$name, 'name' => $t('JBrowse Instance'), 'base' => 'node_content', 'title_label' => $t('Title'), 'description' => $t('Integrates an existing JBrowse instance within these nodes.'), 'custom' => TRUE, ); // set other node defaults not declared above $content_type = node_type_set_defaults($type); // add the body field node_add_body_field($content_type, $t('JBrowse Description')); // save the content type node_type_save($content_type); // add peristant variables that control settings variable_set('additional_settings__active_tab_' . $name, 'edit-menu'); variable_set('node_preview_' . $name, 2); variable_set('node_options_' . $name, array(0 => 'status', 1 => 'promote')); variable_set('node_submitted_' . $name, 0); variable_set('menu_options_' . $name, array()); variable_set('menu_parent_' . $name, 'main-menu:0'); /**** STEP 2: Add Fields ****/ // create all the fields we are adding to our content type foreach (_jbrowse_installed_fields() as $field) { field_create_field($field); } // create all the instances for our fields foreach (_jbrowse_installed_instances() as $instance) { $instance['entity_type'] = 'node'; $instance['bundle'] = $type['type']; field_create_instance($instance); } } /** * Implements hook_uninstall(). */ function tripal_jbrowse_uninstall() { // machine name of the content type $name = 'jbrowse_instance'; // gather all job nodes created $sql = 'SELECT nid FROM {node} n WHERE n.type = :type'; $result = db_query($sql, array(':type' => $name)); $nids = array(); foreach ($result as $row) { $nids[] = $row->nid; } // delete all the job nodes at once node_delete_multiple($nids); // remove peristant variables that control settings variable_del('additional_settings__active_tab_' . $name); variable_del('node_preview_' . $name); variable_del('node_options_' . $name); variable_del('node_submitted_' . $name); variable_del('menu_options_' . $name); variable_del('menu_parent_' . $name); // find all fields and delete them foreach (array_keys(_jbrowse_installed_fields()) as $field) { field_delete_field($field); } // find all fields and delete instance $instances = field_info_instances('node', $name); foreach ($instances as $instance_name => $instance) { field_delete_instance($instance); } // delete our content type node_type_delete($name); // purge all field infromation field_purge_batch(1000); } /** * Defines all the fields needed for the jbrowse_instance content type. * * @return * An associative array specifying the fields we wish to add to our * new node type. */ function _jbrowse_installed_fields() { return array( 'field_jburl' => array( 'translatable' => '0', 'entity_types' => array(), 'settings' => array( 'attributes' => array( 'target' => 'default', 'class' => '', 'rel' => '', ), 'url' => 0, 'title' => 'optional', 'title_value' => '', 'title_maxlength' => 128, 'enable_tokens' => 1, 'display' => array( 'url_cutoff' => 80, ), ), 'storage' => array( 'type' => 'field_sql_storage', 'settings' => array(), 'module' => 'field_sql_storage', 'active' => '1', 'details' => array( 'sql' => array( 'FIELD_LOAD_CURRENT' => array( 'field_data_field_jburl' => array( 'url' => 'field_jburl_url', 'title' => 'field_jburl_title', 'attributes' => 'field_jburl_attributes', ), ), 'FIELD_LOAD_REVISION' => array( 'field_revision_field_jburl' => array( 'url' => 'field_jburl_url', 'title' => 'field_jburl_title', 'attributes' => 'field_jburl_attributes', ), ), ), ), ), 'foreign keys' => array(), 'indexes' => array(), 'field_name' => 'field_jburl', 'type' => 'link_field', 'module' => 'link', 'active' => '1', 'locked' => '0', 'cardinality' => '1', 'deleted' => '0', 'columns' => array( 'url' => array( 'type' => 'varchar', 'length' => 2048, 'not null' => FALSE, 'sortable' => TRUE, ), 'title' => array( 'type' => 'varchar', 'length' => 255, 'not null' => FALSE, 'sortable' => TRUE, ), 'attributes' => array( 'type' => 'text', 'size' => 'medium', 'not null' => FALSE, ), ), 'bundles' => array( 'node' => array( 'jbrowse_instance', ), ), ), 'field_jbloc' => array( 'translatable' => '0', 'entity_types' => array(), 'settings' => array( 