Merge pull request #15 from openeyes/develop

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AppertaFoundation · Apr 9, 2020 · 269b1cf · 269b1cf
2 parents 123511c + a49f3c9
commit 269b1cf
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Showing 115 changed files with 806 additions and 3,086 deletions.
diff --git a/phpcs.xml b/phpcs.xml
@@ -78,12 +78,12 @@
     -->
 
     <!--
-       Include all sniffs in the PEAR standard. Note that the
+       Include all sniffs in the PSR12 standard. Note that the
        path to the standard does not have to be specified as the
-       PEAR standard exists inside the PHP_CodeSniffer install
+       PSR12 standard exists inside the PHP_CodeSniffer install
        directory.
     -->
-    <rule ref="PSR2">
+    <rule ref="PSR12">
         <!-- Too many classes are already defined in OE that do not conform to this rule -->
         <exclude name="Squiz.Classes.ValidClassName.NotCamelCaps"/>
     </rule>

diff --git a/protected/assets/js/OpenEyes.UI.RestrictData.js b/protected/assets/js/OpenEyes.UI.RestrictData.js
@@ -125,7 +125,7 @@ OpenEyes.UI = OpenEyes.UI || {};
         Switch to array for better support
         */
         let arr = Array.prototype.slice.call(collapseData);
-        arr.forEach( ( elem ) => { hideShowBtn( elem ); });
+        arr.forEach( ( elem ) => { hideShowBtn( elem );$(elem).trigger('loaded'); });
     };
 
     exports.RestrictDataController = RestrictDataController;

diff --git a/protected/assets/js/analytics/analytics_cataract.js b/protected/assets/js/analytics/analytics_cataract.js
@@ -273,6 +273,7 @@ var analytics_cataract = (function () {
 
 	function toggleAllSurgeonOpt() {
 		$(this).toggleClass('green hint');
+        $(this).blur();
 		if ($('#analytics_allsurgeons').val() == 'on') {
 			$('#analytics_allsurgeons').val('');
 		} else {
@@ -282,10 +283,11 @@ var analytics_cataract = (function () {
 	}
 
 	function clearDate(event_date) {
-		var date_from = analytics_toolbox.processDate(new Date(event_date['date_from']))
-		var date_to = analytics_toolbox.processDate(new Date(event_date['date_to']))
-		$('#analytics_datepicker_from').val(date_from);
-		$('#analytics_datepicker_to').val(date_to);
+		var date_from = new Date(event_date['date_from']);
+		var date_to = new Date(event_date['date_to']);
+		pickmeup('#analytics_datepicker_from').set_date(date_from);
+
+		pickmeup('#analytics_datepicker_to').set_date(date_to);
 	}
 
 	var init = function (data) {

diff --git a/protected/assets/js/analytics/analytics_drill_down.js b/protected/assets/js/analytics/analytics_drill_down.js
@@ -21,9 +21,9 @@ var analytics_drill_down = (function () {
 
 	var request_url = '/analytics/getdrilldown';
 	function patientDetails() {
-		$('#js-analytics-spinner').show();
 		var link = $(this).data('link');
-		window.location.href = link;
+		$(this).css('background-color', '#28303b');
+		window.open(link, '_blank');
 	}
 
 	function getPatient() {
@@ -187,10 +187,12 @@ var analytics_drill_down = (function () {
 					patient_list_container.addClass('analytics-event-list');
 					$('<th class="text-left" style="vertical-align: center;">Eye</th>').insertBefore('.analytics-patient-list .patient_procedures');
 					$('<th style="vertical-align: center;">Date</th>').insertAfter('.analytics-patient-list .patient_procedures');
-					colGroup.append('<col style="width: 350px;"><col style="width: 50px;"><col style="width: 400px;"><col style="width: 100px;">');
+					// the width for eye, procedures, date columns
+					colGroup.append('<col style="width: 3.5%x;"><col style="width: 24%;"><col style="width: 7%;">');
 				} else {
 					// set up patient list dom layout for non cataract
-					colGroup.append('<col style="width: 450px;"><col style="width: 450px;">');
+					// for procedures column
+					colGroup.append('<col style="width: 24%;">');
 				}
 				// deep copy from passed in data
 				g_data = custom_data.slice();

