<?php
/**
* @file
* Implements the pub node content type
*/
/**
* Implements hook_node_info().
*
* @ingroup tripal_pub
*/
function tripal_pub_node_info() {
return array(
'chado_pub' => array(
'name' => t('Publication'),
'base' => 'chado_pub',
'description' => t('A publication from the Chado database'),
'has_title' => TRUE,
'locked' => TRUE,
'chado_node_api' => array(
'base_table' => 'pub',
'hook_prefix' => 'chado_pub',
'record_type_title' => array(
'singular' => t('Publication'),
'plural' => t('Publications')
),
'sync_filters' => array(
'type_id' => FALSE,
'organism_id' => FALSE
),
),
),
);
}
/**
* Implements hook_form().
*
* @ingroup tripal_pub
*/
function chado_pub_form($node, $form_state) {
$form = array();
// Default values can come in the following ways:
//
// 1) as elements of the $node object. This occurs when editing an existing pub
// 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
$pub_id = null;
$title = '';
$pyear = '';
$uniquename = '';
$type_id = '';
$is_obsolete = '';
// some of the fields in the pub table should show up in the properties
// form elements to make the form more seemless. We will add them
// to this array.
$more_props = array();
// if we are editing an existing node then the pub is already part of the node
if (property_exists($node, 'pub')) {
$pub = $node->pub;
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
$pub = chado_expand_var($pub, 'field', 'pub.uniquename');
$pub_id = $pub->pub_id;
$title = $pub->title;
$pyear = $pub->pyear;
$uniquename = $pub->uniquename;
$type_id = $pub->type_id->cvterm_id;
$is_obsolete = $pub->is_obsolete;
// if the obsolete value is set by the database then it is in the form of
// 't' or 'f', we need to convert to 1 or 0
$is_obsolete = $is_obsolete == 't' ? 1 : $is_obsolete;
$is_obsolete = $is_obsolete == 'f' ? 0 : $is_obsolete;
// set the organism_id in the form
$form['pub_id'] = array(
'#type' => 'value',
'#value' => $pub->pub_id,
);
// get fields from the pub table and convert them to properties. We will add these to the $more_props
// array which gets passed in to the tripal_core_properties_form() API call further down
if ($pub->volumetitle) {
$cvterm = tripal_cv_get_cvterm_by_name('Volume Title', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->volumetitle);
}
if ($pub->volume) {
$cvterm = tripal_cv_get_cvterm_by_name('Volume', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->volume);
}
if ($pub->series_name) {
switch ($pub->type_id->name) {
case 'Journal Article':
$cvterm = tripal_cv_get_cvterm_by_name('Journal Name', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
break;
case 'Conference Proceedings':
$cvterm = tripal_cv_get_cvterm_by_name('Conference Name', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
break;
default:
$cvterm = tripal_cv_get_cvterm_by_name('Series Name', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
}
}
if ($pub->issue) {
$cvterm = tripal_cv_get_cvterm_by_name('Issue', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->issue);
}
if ($pub->pages) {
$cvterm = tripal_cv_get_cvterm_by_name('Pages', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->pages);
}
if ($pub->miniref) {
// not sure what to do with this one
}
if ($pub->publisher) {
$cvterm = tripal_cv_get_cvterm_by_name('Publisher', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->publisher);
}
if ($pub->pubplace) {
$cvterm = tripal_cv_get_cvterm_by_name('Published Location', NULL, 'tripal_pub');
$more_props[] = array('cvterm' => $cvterm, 'value' => $pub->pages);
}
}
// 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', $form_state) and isset($form_state['values']['pubtitle'])) {
$title = $form_state['values']['pubtitle'];
$pyear = $form_state['values']['pyear'];
$uniquename = $form_state['values']['uniquename'];
$type_id = $form_state['values']['type_id'];
$is_obsolete = $form_state['values']['is_obsolete'];
}
// 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'])) {
$title = $form_state['input']['pubtitle'];
$uniquename = $form_state['input']['uniquename'];
$type_id = $form_state['input']['type_id'];
$is_obsolete = array_key_exists('is_obsolete', $form_state['input']) ? $form_state['input']['is_obsolete'] : '';
}
$form['pubtitle'] = array(
'#type' => 'textarea',
'#title' => t('Publication Title'),
'#default_value' => $title,
'#required' => TRUE,
);
$type_cv = tripal_get_default_cv('pub', 'type_id');
if ($type_cv->name == 'tripal_pub') {
// get the list of publication types. In the Tripal publication
// ontologies these are all grouped under the term 'Publication Type'
// we want the default to be 'Journal Article'
$sql = "
SELECT
CVTS.cvterm_id, CVTS.name
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
WHERE
