page_4.php File Reference

Go to the source code of this file.

Functions
	tpps_page_4_create_form (array &$form, array &$form_state)

Detailed Description

Creates GxPxE Data form page and includes helper files.

Definition in file page_4.php.

Function Documentation

tpps_page_4_create_form()

tpps_page_4_create_form	(	array &	$form,
		array &	$form_state
	)

Creates the GxPxE Data form page.

This function creates the genotype, phenotype, and environmental fieldsets based on the data type selection made on page 2. It will then call all necessary helper functions.

Parameters

array	$form	The form to be populated.
array	$form_state	The state of the form to be populated.

Definition at line 23 of file page_4.php.

                                                                   {
  if (isset($form_state['saved_values'][TPPS_PAGE_4])) {
    $values = $form_state['saved_values'][TPPS_PAGE_4];
  }
  else {
    $values = array();
  }

  $form['#tree'] = TRUE;

  $organism_number = $form_state['saved_values'][TPPS_PAGE_1]['organism']['number'];
  $data_type = $form_state['saved_values'][TPPS_PAGE_2]['data_type'];
  for ($i = 1; $i <= $organism_number; $i++) {

    $name = $form_state['saved_values'][TPPS_PAGE_1]['organism']["$i"]['name'];

    $form["organism-$i"] = array(
      '#type' => 'fieldset',
      '#title' => "<div class=\"fieldset-title\">$name:</div>",
      '#tree' => TRUE,
      '#collapsible' => TRUE,
    );

    if (preg_match('/P/', $data_type)) {
      if ($i > 1) {
        $form["organism-$i"]['phenotype-repeat-check'] = array(
          '#type' => 'checkbox',
          '#title' => "Phenotype information for $name is the same as phenotype information for {$form_state['saved_values'][TPPS_PAGE_1]['organism'][$i - 1]['name']}.",
          '#default_value' => isset($values["organism-$i"]['phenotype-repeat-check']) ? $values["organism-$i"]['phenotype-repeat-check'] : 1,
        );
      }

      $form["organism-$i"]['phenotype'] = tpps_phenotype($form, $form_state, $values, "organism-$i");

      if ($i > 1) {
        $form["organism-$i"]['phenotype']['#states'] = array(
          'invisible' => array(
            ":input[name=\"organism-$i\[phenotype-repeat-check]\"]" => array('checked' => TRUE),
          ),
        );
      }

      $normal_check = tpps_get_ajax_value($form_state, array(
        "organism-$i",
        'phenotype',
        'normal-check',
      ), TRUE);
      if (!empty($normal_check)) {
        $image_path = drupal_get_path('module', 'tpps') . '/images/';
        $form["organism-$i"]['phenotype']['format'] = array(
          '#type' => 'radios',
          '#title' => t('Phenotype file format: *'),
          '#options' => array(
            'Type 1',
            'Type 2',
          ),
          '#ajax' => array(
            'callback' => 'tpps_phenotype_file_format_callback',
            'wrapper' => "edit-organism-$i-phenotype-file-ajax-wrapper",
          ),
          '#default_value' => (isset($form_state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype']['format'])) ? $form_state['saved_values'][TPPS_PAGE_4]["organism-$i"]['phenotype']['format'] : 0,
          '#description' => t('Please select a file format type from the listed options. Below please see examples of each format type.'),
          '#states' => array(
            'invisible' => array(
              ":input[name=\"organism-{$i}[phenotype][phenotypes-meta][number]\"]" => array('value' => '0'),
              ":input[name=\"organism-{$i}[phenotype][check]\"]" => array('checked' => FALSE),
            ),
          ),
        );

        $form["organism-$i"]['phenotype']['format'][0]['#prefix'] = "<figure><img src=\"/{$image_path}phenotype_format_1.png\"><figcaption>";
        $form["organism-$i"]['phenotype']['format'][0]['#suffix'] = "</figcaption></figure>";
        $form["organism-$i"]['phenotype']['format'][1]['#prefix'] = "<figure><img src=\"/{$image_path}phenotype_format_2.png\"><figcaption>";
        $form["organism-$i"]['phenotype']['format'][1]['#suffix'] = "</figcaption></figure>";
      
        $form["organism-$i"]['phenotype']['file'] = array(
          '#type' => 'managed_file',
          '#title' => t('Phenotype file: Please upload a file containing columns for Plant Identifier, Phenotype Data: *'),
          '#upload_location' => 'public://' . variable_get('tpps_phenotype_files_dir', 'tpps_phenotype'),
          '#upload_validators' => array(
            'file_validate_extensions' => array('csv tsv xlsx'),
          ),
          '#tree' => TRUE,
          '#states' => array(
            'invisible' => array(
              ":input[name=\"organism-{$i}[phenotype][phenotypes-meta][number]\"]" => array('value' => '0'),
              ":input[name=\"organism-{$i}[phenotype][check]\"]" => array('checked' => FALSE),
            ),
          ),
        );

