|
Tripal v1.0 (6.x-1.0)
|
|
Tripal v1.0 (6.x-1.0)
|
| chado_organism_access | ( | $ | op, |
| $ | node, | ||
| $ | account | ||
| ) |
The following function proves access control for users trying to perform actions on data managed by this module
Definition at line 160 of file tripal_organism.module.
{
if ($op == 'create') {
if (!user_access('create chado_organism content', $account)) {
return FALSE;
}
}
if ($op == 'update') {
if (!user_access('edit chado_organism content', $account)) {
return FALSE;
}
}
if ($op == 'delete') {
if (!user_access('delete chado_organism content', $account)) {
return FALSE;
}
}
if ($op == 'view') {
if (!user_access('access chado_organism content', $account)) {
return FALSE;
}
}
return NULL;
}
| chado_organism_add_image | ( | $ | node | ) |
Definition at line 403 of file tripal_organism.module.
{
// check to see if a file was uploaded. If so then copy it to the images
// directory for display with the organism
if (isset($_FILES['files']) && $_FILES['files']['name']['organism_image'] &&
is_uploaded_file($_FILES['files']['tmp_name']['organism_image'])) {
$dest = file_directory_path() . "/tripal/tripal_organism/images";
$validators = array(
'file_validate_is_image' => array(),
);
file_check_directory($dest, FILE_CREATE_DIRECTORY, 'organism_image');
if (!$file = file_save_upload('organism_image', $validators, $dest)) {
drupal_set_message(t("Organism image was not uploaded."));
}
// move this image into the images directory
file_move($file->filepath, $dest . "/" . $node->nid . ".jpg", FILE_EXISTS_REPLACE);
}
}
| chado_organism_delete | ( | $ | node | ) |
Delete organism from both drupal and chado databases. Check dependency before deleting from chado.
Definition at line 358 of file tripal_organism.module.
{
$organism_id = chado_get_id_for_node('organism', $node);
// if we don't have an organism id for this node then this isn't a node of
// type chado_organism or the entry in the chado_organism table was lost.
if (!$organism_id) {
return;
}
// Remove data from the {chado_organism}, {node}, and {node_revisions} tables
$sql_del = "DELETE FROM {chado_organism} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
$sql_del = "DELETE FROM {node} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
$sql_del = "DELETE FROM {node_revisions} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
// Test dependency before deleting from chado database. If a library or
// feature depends on this organism, don't delete it
$sql = "SELECT feature_id FROM {feature} WHERE organism_id = %d";
$check_feature = db_result(chado_query($sql, $organism_id));
$sql = "SELECT library_id FROM {library} WHERE organism_id = %d";
$check_lib = db_result(chado_query($sql, $organism_id));
if ($check_lib == 0 && $check_feature == 0) {
tripal_core_chado_delete('organism', array('organism_id' => $organism_id));
}
else {
drupal_set_message(t("Organism deleted from drupal. Warning: at least one ".
"library or feature depends on this organism. It was ".
"not removed from chado."));
}
}
| chado_organism_form | ( | $ | node, |
| $ | param | ||
| ) |
When editing or creating a new node of type 'chado_organism' we need a form. This function creates the form that will be used for this.
Definition at line 428 of file tripal_organism.module.
{
$organism = $node->organism;
// add in the comment since it is a text field and may not be included if too big
$organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
// get form defaults
$abbreviation = $node->abbreviation;
if (!$abbreviation) {
$abbreviation = $organism->abbreviation;
}
$genus = $node->genus;
if (!$genus) {
$genus = $organism->genus;
}
$species = $node->species;
if (!$species) {
$species = $organism->species;
}
$common_name = $node->common_name;
if (!$common_name) {
$common_name = $organism->common_name;
}
$description = $node->description;
if (!$description) {
$description = $organism->comment;
}
$organism_image = $node->organism_image;
$form = array();
$form['#attributes']['enctype'] = 'multipart/form-data';
// keep track of the organism id if we have one. If we do have one then
// this would indicate an update as opposed to an insert.
