|
|
@@ -0,0 +1,800 @@
|
|
|
+<?php
|
|
|
+
|
|
|
+/**
|
|
|
+ * @file Stock Node Functionality
|
|
|
+ */
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_node_info(): registers a stock node type
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing various details of the node
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_info() {
|
|
|
+ return array(
|
|
|
+ 'chado_stock' => array(
|
|
|
+ 'name' => t('Stock'),
|
|
|
+ 'base' => 'chado_stock',
|
|
|
+ 'description' => t('A Chado Stock is a collection of material that can be sampled and have experiments performed on it.'),
|
|
|
+ 'has_title' => TRUE,
|
|
|
+ 'has_body' => FALSE,
|
|
|
+ 'chado_node_api' => array(
|
|
|
+ 'base_table' => 'stock',
|
|
|
+ 'hook_prefix' => 'chado_stock',
|
|
|
+ 'title' => array(
|
|
|
+ 'singular' => t('Stock'),
|
|
|
+ 'plural' => t('Stocks')
|
|
|
+ ),
|
|
|
+ 'select_by' => array(
|
|
|
+ 'type_id' => TRUE,
|
|
|
+ 'organism_id' => TRUE
|
|
|
+ ),
|
|
|
+ )
|
|
|
+ ),
|
|
|
+ );
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_load(): Prepares the chado_stock node
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The basic node containing all variables common to all nodes
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A stock node containing all the variables from the basic node and all stock specific variables
|
|
|
+ *
|
|
|
+ * D7 @todo: Make optimizations to take advantage of $nodes
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_load($nodes) {
|
|
|
+
|
|
|
+ $new_nodes = array();
|
|
|
+ foreach ($nodes as $nid => $node) {
|
|
|
+ // get the stock details from chado
|
|
|
+ $stock_id = chado_get_id_for_node('stock', $node->nid);
|
|
|
+ if (empty($stock_id)) {
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_stock',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'Unable to retrieve stock_id for %title (NID = %nid).',
|
|
|
+ array('%title' => $node->title, '%nid' => $node->nid)
|
|
|
+ );
|
|
|
+ }
|
|
|
+ else {
|
|
|
+
|
|
|
+ // build the variable with all the stock details
|
|
|
+ $values = array('stock_id' => $stock_id);
|
|
|
+ $stock = tripal_core_generate_chado_var('stock', $values);
|
|
|
+
|
|
|
+ // by default, the titles are saved using the unique constraint. We will
|
|
|
+ // keep it the same, but remove the duplicate name if the unique name and name
|
|
|
+ // are identical
|
|
|
+ $title_type = variable_get('chado_stock_title', 'unique_constraint');
|
|
|
+ if($title_type == 'unique_constraint') {
|
|
|
+ if (strcmp($stock->name, $stock->uniquename)==0) {
|
|
|
+ $node->title = $stock->name . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
|
|
|
+ }
|
|
|
+ // in previous version of Tripal, the stock title was simply the unique name.
|
|
|
+ // so, we recreate the title just to be sure all of our stock pages are consistent
|
|
|
+ else {
|
|
|
+ $node->title = $stock->name . ", " . $stock->uniquename . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // set the title to be the stock name or uniquename as configured
|
|
|
+ if($title_type == 'stock_name') {
|
|
|
+ $node->title = $stock->name;
|
|
|
+ }
|
|
|
+ if($title_type == 'stock_unique_name') {
|
|
|
+ $node->title = $stock->uniquename;
|
|
|
+ }
|
|
|
+
|
|
|
+ // add this to the node
|
|
|
+ $node->stock = $stock;
|
|
|
+ }
|
|
|
+
|
|
|
+ $new_nodes[$nid] = $node;
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ return $new_nodes;
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_form(): Creates the main Add/Edit/Delete Form for chado stocks
|
|
|
+ *
|
|
|
+ * Parts to be added by this form
|
|
|
+ * name,
|
|
|
+ * uniquename,
|
|
|
+ * description,
|
|
|
+ * type => select from cvterm with key cvterm_id,
|
|
|
+ * organism => select from available with key organism_id
|
|
|
+ * main_db_reference => accession, version, description, db_name(select from dropdown)
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * An empty node object on insert OR the current stock node object on update
