From ab6bf66ef2c5b33229c615bc8cd0be148227ded6 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 20:37:22 +0000
Subject: [PATCH 01/20] Update tracker to version 2.0.4

---
 modules/tracker/configs/module.ini         |   2 +-
 modules/tracker/database/mysql/2.0.4.sql   | 159 +++++++++++++++++++++
 modules/tracker/database/upgrade/2.0.4.php |  37 +++++
 3 files changed, 197 insertions(+), 1 deletion(-)
 create mode 100644 modules/tracker/database/mysql/2.0.4.sql
 create mode 100644 modules/tracker/database/upgrade/2.0.4.php

diff --git a/modules/tracker/configs/module.ini b/modules/tracker/configs/module.ini
index e47190b71..f07b8bff7 100644
--- a/modules/tracker/configs/module.ini
+++ b/modules/tracker/configs/module.ini
@@ -6,4 +6,4 @@ description = "Track scalar results over time"
 category = "Visualization"
 dependencies = api,scheduler
 uuid = "3048a9fa-89ab-4e61-a55e-a49379fa6dc"
-version = "2.0.3"
+version = "2.0.4"
diff --git a/modules/tracker/database/mysql/2.0.4.sql b/modules/tracker/database/mysql/2.0.4.sql
new file mode 100644
index 000000000..389707694
--- /dev/null
+++ b/modules/tracker/database/mysql/2.0.4.sql
@@ -0,0 +1,159 @@
+-- Midas Server. Copyright Kitware SAS. Licensed under the Apache License 2.0.
+
+-- MySQL database for the tracker module, version 2.0.4
+
+CREATE TABLE IF NOT EXISTS `tracker_producer` (
+    `producer_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `community_id` bigint(20) NOT NULL,
+    `repository` varchar(255) NOT NULL,
+    `executable_name` varchar(255) NOT NULL,
+    `display_name` varchar(255) NOT NULL,
+    `description` text NOT NULL,
+    `revision_url` text NOT NULL,
+    `histogram_max_x` double,
+    `producer_definition` text,
+    PRIMARY KEY (`producer_id`),
+    KEY (`community_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_scalar` (
+    `scalar_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `trend_id` bigint(20) NOT NULL,
+    `value` double,
+    `submission_id` bigint(20) NOT NULL,
+    PRIMARY KEY (`scalar_id`),
+    KEY (`trend_id`),
+    KEY (`submission_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_submission` (
+    `submission_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `producer_id` bigint(20) NOT NULL,
+    `name` varchar(255) NOT NULL DEFAULT '',
+    `uuid` varchar(255) NOT NULL DEFAULT '',
+    `submit_time` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    `producer_revision` varchar(255),
+    `user_id` bigint(20) NOT NULL DEFAULT '-1',
+    `official` tinyint(4) NOT NULL DEFAULT '1',
+    `build_results_url` text NOT NULL,
+    `branch` varchar(255) NOT NULL DEFAULT '',
+    `extra_urls` text,
+    `reproduction_command` text,
+    PRIMARY KEY (`submission_id`),
+    UNIQUE KEY (`uuid`),
+    KEY (`user_id`),
+    KEY (`submit_time`),
+    KEY (`branch`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_submission2item` (
+    `submission_id` bigint(20) NOT NULL,
+    `item_id` bigint(20) NOT NULL,
+    `label` varchar(255) NOT NULL,
+    `trendgroup_id` bigint(20) NOT NULL,
+    KEY (`submission_id`),
+    KEY (`item_id`),
+    KEY (`trendgroup_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_threshold_notification` (
+    `threshold_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `trend_id` bigint(20) NOT NULL,
+    `value` double,
+    `comparison` varchar(2),
+    `action` varchar(80) NOT NULL,
+    `recipient_id` bigint(20) NOT NULL,
+    PRIMARY KEY (`threshold_id`),
+    KEY (`trend_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_trend` (
+    `trend_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `trendgroup_id` bigint(20),
+    `metric_name` varchar(255) NOT NULL,
+    `display_name` varchar(255) NOT NULL,
+    `unit` varchar(255) NOT NULL,
+    `key_metric` tinyint(4) NOT NULL DEFAULT '0',
+    PRIMARY KEY (`trend_id`),
+    KEY (`trendgroup_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_trend_threshold` (
+    `trend_threshold_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `producer_id` bigint(20) NOT NULL,