$form['organism_id'] = array(
'#type' => 'value',
'#value' => $organism->organism_id,
);
$form['abbreviation']= array(
'#type' => 'textfield',
'#title' => t('Abbreviation'),
'#required' => TRUE,
'#default_value' => $organism->abbreviation,
'#weight' => 3
);
$form['genus']= array(
'#type' => 'textfield',
'#title' => t('Genus'),
'#required' => TRUE,
'#default_value' => $organism->genus,
'#weight' => 1
);
$form['species']= array(
'#type' => 'textfield',
'#title' => t('Species'),
'#required' => TRUE,
'#default_value' => $organism->species,
'#weight' => 2
);
$form['common_name']= array(
'#type' => 'textfield',
'#title' => t('Common Name'),
'#required' => TRUE,
'#default_value' => $organism->common_name,
'#weight' => 4
);
$form['description']= array(
'#type' => 'textarea',
'#rows' => 15,
'#title' => t('Description'),
'#required' => TRUE,
'#default_value' => $organism->comment,
'#weight' => 5
);
$form['organism_image']= array(
'#type' => 'file',
'#title' => t('Organism Image'),
'#description' => 'Add an image for this organism',
'#weight' => 6
);
return $form;
}
| chado_organism_insert | ( | $ | node | ) |
When a new chado_organism node is created we also need to add information to our chado_organism table. This function is called on insert of a new node of type 'chado_organism' and inserts the necessary information.
Definition at line 271 of file tripal_organism.module.
{
$values = array(
'genus' => $node->genus,
'species' => $node->species,
'abbreviation' => $node->abbreviation,
'common_name' => $node->common_name,
'comment' => $node->description
);
// if there is an organism_id in the $node object then this must be a sync so
// we can skip adding the organism as it is already there, although
// we do need to proceed with the rest of the insert
if (!$node->organism_id) {
$organism = tripal_core_chado_insert('organism', $values);
if (!$organism) {
drupal_set_message(t('Unable to add organism.', 'warning'));
watchdog('tripal_organism',
'Insert Organism: Unable to create organism where values:%values',
array('%values' => print_r($values, TRUE)),
WATCHDOG_WARNING
);
return;
}
$organism_id = $organism['organism_id'];
}
else {
$organism_id = $node->organism_id;
}
// Make sure the entry for this organism doesn't already exist in the
// chado_organism table if it doesn't exist then we want to add it.
if (!chado_get_id_for_node('organism', $node) ) {
// next add the item to the drupal table
$sql = "INSERT INTO {chado_organism} (nid, vid, organism_id) ".
"VALUES (%d, %d, %d)";
chado_query($sql, $node->nid, $node->vid, $organism_id);
}
// set the title for the node
$record = new stdClass();
$record->title = "$node->genus $node->species";
$record->nid = $node->nid;
drupal_write_record('node', $record, 'nid');
drupal_write_record('node_revisions', $record, 'nid');
// add the image
chado_organism_add_image($node);
}
| chado_organism_load | ( | $ | node | ) |
When a node is requested by the user this function is called to allow us to add auxiliary data to the node object.
Definition at line 519 of file tripal_organism.module.
{
// find the organism and add in the details
$organism_id = chado_get_id_for_node('organism', $node);
$values = array('organism_id' => $organism_id);
$organism = tripal_core_generate_chado_var('organism', $values);
// add in the description field
$organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
$additions = new stdClass();
$additions->organism = $organism;
return $additions;
}
| chado_organism_update | ( | $ | node | ) |
Update organisms
Definition at line 325 of file tripal_organism.module.
{
if ($node->revision) {
// there is no way to handle revisions in Chado but leave
// this here just to make not we've addressed it.
}
$match = array(
'organism_id' => chado_get_id_for_node('organism', $node),
);
$values = array(
'genus' => $node->genus,
'species' => $node->species,
'abbreviation' => $node->abbreviation,
'common_name' => $node->common_name,
'comment' => $node->description
);
$org_status = tripal_core_chado_update('organism', $match, $values);
// set the title for the node
$record = new stdClass();
$record->title = "$node->genus $node->species";
$record->nid = $node->nid;
drupal_write_record('node', $record, 'nid');
drupal_write_record('node_revisions', $record, 'nid');
// add the image
chado_organism_add_image($node);
}
| chado_organism_validate | ( | $ | node, |
| &$ | form | ||
| ) |
Definition at line 230 of file tripal_organism.module.