|
|
|
+ * @param $form_state
|
|
|
+ * The current state of the form
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A description of the form to be rendered by drupal_get_form()
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_form($node, $form_state) {
|
|
|
+
|
|
|
+ // If existing stock then expand all fields needed using the chado API
|
|
|
+ if (isset($node->nid)) {
|
|
|
+ $fields_needed = array('stock.uniquename', 'stock.name', 'stock.stock_id', 'stock.type_id', 'stock.organism_id', 'stock.description', 'stock.dbxref_id', 'dbxref.accession', 'dbxref.description', 'dbxref.db_id', 'db.db_id');
|
|
|
+ foreach ($fields_needed as $field_name) {
|
|
|
+ // Check to see if it's excluded and expand it if so
|
|
|
+ if (isset($node->expandable_fields)) {
|
|
|
+ if (in_array($field_name, $node->expandable_fields)) {
|
|
|
+ $node = tripal_core_expand_chado_vars($node, 'field', $field_name);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Default values can come in the following ways:
|
|
|
+ //
|
|
|
+ // 1) as elements of the $node object. This occurs when editing an existing stock
|
|
|
+ // 2) in the $form_state['values'] array which occurs on a failed validation or
|
|
|
+ // ajax callbacks from non submit form elements
|
|
|
+ // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
|
|
|
+ // form elements and the form is being rebuilt
|
|
|
+ //
|
|
|
+ // set form field defaults
|
|
|
+ $sname = '';
|
|
|
+ $uniquename = '';
|
|
|
+ $stock_id = 0;
|
|
|
+ $type_id = 0;
|
|
|
+ $organism_id = 0;
|
|
|
+ $sdescription = '';
|
|
|
+ $dbxref_accession = '';
|
|
|
+ $dbxref_description = '';
|
|
|
+ $dbxref_database = 0;
|
|
|
+
|
|
|
+ // 1) if we are editing an existing node then the stock is already part of the node
|
|
|
+ if (property_exists($node, 'stock')) {
|
|
|
+ $sname = $node->stock->name;
|
|
|
+ $uniquename = $node->stock->uniquename;
|
|
|
+ $stock_id = $node->stock->stock_id;
|
|
|
+ $type_id = $node->stock->type_id->cvterm_id;
|
|
|
+ $organism_id = $node->stock->organism_id->organism_id;
|
|
|
+ $sdescription = $node->stock->description;
|
|
|
+ $dbxref_accession = $node->stock->dbxref_id->accession;
|
|
|
+ $dbxref_description = $node->stock->dbxref_id->description;
|
|
|
+ $dbxref_database = $node->stock->dbxref_id->db_id->db_id;
|
|
|
+ }
|
|
|
+
|
|
|
+ // 2) if we are re constructing the form from a failed validation or ajax callback
|
|
|
+ // then use the $form_state['values'] values
|
|
|
+ if (array_key_exists('values', $form_state)) {
|
|
|
+ $sname = $form_state['values']['sname'];
|
|
|
+ $uniquename = $form_state['values']['uniquename'];
|
|
|
+ $stock_id = $form_state['values']['stock_id'];
|
|
|
+ $type_id = $form_state['values']['type_id'];
|
|
|
+ $organism_id = $form_state['values']['organism_id'];
|
|
|
+ $sdescription = $form_state['values']['description'];
|
|
|
+ $dbxref_accession = $form_state['values']['accession'];
|
|
|
+ $dbxref_description = $form_state['values']['db_description'];
|
|
|
+ $dbxref_database = $form_state['values']['database'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // 3) if we are re building the form from after submission (from ajax call) then
|
|
|
+ // the values are in the $form_state['input'] array
|
|
|
+ if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
|
|
|
+ $sname = $form_state['input']['sname'];
|
|
|
+ $uniquename = $form_state['input']['uniquename'];
|
|
|
+ $stock_id = $form_state['input']['stock_id'];
|
|
|
+ $type_id = $form_state['input']['type_id'];
|
|
|
+ $organism_id = $form_state['input']['organism_id'];
|
|
|
+ $sdescription = $form_state['input']['description'];
|
|
|
+ $dbxref_accession = $form_state['input']['accession'];
|
|
|
+ $dbxref_description = $form_state['input']['db_description'];
|
|
|
+ $dbxref_database = $form_state['input']['database'];
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['names'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Stock Name')