+    `metric_name` varchar(255) NOT NULL,
+    `abbreviation` varchar(255) NOT NULL DEFAULT '',
+    `warning` double,
+    `fail` double,
+    `min` double,
+    `max` double,
+    `lower_is_better` tinyint(4) NOT NULL DEFAULT '0',
+    PRIMARY KEY (`trend_threshold_id`),
+    KEY (`producer_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_trendgroup` (
+    `trendgroup_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `producer_id` bigint(20) NOT NULL,
+    `config_item_id` bigint(20),
+    `test_dataset_id` bigint(20),
+    `truth_dataset_id` bigint(20),
+    PRIMARY KEY (`trendgroup_id`),
+    KEY (`producer_id`),
+    KEY (`config_item_id`),
+    KEY (`test_dataset_id`),
+    KEY (`truth_dataset_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_param` (
+    `param_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `submission_id` bigint(20) NOT NULL,
+    `param_name` varchar(255) NOT NULL,
+    `param_type` enum('text', 'numeric') NOT NULL,
+    `text_value` text,
+    `numeric_value` double,
+    PRIMARY KEY (`param_id`),
+    KEY (`submission_id`),
+    KEY (`param_name`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_aggregate_metric` (
+    `aggregate_metric_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `aggregate_metric_spec_id` bigint(20) NOT NULL,
+    `submission_id` bigint(20) NOT NULL,
+    `value` double,
+    PRIMARY KEY (`aggregate_metric_id`),
+    KEY (`aggregate_metric_spec_id`),
+    KEY (`submission_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_aggregate_metric_spec` (
+    `aggregate_metric_spec_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `producer_id` bigint(20) NOT NULL,
+    `name` varchar(255) NOT NULL DEFAULT '',
+    `description` varchar(255) NOT NULL DEFAULT '',
+    `spec` text NOT NULL DEFAULT '',
+    `abbreviation` varchar(255) NOT NULL DEFAULT '',
+    `warning` double,
+    `fail` double,
+    `max` double,
+    PRIMARY KEY (`aggregate_metric_spec_id`),
+    KEY (`producer_id`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_aggregate_metric_notification` (
+    `aggregate_metric_notification_id` bigint(20) NOT NULL AUTO_INCREMENT,
+    `aggregate_metric_spec_id` bigint(20) NOT NULL,
+    `branch` varchar(255) NOT NULL DEFAULT '',
+    `value` double,
+    `comparison` varchar(2) NOT NULL DEFAULT '',
+    PRIMARY KEY (`aggregate_metric_notification_id`),
+    KEY (`aggregate_metric_spec_id`),
+    KEY (`branch`)
+) DEFAULT CHARSET=utf8;
+
+CREATE TABLE IF NOT EXISTS `tracker_user2aggregate_metric_notification` (
+    `user_id` bigint(20) NOT NULL,
+    `aggregate_metric_notification_id` bigint(20) NOT NULL,
+    PRIMARY KEY (`user_id`, `aggregate_metric_notification_id`)
+) DEFAULT CHARSET=utf8;
diff --git a/modules/tracker/database/upgrade/2.0.4.php b/modules/tracker/database/upgrade/2.0.4.php
new file mode 100644
index 000000000..64ae040bd
--- /dev/null
+++ b/modules/tracker/database/upgrade/2.0.4.php
@@ -0,0 +1,37 @@
+<?php
+/*=========================================================================
+ Midas Server
+ Copyright Kitware SAS, 26 rue Louis Guérin, 69100 Villeurbanne, France.
+ All rights reserved.
+ For more information visit http://www.kitware.com/.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0.txt
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+=========================================================================*/
+
+/** Upgrade the tracker module to version 2.0.4 */
+class Tracker_Upgrade_2_0_4 extends MIDASUpgrade
+{
+    /** Upgrade a MySQL database. */
+    public function mysql()
+    {
+        $this->db->query(
+            'ALTER TABLE `tracker_producer` '.
+            '   ADD COLUMN `producer_definition` text;'
+        );
+        $this->db->query(
+            'ALTER TABLE `tracker_trend_threshold` '.
+            '   ADD COLUMN `min` double,'.
+            '   ADD COLUMN `lower_is_better` tinyint(4) NOT NULL DEFAULT 0;'
+        );
+    }
+}