        $form["organism-$i"]['phenotype']['file']['empty'] = array(
          '#default_value' => isset($values["organism-$i"]['phenotype']['file']['empty']) ? $values["organism-$i"]['phenotype']['file']['empty'] : 'NA',
        );

        $form["organism-$i"]['phenotype']['file']['columns'] = array(
          '#description' => t('Please define which columns hold the required data: Plant Identifier, Phenotype name, and Value(s)'),
        );
        
        
        $format = tpps_get_ajax_value($form_state, array(
          "organism-$i",
          'phenotype',
          'format',
        ), 0);

        if ($format == 0) {
          $column_options = array(
            'Phenotype Data',
            'Plant Identifier',
            'Timepoint',
            'Clone Number',
            'N/A',
          );
        }
        else {
          $column_options = array(
            'N/A',
            'Plant Identifier',
            'Phenotype Name/Identifier',
            'Value(s)',
            'Timepoint',
            'Clone Number',
          );
          $form["organism-$i"]['phenotype']['file']['#title'] = t('Phenotype file: Please upload a file containing columns for Plant Identifier, Phenotype Name, and value for all of your phenotypic data: *');
        }

        $form["organism-$i"]['phenotype']['file']['columns-options'] = array(
          '#type' => 'hidden',
          '#value' => $column_options,
        );

        $form["organism-$i"]['phenotype']['file']['no-header'] = array();
      }
    }

    if (preg_match('/G/', $data_type)) {
      if ($i > 1) {
        $form["organism-$i"]['genotype-repeat-check'] = array(
          '#type' => 'checkbox',
          '#title' => "Genotype information for $name is the same as genotype information for {$form_state['saved_values'][TPPS_PAGE_1]['organism'][$i - 1]['name']}.",
          '#default_value' => isset($values["organism-$i"]['genotype-repeat-check']) ? $values["organism-$i"]['genotype-repeat-check'] : 1,
        );
      }

      $form["organism-$i"]['genotype'] = tpps_genotype($form, $form_state, $values, "organism-$i");

      if ($i > 1) {
        $form["organism-$i"]['genotype']['#states'] = array(
          'invisible' => array(
            ":input[name=\"organism-$i\[genotype-repeat-check]\"]" => array('checked' => TRUE),
          ),
        );
      }

    }

    if (preg_match('/E/', $data_type)) {
      if ($i > 1) {
        $form["organism-$i"]['environment-repeat-check'] = array(
          '#type' => 'checkbox',
          '#title' => "Environmental information for $name is the same as environmental information for {$form_state['saved_values'][TPPS_PAGE_1]['organism'][$i - 1]['name']}.",
          '#default_value' => isset($values["organism-$i"]['environment-repeat-check']) ? $values["organism-$i"]['environment-repeat-check'] : 1,
        );
      }

      $form["organism-$i"]['environment'] = tpps_environment($form, $form_state, "organism-$i");

      if ($i > 1) {
        $form["organism-$i"]['environment']['#states'] = array(
          'invisible' => array(
            ":input[name=\"organism-$i\[environment-repeat-check]\"]" => array('checked' => TRUE),
          ),
        );
      }
    }
  }

  $form['Back'] = array(
    '#type' => 'submit',
    '#value' => t('Back'),
    '#prefix' => '<div class="input-description">* : Required Field</div>',
  );

  $form['Save'] = array(
    '#type' => 'submit',
    '#value' => t('Save'),
  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => t('Review Information and Submit'),
  );

  if (preg_match('/G/', $data_type)) {
    $pre_valid_states = array();
    for ($i = 1; $i <= $organism_number; $i++) {
      $pre_valid_states["input[name=\"organism-{$i}[genotype][files][file-type][VCF]\"]"] = array('checked' => FALSE);
    }
    $form['pre_validate'] = array(
      '#type' => 'button',
      '#value' => t('Pre-validate my VCF files'),
      '#states' => array(
        'invisible' => $pre_valid_states,
      ),
      '#suffix' => '<div>Sometimes large VCF files can cause problems during the validation step. If your VCF file is very large, you can click the "Pre-validate my VCF files" button to validate your VCF file in the background, before clicking "Review Information and Submit".</div>',
    );

    $form['Back']['#prefix'] .= "<div id=\"pre-validate-message\"></div>";
  }
}