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['names']['sname'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Name'),
|
|
|
+ '#default_value' => $sname,
|
|
|
+ '#required' => TRUE
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['names']['uniquename'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Unique Name'),
|
|
|
+ '#default_value' => $uniquename,
|
|
|
+ '#required' => TRUE
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['names']['stock_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $stock_id,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['details'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Stock Details')
|
|
|
+ );
|
|
|
+
|
|
|
+ $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_types_cv', 'NULL') );
|
|
|
+ $type_options[0] = 'Select a Type';
|
|
|
+ $form['details']['type_id'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Type of Stock'),
|
|
|
+ '#options' => $type_options,
|
|
|
+ '#default_value' => $type_id,
|
|
|
+ '#required' => TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+
|
|
|
+ // get the list of organisms
|
|
|
+ $sql = "SELECT * FROM {organism} ORDER BY genus, species";
|
|
|
+ $org_rset = chado_query($sql);
|
|
|
+ $organisms = array();
|
|
|
+ $organisms[''] = '';
|
|
|
+ while ($organism = $org_rset->fetchObject()) {
|
|
|
+ $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
|
|
|
+ }
|
|
|
+ $form['details']['organism_id'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Source Organism for stock'),
|
|
|
+ '#default_value' => $organism_id,
|
|
|
+ '#options' => $organisms,
|
|
|
+ '#required' => TRUE
|
|
|
+ );
|
|
|
+
|
|
|
+
|
|
|
+ $form['details']['stock_description'] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#title' => t('Notes'),
|
|
|
+ '#default_value' => $sdescription,
|
|
|
+ '#description' => t('Briefly enter any notes on the above stock. This should not include phenotypes or genotypes.'),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['database_reference'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Stock Database Reference')
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['database_reference']['accession'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Accession'),
|
|
|
+ '#default_value' => $dbxref_accession,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['database_reference']['db_description'] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#title' => t('Description of Database Reference'),
|
|
|
+ '#default_value' => $dbxref_description,
|
|
|
+ '#description' => t('Optionally enter a description about the database accession.')
|
|
|
+ );
|
|
|
+
|
|
|
+ $db_options = tripal_db_get_db_options();
|
|
|
+ $db_options[0] = 'Select a Database';
|
|
|
+ $form['database_reference']['database'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Database'),
|
|
|
+ '#options' => $db_options,
|
|
|
+ '#default_value' => $dbxref_database
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_validate(): Validate the input from the chado_stock node form
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The current node including fields with the form element names and submitted values
|
|
|
+ * @param $form
|
|
|
+ * A description of the form to be rendered by drupal_get_form()
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_validate($node, $form, &$form_state) {
|
|
|
+
|
|
|
+ // remove surrounding whitespace
|
|
|
+ $node->uniquename = trim($node->uniquename);
|
|
|
+ $node->sname = trim($node->sname);
|
|
|
+ $node->stock_description = trim($node->stock_description);
|
|
|
+ $node->accession = trim($node->accession);
|
|
|
+ $node->db_description = trim($node->db_description);
|
|
|
+
|
|
|
+ // if this is a delete then don't validate
|
|
|
+ if($node->op == 'Delete') {
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ // we are syncing if we do not have a node ID but we do have a stock_id. We don't
|
|
|
+ // need to validate during syncing so just skip it.