From a04f752484b76fcd39980304161d09620951548d Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 20:37:45 +0000
Subject: [PATCH 02/20] Correct tracker db script version number comments

---
 modules/tracker/database/mysql/2.0.2.sql | 2 +-
 modules/tracker/database/mysql/2.0.3.sql | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/tracker/database/mysql/2.0.2.sql b/modules/tracker/database/mysql/2.0.2.sql
index 9f41cb05d..c78792409 100644
--- a/modules/tracker/database/mysql/2.0.2.sql
+++ b/modules/tracker/database/mysql/2.0.2.sql
@@ -1,6 +1,6 @@
 -- Midas Server. Copyright Kitware SAS. Licensed under the Apache License 2.0.
 
--- MySQL database for the tracker module, version 2.0.1
+-- MySQL database for the tracker module, version 2.0.2
 
 CREATE TABLE IF NOT EXISTS `tracker_producer` (
     `producer_id` bigint(20) NOT NULL AUTO_INCREMENT,
diff --git a/modules/tracker/database/mysql/2.0.3.sql b/modules/tracker/database/mysql/2.0.3.sql
index 4b62b26c1..93538a026 100644
--- a/modules/tracker/database/mysql/2.0.3.sql
+++ b/modules/tracker/database/mysql/2.0.3.sql
@@ -1,6 +1,6 @@
 -- Midas Server. Copyright Kitware SAS. Licensed under the Apache License 2.0.
 
--- MySQL database for the tracker module, version 2.0.1
+-- MySQL database for the tracker module, version 2.0.3
 
 CREATE TABLE IF NOT EXISTS `tracker_producer` (
     `producer_id` bigint(20) NOT NULL AUTO_INCREMENT,

From 4ab2214d60fd826076a5965b45e4672be0f7fdc3 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 20:39:22 +0000
Subject: [PATCH 03/20] Add producer_definition to Tracker Producer model

---
 modules/tracker/models/base/ProducerModelBase.php | 1 +
 modules/tracker/models/dao/ProducerDao.php        | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/modules/tracker/models/base/ProducerModelBase.php b/modules/tracker/models/base/ProducerModelBase.php
index e1345562c..322013252 100644
--- a/modules/tracker/models/base/ProducerModelBase.php
+++ b/modules/tracker/models/base/ProducerModelBase.php
@@ -37,6 +37,7 @@ public function __construct()
             'display_name' => array('type' => MIDAS_DATA),
             'description' => array('type' => MIDAS_DATA),
             'histogram_max_x' => array('type' => MIDAS_DATA),
+            'producer_definition' => array('type' => MIDAS_DATA),
             'community' => array(
                 'type' => MIDAS_MANY_TO_ONE,
                 'model' => 'Community',
diff --git a/modules/tracker/models/dao/ProducerDao.php b/modules/tracker/models/dao/ProducerDao.php
index 547662dc1..490d608e2 100644
--- a/modules/tracker/models/dao/ProducerDao.php
+++ b/modules/tracker/models/dao/ProducerDao.php
@@ -39,6 +39,8 @@
  * @method void setCommunity(CommunityDao $communityDao)
  * @method array getTrendgroups()
  * @method void setTrendgroups(array $trendgroupDaos)
+ * @method string getProducerDefinition()
+ * @method void setProducerDefinition(string $producerDefinition)
  */
 class Tracker_ProducerDao extends Tracker_AppDao
 {

From 16a6552568358e439a41f02d5f6b0a078ac1741d Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 20:41:06 +0000
Subject: [PATCH 04/20] Add setAggregatableTrendAsKeyMetrics to Tracker Trend
 model

---
 .../tracker/models/base/TrendModelBase.php    |  9 ++++++++
 modules/tracker/models/pdo/TrendModel.php     | 21 +++++++++++++++++++
 2 files changed, 30 insertions(+)

diff --git a/modules/tracker/models/base/TrendModelBase.php b/modules/tracker/models/base/TrendModelBase.php
index 0a25df14a..717280afa 100644
--- a/modules/tracker/models/base/TrendModelBase.php
+++ b/modules/tracker/models/base/TrendModelBase.php
@@ -96,6 +96,15 @@ abstract public function getScalars($trendDao, $startDate = null, $endDate = nul
      */
     abstract public function getTrendsByGroup($producerDao, $onlyKey = false);
 
+    /**
+     * Set all Trends with the passed in metric_name to key_metrics,
+     * for the passed in Producer.
+     *
+     * @param Tracker_ProducerDao $producerDao producer DAO
+     * @param string $metricName The metric_name to match against trends
+     */
+    abstract public function setAggregatableTrendAsKeyMetrics($producerDao, $metricName);
+
     /**
      * Save the given trend. Ensure that null values are explicitly set in the database.
      *
diff --git a/modules/tracker/models/pdo/TrendModel.php b/modules/tracker/models/pdo/TrendModel.php
index 782dc874c..027f9c304 100644
--- a/modules/tracker/models/pdo/TrendModel.php
+++ b/modules/tracker/models/pdo/TrendModel.php
@@ -151,6 +151,27 @@ public function getTrendsByGroup($producerDao, $onlyKey = false)
         return $results;
     }
 
