criteria);
$num_criteria = $criteria['num_criteria'];
$criteria_str = '';
for ($i = 0; $i <= $num_criteria; $i++) {
$search_terms = $criteria['criteria'][$i]['search_terms'];
$scope = $criteria['criteria'][$i]['scope'];
$operation = $criteria['criteria'][$i]['operation'];
$criteria_str .= "$operation ($scope: $search_terms) ";
}
$rows[] = array(
l(t('Edit/Test'), "admin/tripal/tripal_pub/import/edit/$importer->pub_import_id"),
$importer->name,
$criteria['remote_db'],
$criteria_str,
$importer->disabled ? 'Yes' : 'No',
$importer->do_contact ? 'Yes' : 'No',
l(t('Delete'), "admin/tripal/tripal_pub/import/delete/$importer->pub_import_id"),
);
}
$rows[] = array(
'data' => array(
array('data' => l(t('Create a new publication importer.'), "admin/tripal/tripal_pub/import/new"),
'colspan' => 7),
)
);
$page = theme('table', $header, $rows);
return $page;
}
/*
*
*/
function tripal_pub_importer_setup($action = 'new', $pub_import_id = NULL) {
global $pager_total, $pager_total_items;
$pager_id = 0;
$limit = 10;
// generate the search form
$form = drupal_get_form('tripal_pub_importer_setup_form', $pub_import_id, $action);
$output = l("Return to publication importers list", "admin/tripal/tripal_pub/import_list");
$output .= $form;
// retrieve any results
$remote_db = $_SESSION['tripal_pub_search']['remote_db'];
$num_criteria = $_SESSION['tripal_pub_search']['num_criteria'];
$days = $_SESSION['tripal_pub_search']['days'];
$search_array = array();
$search_array['remote_db'] = $remote_db;
$search_array['num_criteria'] = $num_criteria;
$search_array['days'] = $days;
for ($i = 0; $i <= $num_criteria; $i++) {
$search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'];
$search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_search']['criteria'][$i]['scope'];
$search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_search']['criteria'][$i]['operation'];
}
if ($_SESSION['tripal_pub_search']['perform_search']) {
// get the list of publications from the remote database using the search criteria.
$pubs = tripal_pub_get_remote_search_results($remote_db, $search_array, $limit, $pager_id);
// generate the pager
$total_pages = $pager_total[$pager_id];
$total_items = $pager_total_items[$pager_id];
$page = isset($_GET['page']) ? $_GET['page'] : '0';
$pager = theme('pager');
// iterate through the results and construct the table displaying the publications
$rows = array();
$i = $page * $limit + 1;
if (count($pubs) > 0) {
foreach ($pubs as $pub) {
$rows[] = array(number_format($i), $pub['Citation']);
$i++;
}
}
$headers = array('', 'Citation');
$table = theme('table', $headers, $rows);
// join all to form the results
$output .= "
Found " . number_format($total_items) .
". Page " . ($page + 1) . " of $total_pages. " .
" Results" . $table . '
' . $pager;
}
return $output;
}
/*
*
*/
function theme_tripal_pub_importer_setup_form($form) {
$rows = array();
foreach ($form['criteria'] as $i => $element) {
if(is_numeric($i)) {
$rows[] = array(
array('data' => drupal_render($element["operation-$i"]), 'width' => '10%'),
array('data' => drupal_render($element["scope-$i"]), 'width' => '10%'),
drupal_render($element["search_terms-$i"]),
array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'),
);
}
}
$headers = array('Operation','Scope', 'Search Terms', '');
$markup = '';
$markup .= '' . drupal_render($form['disabled']) . '
';
$markup .= '' . drupal_render($form['do_contact']) . '
';
$markup .= theme('table', $headers, $rows);
$form['criteria'] = array(
'#type' => 'markup',
'#value' => $markup,
'#weight' => -10,
);
return drupal_render($form);
}
/**
* Purpose: Provides the form to search pubmed
*
* @ingroup tripal_pub
*/
function tripal_pub_importer_setup_form(&$form_state = NULL, $pub_import_id = NULL, $action = 'new') {
tripal_core_ahah_init_form();
dpm($form_state);
// Set the default values. If the pub_import_id isn't already defined by the form values
// and one is provided then look it up in the database
$criteria = NULL;
if ($action == "edit" and !$form_state['values']) {
$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
$importer = db_fetch_object(db_query($sql, $pub_import_id));
$criteria = unserialize($importer->criteria);
$remote_db = $criteria['remote_db'];
$days = $criteria['days'];
$disabled = $criteria['disabled'];
$do_contact = $criteria['do_contact'];
$num_criteria = $criteria['num_criteria'];
$loader_name = $criteria['loader_name'];
}
// if the session has variables then use those. This should only happen when
// the 'Test Criteria' button is clicked.
