fetchObject()) {
$criteria = unserialize($importer->criteria);
$num_criteria = $criteria['num_criteria'];
$criteria_str = '';
for ($i = 1; $i <= $num_criteria; $i++) {
$search_terms = $criteria['criteria'][$i]['search_terms'];
$scope = $criteria['criteria'][$i]['scope'];
$is_phrase = $criteria['criteria'][$i]['is_phrase'];
$operation = $criteria['criteria'][$i]['operation'];
$criteria_str .= "$operation ($scope: $search_terms) ";
}
$rows[] = array(
l(t('Edit/Test'), "admin/tripal/chado/tripal_pub/import/edit/$importer->pub_import_id"),
$importer->name,
$criteria['remote_db'],
$criteria_str,
$importer->disabled ? 'Yes' : 'No',
$importer->do_contact ? 'Yes' : 'No',
l(t('Delete'), "admin/tripal/chado/tripal_pub/import/delete/$importer->pub_import_id"),
);
}
$rows[] = array(
'data' => array(
array('data' => l(t('Create a new publication importer.'), "admin/tripal/chado/tripal_pub/import/new"),
'colspan' => 7),
)
);
$page = "";
$page .= ' - ' . l('New Importer', 'admin/tripal/chado/tripal_pub/import/new') . '
';
$page .= '
';
$page .= theme('table', array('header' => $header, 'rows' => $rows));
return $page;
}
/*
*
*/
function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL) {
global $pager_total, $pager_total_items;
$pager_id = 0;
$limit = 20;
// make sure the tripal_pub and tripal_contact ontologies are loaded
$values = array('name' => 'tripal_pub');
$tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
if (count($tpub_cv) == 0) {
drupal_set_message(t('Before importing publications you must first ') . l(t('load the Tripal Pub Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
}
$values = array('name' => 'tripal_contact');
$tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
if (count($tpub_cv) == 0) {
drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
}
// 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/chado/tripal_pub/import_list");
$output .= drupal_render($form);
/*
// retrieve any results
$remote_db = $_SESSION['tripal_pub_import']['remote_db'];
$num_criteria = $_SESSION['tripal_pub_import']['num_criteria'];
$days = $_SESSION['tripal_pub_import']['days'];
$search_array = array();
$search_array['remote_db'] = $remote_db;
$search_array['num_criteria'] = $num_criteria;
$search_array['days'] = $days;
for ($i = 1; $i <= $num_criteria; $i++) {
$search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_import']['criteria'][$i]['search_terms'];
$search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_import']['criteria'][$i]['scope'];
$search_array['criteria'][$i]['is_phrase'] = $_SESSION['tripal_pub_import']['criteria'][$i]['is_phrase'];
$search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_import']['criteria'][$i]['operation'];
}
if ($_SESSION['tripal_pub_import']['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, $pager_id);
//dpm($pubs);
// 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) {
$citation = htmlspecialchars($pub['Citation']);
$raw_link = '';
if($pub['Publication Dbxref']) {
$raw_link = l('raw', 'admin/tripal/chado/tripal_pub/import/raw/' . $pub['Publication Dbxref'], array('attributes' => array('target' => '_blank')));
}
$rows[] = array(
number_format($i),
$citation,
$raw_link,
);
$i++;
}
}
$headers = array('', 'Publication', '');
$table = theme('table', array('header' => $headers, 'rows' => $rows));
// join all to form the results
$output .= "
Found " . number_format($total_items) .
". Page " . ($page + 1) . " of $total_pages. " .
" Results" . $table . '
' . $pager;
}
*/
return $output;
}
/**
* Purpose: Provides the form to search pubmed
*
* @ingroup tripal_pub
*/
function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_id = NULL, $action = 'new') {
// Default values can come in the following ways:
//
// 1) as elements of the $pub_importer object. This occurs when editing an existing importer
// 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
// 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;
$remote_db = '';
$days = '';
$disabled = '';
$do_contact = '';
$num_criteria = '';
$loader_name = '';
// if this is an edit the we are pulling an import object from the database
if ($action == "edit") {
$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :pub_import_id";
$importer = db_query($sql, array(':pub_import_id' => $pub_import_id))->fetchObject();
$criteria = unserialize($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 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)) {
$remote_db = $form_state['values']['remote_db'];
$days = $form_state['values']['days'];
$disabled = $form_state['values']['disabled'];
$do_contact = $form_state['values']['do_contact'];
$num_criteria = $form_state['values']['num_criteria'];
$loader_name = $form_state['values']['loader_name'];
}
// 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'])) {
$remote_db = $form_state['input']['remote_db'];
$days = $form_state['input']['days'];
$disabled = $form_state['input']['disabled'];
$do_contact = $form_state['input']['do_contact'];
$num_criteria = $form_state['input']['num_criteria'];
$loader_name = $form_state['input']['loader_name'];
}
// check if the pub_import_id in the session variable is not the same as the one we've been provided
// if so, then clear the session variable
// if ($pub_import_id and $pub_import_id != $_SESSION['tripal_pub_import']['pub_import_id']) {
// unset($_SESSION['tripal_pub_import']);
// }
// change the number of criteria based on form_state post data.