CV.name = 'tripal_pub' AND CVTO.name = 'Publication Type' AND
NOT CVTS.is_obsolete = 1
ORDER BY CVTS.name ASC
";
$results = chado_query($sql);
$pub_types = array();
while ($pub_type = $results->fetchObject()) {
$pub_types[$pub_type->cvterm_id] = $pub_type->name;
// if we don't have a default type then set the default to be 'Journal Article'
if (strcmp($pub_type->name,"Journal Article") == 0 and !$type_id) {
$type_id = $pub_type->cvterm_id;
}
}
}
else {
$pub_types = tripal_get_cvterm_default_select_options('pub', 'type_id', 'publication types');
$pub_types[0] = 'Select a Type';
}
$form['type_id'] = array(
'#type' => 'select',
'#title' => t('Publication Type'),
'#options' => $pub_types,
'#required' => TRUE,
'#default_value' => $type_id,
);
$form['pyear'] = array(
'#type' => 'textfield',
'#title' => t('Publication Year'),
'#default_value' => $pyear,
'#required' => TRUE,
'#size' => 5,
'#description' => t('Enter the year of publication. Also, if available, please add a <b>Publication Date</b> property to specify the full date of publication.'),
);
$form['uniquename'] = array(
'#type' => 'textarea',
'#title' => t('Citation'),
'#default_value' => $uniquename,
'#description' => t('All publications must have a unique citation.
<b>Please enter the full citation for this publication or leave blank and one will be generated
automatically if possible</b>. For PubMed style citations list
the last name of the author followed by initials. Each author should be separated by a comma. Next comes
the title, followed by the series title (e.g. journal name), publication date (4 digit year, 3 character Month, day), volume, issue and page numbers. You may also use HTML to provide a link in the citation.
Below is an example: <pre>Medeiros PM, Ladio AH, Santos AM, Albuquerque UP. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23462414" target="_blank">Does the selection of medicinal plants by Brazilian local populations
suffer taxonomic influence?</a> J Ethnopharmacol. 2013 Apr 19; 146(3):842-52.</pre>'),
);
$form['is_obsolete'] = array(
'#type' => 'checkbox',
'#title' => t('Is Obsolete? (Check for Yes)'),
'#default_value' => $is_obsolete,
);
// Properties Form
// ----------------------------------
$select_options = array();
$prop_cv = tripal_get_default_cv('pubprop', 'type_id');
$cv_id = $prop_cv ? $prop_cv->cv_id : NULL;
// if the poperty cv is 'tripal_pub' then we need to pass in our own select_options
// for only a subset of the vocabulary
if ($prop_cv->name == 'tripal_pub') {
$select_options[] = 'Select a Property';
$sql = "
SELECT
DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
WHERE CV.name = 'tripal_pub' and
(CVTO.name = 'Publication Details' OR CVTS.name = 'Publication Type') AND
NOT CVTS.is_obsolete = 1
ORDER BY CVTS.name ASC
";
$prop_types = chado_query($sql);
while ($prop = $prop_types->fetchObject()) {
// add all properties except the Citation. That property is set via the uniquename field
if ($prop->name == 'Citation') {
continue;
}
// Publication Dbxref's are handled by the dbxref form addition below
if ($prop->name == 'Publication Dbxref') {
continue;
}
$select_options[$prop->cvterm_id] = $prop->name;
}
}
$details = array(
'property_table' => 'pubprop',
'chado_id' => $pub_id,
'cv_id' => $cv_id,
'select_options' => $select_options,
'default_properties' => $more_props,
);
chado_add_node_form_properties($form, $form_state, $details);
// RELATIONSHIPS FORM
//---------------------------------------------
$relationship_cv = tripal_get_default_cv('pub_relationship', 'type_id');
$cv_id = $relationship_cv ? $relationship_cv->cv_id : NULL;
$details = array(
'relationship_table' => 'pub_relationship', // the name of the _relationship table
'base_table' => 'pub', // the name of your chado base table
'base_foreign_key' => 'pub_id', // the name of the key in your base chado table
'base_key_value' => $pub_id, // the value of example_id for this record
'nodetype' => 'pub', // the human-readable name of your node type
'cv_id' => $cv_id, // the cv.cv_id of the cv containing the properties
'base_name_field' => 'uniquename', // the base table field you want to be used as the name
'select_options' => $select_options
);
// Adds the form elements to your current form
chado_add_node_form_relationships($form, $form_state, $details);
// ADDITIONAL DBXREFS FORM
//---------------------------------------------
$details = array(
'linking_table' => 'pub_dbxref', // the name of the _dbxref table
'base_foreign_key' => 'pub_id', // the name of the key in your base chado table
'base_key_value' => $pub_id // the value of pub_id for this record
);
// Adds the form elements to your current form
chado_add_node_form_dbxrefs($form, $form_state, $details);
return $form;
}
/**
* Implements hook_validate().