{
// if this is an update, we want to make sure that a different organism doesn't
// already have this genus and speces
if ($node->organism_id) {
$sql = "SELECT *
FROM {organism} O
WHERE genus = '%s' and species = '%s' AND NOT organism_id = %d";
$result = db_fetch_object(chado_query($sql, $node->genus, $node->species, $node->organism_id));
if ($result) {
form_set_error('genus', t("Update cannot proceed. The organism genus
'$node->genus' and species '$node->species' is already present in the database."));
watchdog('tripal_organism',
'Update organism: genus and species already exists: %values',
array('%values' => "genus = $node->genus, species = $node->species"),
WATCHDOG_WARNING);
}
}
// if this is an insert then check to make sure the genus and species are unique
else {
$values = array(
'genus' => $node->genus,
'species' => $node->species,
);
$organism = tripal_core_chado_select('organism', array('organism_id'), $values);
if (sizeof($organism) > 0) {
form_set_error('genus', 'Cannot add the organism with this genus and species.
The organism already exists.');
watchdog('tripal_organism',
'Insert organism: genus and species already exists: %values',
array('%values' => "genus = $node->genus, species = $node->species"),
WATCHDOG_WARNING);
}
}
}
| chado_organism_view | ( | $ | node, |
| $ | teaser = FALSE, |
||
| $ | page = FALSE |
||
| ) |
This function customizes the view of the chado_organism node. It allows us to generate the markup.
Definition at line 540 of file tripal_organism.module.
{
// use drupal's default node view:
$node = node_prepare($node, $teaser);
return $node;
}
| get_chado_organisms | ( | ) |
This function uses organism_id's of all drupal organism nodes as input and pull the organism information (genus, species, common_name, comment) from chado database. The return type is an object array that stores $organism objects sorted by common_name
Definition at line 577 of file tripal_organism.module.
{
$sql_drupal = "SELECT COUNT (organism_id) FROM {chado_organism}";
$no_orgs = db_result(db_query($sql_drupal));
if ($no_orgs != 0) {
$sql = "SELECT organism_id, nid FROM {chado_organism}";
$result = chado_query($sql);
$sql = "SELECT genus, species, common_name, comment ".
"FROM {Organism} ".
"WHERE organism_id=%d";
$organisms = array();
$count = 0;
while ($data = db_fetch_object($result)) {
$organism = db_fetch_object(chado_query($sql, $data->organism_id));
$organism->node_id = $data->nid;
// Use common_name plus $count as the key so we can sort by common
// name later. Since common_name is not unique, we need to add $count
// to the key
$key = drupal_strtolower($organism->common_name) . $count;
$organisms [$key] = $organism;
$count ++;
}
//Sort organisms by common name
ksort($organisms, SORT_STRING);
return $organisms;
}
}
| get_tripal_organism_admin_form_cleanup_set | ( | &$ | form | ) |
Definition at line 44 of file tripal_organism.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 organisms in Chado become ".
"\"orphaned\". This can occur if an organism node in Drupal is ".
"deleted but the corresponding chado organism is not and/or vice ".
"versa. Click the button below to resolve these discrepancies."),
'#weight' => 1,
);
$form['cleanup']['button'] = array(
'#type' => 'submit',
'#value' => t('Clean up orphaned organisms'),
'#weight' => 2,
);
}
| get_tripal_organism_admin_form_reindex_set | ( | &$ | form | ) |
Definition at line 113 of file tripal_organism.admin.inc.
{
// define the fieldsets
$form['reindex'] = array(
'#type' => 'fieldset',
'#title' => t('Reindex Organism Features')
);
// get the list of libraries
$sql = "SELECT * FROM {Organism} ORDER BY genus,species";
$org_rset = chado_query($sql);
// iterate through all of the libraries
$org_boxes = array();
while ($organism = db_fetch_object($org_rset)) {
$org_boxes[$organism->organism_id] = "$organism->genus $organism->species";
}
$form['reindex']['description'] = array(
'#type' => 'item',
'#value' => t("This option allows for reindexing of only those features that belong to the selected organisms below. All other features will be unaffected. To reindex all features in the site see the Feature Administration page."),
'#weight' => 1,
);
$form['reindex']['re-organisms'] = array(
'#title' => t('Organisms'),
'#type' => t('checkboxes'),
'#description' => t("Check the organisms whoee features you want to reindex. Note: this list contains all organisms, even those that may not be synced."),
'#required' => FALSE,
'#prefix' => '<div id="lib_boxes">',
'#suffix' => '</div>',
'#options' => $org_boxes,
'#weight' => 2,
);
$form['reindex']['re-button'] = array(
'#type' => 'submit',
'#value' => t('Reindex Features'),
'#weight' => 3,
);
}
| get_tripal_organism_admin_form_sync_set | ( | &$ | form | ) |
Definition at line 155 of file tripal_organism.admin.inc.