'max_length' => '255', ), 'storage' => array( 'type' => 'field_sql_storage', 'settings' => array(), 'module' => 'field_sql_storage', 'active' => '1', 'details' => array( 'sql' => array( 'FIELD_LOAD_CURRENT' => array( 'field_data_field_jbloc' => array( 'value' => 'field_jbloc_value', 'format' => 'field_jbloc_format', ), ), 'FIELD_LOAD_REVISION' => array( 'field_revision_field_jbloc' => array( 'value' => 'field_jbloc_value', 'format' => 'field_jbloc_format', ), ), ), ), ), 'foreign keys' => array( 'format' => array( 'table' => 'filter_format', 'columns' => array( 'format' => 'format', ), ), ), 'indexes' => array( 'format' => array( 'format', ), ), 'field_name' => 'field_jbloc', 'type' => 'text', 'module' => 'text', 'active' => '1', 'locked' => '0', 'cardinality' => '1', 'deleted' => '0', 'columns' => array( 'value' => array( 'type' => 'varchar', 'length' => '255', 'not null' => FALSE, ), 'format' => array( 'type' => 'varchar', 'length' => 255, 'not null' => FALSE, ), ), 'bundles' => array( 'node' => array( 'jbrowse_instance', ), ), ), 'field_jbtracks' => array( 'translatable' => '0', 'entity_types' => array(), 'settings' => array(), 'storage' => array( 'type' => 'field_sql_storage', 'settings' => array(), 'module' => 'field_sql_storage', 'active' => '1', 'details' => array( 'sql' => array( 'FIELD_LOAD_CURRENT' => array( 'field_data_field_jbtracks' => array( 'value' => 'field_jbtracks_value', 'format' => 'field_jbtracks_format', ), ), 'FIELD_LOAD_REVISION' => array( 'field_revision_field_jbtracks' => array( 'value' => 'field_jbtracks_value', 'format' => 'field_jbtracks_format', ), ), ), ), ), 'foreign keys' => array( 'format' => array( 'table' => 'filter_format', 'columns' => array( 'format' => 'format', ), ), ), 'indexes' => array( 'format' => array( 'format', ), ), 'field_name' => 'field_jbtracks', 'type' => 'text_long', 'module' => 'text', 'active' => '1', 'locked' => '0', 'cardinality' => '1', 'deleted' => '0', 'columns' => array( 'value' => array( 'type' => 'text', 'size' => 'big', 'not null' => FALSE, ), 'format' => array( 'type' => 'varchar', 'length' => 255, 'not null' => FALSE, ), ), 'bundles' => array( 'node' => array( 'jbrowse_instance', ), ), ), ); } /** * Defines the field instances needed for the jbrowse_instance content type. * * @return * An associative array specifying the instances we wish to add to our new * node type. */ function _jbrowse_installed_instances() { return array( 'field_jburl' => array( 'label' => 'Existing JBrowse URL', 'widget' => array( 'weight' => '1', 'type' => 'link_field', 'module' => 'link', 'active' => 0, 'settings' => array(), ), 'settings' => array( 'validate_url' => 1, 'url' => 0, 'title' => 'none', 'title_value' => '', 'title_maxlength' => '128', 'enable_tokens' => 0, 'display' => array( 'url_cutoff' => '', ), 'attributes' => array( 'target' => '_blank', 'rel' => '', 'class' => '', 'configurable_title' => 0, 'title' => '', ), 'rel_remove' => 'default', 'user_register_form' => FALSE, ), 'display' => array( 'default' => array( 'label' => 'above', 'type' => 'link_default', 'settings' => array(), 'module' => 'link', 'weight' => 3, ), 'teaser' => array( 'type' => 'hidden', 'label' => 'above', 'settings' => array(), 'weight' => 0, ), ), 'required' => 1, 'description' => 'The URL for the existing JBrowse you wish to integrate into this page. This URL should not include any query parameters.', 'default_value' => NULL, 'field_name' => 'field_jburl', 'entity_type' => 'node', 'bundle' => 'jbrowse_instance', 'deleted' => '0', ), 'field_jbloc' => array( 'label' => 'Start Location', 'widget' => array( 'weight' => '3', 'type' => 'text_textfield', 'module' => 'text', 'active' => 1, 'settings' => array( 'size' => '60', ), ), 'settings' => array( 'text_processing' => '0', 'user_register_form' => FALSE, ), 'display' => array( 'default' => array( 'label' => 'above', 'type' => 'text_default', 'settings' => array(), 'module' => 'text', 'weight' => 1, ), 'teaser' => array( 'type' => 'hidden', 'label' => 'above', 'settings' => array(), 'weight' => 0, ), ), 'required' => 0, 'description' => "

