tripal_jbrowse/tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

<?php

/**
 * @file tripal_jbrowse_mgmt_tracks.form.inc
 */

/**
 * Add a track to an instance form.
 *
 * @param array $form
 *   The drupal form.
 * @param array $form_state
 *   The form state array.
 * @param int $instance_id
 *   The parent instance ID to add the new track to.
 *
 * @return array
 *   The modified form array.
 */
function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
  if (empty(tripal_jbrowse_mgmt_get_instance($instance_id))) {
    drupal_not_found();

    return [];
  }

  $form['label'] = [
    '#type' => 'textfield',
    '#title' => t('Track Label'),
    '#description' => t('This will appear on the sidebar.'),
    '#required' => TRUE,
  ];

  $form['instance_id'] = [
    '#type' => 'hidden',
    '#value' => $instance_id,
  ];

  $form['data'] = [
    '#type' => 'fieldset',
    '#title' => t('Track Files'),
  ];

  $form['data']['track_type'] = [
    '#type' => 'select',
    '#description' => t('See http://gmod.org/wiki/JBrowse_Configuration_Guide#flatfile-to-json.pl for more info.'),
    '#required' => TRUE,
    '#title' => t('Track Type'),
    '#options' => drupal_map_assoc(tripal_jbrowse_mgmt_get_track_types()),
  ];

  $form['data']['file_type'] = [
    '#type' => 'select',
    '#title' => t('File Type'),
    '#options' => drupal_map_assoc(['gff', 'bed', 'gbk', 'vcf', 'bw']),
    '#description' => t('See http://gmod.org/wiki/JBrowse_Configuration_Guide#flatfile-to-json.pl for more info.'),
    '#required' => TRUE,
  ];

  $form['data']['file'] = [
    '#type' => 'file',
    '#title' => t('File'),
  ];

  $form['data']['file2'] = [
    '#type' => 'file',
    '#title' => t('Index File'),
    '#states' => [
      'visible' => [
        ':input[name="file_type"]' => ['value' => 'vcf'],
      ],
    ],
  ];

  $form['data']['file_path'] = [
    '#type' => 'textfield',
    '#title' => t('- OR Path to File on Server -'),
    '#description' => t('This path will be ignored if a file is provided above. Ex: sites/default/files/file.fasta or /data/file.fasta'),
    '#states' => [
      'invisible' => [
        ':input[name="file_type"]' => ['value' => 'vcf'],
      ],
    ],
  ];

  $form['data']['dir_path'] = [
    '#type' => 'textfield',
    '#title' => t('- OR Path to Directory on Server -'),
    '#description' => t('This path will be ignored if a file is provided above. ' . 'The directory must contain both the .tbi and .gz files.'),
    '#states' => [
      'visible' => [
        ':input[name="file_type"]' => ['value' => 'vcf'],
      ],
    ],
  ];

  $form['data']['symbolic_link'] = [
    '#type' => 'checkbox',
    '#title' => t('Symbolic Link'),
    '#description' => t('Create a symbolic link rather than make a copy of the file.'),
  ];

  $form['submit'] = [
    '#type' => 'submit',
    '#value' => 'Add New Track',
  ];
  return $form;
}

/**
 * Validate the add track form.
 *
 * This function also takes care of the uploading of files.
 * TODO: If the file is invalid, delete it!
 *
 * @param array $form
 *   The Drupal form.
 * @param array $form_state
 *   The form state.
 */
function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
  $values = $form_state['values'];
  $file = $_FILES['files']['tmp_name']['file'];
  $settings = tripal_jbrowse_mgmt_get_settings();
  $instance = tripal_jbrowse_mgmt_get_instance($values['instance_id']);
  $data = $settings['data_dir'];
  $file_type = $values['file_type'];
  $symbolic_link = $values['symbolic_link'];
  $path = NULL;

  $base_path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data';

  if ($file_type === 'vcf') {
    $path = $base_path . '/vcf';
  }
  elseif ($file === 'bw') {
    $path = $base_path . '/wig';
  }
  else {
    $path = $base_path;
  }

  switch ($file_type) {
    case 'vcf':
      $index = $_FILES['files']['tmp_name']['file2'];
      $local_dir = isset($values['dir_path']) ? $values['dir_path'] : NULL;

      if (empty($file) && empty($index) && empty($local_dir)) {
        form_set_error('file',
          'Please provide a local directory path or upload files.');
      }
      elseif (empty($file) && empty($index) && !empty($local_dir)) {
        if (!file_exists($local_dir)) {
          form_set_error('file_path', 'The directory provided does not exist.');
        }
        else {
          if (!is_dir($local_dir)) {
            form_set_error('file_path',
              'The file provided is not a directory.');
          }
          else {
            $file_gz = glob($local_dir . '/*.vcf.gz');
            $file_index = glob($local_dir . '/*.vcf.gz.[cti][sbd][ix]');
            if (count($file_gz) != 1 || count($file_index) != 1) {
              form_set_error('file_path',
                'Please provide a directory with exactly one gz and one index file.');
            }
            else {
              try {
                if (!tripal_jbrowse_mgmt_copy_file($file_gz[0], $path, $symbolic_link)) {
                  form_set_error('file_path', 'Failed to copy file' . $file_gz[0] . ' to ' . $path);
                }
                else {
                  if (!tripal_jbrowse_mgmt_copy_file($file_index[0], $path, $symbolic_link)) {
                    form_set_error('file_path', 'Failed to copy file' . $file_gz[0] . ' to ' . $path);
                  }
                }
              } catch (Exception $exception) {
                form_set_error($exception->getMessage());
              }

