<?php
class so__transcript extends ChadoField {
// --------------------------------------------------------------------------
// EDITABLE STATIC CONSTANTS
//
// The following constants SHOULD be set for each descendent class. They are
// used by the static functions to provide information to Drupal about
// the field and it's default widget and formatter.
// --------------------------------------------------------------------------
// The default label for this field.
public static $default_label = 'Transcripts';
// The default description for this field.
public static $description = 'An RNA synthesized on a DNA or RNA template by an RNA polymerase.';
// Provide a list of instance specific settings. These can be accessed within
// the instanceSettingsForm. When the instanceSettingsForm is submitted
// then Drupal will automatically change these settings for the instance.
// It is recommended to put settings at the instance level whenever possible.
// If you override this variable in a child class be sure to replicate the
// term_name, term_vocab, term_accession and term_fixed keys as these are
// required for all TripalFields.
public static $default_instance_settings = [
// The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
'term_vocabulary' => 'SO',
// The name of the term.
'term_name' => 'transcript',
// The unique ID (i.e. accession) of the term.
'term_accession' => '0000673',
// Set to TRUE if the site admin is allowed to change the term
// type. This will create form elements when editing the field instance
// to allow the site admin to change the term settings above.
'term_fixed' => FALSE,
// Contains the list of fields on the transcript child that the
// user wants to have displayed for the transcript. The
// `so__transcript_expanded_formatter will display these.
'transcript_fields' => []
];
// The default widget for this field.
public static $default_widget = 'so__transcript_widget';
// The default formatter for this field.
public static $default_formatter = 'so__transcript_formatter';
// --------------------------------------------------------------------------
// PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
// --------------------------------------------------------------------------
// An array containing details about the field. The format of this array
// is the same as that returned by field_info_fields()
protected $field;
// An array containing details about an instance of the field. A field does
// not have to have an instance. But if dealing with an instance (such as
// when using the widgetForm, formatterSettingsForm, etc.) it should be set.
protected $instance;
/**
* @see TripalField::elementInfo()
*/
public function elementInfo() {
$field_term = $this->getFieldTermID();
return [
$field_term => [
'operations' => [],
'sortable' => FALSE,
'searchable' => FALSE,
'type' => 'xs:complexType',
'readonly' => TRUE,
'elements' => [
'rdfs:type' => [
'name' => 'transcript_type',
'label' => 'Transcript Type',
'help' => 'The type of a transcript.',
'searchable' => FALSE,
'operations' => ['eq', 'ne', 'contains', 'starts'],
'sortable' => FALSE,
'type' => 'xs:string',
'readonly' => TRUE,
'required' => FALSE,
],
'schema:name' => [
'name' => 'transcript_name',
'label' => 'Transcript Name',
'help' => 'The name of a transcript.',
'searchable' => FALSE,
'operations' => ['eq', 'ne', 'contains', 'starts'],
'sortable' => FALSE,
'type' => 'xs:string',
'readonly' => TRUE,
'required' => FALSE,
],
'data:0842' => [
'name' => 'transcript_uniquename',
'label' => 'Transcript Identifier',
'help' => 'The unique identifier of a transcript.',
'searchable' => FALSE,
'operations' => ['eq', 'ne', 'contains', 'starts'],
'sortable' => FALSE,
'type' => 'xs:string',
'readonly' => TRUE,
'required' => FALSE,
],
'SO:0000735' => [
'name' => 'loc',
'label' => 'Transcript Location',
'help' => 'The location of the transcript on a reference feature.',
'searchable' => FALSE,
'operations' => ['eq', 'ne', 'contains', 'starts'],
'sortable' => FALSE,
'type' => 'xs:string',
'readonly' => TRUE,
'required' => FALSE,
],
'entity' => [
'searchable' => FALSE,
'sortable' => FALSE,
],
],
],
];
}
/**
*
* @see TripalField::load()
*/
public function load($entity) {
$record = $entity->chado_record;
$field_name = $this->field['field_name'];
$field_type = $this->field['type'];
$field_table = $this->instance['settings']['chado_table'];
$field_column = $this->instance['settings']['chado_column'];
// Set some defaults for the empty record.
$entity->{$field_name}['und'][0] = [
'value' => '',
];
if (!$record) {
return;
}
// Get the mRNA features for this gene.
$sql = "
SELECT FS.name, FS.uniquename, FS.feature_id, FCVT.name as type
FROM {feature_relationship} FR
INNER JOIN {feature} FS on FS.feature_id = FR.subject_id
INNER JOIN {cvterm} FCVT on FCVT.cvterm_id = FS.type_id
INNER JOIN {cv} CV on CV.cv_id = FCVT.cv_id
WHERE
FR.object_id = :feature_id and
FCVT.name = 'mRNA' and
CV.name = 'sequence'
";
$results = chado_query($sql, [':feature_id' => $record->feature_id]);
$i = 0;
while ($transcript = $results->fetchObject()) {
// Get the location of this mRNA.