+    /**
+     * Set all Trends with the passed in metric_name to key_metrics,
+     * for the passed in Producer.
+     *
+     * @param Tracker_ProducerDao $producerDao producer DAO
+     * @param string $metricName The metric_name to match against trends
+     */
+    public function setAggregatableTrendAsKeyMetrics($producerDao, $metricName)
+    {
+        if (is_null($producerDao) || $producerDao === false) {
+            return false;
+        }
+        $producerIdQ = $this->database->getDB()->quote($producerDao->getProducerId());
+        $metricNameQ = $this->database->getDB()->quote($metricName);
+        $update = 'UPDATE tracker_trend, tracker_trendgroup SET key_metric=1 WHERE'.
+            ' producer_id = ' . $producerIdQ .
+            ' AND tracker_trend.trendgroup_id = tracker_trendgroup.trendgroup_id '.
+            ' AND tracker_trend.metric_name = ' . $metricNameQ;
+        $this->database->getDB()->query($update);
+    }
+
     /**
      * Return the trend DAOs that match the given associative array of database columns and values.
      *

From d19e25b8f05cba8a539b904fea9672b1a3cf0b6a Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 20:48:29 +0000
Subject: [PATCH 05/20] Add upsert to Tracker TrendThreshold model

---
 .../models/base/TrendThresholdModelBase.php   | 25 +++++++++
 .../tracker/models/dao/TrendThresholdDao.php  |  4 ++
 .../models/pdo/TrendThresholdModel.php        | 56 +++++++++++++++++++
 3 files changed, 85 insertions(+)

diff --git a/modules/tracker/models/base/TrendThresholdModelBase.php b/modules/tracker/models/base/TrendThresholdModelBase.php
index 01e469b56..0f6814cb2 100644
--- a/modules/tracker/models/base/TrendThresholdModelBase.php
+++ b/modules/tracker/models/base/TrendThresholdModelBase.php
@@ -36,7 +36,9 @@ public function __construct()
             'abbreviation' => array('type' => MIDAS_DATA),
             'warning' => array('type' => MIDAS_DATA),
             'fail' => array('type' => MIDAS_DATA),
+            'min' => array('type' => MIDAS_DATA),
             'max' => array('type' => MIDAS_DATA),
+            'lower_is_better' => array('type' => MIDAS_DATA),
             'producer' => array(
                 'type' => MIDAS_MANY_TO_ONE,
                 'model' => 'Producer',
@@ -48,4 +50,27 @@ public function __construct()
 
         $this->initialize();
     }
+
+    /**
+     * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
+     *
+     * @param Tracker_ProducerDao $producerDao
+     * @param string $metricName metric name of the trend threshold
+     * @param false|string $abbreviation name abbreviation for the threshold
+     * @param false|float $warning warning value for this threshold
+     * @param false|float $fail fail value for this threshold
+     * @param false|float $min min value for display of this threshold
+     * @param false|float $max max value for display of this threshold
+     * @param false|boolean $lowerIsBetter whether lower values are better for this threshold
+     * @return Tracker_TrendThresholdDao updated or created DAO
+     */
+     abstract public function upsert(
+        $producerDao,
+        $metricName,
+        $abbreviation = false,
+        $warning = false,
+        $fail = false,
+        $min = false,
+        $max = false,
+        $lowerIsBetter = false);
 }
diff --git a/modules/tracker/models/dao/TrendThresholdDao.php b/modules/tracker/models/dao/TrendThresholdDao.php
index ea3c1acd5..a4b3c338c 100644
--- a/modules/tracker/models/dao/TrendThresholdDao.php
+++ b/modules/tracker/models/dao/TrendThresholdDao.php
@@ -33,8 +33,12 @@
  * @method void setWarning(float $warning)
  * @method float getFail()
  * @method void setFail(float $fail)
+ * @method float getMin()
+ * @method void setMin(float $min)
  * @method float getMax()
  * @method void setMax(float $max)
+ * @method boolean getLowerIsBetter()
+ * @method void setLowerIsBetter(boolean $lowerIsBetter)
  * @method Tracker_ProducerDao getProducer()
  * @method void setProducer(Tracker_ProducerDao $producerDao)
  */
diff --git a/modules/tracker/models/pdo/TrendThresholdModel.php b/modules/tracker/models/pdo/TrendThresholdModel.php
index fa73438d7..7959b60cb 100644
--- a/modules/tracker/models/pdo/TrendThresholdModel.php
+++ b/modules/tracker/models/pdo/TrendThresholdModel.php
@@ -23,4 +23,60 @@
 /** Trend Threshold model for the tracker module. */
 class Tracker_TrendThresholdModel extends Tracker_TrendThresholdModelBase
 {
+    /**
+     * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
+     *
+     * @param Tracker_ProducerDao $producerDao
+     * @param string $metricName metric name of the trend threshold
+     * @param false|string $abbreviation name abbreviation for the threshold
+     * @param false|float $warning warning value for this threshold
+     * @param false|float $fail fail value for this threshold
+     * @param false|float $min min value for display of this threshold
+     * @param false|float $max max value for display of this threshold
+     * @param false|boolean $lowerIsBetter whether lower values are better for this threshold
+     * @return Tracker_TrendThresholdDao updated or created DAO
+     */
+     public function upsert(
+        $producerDao,
+        $metricName,
+        $abbreviation = false,
+        $warning = false,
+        $fail = false,
+        $min = false,
+        $max = false,
+        $lowerIsBetter = false)
+    {
+        if (is_null($producerDao) || $producerDao === false) {
+            return false;
+        }
+        $sql = $this->database->select()->setIntegrityCheck(false)
+            ->where('producer_id = ?', $producerDao->getProducerId())
+            ->where('metric_name = ?', $metricName);
+        /** @var Tracker_TrendThresholdDao $trendThresholdDao */
+        $trendThresholdDao = $this->initDao('TrendThreshold', $this->database->fetchRow($sql), $this->moduleName);
+        if ($trendThresholdDao === false) {
+            $trendThresholdDao = MidasLoader::newDao('TrendThresholdDao', $this->moduleName);
+        }
+        if ($abbreviation !== false) {
+           $trendThresholdDao->setAbbreviation($abbreviation);
+        }
+        if ($warning !== false) {
+           $trendThresholdDao->setWarning($warning);
+        }
+        if ($fail !== false) {
+           $trendThresholdDao->setFail($fail);
+        }
+        if ($min !== false) {
+           $trendThresholdDao->setMin($min);
+        }
+        if ($max !== false) {
+           $trendThresholdDao->setMax($max);
+        }
+        if ($lowerIsBetter !== false) {
+           $trendThresholdDao->setLowerIsBetter($lowerIsBetter);
+        }
+        $this->save($trendThresholdDao);
+
+        return $trendThresholdDao;
+    }
 }

