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@@ -178,15 +178,122 @@ function tripal_fields_field_formatter_info() {
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}
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/**
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- * Implements hook_field_formatter_view().
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+ * Implements hook_chado_field_alter().
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+ *
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+ * This function is used to change the default field formatter and widget
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+ * that are assigned to fields of an Entity. This hook is only used for
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+ * those fields that correspond to a column in a Chado table. An implementation
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+ * of this hook can be used to change the default formatters and widgets to
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+ * custom formatters and widgets that are created by the module creating
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+ * this hook.
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*
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- * Two formatters are implemented.
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- * - field_example_simple_text just outputs markup indicating the color that
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- * was entered and uses an inline style to set the text color to that value.
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- * - field_example_color_background does the same but also changes the
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- * background color of div.region-content.
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+ * By default, Tripal will provide custom formatters and widgets for many
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+ * columns in Chado tables, therefore, this hook will most likely be of use
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+ * to extension modules that create custom table inside of Chado.
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*
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- * @see field_example_field_formatter_info()
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+ * @param $field
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+ */
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+function hook_chado_field_alter(&$field) {
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+ // TODO: add example code for how to use this hook.
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+}
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+
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+/**
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+ * Implements hook_chado_field_alter().
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+ *
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+ * This function adds the custom formatters and widgets to many of the Chado
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+ * tables. This way Tripal users get a nice set of already usable fields.
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+ */
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+function tripal_fields_chado_field_alter(&$field) {
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+
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+ if (!array_key_exists('field_settings', $field)) {
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+ return;
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+ }
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+ // If the field doesn't list the Chado table or column then just return.
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+ if (!array_key_exists('chado_table', $field['field_settings']) or
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+ !array_key_exists('chado_column', $field['field_settings'])) {
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+ return;
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+ }
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+ // Here we provide new field types and widgets for FK fields
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+ // and fields that need special attention.
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+ if ($field['field_settings']['chado_column'] =='organism_id') {
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+ $field['field_type'] = 'organism_id';
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+ $field['widget_type'] = 'tripal_fields_organism_select_widget';
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+ $field['label'] = 'Organism';
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+ $field['description'] = 'Select an organism.';
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+ }
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+ else if ($field['field_settings']['chado_column'] =='dbxref_id') {
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+ $field['field_type'] = 'dbxref_id';
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+ $field['widget_type'] = 'tripal_fields_primary_dbxref_widget';
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+ $field['label'] = 'Primary Cross Reference';;
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+ $field['description'] = 'This record can be cross-referenced with a
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+ record in another online database. The primary reference is for the
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+ most prominent reference. At a minimum, the database and accession
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+ must be provided. To remove a set reference, change the database
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+ field to "Select a Database".';
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+ }
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+ else if ($field['field_settings']['chado_table'] == 'feature' and
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+ $field['field_settings']['chado_column'] == 'md5checksum') {
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+ $field['field_type'] = 'md5checksum';
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+ $field['widget_type'] = 'tripal_fields_md5checksum_checkbox_widget';
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+ $field['label'] = 'MD5 Checksum';
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+ $field['description'] = 'Generating MD5 checksum for the sequence.';
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+ }
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+ else if ($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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+ $field['widget_type'] = 'tripal_fields_seqlen_hidden_widget';
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+ $field['label'] = 'Seqlen';
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+ $field['description'] = 'The length of the residues.';
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+ }
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+ else if ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'residues') {
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+ $field['field_type'] = 'residues';
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+ $field['widget_type'] = 'tripal_fields_residues_textarea_widget';
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+ $field['label'] = 'Residues';
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+ $field['description'] = 'Please provide an IUPAC compatible residues for this feature. Spaces and new lines are allowed.';
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+ }
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+ else if ($field['label'] == 'Timeaccessioned') {
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+ $field['label'] = 'Time Accessioned';
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+ $field['description'] = 'Please enter the time that this record was first added to the database.';
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+ }
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+ else if ($field['label'] == 'Timelastmodified') {
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+ $field['label'] = 'Time Last Modified';
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+ $field['description'] = 'Please enter the time that this record was last modified. The default is the current time.';
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+ }
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+}
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+
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+/**
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+ * Implements hook_field_widget_form_alter().
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+ */
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+function tripal_fields_field_widget_form_alter(&$element, &$form_state, $context) {
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+
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+ if (array_key_exists('#field_name', $element)) {
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+ $field_name = $element['#field_name'];
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+ $matches = array();
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+
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+ if (preg_match('/(.+?)__(.+?)$/', $field_name, $matches)) {
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+ $tablename = $matches[1];
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+ $colname = $matches[2];
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+ $schema = chado_get_schema($tablename);
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+
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+ // The timelastmodified field exists in many Chado tables. We want
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+ // the form element to update to the most recent time rather than the time
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+ // in the database.
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+ if ($colname == 'timelastmodified' and $schema['fields'][$colname]['type'] == 'datetime') {
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+ // We want the default value for the field to be the current time.
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+ $element['#default_value']['value'] = format_date(time(), 'custom', "Y-m-d H:i:s", 'UTC');
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+ $element['#date_items']['value'] = $element['#default_value']['value'];
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+ }
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+ // We want the date combo fieldset to be collaspible so we will
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+ // add our own theme_wrapper to replace the one added by the date
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+ // module.
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+ if (array_key_exists($colname, $schema['fields']) and $schema['fields'][$colname]['type'] == 'datetime') {
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+ $element['#theme_wrappers'] = array('tripal_entities_date_combo');
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+ }
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+ }
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+ }
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+}
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+
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+/**
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+ * Implements hook_field_formatter_view().
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*/
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function tripal_fields_field_formatter_view($entity_type, $entity, $field,
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$instance, $langcode, $items, $display) {
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Stephen Ficklin