SRA.',
    'access arguments' => array('administer site configuration'),
    'weight' => 10,
  );

  /**
   * bioproject (use project module in chado)
   */
  $items['admin/tripal/extension/tripal_sra/bioproject'] = array(
    'title' => 'SRA BioProject',
    'description' => 'A collection of biological data related to a single initiative, originating from a single organization or from a consortium.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'tripal_bioproject_admin_bioprojects_view',
    'type' => MENU_NORMAL_ITEM,
  );

  // bioproject settings.
  $items['admin/tripal/extension/tripal_sra/bioproject/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Manage Tripal SRA: BioPorject settings and configurations.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bioproject_admin'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5,
  );

  // bioproject TOC.
  $items['admin/tripal/extension/tripal_sra/bioproject/chado_bioproject_toc'] = array(
    'title' => 'TOC',
    'description' => 'Manage the table of contents for BioProject nodes.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_content_type_toc_form', 'chado_bioproject'),
    'file' => 'includes/tripal_core.toc.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 3,
  );

  // bioproject help.
  $items['admin/tripal/extension/tripal_sra/bioproject/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal BioProject content type including a short description of it's usage.",
    'access arguments' => array('administer site configuration'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_bioproject_help'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

  // bioproject enable view.
  $items['admin/tripal/extension/tripal_sra/bioproject/views/bioprojects/enable'] = array(
    'title' => 'Enable Biosample Administrative View',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'tripal_enable_view',
    'page arguments' => array(
      'tripal_biosample_admin_bioproject',
      'tripal_sra',
      'admin/tripal/extension/tripal_sra/bioproject',
    ),
  );

  /**
   * biomaterial (aka biosample in SRA)
   */
  $items['admin/tripal/extension/tripal_sra/biosample'] = array(
    'title' => 'SRA BioSample',
    'description' => 'Descriptions of biological source materials used in experimental assays.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'tripal_biosample_admin_biosamples_view',
    'type' => MENU_NORMAL_ITEM,
  );

  // biosample loader from txt file.
  $items['admin/tripal/extension/tripal_sra/biosample/biosample_loader'] = array(
    'title' => 'Load',
    'description' => 'Load biosamples into database from tab delimit file.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_biosample_loader'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2,
  );

  // biosample sync node from chado database 
  $items['admin/tripal/extension/tripal_sra/biosample/sync'] = array(
    'title' => 'Sync',
    'description' => 'Create pages on this site for BioSamples stored in Chado.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array(
      'chado_node_sync_form',
      'tripal_sra',
      'chado_biosample',
    ),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2,
  );

  // biosample TOC.
  $items['admin/tripal/extension/tripal_sra/biosample/chado_biosample_toc'] = array(
    'title' => 'TOC',
    'description' => 'Manage the table of contents for biosample nodes.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_content_type_toc_form', 'chado_biosample'),
    'file' => 'includes/tripal_core.toc.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 3,
  );

  // biosample delete.
  $items['admin/tripal/extension/tripal_sra/biosample/delete'] = array(
    'title' => "Delete",
    'description' => 'Delete multiple biosamples from Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_biosample_delete_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_LOCAL_TASK,
    'file path' => drupal_get_path('module', 'tripal_sra'),
    'file' => 'includes/tripal_biosample.delete.inc',
    'weight' => 3,
  );

  // biosample settings.
  $items['admin/tripal/extension/tripal_sra/biosample/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Manage Tripal SRA: Biosample settings and configurations.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_biosample_admin'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5,
  );

  // biosample help.
  $items['admin/tripal/extension/tripal_sra/biosample/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Biosample content type including a short description of it's usage.",
    'access arguments' => array('administer site configuration'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_biosample_help'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

  // biosample enable view.
  /**
  $items['admin/tripal/extension/tripal_sra/biosample/views/biosamples/enable'] = array(
    'title' => 'Enable Biosample Administrative View',
    'access arguments' => array('administer'),
    'page callback' => 'tripal_enable_view',
    'page arguments' => array(
      'tripal_biosample_admin_biosamples',
      'tripal_sra',
      'admin/tripal/extension/tripal_sra/biosample',
    ),
  );
  */

  /**
   * experiment (aka experiment in SRA)
   */
  $items['admin/tripal/extension/tripal_sra/experiment'] = array(
    'title' => 'SRA Experiment',
    'description' => 'SRA Experiment.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'tripal_experiment_admin_experiments_view',
    'type' => MENU_NORMAL_ITEM,
  );

  // biosample loader from txt file.
  $items['admin/tripal/extension/tripal_sra/experiment/experiment_loader'] = array(
    'title' => 'Load',
    'description' => 'Load Experiments into database from tab delimit file.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_experiment_loader'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2,
  );

  // biosample sync node from chado database 
  $items['admin/tripal/extension/tripal_sra/experiment/sync'] = array(
    'title' => 'Sync',
    'description' => 'Create pages on this site for Experiments stored in Chado.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array(
      'chado_node_sync_form',
      'tripal_sra',
      'chado_experiment',
    ),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2,
  );

  // experiment settings.
  $items['admin/tripal/extension/tripal_sra/experiment/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Manage Tripal SRA: Experiment settings and configurations.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_experiment_admin'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5,
  );

