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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Go to the source code of this file.
Functions | |
| tripal_project_admin ($form_state=NULL) | |
| get_tripal_project_admin_form_cleanup_set (&$form) | |
| get_tripal_project_admin_form_sync_set (&$form) | |
| tripal_project_admin_validate ($form, &$form_state) | |
| tripal_project_sync_projects ($project_id=NULL, $job_id=NULL) | |
| tripal_project_sync_projects_form_submit ($form, &$form_state) | |
| tripal_project_sync_all_projects () | |
| tripal_project_cleanup ($dummy=NULL, $job_id=NULL) | |
Definition in file tripal_project.admin.inc.
| get_tripal_project_admin_form_cleanup_set | ( | &$ | form | ) |
Definition at line 42 of file tripal_project.admin.inc.
{
$form['cleanup'] = array(
'#type' => 'fieldset',
'#title' => t('Clean Up')
);
$form['cleanup']['description'] = array(
'#type' => 'item',
'#value' => t("With Drupal and chado residing in different databases ".
"it is possible that nodes in Drupal and projects in Chado become ".
"\"orphaned\". This can occur if an project node in Drupal is ".
"deleted but the corresponding chado project is not and/or vice ".
"versa. Click the button below to resolve these discrepancies."),
'#weight' => 1,
);
$form['cleanup']['button'] = array(
'#type' => 'submit',
'#value' => t('Clean up orphaned projects'),
'#weight' => 2,
);
}
| get_tripal_project_admin_form_sync_set | ( | &$ | form | ) |
Definition at line 66 of file tripal_project.admin.inc.
{
// define the fieldsets
$form['sync'] = array(
'#type' => 'fieldset',
'#title' => t('Sync Projects')
);
// before proceeding check to see if we have any
// currently processing jobs. If so, we don't want
// to give the opportunity to sync libraries
$active_jobs = FALSE;
if (tripal_get_module_active_jobs('tripal_project')) {
$active_jobs = TRUE;
}
if (!$active_jobs) {
// get the list of projects
$sql = "SELECT * FROM {project} ORDER BY name";
$org_rset = chado_query($sql);
// if we've added any projects to the list that can be synced
// then we want to build the form components to allow the user
// to select one or all of them. Otherwise, just present
// a message stating that all projects are currently synced.
$proj_boxes = array();
$added = 0;
while ($project = db_fetch_object($org_rset)) {
// check to see if the project is already present as a node in drupal.
// if so, then skip it.
$sql = "SELECT * FROM {chado_project} WHERE project_id = %d";
if (!db_fetch_object(db_query($sql, $project->project_id))) {
$proj_boxes[$project->project_id] = $project->name;
$added++;
}
}
// if we have projects we need to add to the checkbox then
// build that form element
if ($added > 0) {
$proj_boxes['all'] = "All Projects";
$form['sync']['projects'] = array(
'#title' => t('Available Projects'),
'#type' => t('checkboxes'),
'#description' => t("Check the projects you want to sync. Drupal content will be created for each of the projects listed above. Select 'All Projects' to sync all of them."),
'#required' => FALSE,
'#prefix' => '<div id="org_boxes">',
'#suffix' => '</div>',
'#options' => $proj_boxes,
);
$form['sync']['button'] = array(
'#type' => 'submit',
'#value' => t('Submit Sync Job')
);
}
// we don't have any projects to select from
else {
$form['sync']['value'] = array(
'#value' => t('All projects in Chado are currently synced with Drupal.')
);
}
}
// we don't want to present a form since we have an active job running
else {
$form['sync']['value'] = array(
'#value' => t('Currently, jobs exist related to chado projects. Please check back later for projects that can by synced once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.')
);
}
}
| tripal_project_admin | ( | $ | form_state = NULL | ) |
Definition at line 7 of file tripal_project.admin.inc.
{
$form = array();
// before proceeding check to see if we have any
// currently processing jobs. If so, we don't want
// to give the opportunity to sync libraries
$active_jobs = FALSE;
if (tripal_get_module_active_jobs('tripal_project')) {
$active_jobs = TRUE;
}
// add the field set for syncing libraries
if (!$active_jobs) {
get_tripal_project_admin_form_sync_set($form);
get_tripal_project_admin_form_cleanup_set($form);
// get_tripal_project_admin_form_reindex_set($form);
}
else {
$form['notice'] = array(
'#type' => 'fieldset',
'#title' => t('Project Management Temporarily Unavailable')
);
$form['notice']['message'] = array(
'#value' => t('Currently, project management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete. Please check back later once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.'),
);
}
return system_settings_form($form);
}
| tripal_project_admin_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 140 of file tripal_project.admin.inc.
{
global $user; // we need access to the user info
$job_args = array();
if ($form_state['values']['op'] == t('Submit Sync Job')) {
// check to see if the user wants to sync chado and drupal. If
// so then we need to register a job to do so with tripal
$projects = $form_state['values']['projects'];
$do_all = FALSE;
$to_sync = array();
foreach ($projects as $project_id) {
if (preg_match("/^all$/i" , $project_id)) {
$do_all = TRUE;
}
if ($project_id and preg_match("/^\d+$/i" , $project_id)) {
// get the list of projects
$sql = "SELECT * FROM {Project} WHERE project_id = %d";
$project = db_fetch_object(chado_query($sql, $project_id));
$to_sync[$project_id] = "$project->genus $project->species";
}
}
// submit the job the tripal job manager
if ($do_all) {
tripal_add_job('Sync all projects' , 'tripal_project',
'tripal_project_sync_projects' , $job_args , $user->uid);
}
else{
foreach ($to_sync as $project_id => $name) {
$job_args[0] = $project_id;
tripal_add_job("Sync project: $name" , 'tripal_project',
'tripal_project_sync_projects' , $job_args , $user->uid);
}
}
}
// -------------------------------------
// Submit the Reindex Job if selected
if ($form_state['values']['op'] == t('Reindex Features')) {
$projects = $form_state['values']['re-projects'];
foreach ($projects as $project_id) {
if ($project_id and preg_match("/^\d+$/i" , $project_id)) {
// get the project info
$sql = "SELECT * FROM {project} WHERE project_id = %d";
$project = db_fetch_object(chado_query($sql , $project_id));
$job_args[0] = $project_id;
tripal_add_job("Reindex features for project: $project->genus ".
