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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_views_api () | |
| tripal_project_menu () | |
| tripal_project_perm () | |
| chado_project_access ($op, $node, $account) | |
| tripal_project_node_info () | |
| tripal_project_theme () | |
| chado_project_form (&$node, $form_state) | |
| chado_project_validate ($node) | |
| chado_project_insert ($node) | |
| chado_project_delete ($node) | |
| chado_project_update ($node) | |
| chado_project_load ($node) | |
| tripal_project_block ($op= 'list', $delta= '0', $edit=array()) | |
| tripal_project_preprocess_tripal_project_relationships (&$variables) | |
This file contains the basic functions needed for this drupal module. The drupal tripal_project module maps directly to the chado general module.
For documentation regarding the Chado General module:
Definition in file tripal_project.module.
| chado_project_access | ( | $ | op, |
| $ | node, | ||
| $ | account | ||
| ) |
Implements hook_access()
This function sets the access permission for operations on the database.
$op The operation that is to be performed
$node The specific node that is to have the operation performed
$account The account of the user that is performing the operations
Definition at line 87 of file tripal_project.module.
{
if ($op == 'create') {
// Only users with permission to do so may create this node type.
if (!user_access('create chado_projects', $account)) {
return FALSE;
}
}
// Users who create a node may edit or delete it later, assuming they have the necessary permissions.
if ($op == 'update' || $op == 'delete') {
if (!user_access('edit own chado_projects', $account)) {
return FALSE;
}
if (user_access('edit own chado_projects', $account) &&
$account->uid != $node->uid) {
return FALSE;
}
}
if ($op == 'view') {
if (!user_access('access chado_projects', $account)) {
return FALSE;
}
}
return NULL;
}
| chado_project_delete | ( | $ | node | ) |
Implementation of hook_delete().
| $node | The node which is to be deleted, only chado project and chado_project need to be dealt with since the drupal node is deleted automagically |
Definition at line 315 of file tripal_project.module.
{
$project_id = chado_get_id_for_node('project', $node);
// if we don't have a project id for this node then this isn't a node of
// type chado_project or the entry in the chado_project table was lost.
if (!$project_id) {
return;
}
// Remove data from {chado_project}, {node} and {node_revisions} tables of
// drupal database
$sql_del = "DELETE FROM {chado_project} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($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);
$sql_del = "DELETE FROM {node} ".
"WHERE nid = %d ".
"AND vid = %d";
db_query($sql_del, $node->nid, $node->vid);
// Remove data from project and projectprop tables of chado database as well
chado_query("DELETE FROM {projectprop} WHERE project_id = %d", $project_id);
chado_query("DELETE FROM {project} WHERE project_id = %d", $project_id);
}
| chado_project_form | ( | &$ | node, |
| $ | form_state | ||
| ) |
Implementation of hook_form().
This form takes the Project Title information and description from the user.
&$node The initialized node
$form_state The state of the form, that has the user entered information that is neccessary for adding information to the project
Definition at line 189 of file tripal_project.module.
{
$form = array();
$project = $node->project;
// get the project default values. When this module was first created
// the project description was incorrectly stored in the $node->body field.
// It is better to store it in the Chado tables. However, the 'description'
// field of the project table is only 255 characters. So, we are going
// to follow the same as the project module and store the description in
// the projectprop table and leave the project.description field blank.
// however, for backwards compatibitily, we check to see if the description
// is in the $node->body field. If it is we'll use that. When the node is
// edited the text will be moved out of the body and into the projectprop
// table where it should belong.
if ($node->body) {
$project_description = $node->body;
}
else {
$project_description = $node->project_description;
}
if (!$project_description) {
$projectprop = tripal_project_get_property($project->project_id, 'project_description');
$project_description = $projectprop->value;
}
// keep track of the project id if we have. If we do have one then
// this is an update as opposed to an insert.
$form['project_id'] = array(
'#type' => 'value',
'#value' => $project->project_id,
);
$form['title']= array(
'#type' => 'textfield',
'#title' => t('Project Title'),
'#description' => t('Please enter the title for this project. This appears at the top of the project page.'),
'#required' => TRUE,
'#default_value' => $node->title,
'#weight' => 1
);
$form['project_description']= array(
'#type' => 'textarea',
'#title' => t('Project Description'),
'#description' => t('A brief description of the project'),
'#required' => TRUE,
'#default_value' => $project_description,
'#weight' => 5
);
return $form;
}
| chado_project_insert | ( | $ | node | ) |
Implementation of hook_insert().
$node Then node that has the information stored within, accessed given the nid
Definition at line 271 of file tripal_project.module.