*
* @ingroup tripal_pub
*/
function chado_pub_validate($node, $form, &$form_state) {
// if this is a delete then don't validate
if($node->op == 'Delete') {
return;
}
// we are syncing if we do not have a node ID but we do have a pub_id. We don't
// need to validate during syncing so just skip it.
if (is_null($node->nid) and property_exists($node, 'pub_id') and $node->pub_id != 0) {
return;
}
// get the submitted values
$title = trim($node->pubtitle);
$pyear = trim($node->pyear);
$uniquename = trim($node->uniquename);
$is_obsolete = $node->is_obsolete;
$type_id = $node->type_id;
$pub = array();
// make sure the year is four digits
if(!preg_match('/^\d{4}$/', $pyear)){
form_set_error('pyear', t('The publication year should be a 4 digit year.'));
return;
}
// get the type of publication
$values = array('cvterm_id' => $type_id);
$cvterm = chado_select_record('cvterm', array('name'), $values);
if (count($cvterm) == 0) {
$message = t('Invalid publication type.');
form_set_error('type_id', $message);
return;
}
// get the media name looking at the properties
$series_name = '';
$properties = chado_retrieve_node_form_properties($node);
foreach ($properties as $key => $prop_values) {
$values = array('cvterm_id' => $key);
$prop_type = chado_select_record('cvterm', array('name'), $values);
if ($prop_type[0]->name == 'Conference Name' or
$prop_type[0]->name == 'Journal Name' or
$prop_type[0]->name == 'Series Name') {
$series_name = $prop_values[0];
}
if ($prop_type[0]->name == 'Citation') {
$uniquename = $prop_values[0];
}
if (count($prop_values) == 1) {
$pub[$prop_type[0]->name] = $prop_values[0];
}
else {
$pub[$prop_type[0]->name] = $prop_values;
}
}
// if the citation is missing then try to generate one
if (!$uniquename) {
$pub['Title'] = $title;
$pub['Publication Type'][0] = $cvterm[0]->name;
$pub['Year'] = $pyear;
$uniquename = tripal_pub_create_citation($pub);
if (!$uniquename) {
form_set_error('uniquename', "Cannot automatically generate a citation for this publication type. Please add one manually.");
}
}
$skip_duplicate_check = 0;
// if this publication is a Patent then skip the validation below. Patents can have the title
// name and year but be different
if (strcmp($cvterm[0]->name,'Patent') == 0) {
$skip_duplicate_check = 1;
}
// Validating for an update
if (!is_null($node->nid)) {
$pub_id = $node->pub_id;
// check to see if a duplicate publication already exists
if (!$skip_duplicate_check) {
chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm[0], $pub_id);
}
chado_pub_validate_check_uniquename($uniquename, $pub_id);
}
// Validating for an insert
else {
chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm[0]);
chado_pub_validate_check_uniquename($uniquename);
}
}
/**
* Validate the publication uniquename. To be called from hook_validate().
*
* @param $uniquename
* The uniquename of the publication
* @param $pub_id
* If an update, provide the pub_id so we don't check for a matching
* uniquename of the pub we are editing
*
* @ingroup tripal_pub
*/
function chado_pub_validate_check_uniquename($uniquename, $pub_id = NULL) {
// check to see if a pub exists with this uniquename
$pub = chado_get_publication(array('uniquename' => $uniquename));
if ($pub) {
// if a $pub_id is provided to the function then this is an update
// if the pub_id's don't match then a different pub with the same
// uniquename already exists.
if ($pub->pub_id != $pub_id) {
$message = t('A publication with this unique citation already exists.');
form_set_error('uniquename', $message);
}
}
}
/**
* Check for duplicate publications. To be called from hook_validate(). Sets
* the form error if a duplicate
*
* @param $title
* The title of the publication
* @param $pyear
* The year the publication was published
* @param $series_name
* The series name of the publication
* @param $cvterm
* The type of publication
* @param $pub_id
* the unique id of the publication
*
*
* @ingroup tripal_pub
*/
function chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm, $pub_id = NULL) {
$pub_details = array(
'Title' => $title,
'Year' => $pyear,
'Series Name' => $series_name,
'Publication Type' => $cvterm->name,
);
// TODO: need to include the Publication Dbxref in the $pub_details as well
$pub_ids = tripal_publication_exists($pub_details);
// if we found only one publication and it is our publication then return, we're good.
