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@@ -550,6 +550,19 @@ function tripal_chado_field_info() {
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'active' => TRUE
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),
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),
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+
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+ 'synonym' => array(
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+ 'label' => t('Synonyms'),
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+ 'description' => t('Adds an alternative name (synonym or alias) to this record..'),
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+ 'default_widget' => 'tripal_chado_synonym_widget',
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+ 'default_formatter' => 'tripal_chado_synonym_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ ),
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);
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return $fields;
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}
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@@ -609,6 +622,10 @@ function tripal_chado_field_widget_info() {
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'label' => t('Property'),
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'field types' => array('kvproperty'),
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),
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+ 'tripal_chado_synonym_widget' => array(
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+ 'label' => t('Synonyms'),
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+ 'field types' => array('synonym'),
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+ ),
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);
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}
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/**
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@@ -656,6 +673,10 @@ function tripal_chado_field_formatter_info() {
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'label' => t('Property'),
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'field types' => array('kvproperty')
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),
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+ 'tripal_chado_synonym_formatter' => array(
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+ 'label' => t('Synonyms'),
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+ 'field types' => array('synonym')
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+ ),
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);
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}
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@@ -750,6 +771,11 @@ function tripal_chado_field_formatter_view($entity_type, $entity, $field,
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tripal_chado_kvproperty_formatter($element, $entity_type, $entity, $field,
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$instance, $langcode, $items, $display);
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break;
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+ case 'tripal_chado_synonym_formatter':
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+ module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
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+ tripal_chado_synonym_formatter($element, $entity_type, $entity, $field,
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+ $instance, $langcode, $items, $display);
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+ break;
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}
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return $element;
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}
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@@ -814,6 +840,11 @@ function tripal_chado_field_widget_form(&$form, &$form_state, $field,
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module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
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tripal_chado_kvproperty_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
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break;
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+ case 'tripal_chado_synonym_widget':
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+ form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/synonym');
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+ module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
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+ tripal_chado_synonym_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
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+ break;
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}
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return $widget;
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}
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@@ -961,6 +992,10 @@ function tripal_chado_theme($existing, $type, $theme, $path) {
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'render element' => 'element',
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'file' => 'includes/fields/cvterm.inc',
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),
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+ 'tripal_chado_synonym_widget' => array(
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+ 'render element' => 'element',
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+ 'file' => 'includes/fields/synonym.inc',
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+ ),
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'tripal_chado_kvproperty_addr_widget' => array(
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'render element' => 'element',
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'file' => 'includes/fields/dbxref_id.inc',
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@@ -1097,6 +1132,18 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
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if (chado_table_exists($cvterm_table)) {
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tripal_chado_add_bundle_cvterm_class_adder_field($entity_type, $bundle_name, $cvterm_table, $bundle_data['data_table']);
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}
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+
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+
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+ ////
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+ //
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+ // Synonym table fields.
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+ //
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+ // Check to see if there are any cvterm tables with FKs to this
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+ // base table. If so, add the fields for that type of table.
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+ $syn_table = $bundle_data['data_table'] . '_synonym';
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+ if (chado_table_exists($cvterm_table)) {
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+ tripal_chado_add_bundle_synonym_field($entity_type, $bundle_name, $syn_table, $bundle_data['data_table']);
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+ }
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}
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/**
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@@ -1150,6 +1197,51 @@ function tripal_chado_add_bundle_dbxref_field($entity_type_name, $bundle_name, $
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}
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tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
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}
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+/**
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+ * Adds the fields for managing xrefs that are stored in a [base]_dbxref table.
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+ *
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+ * @param $entity_type
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+ * @param $bundle_name
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+ * @param $base_table
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+ * @param $dbxref_table
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+ */
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+function tripal_chado_add_bundle_synonym_field($entity_type_name, $bundle_name, $syn_table, $base_table) {
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+ // We already have a dbxref_id field.
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+ $field_name = $syn_table;
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+ $schema = chado_get_schema($syn_table);
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+ $pkey = $schema['primary key'][0];
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+
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+ // Initialize the field array.
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+ $field_info = array(
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+ 'field_type' => 'synonym',
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+ 'widget_type' => 'tripal_fields_synonym_widget',
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Synonyms',
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+ 'is_required' => 0,
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+ 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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+ 'storage' => 'field_chado_storage',
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+ 'field_settings' => array(
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+ // The Chado table that this field maps to.
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+ 'chado_table' => $syn_table,
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+ // The column in the chado table that this field maps to.
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+ 'chado_column' => $pkey,
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+ // The base table that this field is connected to.
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+ 'base_table' => $base_table,
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+ 'semantic_web' => array(
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+ // The type is the term from a vocabulary that desribes this field..
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+ 'type' => '',
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+ // The namepsace for the vocabulary (e.g. 'foaf').
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+ 'ns' => '',
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+ // The URL for the namespace. It must be that the type can be
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+ // appended to the URL.
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+ 'nsurl' => '',
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+ ),
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+ ),
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+ );
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+
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+ tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
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+}
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/**
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* Adds the fields for managing properties that are stored in a prop table.
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*
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@@ -1420,7 +1512,7 @@ function tripal_chado_get_table_column_field_default($table_name, $schema, $colu
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$field['field_type'] = 'md5checksum';
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$field['widget_type'] = 'tripal_chado_md5checksum_checkbox_widget';
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$field['label'] = 'MD5 Checksum';
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- $field['description'] = 'Generating MD5 checksum for the sequence.';
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+ $field['description'] = 'Generate an MD5 checksum for the sequence.';
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}
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elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'seqlen') {
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$field['field_type'] = 'seqlen';
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Stephen Ficklin