$num_criteria = $_SESSION['tripal_pub_search']['num_criteria'] ? $_SESSION['tripal_pub_search']['num_criteria'] : $num_criteria;
$loader_name = $_SESSION['tripal_pub_search']['loader_name'] ? $_SESSION['tripal_pub_search']['loader_name'] : $loader_name;
$remote_db = $_SESSION['tripal_pub_search']['remote_db'] ? $_SESSION['tripal_pub_search']['remote_db'] : $remote_db;
$disabled = $_SESSION['tripal_pub_search']['disabled'] ? $_SESSION['tripal_pub_search']['disabled'] : $disabled;
$do_contact = $_SESSION['tripal_pub_search']['do_contact'] ? $_SESSION['tripal_pub_search']['do_contact'] : $do_contact;
$days = $_SESSION['tripal_pub_search']['days'] ? $_SESSION['tripal_pub_search']['days'] : $days;
// If the form_state has variables then use those. This happens when an error occurs on the form or the
// form is resbumitted using AJAX
$num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria;
$loader_name = $form_state['values']['loader_name'] ? $form_state['values']['loader_name'] : $loader_name;
$remote_db = $form_state['values']['remote_db'] ? $form_state['values']['remote_db'] : $remote_db;
$disabled = $form_state['values']['disabled'] ? $form_state['values']['disabled'] : $disabled;
$do_contact = $form_state['values']['do_contact'] ? $form_state['values']['do_contact'] : $do_contact;
$days = $form_state['values']['days'] ? $form_state['values']['days'] : $days;
// change the number of criteria based on form_state post data.
if (!$num_criteria) {
$num_criteria = 0;
}
if($form_state['post']["add-$num_criteria"]) {
$num_criteria++;
}
if($form_state['post']["remove-$num_criteria"]) {
$num_criteria--;
}
$form['pub_import_id'] = array(
'#type' => 'hidden',
'#value' => $pub_import_id,
'#required' => TRUE,
);
$form['action'] = array(
'#type' => 'hidden',
'#value' => $action,
'#required' => TRUE,
);
$form['loader_name'] = array(
'#type' => 'textfield',
'#title' => t('Loader Name'),
'#description' => t('Please provide a name for this loader setup..'),
'#default_value' => $loader_name,
'#required' => TRUE,
);
$remote_dbs = array('PMID' => 'Pubmed');
$form['remote_db'] = array(
'#title' => t('Remote Database'),
'#type' => 'select',
'#options' => $remote_dbs,
'#default_value' => $remote_db,
);
$form['num_criteria']= array(
'#type' => 'hidden',
'#default_value' => $num_criteria,
);
$form['pub_import_id']= array(
'#type' => 'hidden',
'#default_value' => $pub_import_id,
);
$form['days'] = array(
'#type' => 'textfield',
'#title' => t('Days'),
'#description' => t('The number of days from today to search.'),
'#default_value' => $days,
'#size' => 5,
);
$form['disabled'] = array(
'#type' => 'checkbox',
'#title' => t('Disabled'),
'#description' => t('Check to disable this importer.'),
'#default_value' => $disabled,
);
$form['do_contact'] = array(
'#type' => 'checkbox',
'#title' => t('Create Contact'),
'#description' => t('Check to create an entry in the contact table for each author of a matching publication during import. This allows storage of
additional information such as affilation, etc. Otherwise, only authors names are retrieved.'),
'#default_value' => $do_contact,
);
for($i = 0; $i <= $num_criteria; $i++) {
// if we have criteria supplied from the database then use that, othrewise look from the form_state or the session
if ($criteria) {
$search_terms = $criteria['criteria'][$i]['search_terms'];
$scope = $criteria['criteria'][$i]['scope'];
$operation = $criteria['criteria'][$i]['operation'];
}
// first populate defaults using any values in the SESSION variable