{
// define the fieldsets
$form['sync'] = array(
'#type' => 'fieldset',
'#title' => t('Sync Organisms')
);
// 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_organism')) {
$active_jobs = TRUE;
}
if (!$active_jobs) {
// get the list of organisms
$sql = "SELECT * FROM {Organism} ORDER BY genus,species";
$org_rset = chado_query($sql);
// if we've added any organisms 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 organisms are currently synced.
$org_boxes = array();
$added = 0;
while ($organism = db_fetch_object($org_rset)) {
// check to see if the organism is already present as a node in drupal.
// if so, then skip it.
$sql = "SELECT * FROM {chado_organism} WHERE organism_id = %d";
if (!db_fetch_object(db_query($sql, $organism->organism_id))) {
$org_boxes[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
$added++;
}
}
// if we have organisms we need to add to the checkbox then
// build that form element
if ($added > 0) {
$org_boxes['all'] = "All Organisms";
$form['sync']['organisms'] = array(
'#title' => t('Available Organisms'),
'#type' => t('checkboxes'),
'#description' => t("Check the organisms you want to sync. Drupal content will be created for each of the organisms listed above. Select 'All Organisms' to sync all of them."),
'#required' => FALSE,
'#prefix' => '<div id="org_boxes">',
'#suffix' => '</div>',
'#options' => $org_boxes,
);
$form['sync']['button'] = array(
'#type' => 'submit',
'#value' => t('Submit Sync Job')
);
}
// we don't have any organisms to select from
else {
$form['sync']['value'] = array(
'#value' => t('All organisms in Chado are currently synced with Drupal.')
);
}
}
// we don't want to present a form since we have an active job running
else {
$form['sync']['value'] = array(
'#value' => t('Currently, jobs exist related to chado organisms. Please check back later for organisms that can by synced once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.')
);
}
}
| get_tripal_organism_admin_form_taxonomy_set | ( | &$ | form | ) |
Definition at line 69 of file tripal_organism.admin.inc.
{
$form['taxonify'] = array(
'#type' => 'fieldset',
'#title' => t('Assign Drupal Taxonomy to Organism Features')
);
// get the list of libraries
$sql = "SELECT * FROM {Organism} ORDER BY genus,species";
$org_rset = chado_query($sql);
// iterate through all of the libraries
$org_boxes = array();
while ($organism = db_fetch_object($org_rset)) {
$org_boxes[$organism->organism_id] = "$organism->genus $organism->species";
}
$form['taxonify']['description'] = array(
'#type' => 'item',
'#value' => t("Drupal allows for assignment of \"taxonomy\" or catagorical terms to " .
"nodes. These terms allow for advanced filtering during searching. This option allows ".