The initial genomic position which will be visible in the viewing field. Possible input strings are:

\r\n\"Chromosome\"+\":\"+ start point + \"..\" + end point\r\n

A chromosome name/ID followed by “:”, starting position, “..” and end position of the genome to be viewed in the browser is used as an input. Chromosome ID can be either a string or a mix of string and numbers. “CHR” to indicate chromosome may or may not be used. Strings are not case-sensitive. If the chromosome ID is found in the database reference sequence (RefSeq), the chromosome will be shown from the starting position to the end position given in URL.

\r\n
     ctgA:100..200
\r\n

Chromosome ctgA will be displayed from position 100 to 200.

\r\nOR start point + \"..\" + end point\r\n

A string of numerical value, “..” and another numerical value is given with the loc option. JBrowse navigates through the currently selected chromosome from the first numerical value, start point, to the second numerical value, end point.

\r\n
     200..600
\r\n

Displays position 200 to 600 of the current chromosome.

\r\nOR center base\r\n

If only one numerical value is given as an input, JBrowse treats the input as the center position. Then an arbitrary region of the currently selected gene is displayed in the viewing field with the given input position as basepair position on which to center the view.

\r\nOR feature name/ID\r\n

If a string or a mix of string and numbers are entered as an input, JBrowse treats the input as a feature name/ID of a gene. If the ID exists in the database RefSeq, JBrowser displays an arbitrary region of the feature from the the position 0, starting position of the gene, to a certain end point.

\r\n
     ctgA
\r\n

Displays an arbitrary region from the ctgA reference.

", 'default_value' => NULL, 'field_name' => 'field_jbloc', 'entity_type' => 'node', 'bundle' => 'jbrowse_instance', 'deleted' => '0', ), 'field_jbtracks' => array( 'label' => 'Tracks to Display', 'widget' => array( 'weight' => '4', 'type' => 'text_textarea', 'module' => 'text', 'active' => 1, 'settings' => array( 'rows' => '2', ), ), 'settings' => array( 'text_processing' => '0', 'user_register_form' => FALSE, ), 'display' => array( 'default' => array( 'label' => 'above', 'type' => 'text_default', 'settings' => array(), 'module' => 'text', 'weight' => 2, ), 'teaser' => array( 'type' => 'hidden', 'label' => 'above', 'settings' => array(), 'weight' => 0, ), ), 'required' => 0, 'description' => "

A comma-delimited strings containing track names, each of which should correspond to the \"label\" element of the track information dictionaries that are currently viewed in the viewing field.

\r\n
     DNA,knownGene,ccdsGene,snp131,pgWatson,simpleRepeat
", 'default_value' => NULL, 'field_name' => 'field_jbtracks', 'entity_type' => 'node', 'bundle' => 'jbrowse_instance', 'deleted' => '0', ), ); }