Updated project generation from php files to support inclusion criteria and other features

relis_app/controllers/test/Unit_test.php

@@ -98,8 +98,6 @@ function __construct()
         $this->apiQueryUnitTest = new ApiQueryUnitTest();
         $this->opUnitTest = new OpUnitTest();
         $this->inclusion_mode_conflictUnitTest = new inclusion_mode_conflictUnitTest();
-        //$this->screeningInclusionModeConflictsTest = new X
-        //$this->customScreeningPhaseConfigTest = new X
     }
 
     public function relis_unit_test($result = "html_report")

relis_app/helpers/install_project_helper.php

@@ -341,6 +341,8 @@ function update_screening_values($screening, $target_db = 'current')
 	$config['screening_status_to_validate'] = !empty($screening['status_to_validate']) ? $screening['status_to_validate'] : "Excluded";
     $config['validation_default_percentage'] = !empty($screening['validation_percentage']) ? $screening['validation_percentage'] : "20";
 	$config['screening_validator_assignment_type'] = !empty($screening['validation_assigment_mode']) ? $screening['validation_assigment_mode'] : "Normal";
+	$config['screening_inclusion_mode'] = !empty($screening['inclusion_mode']) ? $screening['inclusion_mode'] : "None";
+	$config['use_kappa'] = isset($screening['use_kappa']) ? $screening['use_kappa'] : 1;
 	$config['screening_on'] = 1;
 	$result = $ci->db3->update('config', $config, "config_id=1");
 	//add new phases
@@ -350,24 +352,39 @@ function update_screening_values($screening, $target_db = 'current')
 		//get total number
 		$nbr_phase = count($screening['phases']);
 		$i = 1;
-		$all_phases = array();
 		foreach ($screening['phases'] as $key => $value) {
 			$conf_phase['phase_title'] = !empty($value['title']) ? $value['title'] : "Phase " . $i;
 			$conf_phase['description'] = !empty($value['description']) ? $value['description'] : "";
 			$conf_phase['displayed_fields'] = !empty($value['fields']) ? $value['fields'] : "Title";
 			$conf_phase['screen_phase_final'] = ($nbr_phase == $i) ? '1' : "0";
 			$conf_phase['screen_phase_order '] = $i * 10;
 			$conf_phase['added_by'] = active_user_id();
-			array_push($all_phases, $conf_phase);
+
+			$ci->db3->insert('screen_phase', $conf_phase);
+			//insert corresponding phase config
+			if ($ci->db3->affected_rows() > 0) {
+				$phase_config = array();
+				$phase_config['screen_phase_id'] = $ci->db3->insert_id();
+				$phase_config['config_type'] = isset($value['config']) ? 'Custom' : 'Default';
+				if ($phase_config['config_type'] == 'Custom') {
+					$phase_config['screening_reviewer_number'] = !empty($value['config']['review_per_paper']) ? $value['config']['review_per_paper'] : $config['screening_reviewer_number'];
+					$phase_config['screening_screening_conflict_resolution'] = !empty($value['config']['conflict_resolution']) ? $value['config']['conflict_resolution'] : $config['screening_screening_conflict_resolution'];
+					$phase_config['screening_conflict_type'] = !empty($value['config']['conflict_type']) ? $value['config']['conflict_type'] : $config['screening_conflict_type'];
+					$phase_config['screening_status_to_validate'] = !empty($value['config']['status_to_validate']) ? $value['config']['status_to_validate'] : $config['screening_status_to_validate'];
+					$phase_config['validation_default_percentage'] = !empty($value['config']['validation_percentage']) ? $value['config']['validation_percentage'] : $config['validation_default_percentage'];
+					$phase_config['screening_validator_assignment_type'] = !empty($value['config']['validation_assigment_mode']) ? $value['config']['validation_assigment_mode'] : $config['screening_validator_assignment_type'];
+					$phase_config['screening_inclusion_mode'] = !empty($value['config']['inclusion_mode']) ? $value['config']['inclusion_mode'] : $config['screening_inclusion_mode'];
+					$phase_config['use_kappa'] = isset($screening['use_kappa']) ? $value['config']['use_kappa'] : $config['use_kappa'];
+				}
+				$ci->db3->insert('screen_phase_config', $phase_config);
+			}
 			$i++;
 		}
-		//print_test($all_phases);
-		$result = $ci->db3->insert_batch('screen_phase', $all_phases);
-		//print_test($result);
 	}
 	// Add exclusion criteria , sourcepapers,and searc_strategy
 	$screen_configs_to_save = array(
 		'exclusion_criteria' => array('table' => 'ref_exclusioncrieria'),
+		'inclusion_criteria' => array('table' => 'ref_inclusioncriteria'),
 		'source_papers' => array('table' => 'ref_papers_sources'),
 		'search_startegy' => array('table' => 'ref_search_strategy'),
 	);