From a2cec163a10e50d93571d4b836987a5d5a323ad7 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 21:20:30 +0000
Subject: [PATCH 06/20] Update producer definition based on producer schema

---
 .../controllers/components/ApiComponent.php   | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 8d9defd40..eead42969 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -341,6 +341,7 @@ public function submissionAdd($args)
      * @param uuid The uuid of the submission to validate documents for
      * @param producerConfig (Optional) JSON object describing the pipeline
      * @param submissionDocument (Optional) JSON object describing the submission
+     * @throws Exception
      */
     public function submissionValidate($args)
     {
@@ -370,11 +371,66 @@ public function submissionValidate($args)
 
             if (!$validator->isValid()) {
                 $this->getLogger()->warn('The supplied producerConfig JSON for uuid '.$uuid." does not validate. Violations:\n");
+                /** @var array $error */
                 foreach ($validator->getErrors() as $error) {
                     $this->getLogger()->warn(sprintf("[%s] %s\n", $error['property'], $error['message']));
                 }
             } else {
                 $this->getLogger()->info('The supplied producerConfig JSON for uuid '.$uuid.' is valid.');
+
+                /** @var Tracker_ProducerModel $producerModel */
+                $producerModel = MidasLoader::loadModel('Producer', 'tracker');
+                /** @var Tracker_ProducerDao $producerDao */
+                $producerDao = $submissionDao->getProducer();
+                if (!$producerModel->policyCheck(
+                    $producerDao,
+                    $user,
+                    MIDAS_POLICY_WRITE
+                )) {
+                    throw new Exception('Write permission on the producer required', 403);
+                }
+                /** @var stdClass $producerDefinition */
+                $producerDefinition = json_decode($producerConfig);
+                // Ensure that Producer and Community match.
+                if ($producerDefinition->producer !== $producerDao->getDisplayName()) {
+                    throw new Exception('Producer schema name must match existing Producer display name', 404);
+                }
+                if ($producerDefinition->community !== $producerDao->getCommunity()->getName()) {
+                    throw new Exception('Producer schema community name must match existing Producer Community name', 404);
+                }
+
+                // Save the producer definition to the producer.
+                $producerDao->setProducerDefinition($producerConfig);
+                $producerModel->save($producerDao);
+
+                $defaults = $producerDefinition->defaults;
+                if (!isset($defaults)) {
+                    // Provide a default for $defaults so the below ?: logic works.
+                    $defaults = new stdClass();
+                }
+                $keyMetrics = $producerDefinition->key_metrics;
+                /** @var stdClass $keyMetric */
+                foreach($keyMetrics as $keyMetric) {
+                    /** @var Tracker_TrendModel $trendModel */
+                    $trendModel = MidasLoader::loadModel('Trend', 'tracker');
+                    // Set any needed trends to be key_metrics.
+                    $trendModel->setAggregatableTrendAsKeyMetrics($producerDao, $keyMetric->name);
+                    /** @var Tracker_TrendThresholdModel $trendThresholdModel */
+                    $trendThresholdModel = MidasLoader::loadModel('TrendThreshold', 'tracker');
+                    $trendThresholdModel->upsert($producerDao, $keyMetric->name,
+                        isset($keyMetric->abbreviation) ? $keyMetric->abbreviation : false,
+                        isset($keyMetric->warning) ? $keyMetric->warning :
+                            (isset($defaults->warning) ? $defaults->warning : false),
+                        isset($keyMetric->fail) ? $keyMetric->fail :
+                            (isset($defaults->fail) ? $defaults->fail : false),
+                        isset($keyMetric->min) ? $keyMetric->min :
+                            (isset($defaults->min) ? $defaults->min : false),
+                        isset($keyMetric->max) ? $keyMetric->max :
+                            (isset($defaults->max) ? $defaults->max : false),
+                        isset($keyMetric->lower_is_better) ? $keyMetric->lower_is_better :
+                            (isset($defaults->lower_is_better) ? $defaults->lower_is_better : false)
+                    );
+                }
             }
         }
 

