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Merge branch 'main' into update_ProjectGeneration
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@AbdelhamidRouatbi
AbdelhamidRouatbi authored Aug 25, 2024
2 parents 90f1a86 + fdabe24 commit 9ae4c01
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Showing 3 changed files with 224 additions and 50 deletions.
82 changes: 77 additions & 5 deletions relis_app/controllers/Screening.php
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Original file line number Diff line number Diff line change
Expand Up @@ -738,15 +738,20 @@ public function assignment_screen($data = array())
* The purpose of this function is to retrieve and organize papers for screening based on the provided source,
* source status, current phase, and assignment role
*/
function get_papers_to_screen($source = 'all', $source_status = 'all', $current_phase = "", $assignment_role = "")
function get_papers_to_screen($source = 'all', $source_status = 'all', $current_phase = "", $assignment_role = "", $validation_by_criteria = "")
{
//$source_status="Included";
//$source='1';
if (empty($current_phase)) {
$current_phase = active_screening_phase();
}

$all_papers = $this->Screening_dataAccess->select_screening_all_papers($source, $source_status);
if (empty($validation_by_criteria) or $validation_by_criteria == 'None'){
$all_papers = $this->Screening_dataAccess->select_screening_all_papers($source, $source_status);
}
else{
$all_papers = $this->Screening_dataAccess->select_screening_paper_by_criteria($source_status, $validation_by_criteria, $current_phase);
}

$result['all_papers'] = $all_papers;
// get papers already assigned in current phase
Expand Down Expand Up @@ -2102,6 +2107,9 @@ public function validate_screen_set($data = array())
$data['users'] = $_assign_user;
$data['number_papers'] = count($papers['to_assign']);
$data['number_papers_assigned'] = count($papers['assigned']);
//Get screening criteria
$validation_by_exclusion_criteria = $this->manager_lib->get_reference_select_values('exclusioncrieria;ref_value', False);
$data['validation_by_exclusion_criteria'] = $validation_by_exclusion_criteria;
$data['percentage_of_papers'] = get_appconfig_element('validation_default_percentage');
$data['papers_categories'] = array('Excluded' => 'Excluded', 'Included' => 'Included', 'all' => 'All');
$data['page_title'] = lng('Assign papers for validation ' . $append_title);
Expand All @@ -2115,6 +2123,55 @@ public function validate_screen_set($data = array())
$this->load->view('shared/body', $data);
}

public function get_papers_by_criteria($data = array()) {
header('Content-Type: application/json');
$validation_by_criteria = $this->input->post('validation_by_criteria');
$screening_phase_id = active_screening_phase();
$paper_source = $screening_phase_id;
$screening_phase_info = active_screening_phase_info();
$phase_title = $screening_phase_info['phase_title'];
if(!empty($validation_by_criteria)){
$criteria_list = implode(', ', $validation_by_criteria);
$append_title = "( Excluded papers by $criteria_list from $phase_title )";
}
else{
$append_title = "( Excluded papers from $phase_title )";
}
$page_title = lng('Assign papers for validation ' . $append_title);

// Initialize the result arrays
$papers = array(
'to_assign' => array(),
'assigned' => array(),
'all_papers' => array()
);

if (!empty($validation_by_criteria)) {
foreach ($validation_by_criteria as $criteria) {
$result = $this->get_papers_to_screen($paper_source, 'Excluded', '', 'Validation', $criteria);
// Merge the 'to_assign', 'assigned', and 'all_papers' papers
$papers['to_assign'] = array_merge($papers['to_assign'], $result['to_assign']);
$papers['assigned'] = array_merge($papers['assigned'], $result['assigned']);
$papers['all_papers'] = array_merge($papers['all_papers'], $result['all_papers']);
}
} else {
$papers = $this->get_papers_to_screen($paper_source, 'Excluded', '', 'Validation');
}

$paper_list[0] = array('Key', 'Title');
foreach ($papers['to_assign'] as $key => $value) {
$paper_list[$key + 1] = array($value['bibtexKey'], $value['title']);
}

$updated_data = array(
'number_papers' => count($papers['to_assign']),
'number_papers_assigned' => count($papers['assigned']),
'paper_list' => $paper_list,
'page_title' => $page_title
);
echo json_encode($updated_data);
}