if (count($pub_ids) == 1 and in_array($pub_id, $pub_ids)) {
return;
}
if (count($pub_ids) == 0) {
// there is no match so return
return;
}
// return an appropriate message based on the unique constraint settings
$import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
switch ($import_dups_check) {
case 'title_year':
$message = t('A publication with this title and publication year already exists.');
form_set_error('pubtitle', $message);
break;
case 'title_year_type':
$message = t('A publication with this title, type and publication year already exists.');
form_set_error('pubtitle', $message);
break;
case 'title_year_media':
$message = t('A publication with this title, media name (e.g. Journal Name) and publication year already exists.');
form_set_error('pubtitle', $message);
break;
}
}
/**
* Implement hook_node_access().
*
* This hook allows node modules to limit access to the node types they define.
*
* @param $node
* The node on which the operation is to be performed, or, if it does not yet exist, the
* type of node to be created
*
* @param $op
* The operation to be performed
*
* @param $account
* A user object representing the user for whom the operation is to be performed
*
* @return
* If the permission for the specified operation is not set then return FALSE. If the
* permission is set then return NULL as this allows other modules to disable
* access. The only exception is when the $op == 'create'. We will always
* return TRUE if the permission is set.
*
* @ingroup tripal_pub
*/
function chado_pub_node_access($node, $op, $account) {
$node_type = $node;
if (is_object($node)) {
$node_type = $node->type;
}
if($node_type == 'chado_pub') {
if ($op == 'create') {
if (!user_access('create chado_pub', $account)) {
return NODE_ACCESS_DENY;
}
return NODE_ACCESS_ALLOW;
}
if ($op == 'update') {
if (!user_access('edit chado_pub', $account)) {
return NODE_ACCESS_DENY;
}
}
if ($op == 'delete') {
if (!user_access('delete chado_pub', $account)) {
return NODE_ACCESS_DENY;
}
}
if ($op == 'view') {
if (!user_access('access chado_pub', $account)) {
return NODE_ACCESS_DENY;
}
}
return NODE_ACCESS_IGNORE;
}
}
/**
* Implements hook_insert().
*
* @ingroup tripal_pub
*/
function chado_pub_insert($node) {
$node->pubtitle = trim($node->pubtitle);
$node->pyear = trim($node->pyear);
$node->uniquename = trim($node->uniquename);
$is_obsolete = $node->is_obsolete;
$type_id = $node->type_id;
// we need an array suitable for the tripal_pub_create_citation() function
// to automatically generate a citation if a uniquename doesn't already exist
$pub_arr = array();
// if there is an pub_id in the $node object then this must be a sync so
// we can skip adding the pub as it is already there, although
// we do need to proceed with the rest of the insert
if (!property_exists($node, 'pub_id')) {
$properties = array(); // stores all of the properties we need to add
$cross_refs = array(); // stores any cross references for this publication
// get the properties from the form
$properties = chado_retrieve_node_form_properties($node);
// get the list of properties for easy lookup (without doing lots of database queries
$properties_list = array();
$sql = "
SELECT CVTS.cvterm_id, CVTS.name, CVTS.definition
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and
NOT CVTS.is_obsolete = 1
ORDER BY CVTS.name ASC
";
$prop_types = chado_query($sql);
while ($prop = $prop_types->fetchObject()) {
$properties_list[$prop->cvterm_id] = $prop->name;
// The 'Citation' term is special because it serves
// both as a property and as the uniquename for the
// pub and we want it stored in both the pub table and the pubprop table
if ($prop->name == 'Citation') {
$citation_id = $prop->cvterm_id;
if (!empty($node->uniquename)) {
$properties[$citation_id][0] = $node->uniquename;
}
}
}
// iterate through all of the properties and remove those that really are
// part of the pub table fields
$volume = '';
$volumetitle = '';
$issue = '';
$pages = '';
$publisher = '';
$series_name = '';
$pubplace = '';
$miniref = '';
$cross_refs = array();
foreach ($properties as $type_id => $element) {
$value = trim($element[0]);
$name = $properties_list[$type_id];
// populate our $pub_array for building a citation