{
if ($node->project_id) {
$project['project_id'] = $node->project_id;
}
else {
$values = array(
'name' => $node->title,
'description' => '',
);
$project = tripal_core_chado_insert('project', $values);
}
if ($project) {
// add the description property
tripal_project_insert_property($project['project_id'], 'project_description',
$node->project_description);
// make sure the entry for this feature doesn't already exist in the chado_project table
// if it doesn't exist then we want to add it.
$project_id = chado_get_id_for_node('project', $node) ;
if (!$project_id) {
// next add the item to the drupal table
$sql = "INSERT INTO {chado_project} (nid, vid, project_id) ".
"VALUES (%d, %d, %d)";
db_query($sql, $node->nid, $node->vid, $project['project_id']);
}
}
else {
drupal_set_message(t('Unable to add project.', 'warning'));
watchdog('tripal_project', 'Insert feature: Unable to create project where values: %values',
array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
}
}
| chado_project_load | ( | $ | node | ) |
Implementation of node_load().
| $node | The node that is to have its containing information loaded |
Definition at line 385 of file tripal_project.module.
{
// get the feature details from chado
$project_id = chado_get_id_for_node('project', $node);
$values = array('project_id' => $project_id);
$project = tripal_core_generate_chado_var('project', $values);
$additions = new stdClass();
$additions->project = $project;
return $additions;
}
| chado_project_update | ( | $ | node | ) |
Implements hook_update().
| $node | The node which is to have its containing information updated when the user modifies information pertaining to the specific project |
Definition at line 354 of file tripal_project.module.
{
if ($node->revision) {
// there is no way to handle revisions in Chado but leave
// this here just to make not we've addressed it.
}
// update the project and the description
$project_id = chado_get_id_for_node('project', $node) ;
$match = array(
'project_id' => $project_id,
);
$values = array(
'name' => $node->title,
'description' => '',
);
$status = tripal_core_chado_update('project', $match, $values);
tripal_project_update_property($project_id, 'project_description', $node->project_description, 1);
}
| chado_project_validate | ( | $ | node | ) |
validates submission of form when adding or updating a project node
Definition at line 248 of file tripal_project.module.
{
$project = 0;
// check to make sure the name on the project is unique
// before we try to insert into chado.
if ($node->project_id) {
$sql = "SELECT * FROM {project} WHERE name = '%s' AND NOT project_id = %d";
$project = db_fetch_object(chado_query($sql, $node->title, $node->project_id));
}
else {
$sql = "SELECT * FROM {project} WHERE name = '%s'";
$project = db_fetch_object(chado_query($sql, $node->title));
}
if ($project) {
form_set_error('title', t('The unique project name already exists. Please choose another'));
}
}
| tripal_project_block | ( | $ | op = 'list', |
| $ | delta = '0', |
||
| $ | edit = array() |
||
| ) |
Display block with projects
| 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 407 of file tripal_project.module.
{
switch ($op) {
case 'list':
$blocks['projectbase']['info'] = t('Tripal Project Details');
$blocks['projectbase']['cache'] = BLOCK_NO_CACHE;
$blocks['projectprops']['info'] = t('Tripal Project Properties');
$blocks['projectprops']['cache'] = BLOCK_NO_CACHE;
$blocks['projectpubs']['info'] = t('Tripal Project Publications');
$blocks['projectpubs']['cache'] = BLOCK_NO_CACHE;
$blocks['projectcont']['info'] = t('Tripal Project Contact');
$blocks['projectcont']['cache'] = BLOCK_NO_CACHE;
$blocks['projectrels']['info'] = t('Tripal Project Relationships');
$blocks['projectrels']['cache'] = BLOCK_NO_CACHE;
return $blocks;
case 'view':
if (user_access('access chado_project content') and arg(0) == 'node' and is_numeric(arg(1))) {
$nid = arg(1);
$node = node_load($nid);
$block = array();
switch ($delta) {
case 'projectbase':
$block['subject'] = t('Project Details');
$block['content'] = theme('tripal_project_base', $node);
break;
case 'projectprops':
$block['subject'] = t('Properties');
$block['content'] = theme('tripal_project_properties', $node);
break;
case 'projectpubs':
$block['subject'] = t('Publications');
$block['content'] = theme('tripal_project_publications', $node);
break;
case 'projectcont':
$block['subject'] = t('Contact');
$block['content'] = theme('tripal_project_contact', $node);
break;
case 'projectrels':
$block['subject'] = t('Relationships');
$block['content'] = theme('tripal_project_relationships', $node);
break;
default :
}
return $block;
}
}
}
| tripal_project_menu | ( | ) |
Implements hook_menu
Definition at line 32 of file tripal_project.module.