//responsible for assigning papers for validation based on the previous screening phase.
public function validate_screen_from_previous_set($data = array())
{ //old vesion updated
Expand Down Expand Up @@ -2198,6 +2255,7 @@ function save_assign_screen_validation()
$post_arr = $this->input->post();
$users = array();
$i = 1;
$validation_by_exclusion_criteria_toggle = 'off';
$percentage = intval($post_arr['percentage']);
if (empty($percentage)) {
$data['err_msg'] = lng(' Please provide "Percentage of papers" ');
Expand All @@ -2206,6 +2264,10 @@ function save_assign_screen_validation()
$data['err_msg'] = lng("Please provide a correct value of percentage");
$this->validate_screen_set($data);
} else {
// Check if 'Validation by exclusion criteria' is open
if (!empty($post_arr['validation_by_exclusion_criteria_toggle'])){
$validation_by_exclusion_criteria_toggle = $post_arr['validation_by_exclusion_criteria_toggle'];
}
// Get selected users
if (!empty($post_arr['assign_papers_to'])) { // assign to connected user
array_push($users, $post_arr['assign_papers_to']);
Expand All @@ -2228,11 +2290,21 @@ function save_assign_screen_validation()
$screening_phase_info = active_screening_phase_info();
$phase_title = $screening_phase_info['phase_title'];
$reviews_per_paper = 1;
$papers_all = $this->get_papers_to_screen($papers_sources, $paper_source_status, '', 'Validation');
$papers = $papers_all['to_assign'];
if ($validation_by_exclusion_criteria_toggle == 'on'){
$validation_by_criteria = $post_arr['choose_exclusion_criteria'];
$papers = array();
foreach ($validation_by_criteria as $criteria) {
$result = $this->get_papers_to_screen($papers_sources, 'Excluded', '', 'Validation', $criteria);
$papers = array_merge($papers, $result['to_assign']);
}
}
else {
$papers_all = $this->get_papers_to_screen($papers_sources, $paper_source_status, '', 'Validation');
$papers = $papers_all['to_assign'];
}
$papers_to_validate_nbr = round(count($papers) * $percentage / 100);
$operation_description = "Assign $percentage % ($papers_to_validate_nbr) of " . $paper_source_status . " papers for $phase_title";
// print_test($papers);
// print_test($papers);
shuffle($papers); // randomize the list
$assign_papers = array();
$this->db2 = $this->load->database(project_db(), TRUE);
Expand Down
28 changes: 28 additions & 0 deletions relis_app/models/Screening_dataAccess.php
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,34 @@ function select_screening_paper($current_phase, $condition)
return $paper_assigned;
}

function select_screening_paper_by_criteria($source_status, $exclusion_criteria_name, $screening_phase)
{
//get the id of selected criteria
$ref_id_sql = "SELECT ref_id FROM ref_exclusioncrieria WHERE ref_value = ? AND ref_active = 1";
$ref_id_result = $this->db_current->query($ref_id_sql, $exclusion_criteria_name)->row_array();

if (empty($ref_id_result)) {
return array();
}

$ref_id = $ref_id_result['ref_id'];

$sql = "SELECT paper.id, paper.bibtexKey, paper.title, ref_exclusioncrieria.ref_value AS exclusion
FROM screening_paper
INNER JOIN ref_exclusioncrieria ON ref_exclusioncrieria.ref_id = screening_paper.exclusion_criteria
INNER JOIN paper ON paper.id = screening_paper.paper_id
INNER JOIN screen_decison ON screen_decison.paper_id = screening_paper.paper_id
WHERE screening_paper.screening_phase = ? AND screening_paper.exclusion_criteria = ?
AND screen_decison.screening_decision = ?
GROUP BY paper.id, paper.bibtexKey, paper.title, ref_exclusioncrieria.ref_value
ORDER BY paper.bibtexKey, screening_paper.screening_time
";

$all_papers = $this->db_current->query($sql, array($screening_phase, $ref_id, $source_status))->result_array();

return $all_papers;
}

function get_all_screenings($screening_phase)
{
$sql = "select * from screening_paper where assignment_role='Screening' AND screening_phase = $screening_phase AND screening_status='Done' AND screening_active=1 ";
Expand Down
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