if (!$num_criteria) {
$num_criteria = 1;
}
/*
if($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,
);
$supported_dbs = variable_get('tripal_pub_supported_dbs', array());
$remote_dbs = array();
$values = array(
'name' => $supported_dbs,
);
$dbs = tripal_core_chado_select('db', array('*'), $values);
foreach ($dbs as $index => $db) {
$remote_dbs[$db->name] = $db->description;
};
// use PubMed as the default
if (!$remote_db) {
$remote_db = 'PMID';
}
$form['#prefix'] = '';
$form['#suffix'] = '
';
$form['remote_db'] = array(
'#title' => t('Remote Database'),
'#type' => 'select',
'#options' => $remote_dbs,
'#default_value' => $remote_db,
'#ajax' => array(
'callback' => "tripal_pubs_setup_form_ajax_update",
'wrapper' => 'tripal-pubs-importer-setup',
'effect' => 'fade',
'method' => 'replace',
),
);
$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 since record modified'),
'#description' => t('Limit the search to include pubs that have been added no more than this many days before today.'),
'#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' => $do_contact,
);
// add in the form for the criteria
tripal_pub_importer_setup_add_criteria_fields($form, $form_state, $num_criteria, $criteria);
$form['test'] = array(
'#type' => 'submit',
'#value' => t('Test Importer'),
);
$form['save'] = array(
'#type' => 'submit',
'#value' => t('Save Importer'),
);
/*
$form['import'] = array(
'#type' => 'submit',
'#value' => t('Save & Import Now'),
);
*/
$form['delete'] = array(
'#type' => 'submit',
'#value' => t('Delete Importer'),
);
// allow the selected remote database to make changes to the form if needed
$callback = "tripal_pub_remote_alter_form_$remote_db";
$form = call_user_func($callback, $form, $form_state);
$form['#theme'] = 'tripal_pub_importer_setup_form';
return $form;
}
/**
*
* @param $form
* @param $form_state
* @param $num_criteria
* @param $criteria
*/
function tripal_pub_importer_setup_add_criteria_fields(&$form, &$form_state, $num_criteria, $criteria){
// choices array
$scope_choices = array(
'any' => 'Any Field',
'abstract' => 'Abstract',
'author' => 'Author',
'id' => 'Accession',
'title' => 'Title',
'journal' => 'Journal Name'
);
$first_op_choices = array(
'' => '',
'NOT' => 'NOT'
);
$op_choices = array(
'AND' => 'AND',
'OR' => 'OR',
'NOT' => 'NOT'
);
for($i = 1; $i <= $num_criteria; $i++) {
$is_phrase = 1;
$search_terms = '';
$scope = '';
$is_phrase = '';
$operation = '';
// if we have criteria supplied from the database then use that as the initial defaults
if ($criteria) {
$search_terms = $criteria['criteria'][$i]['search_terms'];
$scope = $criteria['criteria'][$i]['scope'];
$is_phrase = $criteria['criteria'][$i]['is_phrase'];
$operation = $criteria['criteria'][$i]['operation'];
}
/*
// if we're here because the form was posted then load from the session variable (we lost the form state)
$search_terms = isset($_SESSION['tripal_pub_import']['criteria'][$i]['search_terms']) ? $_SESSION['tripal_pub_import']['criteria'][$i]['search_terms'] : $search_terms;
$scope = isset($_SESSION['tripal_pub_import']['criteria'][$i]['scope']) ? $_SESSION['tripal_pub_import']['criteria'][$i]['scope'] : $scope;
$is_phrase = isset($_SESSION['tripal_pub_import']['criteria'][$i]['is_phrase']) ? $_SESSION['tripal_pub_import']['criteria'][$i]['is_phrase'] : $is_phrase;
$operation = isset($_SESSION['tripal_pub_import']['criteria'][$i]['operation']) ? $_SESSION['tripal_pub_import']['criteria'][$i]['operation'] : $operation;
*/
// 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
if (array_key_exists('values', $form_state)) {
$search_terms = $form_state['values']["search_terms-$i"];
$scope = $form_state['values']["scope-$i"];
$is_phrase = $form_state['values']["is_phrase-$i"];
$operation = $form_state['values']["operation-$i"];
}
$form['criteria'][$i]["scope-$i"] = array(
'#type' => 'select',
'#description' => t('Please select the fields to search for this term.'),
'#options' => $scope_choices,
'#default_value' => $scope,
);
$form['criteria'][$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, but do not mix ANDs and ORs. Uncheck the "Is Phrase" checkbox to use conjunctions'),
'#default_value' => $search_terms,
'#required' => TRUE,
'#maxlength' => 2048,
);