relis_app/helpers/tests/inclusion_mode_conflict_ut_helper.php

@@ -18,7 +18,7 @@ function run_tests() {
         $this->defaultCriteria_one();
         $this->keepOneFromAny();
         $this->keepOneFromAll();
-        $this->resetScreening(); 
+        $this->resetScreening();
     }
 
     private function TestInitialize() {
@@ -75,14 +75,14 @@ private function affected_phases() {
         $action = "get_affected_phases (Model method)";
         $test_name = "Testing is changes are made to the right affected phases";
         $test_aspect = "Affected phases";
-        $expected_value = json_encode(array(1));
+        $expected_value = json_encode(array(3));
         $actual_value = "";
 
         addScreeningPhase("Link");
-        $this->ci->db->query("UPDATE relis_dev_correct_" . getProjectShortName() . ".screen_phase_config SET config_type = 'Custom' WHERE screen_phase_config_id = 2");
+        $this->ci->db->query("UPDATE relis_dev_correct_" . getProjectShortName() . ".screen_phase_config SET config_type = 'Custom' WHERE screen_phase_config_id = 3");
 
         $model = new Screening_dataAccess();
-        $actual_value = json_encode($model->get_affected_phases(getScreeningPhaseId("Abstract")));
+        $actual_value = json_encode($model->get_affected_phases(getScreeningPhaseId("Link")));
 
         run_test($this->controller, $action, $test_name, $test_aspect, $actual_value, $actual_value);
     }
@@ -209,7 +209,7 @@ private function keepOneFromAny() {
         run_test($this->controller, $action, $test_name, $test_aspect, $expected_value, $actual_value);
     }
 
-    private function keepOneFromAll() {
+    private function    keepOneFromAll() {
         $action = "solve_mode_conflict";
         $test_name = "Testing if one random criteria is added properly when switching from All to One inclusion mode";
         $test_aspect = "How many criteria were added?";

relis_app/helpers/tests/testFiles/project/classification_install_demoTestProject.php

@@ -638,9 +638,14 @@ function get_classification_demoTestProject()
 	$screening['validation_assigment_mode'] = 'Normal';
     $screening['status_to_validate'] = 'Excluded';
 	$screening['validation_percentage'] = '10';
+	//$screening['inclusion_mode'] = 'One';
+	$screening['use_kappa'] = true;
 	$screening['exclusion_criteria'] = array();
 	array_push($screening['exclusion_criteria'], "EC1: Too short ");
 	array_push($screening['exclusion_criteria'], "EC2: Not abour chocolate");
+	/* $screening['inclusion_criteria'] = array();
+	array_push($screening['inclusion_criteria'], "IC1: Published at most 2 years ago");
+	array_push($screening['inclusion_criteria'], "IC2: Longer than 10 pages"); */
 	$screening['source_papers'] = array();
 	array_push($screening['source_papers'], "Google Scholar");
 	array_push($screening['source_papers'], "Chocolate DB");

relis_app/helpers/tests/testFiles/project/classification_install_demoTestProject2.php

@@ -762,4 +762,4 @@ function get_classification_demoTestProject2()
 	//REPORTING
 
 	return $result;
-}
+}