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@@ -0,0 +1,153 @@
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+<?php
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+
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+class local__gbrowse_image extends ChadoField {
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+
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+
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+ // --------------------------------------------------------------------------
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+ // EDITABLE STATIC CONSTANTS
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+ //
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+ // The following constants SHOULD be set for each descendent class. They are
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+ // used by the static functions to provide information to Drupal about
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+ // the field and it's default widget and formatter.
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+ // --------------------------------------------------------------------------
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+
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+ // The default lable for this field.
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+ public static $default_label = 'GBrowse View';
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+
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+ // The default description for this field.
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+ public static $description = 'A GBrowse image of a feature alignment to another sequence.';
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+
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+ // Provide a list of instance specific settings. These can be access within
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+ // the instanceSettingsForm. When the instanceSettingsForm is submitted
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+ // then Drupal with automatically change these settings for the instnace.
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+ // It is recommended to put settings at the instance level whenever possible.
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+ // If you override this variable in a child class be sure to replicate the
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+ // term_name, term_vocab, term_accession and term_fixed keys as these are
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+ // required for all TripalFields.
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+ public static $default_instance_settings = array(
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+ // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
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+ 'term_vocabulary' => 'local',
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+ // The name of the term.
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+ 'term_name' => 'Gbrowse Image',
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+ // The unique ID (i.e. accession) of the term.
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+ 'term_accession' => 'gbrowse_image',
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+ // Set to TRUE if the site admin is allowed to change the term
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+ // type. This will create form elements when editing the field instance
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+ // to allow the site admin to change the term settings above.
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+ 'term_fixed' => FALSE,
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+ // The URL for the GBrowse image
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+ 'gbrowse_url' => '',
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+ );
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+
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+ // The default widget for this field.
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+ public static $default_widget = 'local__gbrowse_image_widget';
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+
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+ // The default formatter for this field.
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+ public static $default_formatter = 'local__gbrowse_image_formatter';
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+
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+
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+ /**
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+ * @see TripalField::elementInfo()
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+ */
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+ public function elementInfo() {
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+ $field_term = $this->getFieldTermID();
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+ return array(
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+ $field_term => array(
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+ 'sortable' => FALSE,
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+ 'searchable' => FALSE,
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+ 'type' => 'xs:string',
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+ 'readonly' => TRUE,
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+ ),
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+ );
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+ }
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+
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+ /**
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+ * @see TripalField::load()
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+ */
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+ public function load($entity) {
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+ $field_name = $this->field['field_name'];
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+ $feature = $entity->chado_record;
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+
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+ $record = $entity->chado_record;
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+ $settings = $this->instance['settings'];
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+
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+ // Set some defauls for the empty record
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+ $entity->{$field_name}['und'][0] = array(
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+ 'value' => '',
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+ );
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+
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+ // If we don't have a record then just return
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+ if (!$record) {
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+ return;
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+ }
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+
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+ // Replace any tokens in the string.
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+ $bundle = tripal_load_bundle_entity(['name' => $this->instance['bundle']]);
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+ $gbrowse_url = $settings['gbrowse_url'];
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+ $gbrowse_url = tripal_replace_entity_tokens($gbrowse_url, $entity, $bundle);
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+
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+ // Use the term associated to the db.url table of Chado.
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+ $url_term = chado_get_semweb_term('db', 'url');
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+
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+ // Add the URL to the values
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+ $entity->{$field_name}['und'][0]['value'] = [
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+ $url_term => $gbrowse_url
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+ ];
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+ }
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+
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+ /**
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+ * @see TripalField::globalSettingsForm()
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+ */
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+ public function instanceSettingsForm() {
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+ $element = parent::instanceSettingsForm();
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+
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+ $settings = $this->instance['settings'];
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+
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+ $element['gbrowse_url'] = array(
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+ '#type' => 'textarea',
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+ '#title' => 'GBrowse URL',
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+ '#description' => t('Please enter the URL for generating feature ' .
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+ 'images on the remote GBrowse site. You may use tokens to substitute ' .
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+ 'field values from this content type. Open the "Available Tokens" fieldset below. ' .
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+ 'For example, to show a view of a gene from the rice genome GBrowse the ' .
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+ 'following URL with tokens can be used: ' .
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+ 'http://rice.plantbiology.msu.edu/cgi-bin/gbrowse_img/rice/?name=[schema__name];type=Landmarks%3Aregion+Genes+Rice_Annotation'),
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+ '#default_value' => $settings['gbrowse_url'],
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+ );
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+
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+ $element['tokens'] = array(
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+ '#type' => 'fieldset',
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+ '#collapsed' => TRUE,
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+ '#collapsible' => TRUE,
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+ '#title' => 'Available Tokens'
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+ );
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+ $headers = array('Token', 'Description');
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+ $rows = array();
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+
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+ // Get the bundle tokens
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+ $bundle = tripal_load_bundle_entity(['name' => $this->instance['bundle']]);
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+ $tokens = tripal_get_entity_tokens($bundle);
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+ foreach ($tokens as $token) {
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+ $rows[] = array(
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+ $token['token'],
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+ $token['description'],
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+ );
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+ }
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+
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+ $table_vars = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(),
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+ 'sticky' => FALSE,
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+ 'caption' => '',
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+ 'colgroups' => array(),
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+ 'empty' => 'There are no tokens',
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+ );
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+ $element['tokens']['list'] = array(
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+ '#type' => 'item',
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+ '#markup' => theme_table($table_vars),
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+ );
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+
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+ return $element;
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+ }
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+}
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Stephen Ficklin