From 2c2915516d1db01e3342f64d480327c810fad562 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Thu, 28 Jul 2016 17:26:49 -0400
Subject: [PATCH 07/20] Applied fixes from StyleCI

---
 .../controllers/components/ApiComponent.php   |  2 +-
 .../models/base/TrendThresholdModelBase.php   | 26 +++---
 .../tracker/models/dao/TrendThresholdDao.php  |  2 +-
 modules/tracker/models/pdo/TrendModel.php     |  4 +-
 .../models/pdo/TrendThresholdModel.php        | 82 +++++++++----------
 5 files changed, 58 insertions(+), 58 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index eead42969..41c6e66e0 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -410,7 +410,7 @@ public function submissionValidate($args)
                 }
                 $keyMetrics = $producerDefinition->key_metrics;
                 /** @var stdClass $keyMetric */
-                foreach($keyMetrics as $keyMetric) {
+                foreach ($keyMetrics as $keyMetric) {
                     /** @var Tracker_TrendModel $trendModel */
                     $trendModel = MidasLoader::loadModel('Trend', 'tracker');
                     // Set any needed trends to be key_metrics.
diff --git a/modules/tracker/models/base/TrendThresholdModelBase.php b/modules/tracker/models/base/TrendThresholdModelBase.php
index 0f6814cb2..bc75738b3 100644
--- a/modules/tracker/models/base/TrendThresholdModelBase.php
+++ b/modules/tracker/models/base/TrendThresholdModelBase.php
@@ -51,19 +51,19 @@ public function __construct()
         $this->initialize();
     }
 
-    /**
-     * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
-     *
-     * @param Tracker_ProducerDao $producerDao
-     * @param string $metricName metric name of the trend threshold
-     * @param false|string $abbreviation name abbreviation for the threshold
-     * @param false|float $warning warning value for this threshold
-     * @param false|float $fail fail value for this threshold
-     * @param false|float $min min value for display of this threshold
-     * @param false|float $max max value for display of this threshold
-     * @param false|boolean $lowerIsBetter whether lower values are better for this threshold
-     * @return Tracker_TrendThresholdDao updated or created DAO
-     */
+     /**
+      * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
+      *
+      * @param Tracker_ProducerDao $producerDao
+      * @param string $metricName metric name of the trend threshold
+      * @param false|string $abbreviation name abbreviation for the threshold
+      * @param false|float $warning warning value for this threshold
+      * @param false|float $fail fail value for this threshold
+      * @param false|float $min min value for display of this threshold
+      * @param false|float $max max value for display of this threshold
+      * @param false|bool $lowerIsBetter whether lower values are better for this threshold
+      * @return Tracker_TrendThresholdDao updated or created DAO
+      */
      abstract public function upsert(
         $producerDao,
         $metricName,
diff --git a/modules/tracker/models/dao/TrendThresholdDao.php b/modules/tracker/models/dao/TrendThresholdDao.php
index a4b3c338c..c7a3d42c9 100644
--- a/modules/tracker/models/dao/TrendThresholdDao.php
+++ b/modules/tracker/models/dao/TrendThresholdDao.php
@@ -37,7 +37,7 @@
  * @method void setMin(float $min)
  * @method float getMax()
  * @method void setMax(float $max)
- * @method boolean getLowerIsBetter()
+ * @method bool getLowerIsBetter()
  * @method void setLowerIsBetter(boolean $lowerIsBetter)
  * @method Tracker_ProducerDao getProducer()
  * @method void setProducer(Tracker_ProducerDao $producerDao)
diff --git a/modules/tracker/models/pdo/TrendModel.php b/modules/tracker/models/pdo/TrendModel.php
index 027f9c304..e7ce0d95f 100644
--- a/modules/tracker/models/pdo/TrendModel.php
+++ b/modules/tracker/models/pdo/TrendModel.php
@@ -166,9 +166,9 @@ public function setAggregatableTrendAsKeyMetrics($producerDao, $metricName)
         $producerIdQ = $this->database->getDB()->quote($producerDao->getProducerId());
         $metricNameQ = $this->database->getDB()->quote($metricName);
         $update = 'UPDATE tracker_trend, tracker_trendgroup SET key_metric=1 WHERE'.
-            ' producer_id = ' . $producerIdQ .
+            ' producer_id = '.$producerIdQ.
             ' AND tracker_trend.trendgroup_id = tracker_trendgroup.trendgroup_id '.
-            ' AND tracker_trend.metric_name = ' . $metricNameQ;
+            ' AND tracker_trend.metric_name = '.$metricNameQ;
         $this->database->getDB()->query($update);
     }
 