            }
          }
        }
      }
      elseif (empty($file) && !empty($index)) {
        form_set_error('file', 'Please upload both a gz and an index file.');
      }
      elseif (!empty($file) && empty($index)) {
        form_set_error('file2', 'Please upload both a gz and an index file.');
      }
      else {
        $gz_uploaded = tripal_jbrowse_mgmt_upload_file('file');
        if (!$gz_uploaded) {
          form_set_error('file', 'Unable to upload file');
        }
        else {
          $gz_uploaded = tripal_jbrowse_mgmt_move_file($gz_uploaded, $path);
          if (!isset($gz_uploaded)) {
            form_set_error('file', 'Failed to move gz file to ' . $path . '.');
          }
          else {
            $form_state['values']['uploaded_gz'] = $gz_uploaded;
          }
        }

        $index_uploaded = tripal_jbrowse_mgmt_upload_file('file2');
        if (!$index_uploaded) {
          form_set_error('file2', 'Unable to upload file');
        }
        else {
          $index_uploaded = tripal_jbrowse_mgmt_move_file($index_uploaded, $path);
          if (!isset($index_uploaded)) {
            form_set_error('file2', 'Failed to move index file to ' . $path . '.');
          }
          else {
            $form_state['values']['uploaded_tbi'] = $index_uploaded;
          }
        }
      }

      break;

    default:
      $local_file = isset($values['file_path']) ? $values['file_path'] : NULL;

      if (empty($file) && empty($local_file)) {
        form_set_error('file',
          'Please provide a local file path or upload a new file.');
      }
      elseif (empty($file) && !empty($local_file)) {
        if (!file_exists($local_file)) {
          form_set_error('file_path', 'The file path provided does not exist.');
        }
        else {
          try {
            if (!tripal_jbrowse_mgmt_copy_file($local_file, $path, $symbolic_link)) {
              form_set_error('file_path', 'Failed to copy file ' . $local_file . ' to ' . $path);
            }
          } catch (Exception $exception) {
            form_set_error('file_path', 'Failed to copy file ' . $local_file . ' to ' . $path);
          }
        }
      }
      else {
        $uploaded = tripal_jbrowse_mgmt_upload_file('file');
        if (!$uploaded) {
          form_set_error('file', 'Unable to upload file');
        }
        else {
          $uploaded = tripal_jbrowse_mgmt_move_file($uploaded, $path);
          if (!isset($uploaded)) {
            form_set_error('file', 'Failed to move file to ' . $path);
          }
          else {
            $form_state['values']['uploaded_file'] = $uploaded;
          }
        }
      }

      break;
  }
}

/**
 * Handle form submission for adding a track.
 *
 * @param array $form
 * @param array $form_state
 *
 * @throws \Exception
 */
function tripal_jbrowse_mgmt_add_track_form_submit($form, &$form_state) {
  global $user;
  $values = $form_state['values'];

  $file = isset($values['file_path']) ? $values['file_path'] : NULL;
  if (!empty($values['dir_path'])) {
    $file = $values['dir_path'];
  }
  if (!empty($values['uploaded_gz'])) {
    $file = $values['uploaded_gz'];
  }
  if (!empty($values['uploaded_file'])) {
    $file = $values['uploaded_file'];
  }

  $instance = tripal_jbrowse_mgmt_get_instance($values['instance_id']);

  $track_id = tripal_jbrowse_mgmt_create_track($instance, [
    'label' => $values['label'],
    'track_type' => $values['track_type'],
    'file_type' => $values['file_type'],
    'file' => $file,
    'created_at' => time(),
  ]);

  tripal_add_job('Add JBrowse track to ' . $instance->title, 'tripal_jbrowse_mgmt',
    'tripal_jbrowse_mgmt_add_track_to_instance', [$track_id], $user->uid);

  drupal_goto('admin/tripal/extension/tripal_jbrowse/management/instances/' . $instance->id);
}

/**
 * Delete a track form.
 *
 * @param array $form
 * @param array $form_state
 * @param int $track_id
 *
 * @return array
 */
function tripal_jbrowse_mgmt_delete_track_form($form, &$form_state, $track_id) {

  $track = tripal_jbrowse_mgmt_get_track($track_id);

  if (!$track->id) {
    $form['error'] = [
      '#type' => 'item',
      '#markup' => '<p style="color: red">Unable to find track.</p>',
    ];

    return $form;
  }

  $form['description'] = [
    '#type' => 'item',
    '#markup' => 'Are you sure you want to delete the ' . $track->label . ' track?',
  ];

