';
$output .= 'All Database References should strictly pertain to THE CURRENT Individual ';
$output .= ' ';
$output .= theme('tripal_stock_references', $node);
$output .= '
';
$output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
$output .= ' ';
$output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'db_references', $node->nid);
return $output;
}
/**
* Implements Hook_form(): Handles adding of Database References to Stocks
*
* @param $form_state
* An array describing the current state of the form
* @param $node
* The stock node to add the database reference to
*
* @return
* An array describing the form to be rendered
*
* @ingroup tripal_stock
*/
function tripal_stock_add_ONE_dbreference_form($form_state, $node) {
$stock_id = $node->stock->stock_id;
$form['db_nid'] = array(
'#type' => 'hidden',
'#value' => $node->nid
);
$form['add_dbreference'] = array(
'#type' => 'fieldset',
'#title' => t('Add Database References') . '(optional)',
);
$form['add_properties']['db_stock_id'] = array(
'#type' => 'value',
'#value' => $stock_id,
'#required' => TRUE
);
$form['add_dbreference']['accession'] = array(
'#type' => 'textfield',
'#title' => t('Accession Number'),
);
$form['add_dbreference']['db_description'] = array(
'#type' => 'textarea',
'#title' => t('Description of Database Reference') . '+',
'#description' => t('Optionally enter a description about the database accession.')
);
$db_options = tripal_db_get_db_options();
$db_options[0] = 'Select a Database';
ksort($db_options);
$form['add_dbreference']['database'] = array(
'#type' => 'select',
'#title' => t('Database'),
'#options' => $db_options,
);
$form['add_dbreference']['submit'] = array(
'#type' => 'submit',
'#value' => t('Add Database Reference')
);
return $form;
}
/**
* Implements hook_form_validate(): Validates the input from tripal_stock_add_ONE_dbreference_form()
*
* @param $form
* An array describing the form that was rendered
* @param $form_state
* An array describing the current state of the form including user input
*
* @ingroup tripal_stock
*/
function tripal_stock_add_ONE_dbreference_form_validate($form, &$form_state) {
// Only ensure db reference valid if adding
if ($form_state['clicked_button']['#value'] == t('Add Database Reference') ) {
//Do work of required validators
if ($form_state['values']['accession'] == '') {
form_set_error('accession', 'Accession field is Required.');
}
// Check database is valid db_id in chado
if ( $form_state['values']['database'] > 0) {
$tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $form_state['values']['database']));
if ($tmp_obj->count != 1) {
form_set_error('database', 'The database you selected is not valid. Please choose another one.');
}
}
else {
form_set_error('database', 'Please select a database');
}
// Check Accession is unique for database
$tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {dbxref} WHERE accession='%s'", $form_state['values']['accession']));
if ($tmp_obj->count > 0) {
form_set_error('accession', 'This accession has already been assigned to another stock.');
}
} //end of if adding
}
/**
* Implements hoook_form_submit(): Actually adds the db reference to the stock
*
* @param $form
* An array describing the form that was rendered
* @param $form_state
* An array describing the current state of the form including user input
*
* @ingroup tripal_stock
*/
function tripal_stock_add_ONE_dbreference_form_submit($form, &$form_state) {
// FIX: Sometimes on programatic submission of form (drupal_execute) values in the form state get lost
// however, the post values always seem to be correct
if (empty($form_state['values']['db_stock_id'])) {
$form_state['values']['db_stock_id'] = $form_state['clicked_button']['#post']['db_stock_id']; }
// Only Create if valid
if ($form_state['values']['database'] > 0) {
// create dbxref
chado_query(
"INSERT INTO {dbxref} (db_id, accession, description) VALUES (%d, '%s', '%s')",
$form_state['values']['database'],
$form_state['values']['accession'],
$form_state['values']['db_description']
);
//create stock_dbxref
$dbxref = tripal_db_get_dbxref_by_accession($form_state['values']['accession'], $form_state['values']['database']);
if (!empty($dbxref->dbxref_id)) {
chado_query(
"INSERT INTO {stock_dbxref} (stock_id, dbxref_id) VALUES (%d, %d)",
$form_state['values']['db_stock_id'],
$dbxref->dbxref_id
);
drupal_set_message(t('Successfully Added Database Reference'));
}
else {
drupal_set_message(t('Database reference NOT successfully created...'), 'error');
} //end of if dbxref was created successfully
} //end of if valid db reference
}
/**
* Display the EDIT Database References to Stock Page
*
* This page is displayed as a tab on each stock details page (by default)
*
* @param $node
* The stock node to add the database references to
*
* @return
* HTML formatted output
*
* @ingroup tripal_stock
*/
function tripal_stock_edit_ALL_dbreferences_page($node) {
$output = '';
$output .= drupal_get_form('tripal_stock_edit_ALL_db_references_form', $node);
$output .= ' ';
$output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
$output .= ' ';
$output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid);
return $output;
}
/**
* Implements Hook_form(): Handles adding of Database References to Stocks
*
* Specifically this adds dbxrefs to a current stock using the stock_dbxref table
*
* @param $form_state
* An array describing the current state of the form
* @param $node
* The stock node whose database references should be edited
*
* @return
* An array describing the form to be rendered
*
* @ingroup tripal_stock
*/
function tripal_stock_edit_ALL_db_references_form($form_state, $node) {
$form = array();
// Add database references to the node
$node = tripal_core_expand_chado_vars($node, 'table', 'stock_dbxref');
$form['nid'] = array(
'#type' => 'hidden',
'#value' => $node->nid
);
$i=0;
if (!$node->stock->stock_dbxref) {
$node->stock->stock_dbxref = array();
}
elseif (!is_array($node->stock->stock_dbxref)) {
$node->stock->stock_dbxref = array($node->stock->stock_dbxref);
}
if (sizeof($node->stock->stock_dbxref) != 0) {
foreach ($node->stock->stock_dbxref as $ref) {
$i++;
$form["num-$i"] = array(
'#type' => 'item',
'#value' => $i . '.'