"for setting taxonomy only for features that belong to the selected organisms below. All other features will be unaffected. To set taxonomy for all features in the site see the Feature Administration page."),
'#weight' => 1,
);
$form['taxonify']['tx-organisms'] = array(
'#title' => t('Organisms'),
'#type' => t('checkboxes'),
'#description' => t("Check the organisms whose features you want to reset taxonomy. Note: this list contains all organisms, even those that may not be synced."),
'#required' => FALSE,
'#prefix' => '<div id="lib_boxes">',
'#suffix' => '</div>',
'#options' => $org_boxes,
'#weight' => 2
);
$form['taxonify']['tx-button'] = array(
'#type' => 'submit',
'#value' => t('Set Feature Taxonomy'),
'#weight' => 3
);
}
| tripal_organism_admin | ( | ) |
Administrative settings for chado_orgnism
Definition at line 8 of file tripal_organism.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_organism')) {
$active_jobs = TRUE;
}
// add the field set for syncing libraries
if (!$active_jobs) {
get_tripal_organism_admin_form_sync_set($form);
get_tripal_organism_admin_form_reindex_set($form);
get_tripal_organism_admin_form_taxonomy_set($form);
get_tripal_organism_admin_form_cleanup_set($form);
}
else {
$form['notice'] = array(
'#type' => 'fieldset',
'#title' => t('Organism Management Temporarily Unavailable')
);
$form['notice']['message'] = array(
'#value' => t('Currently, organism management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete. Please check back later once these jobs have finished. You can view the status of pending jobs in the Tripal jobs page.'),
);
}
return system_settings_form($form);
}
| tripal_organism_admin_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 229 of file tripal_organism.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
$organisms = $form_state['values']['organisms'];
$do_all = FALSE;
$to_sync = array();
foreach ($organisms as $organism_id) {
if (preg_match("/^all$/i" , $organism_id)) {
$do_all = TRUE;
}
if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
// get the list of organisms
$sql = "SELECT * FROM {Organism} WHERE organism_id = %d";
$organism = db_fetch_object(chado_query($sql, $organism_id));
$to_sync[$organism_id] = "$organism->genus $organism->species";
}
}
// submit the job the tripal job manager
if ($do_all) {
tripal_add_job('Sync all organisms' , 'tripal_organism',
'tripal_organism_sync_organisms' , $job_args , $user->uid);
}
else{
foreach ($to_sync as $organism_id => $name) {
$job_args[0] = $organism_id;
tripal_add_job("Sync organism: $name" , 'tripal_organism',
'tripal_organism_sync_organisms' , $job_args , $user->uid);
}
}
}
// -------------------------------------
// Submit the Reindex Job if selected
if ($form_state['values']['op'] == t('Reindex Features')) {
$organisms = $form_state['values']['re-organisms'];
foreach ($organisms as $organism_id) {
if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
// get the organism info
$sql = "SELECT * FROM {organism} WHERE organism_id = %d";
$organism = db_fetch_object(chado_query($sql , $organism_id));
$job_args[0] = $organism_id;
tripal_add_job("Reindex features for organism: $organism->genus ".
"$organism->species", 'tripal_organism' ,
'tripal_organism_reindex_features', $job_args, $user->uid);
}
}
}
// -------------------------------------
// Submit the taxonomy Job if selected
if ($form_state['values']['op'] == t('Set Feature Taxonomy')) {
$organisms = $form_state['values']['tx-organisms'];
foreach ($organisms as $organism_id) {
if ($organism_id and preg_match("/^\d+$/i", $organism_id)) {
// get the organism info
$sql = "SELECT * FROM {organism} WHERE organism_id = %d";
$organism = db_fetch_object(chado_query($sql , $organism_id));
$job_args[0] = $organism_id;
tripal_add_job("Set taxonomy for features in organism: ".
"$organism->genus $organism->species" , 'tripal_organism',
'tripal_organism_taxonify_features', $job_args, $user->uid);
}
}
}
// -------------------------------------
// Submit the Cleanup Job if selected
if ($form_state['values']['op'] == t('Clean up orphaned organisms')) {
tripal_add_job('Cleanup orphaned organisms', 'tripal_organism',
'tripal_organism_cleanup', $job_args, $user->uid);
}
}
| tripal_organism_block | ( | $ | op = 'list', |
| $ | delta = '0', |
||
| $ | edit = array() |
||
| ) |
Display block with organisms
| op | - parameter to define the phase being called for the block |
| delta | - id of the block to return (ignored when op is list) |
| edit | - when op is save, contains the submitted form data |
Definition at line 51 of file tripal_organism.module.