$form['criteria'][$i]["is_phrase-$i"] = array(
'#type' => 'checkbox',
'#title' => t('Is Phrase?'),
'#default_value' => $is_phrase,
);
if ($i == 1) {
/*
$form['criteria'][$i]["operation-$i"] = array(
'#type' => 'select',
'#options' => $first_op_choices,
'#default_value' => $operation,
);*/
}
if ($i > 1) {
$form['criteria'][$i]["operation-$i"] = array(
'#type' => 'select',
'#options' => $op_choices,
'#default_value' => $operation,
);
}
if ($i == $num_criteria) {
if($i > 1) {
$form['criteria'][$i]["remove-$i"] = array(
'#type' => 'button',
'#name' => 'remove',
'#value' => t('Remove'),
'#ajax' => array(
'callback' => "tripal_pubs_setup_form_ajax_update",
'wrapper' => 'tripal-pubs-importer-setup',
'effect' => 'fade',
'method' => 'replace',
'prevent' => 'click'
),
// When this button is clicked, the form will be validated and submitted.
// Therefore, we set custom submit and validate functions to override the
// default form submit. In the validate function we set the form_state
// to rebuild the form so the submit function never actually gets called,
// but we need it or Drupal will run the default validate anyway.
// we also set #limit_validation_errors to empty so fields that
// are required that don't have values won't generate warnings.
'#submit' => array('tripal_pub_setup_form_criteria_button_submit'),
'#validate' => array('tripal_pub_setup_form_criteria_button_validate'),
'#limit_validation_errors' => array(),
);
}
$form['criteria'][$i]["add-$i"] = array(
'#type' => 'button',
'#name' => 'add',
'#value' => t('Add'),
'#ajax' => array(
'callback' => "tripal_pubs_setup_form_ajax_update",
'wrapper' => 'tripal-pubs-importer-setup',
'effect' => 'fade',
'method' => 'replace',
'prevent' => 'click'
),
// When this button is clicked, the form will be validated and submitted.
// Therefore, we set custom submit and validate functions to override the
// default form submit. In the validate function we set the form_state
// to rebuild the form so the submit function never actually gets called,
// but we need it or Drupal will run the default validate anyway.
// we also set #limit_validation_errors to empty so fields that
// are required that don't have values won't generate warnings.
'#submit' => array('tripal_pub_setup_form_criteria_button_submit'),
'#validate' => array('tripal_pub_setup_form_criteria_button_validate'),
'#limit_validation_errors' => array(),
);
}
}
}
/**
* This function is used to rebuild the form if an ajax call is made vai a button.
* The button causes the form to be submitted. We don't want this so we override
* the validate and submit routines on the form button. Therefore, this function
* only needs to tell Drupal to rebuild the form
*/
function tripal_pub_setup_form_criteria_button_validate($form, &$form_state){
$form_state['rebuild'] = TRUE;
}
/**
* This function is just a dummy to override the default form submit on ajax calls for buttons
*/
function tripal_pub_setup_form_criteria_button_submit($form, &$form_state){
// do nothing
}
/**
*
*/
function tripal_pub_importer_setup_form_validate($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 = 1; $i <= $num_criteria; $i++) {
$search_terms = trim($form_state['values']["search_terms-$i"]);
$scope = $form_state['values']["scope-$i"];
$is_phrase = $form_state['values']["is_phrase-$i"];
$operation = $form_state['values']["operation-$i"];
if (!$is_phrase) {
if (preg_match('/and/i', $search_terms) and preg_match('/or/i', $search_terms)) {
form_set_error("search_terms-$i", "You may use 'AND' or 'OR' but cannot use both. Add a new entry below with the same scope for the other conunction.");
$_SESSION['tripal_pub_import']['perform_search'] = 0;
}
}
}
if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
form_set_error("days", "Please enter a numeric, non decimal value, for the number of days.");
$_SESSION['tripal_pub_import']['perform_search'] = 0;
}
// allow the selected remote database to validate any changes to the form if needed
$callback = "tripal_pub_remote_validate_form_$remote_db";
$form = call_user_func($callback, $form, $form_state);
}
/**
*
*/
function tripal_pub_importer_setup_form_submit($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_import']['remote_db'] = $remote_db;
$_SESSION['tripal_pub_import']['days'] = $days;