diff --git a/protected/assets/js/analytics/analytics_toolbox.js b/protected/assets/js/analytics/analytics_toolbox.js
@@ -70,21 +70,16 @@ var analytics_toolbox = (function () {
 	function initDatePicker(def) {
 		var date_from = typeof (def) === 'undefined' ? false : new Date(def['date_from']);
 		var date_to = typeof (def) === 'undefined' ? false : new Date(def['date_to']);
-		if (date_from && date_to) {
-			date_from = processDate(date_from);
-
-			date_to = processDate(date_to);
-		}
 
 		pickmeup('#analytics_datepicker_from', {
-			format: 'Y-m-d',
+			format: 'd-b-Y',
 			date: date_from,
 			hide_on_select: true,
 			default_date: date_from,
 		});
 
 		pickmeup('#analytics_datepicker_to', {
-			format: 'Y-m-d',
+			format: 'd-b-Y',
 			date: date_to,
 			hide_on_select: true,
 			default_date: date_to,

diff --git a/protected/assets/js/dashboard/OpenEyes.Dash.js b/protected/assets/js/dashboard/OpenEyes.Dash.js
@@ -456,6 +456,9 @@
             chart.data[1]['customdata'] = incompletedData.map(function (item) {
                 return item;
             });
+            hovertemplate = '%{x} %{y} of Total ' + data['total'] + ' Ops';
+            chart.data[0]['hovertemplate'] = hovertemplate;
+            chart.data[1]['hovertemplate'] = hovertemplate;
             Plotly.redraw(chart);
         },
 

diff --git a/protected/commands/ImportDrugsCommand.php b/protected/commands/ImportDrugsCommand.php
@@ -899,7 +899,7 @@ public function copyToOE()
 
         $cmd = "UPDATE medication
                 SET default_dose_unit_term = 'drop' 
-	            WHERE m.preferred_term like '%eye drop%'";
+	            WHERE preferred_term like '%eye drop%'";
 
         Yii::app()->db->createCommand($cmd)->execute();
 
@@ -948,7 +948,7 @@ private function convertMappedUOMsToPlural()
 
         $cmd = "UPDATE medication_attribute_option SET description = CONCAT(description,\"(s)\") WHERE ";
         foreach ($this->uom_to_forms_mapping as $uom => $forms) {
-            if ($uom != "Drop"){ // we don't want plural for Drop(s) as they are almost always 1 drop in opthalmology (DA decision 02/04/2020)
+            if (strtolower($uom) != "drop") { // we don't want plural for Drop(s) as they are almost always 1 drop in opthalmology (DA decision 02/04/2020)
                 $cmd .= "(BINARY description = \"$uom\") OR ";
             }
         }
@@ -976,20 +976,21 @@ private function applyUOMToMedications()
                 ";
         Yii::app()->db->createCommand($cmd)->execute();
 
-
-        $cmd = "UPDATE medication as med 
-            JOIN ( 
+        foreach (['UNIT_OF_MEASURE', 'UNIT_DOSE_UNIT_OF_MEASURE'] as $uom_attr) {
+            $cmd = "UPDATE medication as med 
+            INNER JOIN ( 
                 SELECT maa.medication_id AS med_id, mao.description AS UOM
                 FROM medication_attribute_option mao
-                JOIN medication_attribute_assignment maa
+                INNER JOIN medication_attribute_assignment maa
                     ON maa.medication_attribute_option_id = mao.id
-                JOIN medication_attribute ma
+                INNER JOIN medication_attribute ma
                     ON mao.medication_attribute_id = ma.id
-                WHERE ma.name = \"UNIT_OF_MEASURE\"
+                WHERE ma.name = \"{$uom_attr}\"
             ) AS uom_table ON med.id = uom_table.med_id
             SET med.default_dose_unit_term = uom_table.UOM";
 
-        Yii::app()->db->createCommand($cmd)->execute();
+            Yii::app()->db->createCommand($cmd)->execute();
+        }
 