$search_terms = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] : $search_terms;
$scope = $_SESSION['tripal_pub_search']['criteria'][$i]['scope'] ? $_SESSION['tripal_pub_search']['criteria'][$i]['scope'] : $scope;
$operation = $_SESSION['tripal_pub_search']['criteria'][$i]['operation'] ? $_SESSION['tripal_pub_search']['criteria'][$i]['operation'] : $operation;
// next populate defaults using any form values
$search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $search_terms;
$scope = $form_state['values']["scope-$i"] ? $form_state['values']["scope-$i"] : $scope;
$operation = $form_state['values']["operation-$i"] ? $form_state['values']["operation-$i"] : $operation;
// default to searching the title and abstract
if (!$scope) {
$scope = 'abstract';
}
$form['criteria'][$i]["search_terms-$i"] = array(
'#type' => 'textfield',
'#description' => t('Please provide a list of words for searching. You may use conjunctions such as "AND" or "OR" to separate words if they are expected in the same scope"'),
'#default_value' => $search_terms,
'#required' => TRUE,
);
$form['criteria'][$i]["scope-$i"] = array(
'#type' => 'select',
'#description' => t('Please select the fields to search for this term.'),
'#options' => array(
'any' => 'Any Field',
'title' => 'Title',
'abstract' => 'Title/Abstract',
'author' => 'Author'),
'#default_value' => $scope,
);
if ($i > 0) {
$form['criteria'][$i]["operation-$i"] = array(
'#type' => 'select',
'#options' => array(
'AND' => 'AND',
'OR' => 'OR',
'NOT' => 'NOT'),
'#default_value' => $operation,
);
}
if ($i == $num_criteria) {
if($i > 0) {
$form['criteria'][$i]["remove-$i"] = array(
'#type' => 'image_button',
'#value' => t('Remove'),
'#src' => drupal_get_path('theme', 'tripal') . '/images/minus.png',
'#ahah' => array(
'path' => "admin/tripal/tripal_pub/import/criteria/minus/$i",
'wrapper' => 'tripal-pub-importer-setup-form',
'event' => 'click',
'method' => 'replace',
),
'#attributes' => array('onClick' => 'return false;'),
);
}
$form['criteria'][$i]["add-$i"] = array(
'#type' => 'image_button',
'#value' => t('Add'),
'#src' => drupal_get_path('theme', 'tripal') . '/images/add.png',
'#ahah' => array(
'path' => "admin/tripal/tripal_pub/import/criteria/add/$i",
'wrapper' => 'tripal-pub-importer-setup-form',
'event' => 'click',
'method' => 'replace',
),
'#attributes' => array('onClick' => 'return false;'),
);
}
}
$form['test'] = array(
'#type' => 'submit',
'#value' => t('Test Importer'),
);
$form['save'] = array(
'#type' => 'submit',
'#value' => t('Save Importer'),
);
$form['delete'] = array(
'#type' => 'submit',
'#value' => t('Delete Importer'),
);
return $form;
}
/**
*
*/
function tripal_pub_importer_setup_form_validate($form, &$form_state) {
$num_criteria = $form_state['values']['num_criteria'];
$remote_db = $form_state['values']["remote_db"];
$days = trim($form_state['values']["days"]);
$disabled = $form_state['values']["disabled"];
$do_contact = $form_state['values']["do_contact"];
$loader_name = trim($form_state['values']["loader_name"]);
for ($i = 0; $i <= $num_criteria; $i++) {
$search_terms = trim($form_state['values']["search_terms-$i"]);
$scope = $form_state['values']["scope-$i"];
$operation = $form_state['values']["operation-$i"];
if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
form_set_error("days-$i", "Please enter a numeric, non decimal value, for the number of days.");
}
}
}
/**
*
*/
function tripal_pub_importer_setup_form_submit($form, &$form_state) {
$pub_import_id = $form_state['values']['pub_import_id'];
$num_criteria = $form_state['values']['num_criteria'];