$_SESSION['tripal_pub_import']['num_criteria'] = $num_criteria;
$_SESSION['tripal_pub_import']['loader_name'] = $loader_name;
$_SESSION['tripal_pub_import']['disabled'] = $disabled;
$_SESSION['tripal_pub_import']['do_contact'] = $do_contact;
$_SESSION['tripal_pub_import']['pub_import_id'] = $pub_import_id;
unset($_SESSION['tripal_pub_import']['criteria']);
for ($i = 1; $i <= $num_criteria; $i++) {
$search_terms = trim($form_state['values']["search_terms-$i"]);
$scope = $form_state['values']["scope-$i"];
$is_phrase = $form_state['values']["is_phrase-$i"];
$operation = $form_state['values']["operation-$i"];
$_SESSION['tripal_pub_import']['criteria'][$i] = array(
'search_terms' => $search_terms,
'scope' => $scope,
'is_phrase' => $is_phrase,
'operation' => $operation
);
}
// now perform the appropriate action for the button clicked
if ($form_state['values']['op'] == 'Test Importer') {
$_SESSION['tripal_pub_import']['perform_search'] = 1;
}
if ($form_state['values']['op'] == 'Save Importer' or
$form_state['values']['op'] == 'Save & Import Now') {
$record = array(
'name' => $loader_name,
'criteria' => serialize($_SESSION['tripal_pub_import']),
'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 = :pub_import_id";
$importer = db_query($sql, array(':pub_import_id' => $pub_import_id))->fetchObject();
if($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_import']);
drupal_set_message('Publication import settings updated.');
drupal_goto('admin/tripal/chado/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_import']);
drupal_set_message('Publication import settings saved.');
// if the user wants to do the import now then do it (may time out
// for long jobs)
if ($form_state['values']['op'] == 'Save & Import Now') {
tripal_pub_import_publications($record['pub_import_id']);
}
drupal_goto('admin/tripal/chado/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 = :pub_import_id";
$success = db_query($sql, array(':pub_import_id' => $pub_import_id));
if ($success) {
drupal_set_message('Publication importer deleted.');
drupal_goto('admin/tripal/chado/tripal_pub/import_list');
}
else {
drupal_set_message('Could not delete publication importer.', 'error');
}
}
}
/**
* AJAX callback for updating the form. Because we are replacing
* the entire form we just need to return it
*/
function tripal_pubs_setup_form_ajax_update($form, $form_state) {
dpm('Hi');
return $form;
}
/*
*
*/
function tripal_pub_importer_delete($pub_import_id) {
$sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = :pub_import_id";
$success = db_query($sql, array(':pub_import_id' => $pub_import_id));
if ($success) {
drupal_set_message('Publication importer deleted.');
drupal_goto('admin/tripal/chado/tripal_pub/import_list');
}
else {
drupal_set_message('Could not delete publication importer.', 'error');
}
}
/*
* AHAH callback
*/
function tripal_pub_importer_setup_page_update_remotedb() {
$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' => $settings,
)
);
}
/*
* AHAH callback
*/
function tripal_pub_importer_setup_page_update_criteria($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,
)
);
}
/**
*
* @param $form
*/
function theme_tripal_pub_importer_setup_form($variables) {
$form = $variables['form'];
$rows = array();
foreach ($form['criteria'] as $i => $element) {
if(is_numeric($i)) {
$rows[] = array(
drupal_render($element["operation-$i"]),
drupal_render($element["scope-$i"]),
drupal_render($element["search_terms-$i"]),
drupal_render($element["is_phrase-$i"]),
drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]),
);
}
}
// now build the table containing the criteria elements
$headers = array('Operation','Scope', 'Search Terms', '','');
$table = array(
'header' => $headers,
'rows' => $rows,
'attributes' => array(),
'sticky' => TRUE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
$criteria_table = theme_table($table);
$markup = '';
$markup .= '' . drupal_render($form['remote_db']) . '
';
$markup .= '';
$markup .= '' . drupal_render($form['disabled']) . '
';
$markup .= '' . drupal_render($form['do_contact']) . '
';
$markup .= $criteria_table;
$markup .= drupal_render($form['test']);
$markup .= drupal_render($form['save']);
$markup .= drupal_render($form['delete']);
return $markup;
}