  $form['track_id'] = [
    '#type' => 'hidden',
    '#value' => $track_id,
  ];

  $form['submit'] = [
    '#type' => 'submit',
    '#value' => 'Delete Track',
  ];

  $form['cancel'] = [
    '#type' => 'markup',
    '#markup' => l('Cancel',
      'admin/tripal/extension/tripal_jbrowse/management/instances/' . $track->instance_id),
  ];

  return $form;
}

/**
 * @param $form
 * @param $form_state
 *
 * @throws \Exception
 */
function tripal_jbrowse_mgmt_delete_track_form_submit($form, &$form_state) {
  global $user;
  $values = $form_state['values'];

  $track = tripal_jbrowse_mgmt_get_track($values['track_id']);

  tripal_add_job('Delete JBrowse track', 'tripal_jbrowse_mgmt',
    'tripal_jbrowse_mgmt_delete_track_from_instance', [$values['track_id']],
    $user->uid);

  tripal_jbrowse_mgmt_update_track($track, ['is_deleted' => 1]);

  drupal_goto('admin/tripal/extension/tripal_jbrowse/management/instances/' . $track->instance_id);
}

/**
 * Track json editor advance form.
 * allow user to make all configurations of a track
 *
 * @param array $form
 * @param array $form_state
 * @param int $track_id
 *
 * @return array
 * @throws \Exception
 */
function tripal_jbrowse_mgmt_json_editor_advance_form($form, &$form_state, $track_id) {
  $track = tripal_jbrowse_mgmt_get_track($track_id);

  if (!$track->id) {
    $form['error'] = [
      '#type' => 'item',
      '#markup' => '<p style="color: red">Unable to find track.</p>',
    ];

    return $form;
  }

  $instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
  $json = tripal_jbrowse_mgmt_get_json($instance);
  $form_state['track_json'] = $json;

  $key = tripal_jbrowse_mgmt_make_slug($track->label);
  $track_json = NULL;
  $track_index = NULL;
  foreach ($json['tracks'] as $index => $jtrack) {
    if ($jtrack['label'] === $key) {
      $track_json = $jtrack;
      $track_index = $index;
      break;
    }
  }

  if (!$track_json) {
    $form['error'] = [
      '#type' => 'item',
      '#markup' => '<p style="color: red">Unable to find track in json!</p>',
    ];
    return $form;
  }

  $form['track_index'] = [
    '#type' => 'hidden',
    '#value' => $track_index,
  ];

  $form['track_id'] = [
    '#type' => 'hidden',
    '#value' => $track->id,
  ];

  $instr_detail = '<strong>Only use this function if wanted configuration option is not included in Track Manage.</strong><br>Details of JBrowse track configuration can be found in '.l('JBrowse Documentation', 'http://jbrowse.org/docs/canvas_features.html').'.
    <br><strong>Please</strong> be extra cautious while editing track configuration since it will make changes in file trackList.json directly.<br>';

  $form['Instruction']=[
    '#type' => 'markup',
    '#markup' => $instr_detail,
  ];

  $form['track_all_config'] = [
    '#type' => 'textarea',
    '#title' => t('Track configuration in json'),
    '#description' => t('The track info from trackList.json. Only '),
    '#default_value' => json_encode($track_json, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES),
    '#rows' => '10',
    '#required' => TRUE,
  ];


  $form['submit'] = [
    '#type' => 'submit',
    '#value' => 'Save Track Configuration',
  ];

  return $form;
}

/**
 * Validate the form.
 *
 * @param $form
 * @param $form_state
 */
function tripal_jbrowse_mgmt_json_editor_advance_form_validate($form, &$form_state) {
  $values = $form_state['values'];
  $track_all_config = $values['track_all_config'] ?? NULL;

  if ($track_all_config && !empty($track_all_config)) {
    if (!json_decode($track_all_config)) {
      form_set_error(
        'track_all_config',
        'Invalid JSON. Please verify that the menu template contains only valid JSON.'
      );
    }
  }

}

/**
 * @param array $form
 * @param array $form_state
 *
 * @throws \Exception
 */
function tripal_jbrowse_mgmt_json_editor_advance_form_submit($form, &$form_state) {
  $values = $form_state['values'];
  $track_index = $values['track_index'];
  $track_all_config = $values['track_all_config'] ?? NULL;

  $track = tripal_jbrowse_mgmt_get_track($values['track_id']);

  $json = $form_state['track_json'];
  $json['tracks'][$track_index] = json_decode($track_all_config, TRUE);
  tripal_jbrowse_mgmt_update_track($track, ['label' => $json['tracks'][$track_index]['key']]);

  if (tripal_jbrowse_mgmt_save_json($track->instance, $json) === FALSE) {
    drupal_set_message(
      'Unable to save JSON file. Please make sure it\'s editable.'
    );
    return;
  }

  drupal_set_message('Track updated successfully');
}