$pub_arr[$name] = $value;
// remove properties that are stored in the pub table
if ($name == "Volume") {
$volume = $value;
unset($properties[$type_id]);
}
elseif ($name == "Volume Title") {
$volumetitle = $value;
unset($properties[$type_id]);
}
elseif ($name == "Issue") {
$issue = $value;
unset($properties[$type_id]);
}
elseif ($name == "Pages") {
$pages = $value;
unset($properties[$type_id]);
}
elseif ($name == "Publisher") {
$publisher = $value;
unset($properties[$type_id]);
}
elseif ($name == "Series Name" or $name == "Journal Name" or $name == "Conference Name") {
$series_name = $value;
unset($properties[$type_id]);
}
elseif ($name == "Journal Country" or $name == "Published Location") {
$pubplace = $value;
// allow this property to go into the pubprop table so we don't loose info
// so don't unset it. But it will also go into the pub.pubplace field
}
elseif ($name == "Publication Dbxref") {
// we will add the cross-references to the pub_dbxref table
// but we also want to keep the property in the pubprop table so don't unset it
$cross_refs[] = $value;
}
}
// generate a citation for this pub if one doesn't already exist
if (!$node->uniquename and !array_key_exists($citation_id, $properties)) {
$pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
$pub_arr['Title'] = $node->pubtitle;
$pub_arr['Publication Type'][0] = $pub_type->name;
$pub_arr['Year'] = $node->pyear;
$node->uniquename = tripal_pub_create_citation($pub_arr);
$properties[$citation_id][0] = $node->uniquename;
}
// insert the pub record
$values = array(
'title' => $node->pubtitle,
'series_name' => substr($series_name, 0, 255),
'type_id' => $node->type_id,
'pyear' => $node->pyear,
'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
'uniquename' => $node->uniquename,
'volumetitle' => $volumetitle,
'volume' => $volume,
'issue' => $issue,
'pages' => $pages,
'miniref' => substr($miniref, 0, 255),
'publisher' => substr($publisher, 0, 255),
'pubplace' => substr($pubplace, 0, 255),
);
$pub = chado_insert_record('pub', $values);
if (!$pub) {
drupal_set_message("Error inserting publication", "error");
watchdog('tripal_pub', "Error inserting publication", array(), WATCHDOG_ERROR);
return;
}
$pub_id = $pub['pub_id'];
// now add in the properties
// Only adds in those not used in the pub record
$details = array(
'property_table' => 'pubprop',
'base_table' => 'pub',
'foreignkey_name' => 'pub_id',
'foreignkey_value' => $pub_id
);
chado_update_node_form_properties($node, $details, $properties);
// * Relationships Form *
$details = array(
'relationship_table' => 'pub_relationship', // name of the _relationship table
'foreignkey_value' => $pub_id // value of the pub_id key
);
chado_update_node_form_relationships($node, $details);
// add in any database cross-references
foreach ($cross_refs as $index => $ref) {
$dbxref = array();
if(preg_match('/^(.*?):(.*?)$/', trim($ref), $matches)) {
$dbxref['db_name'] = $matches[1];
$dbxref['accession'] = $matches[2];
}
$success = chado_associate_dbxref('pub', $pub['pub_id'], $dbxref);
if (!$success) {
drupal_set_message("Error cannot add publication cross reference: $ref", "error");
watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
array('%ref' => $ref), WATCHDOG_ERROR);
}
}
// * Additional DBxrefs Form *
$details = array(
'linking_table' => 'pub_dbxref', // the name of your _dbxref table
'foreignkey_name' => 'pub_id', // the name of the key in your base table
'foreignkey_value' => $pub_id // the value of the pub_id key
);
chado_update_node_form_dbxrefs($node, $details);
}
else {
$pub_id = $node->pub_id;
}
// Make sure the entry for this pub doesn't already exist in the
// chado_pub table if it doesn't exist then we want to add it.
$check_org_id = chado_get_id_from_nid('pub', $node->nid);
if (!$check_org_id) {
$record = new stdClass();
$record->nid = $node->nid;
$record->vid = $node->vid;
$record->pub_id = $pub_id;
drupal_write_record('chado_pub', $record);
}
}
/**
* Implements hook_update().
*
* The purpose of the function is to allow the module to take action when an edited node is being
* updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
* As well, the database will be changed, so the user changed information will be saved to the database.