$remote_db = $form_state['values']["remote_db"];
$days = trim($form_state['values']["days"]);
$loader_name = trim($form_state['values']["loader_name"]);
$disabled = $form_state['values']["disabled"];
$do_contact = $form_state['values']["do_contact"];
// set the session variables
$_SESSION['tripal_pub_search']['remote_db'] = $remote_db;
$_SESSION['tripal_pub_search']['days'] = $days;
$_SESSION['tripal_pub_search']['num_criteria'] = $num_criteria;
$_SESSION['tripal_pub_search']['loader_name'] = $loader_name;
$_SESSION['tripal_pub_search']['disabled'] = $disabled;
$_SESSION['tripal_pub_search']['do_contact'] = $do_contact;
unset($_SESSION['tripal_pub_search']['criteria']);
for ($i = 0; $i <= $num_criteria; $i++) {
$search_terms = trim($form_state['values']["search_terms-$i"]);
$scope = $form_state['values']["scope-$i"];
$operation = $form_state['values']["operation-$i"];
$_SESSION['tripal_pub_search']['criteria'][$i] = array(
'search_terms' => $search_terms,
'scope' => $scope,
'operation' => $operation
);
}
// now perform the appropriate action for the button clicked
if ($form_state['values']['op'] == 'Test Importer') {
$_SESSION['tripal_pub_search']['perform_search'] = 1;
}
if ($form_state['values']['op'] == 'Save Importer') {
$record = array(
'name' => $loader_name,
'criteria' => serialize($_SESSION['tripal_pub_search']),
'disabled' => $disabled,
'do_contact' => $do_contact
);
// first check to see if this pub_import_id is already present. If so,
// do an update rather than an insert
$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
$importer = db_fetch_object(db_query($sql, $pub_import_id));
if($importer) {
// do the update
$record['pub_import_id'] = $pub_import_id;
if(drupal_write_record('tripal_pub_import', $record, 'pub_import_id')){
unset($_SESSION['tripal_pub_search']);
drupal_set_message('Publication import settings updated.');
drupal_goto('admin/tripal/tripal_pub/import_list');
}
else {
drupal_set_message('Could not update publication import settings.', 'error');
}
}
else {
// do the insert
if(drupal_write_record('tripal_pub_import', $record)){
unset($_SESSION['tripal_pub_search']);
drupal_set_message('Publication import settings saved.');
drupal_goto('admin/tripal/tripal_pub/import_list');
}
else {
drupal_set_message('Could not save publication import settings.', 'error');
}
}
}
if ($form_state['values']['op'] == 'Delete Importer') {
$sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
$success = db_query($sql, $pub_import_id);
if ($success) {
drupal_set_message('Publication importer deleted.');
drupal_goto('admin/tripal/tripal_pub/import_list');
}
else {
drupal_set_message('Could not delete publication importer.', 'error');
}
}
}
/*
*
*/
function tripal_pub_importer_delete($pub_import_id) {
$sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
$success = db_query($sql, $pub_import_id);
if ($success) {
drupal_set_message('Publication importer deleted.');
drupal_goto('admin/tripal/tripal_pub/import_list');
}
else {
drupal_set_message('Could not delete publication importer.', 'error');
}
}
/*
* AHAH callback
*/
function tripal_pub_importer_setup_page_update_criteria($action, $i) {
$status = TRUE;
// prepare and render the form
$form = tripal_core_ahah_prepare_form();
$data = theme('tripal_pub_importer_setup_form', $form);
// bind javascript events to the new objects that will be returned
// so that AHAH enabled elements will work.
$settings = tripal_core_ahah_bind_events();
// return the updated JSON
drupal_json(
array(
'status' => $status,
'data' => $data,
'settings' => $settings,
)
);
}