|
|
|
+ if (is_null($node->nid) and property_exists($node, 'stock_id') and $node->stock_id != 0) {
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ $int_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
|
|
|
+ $string_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
|
|
|
+
|
|
|
+ // if this is an update, we want to make sure that a different stock for
|
|
|
+ // the organism doesn't already have this uniquename. We don't want to give
|
|
|
+ // two sequences the same uniquename
|
|
|
+ if (property_exists($node, 'nid')) {
|
|
|
+ $sql = "
|
|
|
+ SELECT *
|
|
|
+ FROM {stock} S
|
|
|
+ INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
|
|
|
+ WHERE
|
|
|
+ uniquename = :uname AND organism_id = :organism_id AND
|
|
|
+ CVT.name = :cvtname AND NOT stock_id = :stock_id
|
|
|
+ ";
|
|
|
+ $result = chado_query($sql, array(':uname' => $node->uniquename,
|
|
|
+ ':organism_id' => $node->organism_id, ':cvtname' => $node->type_id,
|
|
|
+ ':stock_id' => $node->stock_id))->fetchObject();
|
|
|
+ if ($result) {
|
|
|
+ form_set_error('uniquename', t("Stock update cannot proceed. The stock name '$node->uniquename' is not unique for this organism. Please provide a unique name for this stock."));
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // if this is an insert then we just need to make sure this name doesn't
|
|
|
+ // already exist for this organism if it does then we need to throw an error
|
|
|
+ else {
|
|
|
+ $sql = "
|
|
|
+ SELECT *
|
|
|
+ FROM {Stock} S
|
|
|
+ INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
|
|
|
+ WHERE uniquename = :uname AND organism_id = :organism_id AND CVT.name = :cvtname";
|
|
|
+ $result = chado_query($sql, array(':uname' => $node->uniquename,
|
|
|
+ ':organism_id' => $node->organism_id, ':cvtname' => $node->type_id))->fetchObject();
|
|
|
+ if ($result) {
|
|
|
+ form_set_error('uniquename', t("Stock insert cannot proceed. The stock name '$node->uniquename' already exists for this organism. Please provide a unique name for this stock."));
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+ // Check Type of Stock is valid cvterm_id in chado ( $form['values']['details']['type_id'] )
|
|
|
+ if ($node->type_id == 0) {
|
|
|
+ form_set_error('type_id', 'Please select a type of stock.');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $replace = array(':table' => 'cvterm', ':column' => 'cvterm_id');
|
|
|
+ $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
|
|
|
+ $num_rows = chado_query($new_sql, array(':value' => $node->type_id))->fetchObject();
|
|
|
+ if ( $num_rows->count != 1) {
|
|
|
+ form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Check Source Organism is valid organism_id in chado ( $form['values']['details']['organism_id'] )
|
|
|
+ if ( $node->organism_id == 0) {
|
|
|
+ form_set_error('organism_id', 'Please select a source organism for this stock');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $replace = array(':table' => 'organism', ':column' => 'organism_id');
|
|
|
+ $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
|
|
|
+ $num_rows = chado_query($new_sql, array(':value' => $node->organism_id))->fetchObject();
|
|
|
+ if ( $num_rows->count != 1 ) {
|
|
|
+ form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Check if Accession also database
|
|
|
+ if ($node->accession != '') {
|
|
|
+ if ($node->database == 0) {
|
|
|
+ // there is an accession but no database selected
|
|
|
+ form_set_error('database', 'You need to enter both a database and an accession for that database in order to add a database reference.');
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ if ($node->database > 0) {
|
|
|
+ // there is a database selected but no accession
|
|
|
+ form_set_error('accession', 'You need to enter both a database and an accession for that database in order to add a database reference.');
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
|
|
|
+ if ( $node->database > 0) {
|
|
|
+ $replace = array(':table' => 'db', ':column' => 'db_id');
|
|
|
+ $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
|
|
|
+ $num_rows = chado_query($new_sql, array(':value' => $node->database))->fetchObject();
|
|
|
+ if ($num_rows->count != 1) {
|
|
|
+ form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_insert(): Inserts data from chado_stock_form() into drupal and chado
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The current node including fields with the form element names and submitted values
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * TRUE if the node was successfully inserted into drupal/chado; FALSE otherwise
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_insert($node) {
|
|
|
+
|
|
|
+ // If the chado stock exists (e.g. this is only a syncing operation)
|
|
|
+ // then don't create but simply link to node
|
|
|
+ if (isset($node->chado_stock_exists)) {
|
|
|
+ if ($node->chado_stock_exists) {
|
|
|
+ if (!empty($node->stock_id)) {
|
|
|
+ db_insert('chado_stock')->fields(array(
|
|
|
+ 'nid' => $node->nid,
|
|
|
+ 'vid' => $node->vid,
|
|
|
+ 'stock_id' => $node->stock_id
|
|
|
+ ));
|
|
|
+ }
|
|
|
+
|
|
|
+ return $node;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // if there is an stock_id in the $node object then this must be a sync so
|
|
|
+ // we can skip adding the stock to chado as it is already there, although
|
|
|
+ // we do need to proceed with the rest of the insert
|
|
|
+ if (!property_exists($node, 'stock_id')) {
|
|
|
+
|
|
|
+ // before we can add the stock, we must add the dbxref if one has been
|
|
|
+ // provided by the user.