diff --git a/modules/tracker/models/pdo/TrendThresholdModel.php b/modules/tracker/models/pdo/TrendThresholdModel.php
index 7959b60cb..d8e668234 100644
--- a/modules/tracker/models/pdo/TrendThresholdModel.php
+++ b/modules/tracker/models/pdo/TrendThresholdModel.php
@@ -24,18 +24,18 @@
 class Tracker_TrendThresholdModel extends Tracker_TrendThresholdModelBase
 {
     /**
-     * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
-     *
-     * @param Tracker_ProducerDao $producerDao
-     * @param string $metricName metric name of the trend threshold
-     * @param false|string $abbreviation name abbreviation for the threshold
-     * @param false|float $warning warning value for this threshold
-     * @param false|float $fail fail value for this threshold
-     * @param false|float $min min value for display of this threshold
-     * @param false|float $max max value for display of this threshold
-     * @param false|boolean $lowerIsBetter whether lower values are better for this threshold
-     * @return Tracker_TrendThresholdDao updated or created DAO
-     */
+      * Create or update a Tracker TrendThreshold tied to the Producer and metric_name.
+      *
+      * @param Tracker_ProducerDao $producerDao
+      * @param string $metricName metric name of the trend threshold
+      * @param false|string $abbreviation name abbreviation for the threshold
+      * @param false|float $warning warning value for this threshold
+      * @param false|float $fail fail value for this threshold
+      * @param false|float $min min value for display of this threshold
+      * @param false|float $max max value for display of this threshold
+      * @param false|bool $lowerIsBetter whether lower values are better for this threshold
+      * @return Tracker_TrendThresholdDao updated or created DAO
+      */
      public function upsert(
         $producerDao,
         $metricName,
@@ -45,38 +45,38 @@ public function upsert(
         $min = false,
         $max = false,
         $lowerIsBetter = false)
-    {
-        if (is_null($producerDao) || $producerDao === false) {
-            return false;
-        }
-        $sql = $this->database->select()->setIntegrityCheck(false)
+     {
+         if (is_null($producerDao) || $producerDao === false) {
+             return false;
+         }
+         $sql = $this->database->select()->setIntegrityCheck(false)
             ->where('producer_id = ?', $producerDao->getProducerId())
             ->where('metric_name = ?', $metricName);
         /** @var Tracker_TrendThresholdDao $trendThresholdDao */
         $trendThresholdDao = $this->initDao('TrendThreshold', $this->database->fetchRow($sql), $this->moduleName);
-        if ($trendThresholdDao === false) {
-            $trendThresholdDao = MidasLoader::newDao('TrendThresholdDao', $this->moduleName);
-        }
-        if ($abbreviation !== false) {
-           $trendThresholdDao->setAbbreviation($abbreviation);
-        }
-        if ($warning !== false) {
-           $trendThresholdDao->setWarning($warning);
-        }
-        if ($fail !== false) {
-           $trendThresholdDao->setFail($fail);
-        }
-        if ($min !== false) {
-           $trendThresholdDao->setMin($min);
-        }
-        if ($max !== false) {
-           $trendThresholdDao->setMax($max);
-        }
-        if ($lowerIsBetter !== false) {
-           $trendThresholdDao->setLowerIsBetter($lowerIsBetter);
-        }
-        $this->save($trendThresholdDao);
+         if ($trendThresholdDao === false) {
+             $trendThresholdDao = MidasLoader::newDao('TrendThresholdDao', $this->moduleName);
+         }
+         if ($abbreviation !== false) {
+             $trendThresholdDao->setAbbreviation($abbreviation);
+         }
+         if ($warning !== false) {
+             $trendThresholdDao->setWarning($warning);
+         }
+         if ($fail !== false) {
+             $trendThresholdDao->setFail($fail);
+         }
+         if ($min !== false) {
+             $trendThresholdDao->setMin($min);
+         }
+         if ($max !== false) {
+             $trendThresholdDao->setMax($max);
+         }
+         if ($lowerIsBetter !== false) {
+             $trendThresholdDao->setLowerIsBetter($lowerIsBetter);
+         }
+         $this->save($trendThresholdDao);
 