{
$items[ 'admin/tripal/tripal_project' ]= array(
'title' => 'Projects',
'page callback' => 'theme',
'page arguments' => array('tripal_project_admin'),
'access arguments' => array('adminster tripal projects'),
'type' => MENU_NORMAL_ITEM
);
$items[ 'admin/tripal/tripal_project/configuration' ]= array(
'title' => 'Configuration',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_project_admin'),
'access arguments' => array('adminster tripal projects'),
'type' => MENU_NORMAL_ITEM
);
return $items;
}
| tripal_project_node_info | ( | ) |
Implementation of hook_node_info().
This node_info, is a simple node that describes the functionallity of the module. It specifies that the title(Project Name) and body(Description) set to true so that they information can be entered
Definition at line 124 of file tripal_project.module.
{
return array(
'chado_project' => array(
'name' => t('Project'),
'module' => 'chado_project',
'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
'has_title' => TRUE,
'title_label' => t('Project Name'),
'had_body' => TRUE,
'body_label' => t('Full Description'),
)
);
}
| tripal_project_perm | ( | ) |
Implements hook_perm()
This function sets the permission for the user to access the information in the database. This includes creating, inserting, deleting and updating of information in the database
Definition at line 59 of file tripal_project.module.
{
return array(
'access chado_projects content',
'create chado_projects content',
'delete chado_projects content',
'edit chado_projects content',
'adminster tripal projects',
);
}
| tripal_project_preprocess_tripal_project_relationships | ( | &$ | variables | ) |
Definition at line 466 of file tripal_project.module.
{
// we want to provide a new variable that contains the matched projects.
$project = $variables['node']->project;
// normally we would use tripal_core_expand_chado_vars to expand our
// organism object and add in the relationships, however whan a large
// number of relationships are present this significantly slows the
// query, therefore we will manually perform the query
$sql = "
SELECT P.name, P.project_id, CP.nid, CVT.name as rel_type
FROM project_relationship PR
INNER JOIN project P ON PR.object_project_id = P.project_id
INNER JOIN cvterm CVT ON PR.type_id = CVT.cvterm_id
LEFT JOIN chado_project CP ON P.project_id = CP.project_id
WHERE PR.subject_project_id = %d
";
$as_subject = chado_query($sql, $project->project_id);
$sql = "
SELECT P.name, P.project_id, CP.nid, CVT.name as rel_type
FROM project_relationship PR
INNER JOIN project P ON PR.subject_project_id = P.project_id
INNER JOIN cvterm CVT ON PR.type_id = CVT.cvterm_id
LEFT JOIN chado_project CP ON P.project_id = CP.project_id
WHERE PR.object_project_id = %d
";
$as_object = chado_query($sql, $project->project_id);
// combine both object and subject relationshisp into a single array
$relationships = array();
$relationships['object'] = array();
$relationships['subject'] = array();
// iterate through the object relationships
while ($relationship = db_fetch_object($as_object)) {
// get the relationship and child types
$rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
$sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));
if (!array_key_exists($rel_type, $relationships['object'])) {
$relationships['object'][$rel_type] = array();
}
if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
$relationships['object'][$rel_type][$sub_type] = array();
}
$relationships['object'][$rel_type][$sub_type][] = $relationship;
}
// now add in the subject relationships
while ($relationship = db_fetch_object($as_subject)) {
// get the relationship and child types
$rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
$obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));
if (!array_key_exists($rel_type, $relationships['subject'])) {
$relationships['subject'][$rel_type] = array();
}
if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
$relationships['subject'][$rel_type][$obj_type] = array();
}
$relationships['subject'][$rel_type][$obj_type][] = $relationship;
}
$project->all_relationships = $relationships;
}| tripal_project_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 144 of file tripal_project.module.
{
return array(
'tripal_project_base' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_project_base',
),
'tripal_project_contact' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_project_contact',
),
'tripal_project_publications' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_project_publications',
),
'tripal_project_relationships' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_project_relationships',
),
'tripal_project_properties' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_project_properties',
),
'tripal_project_admin' => array(
'template' => 'tripal_project_admin',
'arguments' => array(NULL),
'path' => drupal_get_path('module', 'tripal_project') . '/theme'
),
);
}
| tripal_project_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_project.views.inc where all the views integration code is
Definition at line 23 of file tripal_project.module.
{
return array(
'api' => 2.0,
);
}
1.7.4