|
|
|
+ $dbxref_status = 0;
|
|
|
+ if (!empty($node->accession) ) {
|
|
|
+ if (!empty($node->database) ) {
|
|
|
+ $values = array(
|
|
|
+ 'db_id' => $node->database,
|
|
|
+ 'accession' => $node->accession,
|
|
|
+ );
|
|
|
+ if (!tripal_core_chado_select('dbxref', array('dbxref_id'), $values)) {
|
|
|
+ $values['description'] = $node->db_description;
|
|
|
+ $values['version'] = '1';
|
|
|
+ $dbxref_status = tripal_core_chado_insert('dbxref', $values);
|
|
|
+ if (!$dbxref_status) {
|
|
|
+ drupal_set_message(t('Unable to add database reference to this stock.'), 'warning');
|
|
|
+ watchdog('tripal_stock',
|
|
|
+ 'Insert Stock: Unable to create dbxref where values:%values',
|
|
|
+ array('%values' => print_r($values, TRUE)),
|
|
|
+ WATCHDOG_WARNING
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $dbxref_status = 1;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // create stock including the dbxref
|
|
|
+ $stock = '';
|
|
|
+ if ($dbxref_status) {
|
|
|
+ $values = array(
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'db_id' => $node->database,
|
|
|
+ 'accession' => $node->accession
|
|
|
+ ),
|
|
|
+ 'organism_id' => $node->organism_id,
|
|
|
+ 'name' => $node->sname,
|
|
|
+ 'uniquename' => $node->uniquename,
|
|
|
+ 'description' => $node->stock_description,
|
|
|
+ 'type_id' => $node->type_id
|
|
|
+ );
|
|
|
+ $stock = tripal_core_chado_insert('stock', $values);
|
|
|
+ }
|
|
|
+ // create a stock without a dbxref
|
|
|
+ else {
|
|
|
+ $values = array(
|
|
|
+ 'organism_id' => $node->organism_id,
|
|
|
+ 'name' => $node->sname,
|
|
|
+ 'uniquename' => $node->uniquename,
|
|
|
+ 'description' => $node->stock_description,
|
|
|
+ 'type_id' => $node->type_id
|
|
|
+ );
|
|
|
+ $stock = tripal_core_chado_insert('stock', $values);
|
|
|
+ }
|
|
|
+
|
|
|
+ if (is_array($stock)) {
|
|
|
+ $stock_added = TRUE;
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $stock_added = FALSE;
|
|
|
+ }
|
|
|
+ } //end of adding stock to chado
|
|
|
+ else {
|
|
|
+ // stock already exists since this is a sync
|
|
|
+ $stock_added = TRUE;
|
|
|
+ $stock['stock_id'] = $node->stock_id;
|
|
|
+ }
|
|
|
+
|
|
|
+ // if the stock creation was succesful then add the URL and the entry in the
|
|
|
+ // chado_stock table
|
|
|
+ if ($stock_added) {
|
|
|
+
|
|
|
+ // add the entry to the chado_stock table
|
|
|
+ db_insert('chado_stock')->fields(array(
|
|
|
+ 'nid' => (int) $node->nid,
|
|
|
+ 'vid' => (int) $node->vid,
|
|
|
+ 'stock_id' => (int) $stock['stock_id']
|
|
|
+ ))->execute();
|
|
|
+
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message(t('Error during stock creation.'), 'error');
|
|
|
+ watchdog('tripal_stock',
|
|
|
+ 'Insert Stock: Unable to create stock where values:%values',
|
|
|
+ array('%values' => print_r($values, TRUE)),
|
|
|
+ WATCHDOG_WARNING
|
|
|
+ );
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_update(): Handles Editing/Updating of main stock info
|
|
|
+ *
|
|
|
+ * NOTE: Currently just writes over all old data
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The current node including fields with the form element names and submitted values
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * TRUE if the node was successfully updated in drupal/chado; FALSE otherwise
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_update($node) {
|
|
|
+
|
|
|
+ if ($node->revision) {
|
|
|
+ // there is no way to handle revisions in Chado but leave
|
|
|
+ // this here just to make not we've addressed it.