*
* @param $node
* The node being updated
*
* @ingroup tripal_pub
*/
function chado_pub_update($node) {
$node->pubtitle = trim($node->pubtitle);
$node->pyear = trim($node->pyear);
$node->uniquename = trim($node->uniquename);
$is_obsolete = $node->is_obsolete;
$type_id = $node->type_id;
// we need an array suitable for the tripal_pub_create_citation() function
// to automatically generate a citation if a uniquename doesn't already exist
$pub_arr = array();
// get the publication ID for this publication
$pub_id = chado_get_id_from_nid('pub', $node->nid) ;
$properties = array(); // stores all of the properties we need to add
$cross_refs = array(); // stores any cross references for this publication
// get the properties from the form
$properties = chado_retrieve_node_form_properties($node);
// get the list of properties for easy lookup (without doing lots of database queries
$properties_list = array();
$sql = "
SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
WHERE CV.name = 'tripal_pub' and
(CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and
NOT CVTS.is_obsolete = 1
ORDER BY CVTS.name ASC
";
$prop_types = chado_query($sql);
while ($prop = $prop_types->fetchObject()) {
$properties_list[$prop->cvterm_id] = $prop->name;
// The 'Citation' term is special because it serves
// both as a property and as the uniquename for the
// pub and we want it stored in both the pub table and the pubprop table
if ($prop->name == 'Citation') {
$citation_id = $prop->cvterm_id;
if (!empty($node->uniquename)) {
$properties[$citation_id][0] = $node->uniquename;
}
}
}
// iterate through all of the properties and remove those that really are
// part of the pub table fields
$volume = '';
$volumetitle = '';
$issue = '';
$pages = '';
$publisher = '';
$series_name = '';
$pubplace = '';
$miniref = '';
$cross_refs = array();
foreach ($properties as $type_id => $element) {
foreach ($element as $index => $value) {
$name = $properties_list[$type_id];
// populate our $pub_array for building a citation
$pub_arr[$name] = $value;
// remove properties that are stored in the pub table
if ($name == "Volume") {
$volume = $value;
unset($properties[$type_id]);
}
elseif ($name == "Volume Title") {
$volumetitle = $value;
unset($properties[$type_id]);
}
elseif ($name == "Issue") {
$issue = $value;
unset($properties[$type_id]);
}
elseif ($name == "Pages") {
$pages = $value;
unset($properties[$type_id]);
}
elseif ($name == "Publisher") {
$publisher = $value;
unset($properties[$type_id]);
}
elseif ($name == "Journal Name" or $name == "Conference Name") {
$series_name = $value;
unset($properties[$type_id]);
}
elseif ($name == "Journal Country" or $name == "Published Location") {
$pubplace = $value;
// allow this property to go into the pubprop table so we don't loose info
// so don't unset it. But it will also go into the pub.pubplace field
}
elseif ($name == "Publication Dbxref") {
// we will add the cross-references to the pub_dbxref table
// but we also want to keep the property in the pubprop table so don't unset it
$cross_refs[] = $value;
}
}
}
// generate a citation for this pub if one doesn't already exist
if (!$node->uniquename) {
$pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
$pub_arr['Title'] = $node->pubtitle;
$pub_arr['Publication Type'][0] = $pub_type->name;
$pub_arr['Year'] = $node->pyear;
$node->uniquename = tripal_pub_create_citation($pub_arr);
$properties[$citation_id][0] = $node->uniquename;
}
// update the pub record
$match = array(
'pub_id' => $pub_id,
);
$values = array(
'title' => $node->pubtitle,
'type_id' => $node->type_id,
'pyear' => $node->pyear,
'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
'uniquename' => $node->uniquename,
'series_name' => substr($series_name, 0, 255),
'volumetitle' => $volumetitle,
'volume' => $volume,
'issue' => $issue,
'pages' => $pages,
'miniref' => substr($miniref, 0, 255),
'publisher' => substr($publisher, 0, 255),
'pubplace' => substr($pubplace, 0, 255),
);
$status = chado_update_record('pub', $match, $values);
if (!$status) {
drupal_set_message("Error updating publication", "error");
watchdog('tripal_pub', "Error updating publication", array(), WATCHDOG_ERROR);
return;
}
// now add in the properties by first removing any the publication
// already has and adding the ones we have
$details = array(
'property_table' => 'pubprop',
'base_table' => 'pub',
'foreignkey_name' => 'pub_id',
'foreignkey_value'=> $pub_id
);
chado_update_node_form_properties($node, $details, $properties);
// * Relationships Form *
$details = array(
'relationship_table' => 'pub_relationship', // name of the _relationship table
'foreignkey_value' => $pub_id // value of the pub_id key
);
chado_update_node_form_relationships($node, $details);
// add in any database cross-references after first removing
chado_delete_record('pub_dbxref', array('pub_id' => $pub_id));
foreach ($cross_refs as $index => $ref) {
$dbxref = array();
if(preg_match('/^(.*?):(.*?)$/', trim($ref), $matches)) {
$dbxref['db_name'] = $matches[1];
$dbxref['accession'] = $matches[2];
}
$success = chado_associate_dbxref('pub', $pub_id, $dbxref);
if (!$success) {
drupal_set_message("Error cannot add publication cross reference: $ref", "error");
watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
array('%ref' => $ref), WATCHDOG_ERROR);
}
}
// * Additional DBxrefs Form *
$details = array(
'linking_table' => 'pub_dbxref', // the name of your _dbxref table
'foreignkey_name' => 'pub_id', // the name of the key in your base table
'foreignkey_value' => $pub_id // the value of the pub_id key
);
chado_update_node_form_dbxrefs($node, $details);
}
/**
* Implements hook_load().