  // experiment TOC.
  $items['admin/tripal/extension/tripal_sra/experiment/chado_experiment_toc'] = array(
    'title' => 'TOC',
    'description' => 'Manage the table of contents for Experiment nodes.',
    'access arguments' => array('administer site configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_content_type_toc_form', 'chado_experiment'),
    'file' => 'includes/tripal_core.toc.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 3,
  );

  // experiment delete.
  $items['admin/tripal/extension/tripal_sra/experiment/delete'] = array(
    'title' => "Delete",
    'description' => 'Delete multiple Experiments from Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_experiment_delete_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_LOCAL_TASK,
    'file path' => drupal_get_path('module', 'tripal_sra'),
    'file' => 'includes/tripal_experiment.delete.inc',
    'weight' => 3,
  );

  // experiment help.
  $items['admin/tripal/extension/tripal_sra/experiment/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Experiment content type including a short description of it's usage.",
    'access arguments' => array('administer site configuration'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_experiment_help'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

  return $items;
}

/**
 * Implements hook_views_api().
 *
 * Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is located.
 *
 * @ingroup tripal_sra
 */
function tripal_sra_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * Implements hook_theme().
 *
 * This function informs drupal of the themes included in this modules.
 *  An base, help, and teaser template are included for the four content
 *  types defined by this module: 
         analysis: expression, arraydesign,
 *  biosample, and project. Additional templates include a protocol
 *  template for the analysis: expression content type and a variable
 *  expression template for the feature content type.
 *
 * ***documentation of parameters here????
 *
 * @ingroup tripal_sra
 */
function tripal_sra_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  $items = array(
    'node__chado_bioproject' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    'tripal_bioproject_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_bioproject_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_bioproject_experiments' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_bioproject_experiments',
      'path' => "$path/theme/templates",
    ),
    'tripal_bioproject_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_bioproject_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_bioproject_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_bioproject_teaser',
      'path' => "$path/theme/templates",
    ),
    'tripal_bioproject_help' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_bioproject_help',
      'path' => "$path/theme/templates",
    ),

    'node__chado_biosample' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    'tripal_biosample_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_biosample_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_biosample_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_biosample_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_biosample_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_biosample_teaser',
      'path' => "$path/theme/templates",
    ),
    'tripal_biosample_help' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_biosample_help',
      'path' => "$path/theme/templates",
    ),

    'node__chado_experiment' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    'tripal_experiment_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_experiment_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_experiment_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_experiment_teaser',
      'path' => "$path/theme/templates",
    ),
    'tripal_experiment_help' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_experiment_help',
      'path' => "$path/theme/templates",
    ),
  );
  /**
    'tripal_organism_biomaterial' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_biomaterial',
      'path' => "$path/theme/templates",
    ),
    'tripal_feature_expression' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_expression',
      'path' => "$path/theme/templates",
    ),
    'tripal_analysis_biomaterial' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_analysis_biomaterial',
      'path' => "$path/theme/templates",
    ),
  );
  */

  return $items;
}


/*
 * Implement hook_block_info()
 * Define two blocks one for input features
 * the other one for display heatmap
 */
/**
function tripal_sra_block_info(){
  // Define two blocks: one for features input form
  // the other one for heatmap display
  $blocks = array();
  $blocks['input_features'] = array(
    'info' => t('tripal_analysis_expression features form for heatmap'),
    'status' => 1,
    'region' => 'content',
    'weight' => 24,
    'cache' => DRUPAL_NO_CACHE
  );

  $blocks['heatmap_features'] = array(
    'info' => t('tripal_analysis_expression heatmap display'),
    'status' => 1,
    'region' => 'content',
    'weight' => 25,
    'cache' => DRUPAL_NO_CACHE
  );

  return $blocks;
}
*/
/*
 * Implement hook_block_view()
 */
/**
function tripal_analysis_expression_block_view($delta = ''){
  $block = array();
  switch($delta){
    case 'input_features':
      //$block['subject'] = t('Feature Expression');
      //$block['content'] = drupal_get_form('feature_heatmap_form');
      break;
    case 'heatmap_features':
      if(!empty($_SESSION['heatmap_data'])){
        $block['subject'] = t('Feature Expression Heatmap');
        $block['content'] = '<div id="vis_expression"></div>';
        drupal_add_js(array('tripal_analysis_expression' => array('heatmap_data' => $_SESSION['heatmap_data'])), array('type' => 'setting'));
        drupal_add_js(array('tripal_analysis_expression' => array('left_margin' => $_SESSION['left_margin'])), array('type' => 'setting'));
        drupal_add_js(array('tripal_analysis_expression' => array('bottom_margin' => $_SESSION['bottom_margin'])), array('type' => 'setting'));
      } else {
        //$block['subject'] = '';
        //$block['content'] = t('<b><span style="color:red">Either you have not entered any features or no expression data available for the features you entered.</span></b>');
      }
      break;
  }

  //drupal_add_js(array('tripal_analysis_expression' => array('heatmap_data' => $_SESSION['heatmap_data'])), array('type' => 'setting'));
  //drupal_add_js('https://cdn.plot.ly/plotly-latest.min.js', 'external');
  drupal_add_js(drupal_get_path('module', 'tripal_analysis_expression').'/theme/js/plotly-latest.min.js');
  drupal_add_js(drupal_get_path('module', 'tripal_analysis_expression').'/theme/js/heatmap.js');

  return $block;
}
*/