|
|
|
+ }
|
|
|
+
|
|
|
+ //update dbxref
|
|
|
+ if ($node->database) {
|
|
|
+ if ($node->accession) {
|
|
|
+ $dbxref_mode = '';
|
|
|
+ $stock = tripal_core_chado_select(
|
|
|
+ 'stock',
|
|
|
+ array('dbxref_id', 'type_id'),
|
|
|
+ array('stock_id' => $node->stock_id)
|
|
|
+ );
|
|
|
+
|
|
|
+ if ($stock[0]->dbxref_id) {
|
|
|
+ $values = array(
|
|
|
+ 'db_id' => $node->database,
|
|
|
+ 'accession' => $node->accession,
|
|
|
+ 'description' => $node->db_description
|
|
|
+ );
|
|
|
+ $dbxref_status = tripal_core_chado_update(
|
|
|
+ 'dbxref',
|
|
|
+ array('dbxref_id' => $stock[0]->dbxref_id),
|
|
|
+ $values
|
|
|
+ );
|
|
|
+ $dbxref_mode = 'Update';
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ if ($stock[0]->type_id) {
|
|
|
+ //create the dbxref
|
|
|
+ //used the type_id as a control to check we have a stock but not a dbxref
|
|
|
+ $values = array(
|
|
|
+ 'db_id' => $node->database,
|
|
|
+ 'accession' => $node->accession,
|
|
|
+ 'description' => $node->db_description,
|
|
|
+ 'version' => '1',
|
|
|
+ );
|
|
|
+ $dbxref_status = tripal_core_chado_insert(
|
|
|
+ 'dbxref',
|
|
|
+ $values
|
|
|
+ );
|
|
|
+ $dbxref_mode = 'Create';
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message(t('Unable to find stock to Update'), 'error');
|
|
|
+ watchdog(
|
|
|
+ 'tripal_stock',
|
|
|
+ 'Stock Update: Unable to find stock to update using values: %values',
|
|
|
+ array('%values', print_r($values, TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ if (!$dbxref_status) {
|
|
|
+ watchdog(
|
|
|
+ 'tripal_stock',
|
|
|
+ 'Stock Update: Unable to %mode main stock dbxref with values: %values',
|
|
|
+ array('%values' => print_r($values, TRUE), '%mode' => $dbxref_mode),
|
|
|
+ WATCHDOG_WARNING
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ //can't change stock id which is all thats stored in drupal thus only update chado
|
|
|
+ $update_values = array(
|
|
|
+ 'organism_id' => $node->organism_id,
|
|
|
+ 'name' => $node->sname,
|
|
|
+ 'uniquename' => $node->uniquename,
|
|
|
+ 'description' => $node->stock_description,
|
|
|
+ 'type_id' => $node->type_id,
|
|
|
+ );
|
|
|
+ if ($dbxref_status) {
|
|
|
+ $update_values['dbxref_id'] = array(
|
|
|
+ 'db_id' => $node->database,
|
|
|
+ 'accession' => $node->accession
|
|
|
+ );
|
|
|
+ }
|
|
|
+ $status = tripal_core_chado_update('stock', array('stock_id' => $node->stock_id), $update_values);
|
|
|
+
|
|
|
+
|
|
|
+ if (!$status) {
|
|
|
+ drupal_set_message(t('Unable to update stock'), 'error');
|
|
|
+ watchdog(
|
|
|
+ 'tripal_stock',
|
|
|
+ 'Stock Update: Unable to update stock using match values: %mvalues and update values: %uvalues',
|
|
|
+ array('%mvalues' => print_r(array('stock_id' => $node->stock_id), TRUE), '%uvalues' => print_r($update_values, TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ // set the URL for this stock page
|
|
|
+ $values = array('stock_id' => $node->stock_id);
|
|
|
+ $stock = tripal_core_chado_select('stock', array('*'), $values);
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implements hook_delete(): Handles deleting of chado_stocks
|
|
|
+ *
|
|
|
+ * NOTE: Currently deletes data -no undo or record-keeping functionality
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The current node including fields with the form element names and submitted values
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * TRUE if the node was successfully deleted from drupal/chado; FALSE otherwise
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function chado_stock_delete($node) {
|
|
|
+
|
|
|
+ // Set stock in chado: is_obsolete = TRUE
|
|
|
+ chado_query("DELETE FROM {stock} WHERE stock_id = :stock_id", array(':stock_id' => $node->stock->stock_id));
|
|
|
+
|
|
|
+ //remove drupal node and all revisions
|
|
|
+ db_query("DELETE FROM {chado_stock} WHERE nid = :nid", array(':nid' => $node->nid));