*
* @param $node
* The node that is to be loaded
*
* @return $node
* The node with the information to be loaded into the database
*
* @ingroup tripal_pub
*/
function chado_pub_load($nodes) {
foreach ($nodes as $nid => $node) {
// find the pub and add in the details
$pub_id = chado_get_id_from_nid('pub', $nid);
// if the nid does not have a matching record then skip this node.
// this can happen with orphaned nodes.
if (!$pub_id) {
continue;
}
// get the pub
$values = array('pub_id' => $pub_id);
$pub = chado_generate_var('pub', $values);
// expand the 'text' fields as those aren't included by default
// and they really shouldn't be so large to cause problems
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
$pub = chado_expand_var($pub, 'field', 'pub.uniquename');
// set the URL path
$nodes[$nid]->path = "pub/$pub_id";
$nodes[$nid]->pub = $pub;
// Now get the title
$node->title = chado_get_node_title($node);
}
}
/**
* Implements hook_delete().
*
* This function takes a node and if the delete button has been chosen by the user, the publication
* and it's details will be removed.Following,given the node-ID, the instance will be deleted from
* the 'chado_pub' table.
*
* @parm $node
* Then node to be deleted
*
* @ingroup tripal_pub
*/
function chado_pub_delete(&$node) {
$pub_id = chado_get_id_from_nid('pub', $node->nid);
// if we don't have a pub id for this node then this isn't a node of
// type chado_pub or the entry in the chado_pub table was lost.
if (!$pub_id) {
return;
}
// Remove data from {chado_pub}, {node} and {node_revision} tables of
// drupal database
$sql_del = "DELETE FROM {chado_pub} WHERE nid = :nid AND vid = :vid";
db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
$sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
$sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
// Remove data from pub and pubprop tables of chado database as well
chado_query("DELETE FROM {pubprop} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
chado_query("DELETE FROM {pub} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
}
/**
* Implements hook_node_view(). Acts on all content types.
*
* @ingroup tripal_pub
*/
function tripal_pub_node_view($node, $view_mode, $langcode) {
switch ($node->type) {
case 'chado_pub':
// Show feature browser and counts
if ($view_mode == 'full') {
$node->content['tripal_pub_authors'] = array(
'#markup' => theme('tripal_pub_authors', array('node' => $node)),
'#tripal_toc_id' => 'authors',
'#tripal_toc_title' => 'Author Details',
);
$node->content['tripal_pub_base'] = array(
'#markup' => theme('tripal_pub_base', array('node' => $node)),
'#tripal_toc_id' => 'base',
'#tripal_toc_title' => 'Overview',
'#weight' => -100,
);
$node->content['tripal_pub_featuremaps'] = array(
'#markup' => theme('tripal_pub_featuremaps', array('node' => $node)),
'#tripal_toc_id' => 'featuremaps',
'#tripal_toc_title' => 'Maps',
);
$node->content['tripal_pub_features'] = array(
'#markup' => theme('tripal_pub_features', array('node' => $node)),
'#tripal_toc_id' => 'features',
'#tripal_toc_title' => 'Features',
);
$node->content['tripal_pub_libraries'] = array(
'#markup' => theme('tripal_pub_libraries', array('node' => $node)),
'#tripal_toc_id' => 'libraries',
'#tripal_toc_title' => 'Libraries',
);
$node->content['tripal_pub_projects'] = array(
'#markup' => theme('tripal_pub_projects', array('node' => $node)),
'#tripal_toc_id' => 'projects',
'#tripal_toc_title' => 'Projects',
);
$node->content['tripal_pub_properties'] = array(
'#markup' => theme('tripal_pub_properties', array('node' => $node)),
'#tripal_toc_id' => 'properties',
'#tripal_toc_title' => 'Properties',
);
$node->content['tripal_pub_references'] = array(
'#markup' => theme('tripal_pub_references', array('node' => $node)),
'#tripal_toc_id' => 'references',
'#tripal_toc_title' => 'Cross References',
);
$node->content['tripal_pub_relationships'] = array(
'#markup' => theme('tripal_pub_relationships', array('node' => $node)),
'#tripal_toc_id' => 'relationships',
'#tripal_toc_title' => 'Relationships',
);
$node->content['tripal_pub_stocks'] = array(
'#markup' => theme('tripal_pub_stocks', array('node' => $node)),
'#tripal_toc_id' => 'stocks',
'#tripal_toc_title' => 'Stocks',
);
}
if ($view_mode == 'teaser') {
$node->content['tripal_pub_teaser'] = array(
'#markup' => theme('tripal_pub_teaser', array('node' => $node)),
);
}
break;
}
}
/**
* Implements hook_node_insert(). Acts on all content types.