{
switch ($op) {
case 'list':
$blocks['base']['info'] = t('Tripal Organism Details');
$blocks['base']['cache'] = BLOCK_NO_CACHE;
$blocks['description']['info'] = t('Tripal Organism Description');
$blocks['description']['cache'] = BLOCK_NO_CACHE;
$blocks['image']['info'] = t('Tripal Organism Image');
$blocks['image']['cache'] = BLOCK_NO_CACHE;
return $blocks;
case 'view':
if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
$nid = arg(1);
$node = node_load($nid);
$block = array();
switch ($delta) {
case 'base':
$block['subject'] = t('Organism Details');
$block['content'] = theme('tripal_organism_base', $node);
break;
case 'description':
$block['subject'] = t('Organism Description');
$block['content'] = theme('tripal_organism_description', $node);
break;
case 'image':
$block['subject'] = t('Organism Image');
$block['content'] = theme('tripal_organism_image', $node);
break;
default:
}
return $block;
}
}
}
| tripal_organism_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 454 of file tripal_organism.admin.inc.
{
return tripal_core_clean_orphaned_nodes('organism', $job_id);
}| tripal_organism_cron | ( | ) |
Definition at line 219 of file tripal_organism.module.
{
// we want to make sure that any new organisms or features that were
// added to the database external to drupal automatically get new
// nodes created for themselves in drupal.
// tripal_organism_sync_organisms();
}
| tripal_organism_help | ( | $ | path, |
| $ | arg | ||
| ) |
Display help and module information
| path | which path of the site we're displaying help |
| arg | array that holds the current path as would be returned from arg() function |
Definition at line 556 of file tripal_organism.module.
{
$output = '';
switch ($path) {
case "admin/help#tripal_organism":
$output = '<p>'.
t("Displays links to nodes created on this date") .
'</p>';
break;
}
return $output;
}
| tripal_organism_init | ( | ) |
Definition at line 16 of file tripal_organism.module.
{
// add the jGCharts JS and CSS
drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_organism.js');
drupal_add_css(drupal_get_path('theme', 'tripal') . '/css/tripal_organism.css');
}
| tripal_organism_job_describe_args | ( | $ | callback, |
| $ | args | ||
| ) |
Definition at line 624 of file tripal_organism.module.
{
$new_args = array();
if ($callback == 'tripal_organism_sync_organisms') {
$organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
$new_args['Organism'] = $organism[0]->genus ." ". $organism[0]->species;
}
return $new_args;
}
| tripal_organism_menu | ( | ) |
Menu items are automatically added for the new node types created by this module to the 'Create Content' Navigation menu item. This function adds more menu items needed for this module.
Definition at line 97 of file tripal_organism.module.
{
$items = array();
// the administative settings menu
$items['admin/tripal/tripal_organism'] = array(
'title' => 'Organisms',
'description' => 'Basic Description of Tripal Organism Module Functionality',
'page callback' => 'theme',
'page arguments' => array('tripal_organism_admin'),
'access arguments' => array('adminster tripal organism'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_organism/configuration'] = array(
'title' => 'Configuration',
'description' => 'Manage integration of Chado organisms including associated features',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_organism_admin'),
'access arguments' => array('adminster tripal organism'),
'type' => MENU_NORMAL_ITEM,
);
return $items;
}
| tripal_organism_node_info | ( | ) |
Provide information to drupal about the node types that we're creating in this module
Definition at line 28 of file tripal_organism.module.
{
$nodes = array();
$nodes['chado_organism'] = array(
'name' => t('Organism'),
'module' => 'chado_organism',
'description' => t('An organism from the chado database'),
'has_title' => FALSE,
'title_label' => t('Organism'),
'has_body' => FALSE,
'body_label' => t('Organism Description'),
'locked' => TRUE
);
return $nodes;
}
| tripal_organism_nodeapi | ( | &$ | node, |
| $ | op, | ||
| $ | teaser, | ||
| $ | page | ||
| ) |
Definition at line 206 of file tripal_organism.module.
{
switch ($op) {
case 'view':
switch ($node->type) {
}
}
}
| tripal_organism_perm | ( | ) |
Set the permission types that the chado module uses. Essentially we want permissionis that protect creation, editing and deleting of chado data objects
Definition at line 191 of file tripal_organism.module.
{
return array(
'access chado_organism content',
'create chado_organism content',
'delete chado_organism content',
'edit chado_organism content',
'adminster tripal organism',
);
}
| tripal_organism_reindex_features | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Definition at line 368 of file tripal_organism.admin.inc.
{
$i = 0;
if (!$organism_id) {
return;
}
$sql = "SELECT * ".