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Used by Tripal Chado Node API during sync'ing of nodes
|
|
|
+ */
|
|
|
+function chado_stock_chado_node_sync_create_new_node($new_node, $record) {
|
|
|
+
|
|
|
+ $new_node->organism_id = $record->organism_id;
|
|
|
+ $new_node->sname = $record->name;
|
|
|
+ $new_node->uniquename = $record->uniquename;
|
|
|
+ $new_node->type_id = $record->type_id;
|
|
|
+
|
|
|
+ return $new_node;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_presave($node) {
|
|
|
+
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+ $values = array('organism_id' => $node->organism_id);
|
|
|
+ $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
|
|
|
+ $values = array('cvterm_id' => $node->type_id);
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
|
|
|
+ $node->title = $node->sname . ', ' . $node->uniquename . ' (' . $cvterm[0]->name . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_insert($node) {
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+ if (!$node->stock_id) {
|
|
|
+ $sql = "SELECT * FROM {chado_stock} WHERE nid = :nid";
|
|
|
+ $chado_stock = db_query($sql, array(':nid' => $node->nid))->fetchObject();
|
|
|
+ $node->stock_id = $chado_stock->stock_id;
|
|
|
+ }
|
|
|
+
|
|
|
+ // remove any previous alias
|
|
|
+ db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
|
|
|
+
|
|
|
+ // set the URL for this stock page
|
|
|
+ $url_alias = tripal_stock_get_stock_url($node);
|
|
|
+ $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
|
|
|
+ path_save($path_alias);
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_update($node) {
|
|
|
+
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+
|
|
|
+ // remove any previous alias
|
|
|
+ db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
|
|
|
+
|
|
|
+ // set the URL for this stock page
|
|
|
+ $url_alias = tripal_stock_get_stock_url($node);
|
|
|
+ $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
|
|
|
+ path_save($path_alias);
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_view($node, $view_mode, $langcode) {
|
|
|
+
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_organism':
|
|
|
+ if ($view_mode == 'full') {
|
|
|
+ // Show stock if the organism/feature is not at teaser view
|
|
|
+ $node->content['tripal_organism_stocks'] = array(
|
|
|
+ '#value' => theme('tripal_organism_stocks', $node),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ case 'chado_stock':
|
|
|
+ if ($view_mode == 'full') {
|
|
|
+ $node->content['tripal_stock_base'] = array(
|
|
|
+ '#value' => theme('tripal_stock_base', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Cross References
|
|
|
+ $node->content['tripal_stock_references'] = array(
|
|
|
+ '#value' => theme('tripal_stock_references', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Properties
|
|
|
+ $node->content['tripal_stock_properties'] = array(
|
|
|
+ '#value' => theme('tripal_stock_properties', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Synonyms
|
|
|
+ $node->content['tripal_stock_synonyms'] = array(
|
|
|
+ '#value' => theme('tripal_stock_synonyms', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Relationships
|
|
|
+ $node->content['tripal_stock_relationships'] = array(
|
|
|
+ '#value' => theme('tripal_stock_relationships', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Stock Collections
|
|
|
+ $node->content['tripal_stock_collections'] = array(
|
|
|
+ '#value' => theme('tripal_stock_collections', array('node' => $node)),
|
|
|
+ );
|
|
|
+ // Stock Genotypes
|
|
|
+ $node->content['tripal_stock_genotypes'] = array(
|
|
|
+ '#value' => theme('tripal_stock_genotypes', array('node' => $node)),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ if ($view_mode == 'teaser') {
|
|
|
+ $node->content['tripal_stock_teaser'] = array(
|
|
|
+ '#value' => theme('tripal_stock_teaser', array('node' => $node)),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
Lacey Sanderson