*
* We want the publications to always have a URL of http://[base url]/pub/[pub id]
* where [pub id] is the Chado publication ID. This will allow for easy linking
* into the publication without needing to know the node. Of course if you know the
* node that will still work too (e.g. http://[base url]/node/[node id]
* so the nodeapi function ensures that the URL path is set after insert or update
* of the node and when the node is loaded if it hasn't yet been set.
*
* @ingroup tripal_pub
*/
function tripal_pub_node_insert($node) {
if ($node->type == 'chado_pub') {
// get the pub
$pub_id = chado_get_id_from_nid('pub', $node->nid);
$values = array('pub_id' => $pub_id);
$pub = chado_generate_var('pub', $values);
// expand the 'text' fields as those aren't included by default
// and they really shouldn't be so large to cause problems
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
$pub = chado_expand_var($pub, 'field', 'pub.uniquename');
$node->pub = $pub;
// Now get the title
$node->title = chado_get_node_title($node);
tripal_pub_set_pub_url($node, $pub_id);
}
}
/**
* Implements hook_node_load(). Acts on all content types.
*
* We want the publications to always have a URL of http://[base url]/pub/[pub id]
* where [pub id] is the Chado publication ID. This will allow for easy linking
* into the publication without needing to know the node. Of course if you know the
* node that will still work too (e.g. http://[base url]/node/[node id]
* so the nodeapi function ensures that the URL path is set after insert or update
* of the node and when the node is loaded if it hasn't yet been set.
*
* @ingroup tripal_pub
*/
function tripal_pub_node_load($nodes, $types) {
if (count(array_intersect(array('chado_pub'), $types))) {
foreach ($nodes as $nid => $node) {
if ($node->type == 'chado_pub' and !property_exists($node, 'path')) {
$pub_id = chado_get_id_from_nid('pub', $node->nid);
$path = tripal_pub_set_pub_url($node, $pub_id);
}
}
}
}
/**
* Implements hook_node_update(). Acts on all content types.
*
* We want the publications to always have a URL of http://[base url]/pub/[pub id]
* where [pub id] is the Chado publication ID. This will allow for easy linking
* into the publication without needing to know the node. Of course if you know the
* node that will still work too (e.g. http://[base url]/node/[node id]
* so the nodeapi function ensures that the URL path is set after insert or update
* of the node and when the node is loaded if it hasn't yet been set.
*
* @ingroup tripal_pub
*/
function tripal_pub_node_update($node) {
if ($node->type == 'chado_pub') {
// get the pub
$pub_id = chado_get_id_from_nid('pub', $node->nid);
$values = array('pub_id' => $pub_id);
$pub = chado_generate_var('pub', $values);
// expand the 'text' fields as those aren't included by default
// and they really shouldn't be so large to cause problems
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
$pub = chado_expand_var($pub, 'field', 'pub.uniquename');
$node->pub = $pub;
// Now get the title
$node->title = chado_get_node_title($node);
tripal_pub_set_pub_url($node, $pub_id);
}
}
/**
* Implements hook_node_presave(). Acts on all content types.
*
* @ingroup tripal_pub
*/
function tripal_pub_node_presave($node) {
switch ($node->type) {
case 'chado_pub':
// when syncing the details are not present in the $node object
// as they are when submitted via the form. Therefore, if we do
// not see any field values from the form, we assume this fucntion
// is being called for syncing, so we must set the title accordingly
if (property_exists($node, 'title')) {
// do nothing, the title is set
}
else if (property_exists($node, 'pub')) {
// in Drupal a node title can only be 255 characters so we truncate
// it just in case
$node->title = substr($node->pub->title, 0, 255);
}
break;
}
}
/**
* Implements [content_type]_chado_node_default_title_format().
*
* Defines a default title format for the Chado Node API to set the titles on
* Chado pub nodes based on chado fields.
*/
function chado_pub_chado_node_default_title_format() {
return '[pub.title]';
}