"FROM {feature} ".
"WHERE organism_id = $organism_id ".
"ORDER BY feature_id";
$results = chado_query($sql);
// load into ids array
$count = 0;
$ids = array();
while ($id = db_fetch_object($results)) {
$ids[$count] = $id->feature_id;
$count++;
}
$interval = intval($count * 0.01);
foreach ($ids as $feature_id) {
// update the job status every 1% features
if ($job_id and $i % $interval == 0) {
tripal_job_set_progress($job_id , intval(($i/$count)*100));
}
tripal_feature_sync_feature($feature_id);
$i++;
}
}
| tripal_organism_sync_organisms | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Synchronize organisms from chado to drupal
Definition at line 314 of file tripal_organism.admin.inc.
{
global $user;
$page_content = '';
if (!$organism_id) {
$sql = "SELECT * FROM {Organism} O";
$results = chado_query($sql);
}
else {
$sql = "SELECT * FROM {Organism} L WHERE organism_id = %d";
$results = chado_query($sql, $organism_id);
}
// We'll use the following SQL statement for checking if the organism
// already exists as a drupal node.
$sql = "SELECT * FROM {chado_organism} ".
"WHERE organism_id = %d";
while ($organism = db_fetch_object($results)) {
// check if this organism already exists in the drupal database. if it
// does then skip this organism and go to the next one.
if (!db_fetch_object(db_query($sql, $organism->organism_id))) {
$new_node = new stdClass();
$new_node->type = 'chado_organism';
$new_node->uid = $user->uid;
$new_node->title = "$organism->genus $organism->species";
$new_node->organism_id = $organism->organism_id;
$new_node->genus = $organism->genus;
$new_node->species = $organism->species;
$new_node->description = '';
node_validate($new_node);
if (!form_get_errors()) {
$node = node_submit($new_node);
node_save($node);
if ($node->nid) {
print "Added $organism->common_name\n";
}
}
else {
print "Failed to insert organism $organism->common_name\n";
}
}
else {
print "Skipped $organism->common_name\n";
}
}
return $page_content;
}
| tripal_organism_taxonify_features | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Definition at line 403 of file tripal_organism.admin.inc.
{
$i = 0;
if (!$organism_id) {
return;
}
$sql = "SELECT * ".
"FROM {feature} ".
"WHERE organism_id = $organism_id ".
"ORDER BY feature_id";
$results = chado_query($sql);
// load into ids array
$count = 0;
$ids = array();
while ($id = db_fetch_object($results)) {
$ids[$count] = $id->feature_id;
$count++;
}
// make sure our vocabularies are set before proceeding
tripal_feature_set_vocabulary();
// use this SQL for getting the nodes
$nsql = "SELECT * FROM {chado_feature} CF ".
" INNER JOIN {node} N ON N.nid = CF.nid ".
"WHERE feature_id = %d";
// iterate through the features and set the taxonomy
$interval = intval($count * 0.01);
foreach ($ids as $feature_id) {
// update the job status every 1% features
if ($job_id and $i % $interval == 0) {
tripal_job_set_progress($job_id, intval(($i/$count)*100));
}
$node = db_fetch_object(db_query($nsql, $feature_id));
tripal_feature_set_taxonomy($node, $feature_id);
$i++;
}
}
| tripal_organism_theme | ( | ) |
We need to let drupal know about our theme functions and their arguments. We create theme functions to allow users of the module to customize the look and feel of the output generated in this module
Definition at line 129 of file tripal_organism.module.
{
return array(
'tripal_organism_base' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_base',
),
'tripal_organism_description' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_description',
),
'tripal_organism_image' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_image',
),
'tripal_organism_teaser' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_teaser',
),
'tripal_organism_admin' => array(
'template' => 'tripal_organism_admin',
'arguments' => array(NULL),
'path' => drupal_get_path('module', 'tripal_organism') . '/theme'
),
);
}
| tripal_organism_views_api | ( | ) |
Implements hook_views_api() Purpose: Essentially this hook tells drupal that there is views support for for this module which then includes tripal_db.views.inc where all the views integration code is
Definition at line 614 of file tripal_organism.module.
{
return array(
'api' => 2.0,
);
}
1.7.4