);
$form["accession-$i"] = array(
'#type' => 'textfield',
//'#title' => t('Accession'),
'#size' => 30,
'#required' => TRUE,
'#default_value' => $ref->dbxref_id->accession
);
$db_options = tripal_db_get_db_options();
$db_options[0] = 'Select a Database';
ksort($db_options);
$form["database-$i"] = array(
'#type' => 'select',
//'#title' => t('Database'),
'#options' => $db_options,
'#default_value' => $ref->dbxref_id->db_id->db_id
);
$form["id-$i"] = array(
'#type' => 'hidden',
'#value' => $ref->dbxref_id->dbxref_id
);
$form["submit-$i"] = array(
'#type' => 'submit',
'#value' => t("Delete #$i")
);
}} //end of foreach db ref
$form['num_db_references'] = array(
'#type' => 'hidden',
'#value' => $i
);
$form["submit-edits"] = array(
'#type' => 'submit',
'#value' => t('Update DB References')
);
return $form;
}
/**
* Implements hook_form_submit(): Actually edits the database references
*
* @param $form
* An array representing the form
* @param $form_state
* An array representing the current state of the form including user input
*
* @ingroup tripal_stock
*/
function tripal_stock_edit_ALL_db_references_form_submit($form, &$form_state) {
if ($form_state['clicked_button']['#value'] == t('Update DB References') ) {
//Update all
for ($i=1; $i<=$form_state['values']['num_db_references']; $i++) {
tripal_stock_update_db_reference(
$form_state['values']["id-$i"],
$form_state['values']["database-$i"],
$form_state['values']["accession-$i"]
);
}
drupal_set_message(t("Updated all Database References"));
drupal_goto('node/' . $form_state['values']['nid']);
}
elseif ( preg_match('/Delete #(\d+)/', $form_state['clicked_button']['#value'], $matches) ) {
$i = $matches[1];
tripal_stock_delete_db_reference($form_state['values']["id-$i"]);
drupal_set_message(t("Deleted Database Reference"));
}
else {
drupal_set_message(t("Unrecognized Button Pressed"), 'error');
}
}
/**
* Updates a Database Reference
*
* @todo Make this function more generic ie: update all parts of the dbxref and db
*
* @param $dbxref_id
* The unique chado identifier of the database reference to be updated
* @param $database_id
* The new database ID
* @param $accession
* The new accession
*
* @ingroup tripal_stock
*/
function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession) {
chado_query(
"UPDATE {dbxref} SET db_id=%d, accession='%s' WHERE dbxref_id=%d",
$database_id,
$accession,
$dbxref_id
);
}
/**
* Deletes a given database reference
*
* @param $dbxref_id
* The chado unique idenfier for the database reference to be deleted
*
* @return
* TRUE on success; FALSE otherwise
*
* @ingroup tripal_stock
*/
function tripal_stock_delete_db_reference($dbxref_id) {
chado_query(
"DELETE FROM {dbxref} WHERE dbxref_id=%d",
$dbxref_id
);
chado_query(
"DELETE FROM {stock_dbxref} WHERE dbxref_id=%d",
$dbxref_id
);
}
/**
* Themes the Edit All Database References for a stock form
*
* @param $form
* An array describing the form to be themed
*
* @return
* An HTML rendering of the form
*
* @ingroup tripal_stock
*/
function theme_tripal_stock_edit_ALL_db_references_form($form) {
$output = '';
$output .= ' ';
return $output;
}
/**
* List all database references for a given node
*
* @todo Make this function a theme function
*
* @param $db_references
* An array of database references to be listed
*
* @return
* HTML representation of the list
*
* @ingroup tripal_stock
*/
function tripal_stock_list_dbreferences_for_node($db_references) {
if (!empty($db_references) ) {
$output = '
';
$output .= '
Database
Accession
';
foreach ($db_references as $db) {
$output .= '
' . $db->db_name . '
' . $db->accession . '
';
} // end of foreach db reference
$output .= '
';
}
else {
$output = 'No Database References Added to the Current Stock';
}
return $output;
}