$sql = "
SELECT FL.*, F.name as srcfeature_name
FROM {featureloc} FL
INNER JOIN {feature} F on F.feature_id = FL.srcfeature_id
WHERE FL.feature_id = :object_id
";
$floc_results = chado_query($sql, [':object_id' => $transcript->feature_id]);
$loc = "";
while ($location = $floc_results->fetchObject()) {
$loc .= $location->srcfeature_name . ":" . $location->fmin . ".." . $location->fmax;
}
$entity->{$field_name}['und'][$i]['value'] = [
'rdfs:type' => $transcript->type,
'schema:name' => $transcript->name,
'data:0842' => $transcript->uniquename,
'SO:0000735' => $loc,
];
$feature = chado_generate_var('feature', ['feature_id' => $transcript->feature_id]);
if (property_exists($feature, 'entity_id')) {
$entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $feature->entity_id;
}
$i++;
}
}
/**
* @see TripalField::globalSettingsForm()
*/
public function instanceSettingsForm() {
$element = parent::instanceSettingsForm();
$settings = $this->instance['settings'];
$element['transcript_fields'] = [
'#type' => 'value',
'#default_value' => $settings['transcript_fields'],
];
// Get the content type for the mRNA term (SO:0000234) and it's feilds.
// If it isn't published then don't show the form below.
$bundle = tripal_load_bundle_entity(['accession' => 'SO:0000234']);
if (!$bundle) {
return $element;
}
$fields = field_info_instances('TripalEntity', $bundle->name);
foreach ($fields as $field_name => $details) {
$defaults = [];
if (array_key_exists($field_name, $settings['transcript_fields'])) {
$defaults = $settings['transcript_fields'][$field_name];
}
$weight = array_key_exists('weight', $defaults) ? $defaults['weight'] : $details['display']['default']['weight'];
$checked = array_key_exists('show', $defaults) ? $defaults['show'] : 0;
$element['themeable']['field-'. $weight] = [
'#type' => 'value',
'#value' => $field_name,
'#weight' => $weight,
];
$element['themeable']['field-'. $weight . '-check'] = [
'#type' => 'checkbox',
'#weight' => $weight,
'#default_value' => $checked,
];
$element['themeable']['field-'. $weight . '-label'] = [
'#type' => 'markup',
'#markup' => t($details['label']),
'#weight' => $weight,
];
$element['themeable']['field-'. $weight . '-description'] = [
'#type' => 'markup',
'#markup' => t($details['description']),
'#weight' => $weight,
];
$element['themeable']['field-'. $weight . '-weight'] = [
'#type' => 'textfield',
'#default_value' => $weight,
'#weight' => $weight,
'#size' => 3,
'#attributes' => [
'class' => ['tripal-field-settings-table-weights'],
],
];
}
return $element;
}
/**
* @see TripalField::instanceSettingsFormValidate()
*/
public function instanceSettingsFormValidate($form, &$form_state) {
$settings = $form_state['values']['instance']['settings']['themeable'];
// Iterate through the themable elements to get the weights and
// checks for each field. Store that info in a temp array.
$temp = [];
foreach ($settings as $element => $value) {
$matches = [];
if (preg_match('/^field-(\d+)-check$/', $element, $matches)) {
$orig_weight = $matches[1];
$new_weight = $settings['field-' . $orig_weight . '-weight'];
$field_name = $settings['field-' . $orig_weight];
$temp[$new_weight]['name'] = $field_name;
$temp[$new_weight]['show'] = $value;
}
}
// Sort and resstart the weights from zero.
ksort($temp);
$temp = array_values($temp);
// Now build the transcirpt_fields setting value.
$transcript_fields = [];
foreach ($temp as $weight => $field) {
$field_name = $field['name'];
$transcript_fields[$field_name] = [
'weight' => $weight,
'show' => $field['show'],
];
}
// Now store the values for the setting properly and remove the unwanted.
$form_state['values']['instance']['settings']['transcript_fields'] = $transcript_fields;
unset($form_state['values']['instance']['settings']['themeable']);
}
/**
* @see TripalField::settingsTheme()
*/
public function settingsTheme($element) {
$headers = ['', 'Field', 'Description', ''];
$rows = [];
foreach (element_children($element) as $child) {
$matches = [];
if (preg_match('/^field-(\d+)-(.+)$/', $child, $matches)) {
$weight = $matches[1];
switch ($matches[2]) {
case 'check':
$rows[$weight]['data'][0] = drupal_render($element[$child]);
break;
case 'label':
$rows[$weight]['data'][1] = drupal_render($element[$child]);
break;
case 'description':
$rows[$weight]['data'][2] = drupal_render($element[$child]);
break;
case 'weight':
$rows[$weight]['data'][3] = drupal_render($element[$child]);
break;
}
ksort($rows[$weight]['data']);
$rows[$weight]['class'] = ['draggable'];
}
}
ksort($rows);
$table = [
'header' => $headers,
'rows' => $rows,
'attributes' => ["id" => 'tripal-field-settings-table'],
'sticky' => TRUE,
'caption' => t('Content Panes Available in the TOC'),
'colgroups' => [],
'empty' => t('There are no content panes for this page. The mRNA content type must exist to customize.'),
];
drupal_add_tabledrag('tripal-field-settings-table', 'order', 'sibling', 'tripal-field-settings-table-weights');
$fset = [];
$fset['fields'] = [
'#type' => 'fieldset',
'#title' => 'Transcript (mRNA) Field Selection',
'#description' => t('Here, you can customize what information is provided to the end-user about transcripts. Select the fields that you want displayed on the page. If no fields are selected then a default display is provided. All mRNA for a gene must be published or the default display will be provided.'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
'#attributes' => ['class' => ['collapsible', 'collapsed']],
];
drupal_add_library('system', 'drupal.collapse');
$fset['fields']['table'] = [
'#type' => 'markup',
'#markup' => theme_table($table),
];
return drupal_render($fset['fields']);
}
}