         $cmd = "UPDATE medication 
         SET default_dose = 1 

diff --git a/protected/commands/OldMedicationAndDrugDeletionCommand.php b/protected/commands/OldMedicationAndDrugDeletionCommand.php
@@ -75,9 +75,9 @@ private function deleteOldDrugAndMedicationTables()
                      'site_subspecialty_drug',
                      'medication_drug',
                  ];
-        $tables_to_ignore = ['drug_duration'];
+
         foreach (Yii::app()->db->getSchema()->getTableNames() as $table_to_rename) {
-            if (((substr($table_to_rename, 0, strlen($drugTableSuffix)) === $drugTableSuffix) || in_array($table_to_rename, $tables_to_rename)) && !in_array($table_to_rename, $tables_to_ignore)) {
+            if (((substr($table_to_rename, 0, strlen($drugTableSuffix)) === $drugTableSuffix) || in_array($table_to_rename, $tables_to_rename))) {
                 Yii::app()->db->createCommand("RENAME TABLE " . $table_to_rename . " TO archive_" . $table_to_rename)->execute();
             }
         }

diff --git a/protected/commands/PopulateAutoMedicationSetsCommand.php b/protected/commands/PopulateAutoMedicationSetsCommand.php
@@ -17,8 +17,7 @@
 
 class PopulateAutoMedicationSetsCommand extends CConsoleCommand
 {
-    private $_pid;
-    private $_pidfile = '/tmp/oe_populatesets.pid';
+    private $lock_name = "PopulateAutoMedicationSetsCommand_lock";
 
     public function getHelp()
     {
@@ -30,13 +29,15 @@ public function run($args)
         $t = microtime(true);
         echo "[" . (date("Y-m-d H:i:s")) . "] PopulateAutoMedicationSets ... ";
 
-        $this->_pid = getmypid();
-
-        if ($this->_isRunning()) {
+        if ($this->_isRunning() || !$this->acquireLock()) {
             echo "Another process is already being run." . PHP_EOL;
             exit(1);
         }
 
+        register_shutdown_function(function () {
+            $this->releaseLock();
+        });
+
         //populate whole set unless we are given specific set number to reduce time on rebuilding sets on admin page
         if (empty($args)) {
             MedicationSet::populateAutoSets();
@@ -53,12 +54,33 @@ public function run($args)
 
     private function _isRunning()
     {
-        if (file_exists($this->_pidfile)) {
-            $pid = filter_var(file_get_contents($this->_pidfile), FILTER_SANITIZE_NUMBER_INT);
-            return file_exists("/proc/$pid");
-        } else {
-            return false;
-        }
+        return (bool) Yii::app()->db->createCommand(
+            'SELECT IS_USED_LOCK(:name)'
+        )->bindValue(':name', $this->lock_name)
+        ->queryScalar();
+    }
+
+    /**
+     * @return bool acquiring result
+     */
+    private function acquireLock()
+    {
+        return (bool) Yii::app()->db->createCommand(
+            'SELECT GET_LOCK(:name, :timeout)',
+        )->bindValue(':name', $this->lock_name)
+        ->bindValue(':timeout', 0) // timeout = 0 means that the method will return false immediately in case lock is used
+        ->queryScalar();
+    }
+
+    /**
+     * @return bool release result
+     */
+    private function releaseLock()
+    {
+        return (bool) Yii::app()->db->createCommand(
+            'SELECT RELEASE_LOCK(:name)'
+        )->bindValue(':name', $this->lock_name)
+        ->queryScalar();
     }
 
     public function actionCheckRunning()

diff --git a/protected/components/DbFixtureManager.php b/protected/components/DbFixtureManager.php
@@ -21,6 +21,10 @@ class DbFixtureManager extends CDbFixtureManager
 {
     protected $fixtures = array();
 
+    /**
+     * @throws CDbException
+     * @throws CException
+     */
     public function init()
     {
         $paths = array($this->basePath ?: Yii::getPathOfAlias('application.tests.fixtures'));
@@ -64,6 +68,7 @@ public function getFixtures()
 
     /**
      * @param string $tableName
+     * @throws CException
      */
     public function resetTable($tableName)
     {
@@ -79,6 +84,8 @@ public function resetTable($tableName)
      * @param string $table_name
      *
      * @return array|false
+     * @throws CDbException
+     * @throws CException
      */
     public function loadFixture($table_name)
     {