"$project->species", 'tripal_project' ,
'tripal_project_reindex_features', $job_args, $user->uid);
}
}
}
// -------------------------------------
// Submit the taxonomy Job if selected
if ($form_state['values']['op'] == t('Set Feature Taxonomy')) {
$projects = $form_state['values']['tx-projects'];
foreach ($projects as $project_id) {
if ($project_id and preg_match("/^\d+$/i", $project_id)) {
// get the project info
$sql = "SELECT * FROM {project} WHERE project_id = %d";
$project = db_fetch_object(chado_query($sql , $project_id));
$job_args[0] = $project_id;
tripal_add_job("Set taxonomy for features in project: ".
"$project->genus $project->species" , 'tripal_project',
'tripal_project_taxonify_features', $job_args, $user->uid);
}
}
}
// -------------------------------------
// Submit the Cleanup Job if selected
if ($form_state['values']['op'] == t('Clean up orphaned projects')) {
tripal_add_job('Cleanup orphaned projects', 'tripal_project',
'tripal_project_cleanup', $job_args, $user->uid);
}
}
| tripal_project_cleanup | ( | $ | dummy = NULL, |
| $ | job_id = NULL |
||
| ) |
Remove orphaned drupal nodes
| $dummy | Not Used -kept for backwards compatibility |
| $job_id | The id of the tripal job executing this function |
Definition at line 348 of file tripal_project.admin.inc.
{
return tripal_core_clean_orphaned_nodes('project', $job_id);
}| tripal_project_sync_all_projects | ( | ) |
Definition at line 288 of file tripal_project.admin.inc.
{
//retrieve all projects in drupal
$resource = db_query('SELECT project_id FROM {chado_project}');
$drupal_projects = array();
while ($r = db_fetch_object($resource)) {
$drupal_projects[$r->project_id] = $r->project_id;
}
// retrieve all projects in chado
$chado_projects = array();
$resource = chado_query('SELECT project_id FROM {project}');
while ($r = db_fetch_object($resource)) {
// if not already in drupal add to list to be sync'd
if (!isset($drupal_projects[$r->project_id])) {
$chado_projects[$r->project_id] = $r->project_id;
}
}
print 'Number of Projects to Sync: ' . sizeof($chado_projects) . "\n";
foreach ($chado_projects as $project_id) {
$project = tripal_core_chado_select('project', array('name', 'description'), array('project_id' => $project_id));
// create node
$new_node = new stdClass();
$new_node->type = 'chado_project';
$new_node->uid = $user->uid;
$new_node->title = $project[0]->name;
$new_node->project_id = $project_id;
$new_node->description = $project[0]->description;
node_validate($new_node);
$errors = form_get_errors();
if (!$errors) {
$node = node_submit($new_node);
node_save($node);
if ($node->nid) {
print "Added " . $project[0]->name . " (Node ID:" . $node->nid . ")\n";
}
}
else {
print "Failed to insert project: " . $project[0]->name . "\n";
print "Errors: " . print_r($errors, TRUE) . "\n";
}
}
}
| tripal_project_sync_projects | ( | $ | project_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Synchronize projects from chado to drupal
Definition at line 224 of file tripal_project.admin.inc.
{
global $user;
$page_content = '';
if (!$project_id) {
$sql = "SELECT * FROM {project} P";
$results = chado_query($sql);
}
else {
$sql = "SELECT * FROM {project} P WHERE project_id = %d";
$results = chado_query($sql, $project_id);
}
// We'll use the following SQL statement for checking if the project
// already exists as a drupal node.
$sql = "SELECT * FROM {chado_project} ".
"WHERE project_id = %d";
while ($project = db_fetch_object($results)) {
// check if this project already exists in the drupal database. if it
// does then skip this project and go to the next one.
if (!db_fetch_object(db_query($sql, $project->project_id))) {
$new_node = new stdClass();
$new_node->type = 'chado_project';
$new_node->uid = $user->uid;
$new_node->title = "$project->name";
$new_node->project_id = $project->project_id;
$new_node->name = $project->name;
$new_node->description = $project->description;
node_validate($new_node);
if (!form_get_errors()) {
$node = node_submit($new_node);
node_save($node);
if ($node->nid) {
print "Added $project->name\n";
}
}
else {
print "Failed to insert project $project->name\n";
}
}
else {
print "Skipped $project->name\n";
}
}
return $page_content;
}
| tripal_project_sync_projects_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 276 of file tripal_project.admin.inc.
{
global $user;
//sync'ing is done by a tripal_job that is added here
$job_id = tripal_add_job('Sync Projects', 'tripal_project',
'tripal_project_sync_all_projects', array(), $user->uid);
}
1.7.4