-        return $trendThresholdDao;
-    }
+         return $trendThresholdDao;
+     }
 }

From 766b5e204014f065524decb22ee37ee9277ff28d Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Sun, 31 Jul 2016 20:17:10 +0000
Subject: [PATCH 08/20] Add fields to producer definition

---
 modules/tracker/database/mysql/2.0.4.sql          | 2 ++
 modules/tracker/database/upgrade/2.0.4.php        | 2 ++
 modules/tracker/models/base/ProducerModelBase.php | 9 +++++++++
 modules/tracker/models/dao/ProducerDao.php        | 8 ++++++++
 4 files changed, 21 insertions(+)

diff --git a/modules/tracker/database/mysql/2.0.4.sql b/modules/tracker/database/mysql/2.0.4.sql
index 389707694..2ac28096c 100644
--- a/modules/tracker/database/mysql/2.0.4.sql
+++ b/modules/tracker/database/mysql/2.0.4.sql
@@ -11,6 +11,8 @@ CREATE TABLE IF NOT EXISTS `tracker_producer` (
     `description` text NOT NULL,
     `revision_url` text NOT NULL,
     `histogram_max_x` double,
+    `grid_across_metric_groups` tinyint(4) NOT NULL DEFAULT '0',
+    `histogram_number_of_bins` int(11) NOT NULL DEFAULT '10',
     `producer_definition` text,
     PRIMARY KEY (`producer_id`),
     KEY (`community_id`)
diff --git a/modules/tracker/database/upgrade/2.0.4.php b/modules/tracker/database/upgrade/2.0.4.php
index 64ae040bd..16211dfff 100644
--- a/modules/tracker/database/upgrade/2.0.4.php
+++ b/modules/tracker/database/upgrade/2.0.4.php
@@ -26,6 +26,8 @@ public function mysql()
     {
         $this->db->query(
             'ALTER TABLE `tracker_producer` '.
+            '   ADD COLUMN `grid_across_metric_groups` tinyint(4) NOT NULL DEFAULT 0,'.
+            '   ADD COLUMN `histogram_number_of_bins` int(11) NOT NULL DEFAULT 10,'.
             '   ADD COLUMN `producer_definition` text;'
         );
         $this->db->query(
diff --git a/modules/tracker/models/base/ProducerModelBase.php b/modules/tracker/models/base/ProducerModelBase.php
index 322013252..56e6d6827 100644
--- a/modules/tracker/models/base/ProducerModelBase.php
+++ b/modules/tracker/models/base/ProducerModelBase.php
@@ -37,6 +37,8 @@ public function __construct()
             'display_name' => array('type' => MIDAS_DATA),
             'description' => array('type' => MIDAS_DATA),
             'histogram_max_x' => array('type' => MIDAS_DATA),
+            'grid_across_metric_groups' => array('type' => MIDAS_DATA),
+            'histogram_number_of_bins' => array('type' => MIDAS_DATA),
             'producer_definition' => array('type' => MIDAS_DATA),
             'community' => array(
                 'type' => MIDAS_MANY_TO_ONE,
@@ -51,6 +53,13 @@ public function __construct()
                 'parent_column' => 'producer_id',
                 'child_column' => 'producer_id',
             ),
+            'trendthresholds' => array(
+                'type' => MIDAS_ONE_TO_MANY,
+                'model' => 'TrendThreshold',
+                'module' => $this->moduleName,
+                'parent_column' => 'producer_id',
+                'child_column' => 'producer_id',
+            ),
         );
 
         $this->initialize();
diff --git a/modules/tracker/models/dao/ProducerDao.php b/modules/tracker/models/dao/ProducerDao.php
index 490d608e2..24e2e075d 100644
--- a/modules/tracker/models/dao/ProducerDao.php
+++ b/modules/tracker/models/dao/ProducerDao.php
@@ -39,6 +39,14 @@
  * @method void setCommunity(CommunityDao $communityDao)
  * @method array getTrendgroups()
  * @method void setTrendgroups(array $trendgroupDaos)
+ * @method array getTrendthresholds()
+ * @method void setTrendthresholds(array $trendthresholdDaos)
+ * @method void setHistogramMaxX(float $histogramMaxX)
+ * @method float getHistogramMaxX()
+ * @method bool getGridAcrossMetricGroups()
+ * @method void setGridAcrossMetricGroups(boolean $gridAcrossMetricGroups)
+ * @method int getHistogramNumberOfBins()
+ * @method void setHistogramNumberOfBins(int $histogramNumberOfBins)
  * @method string getProducerDefinition()
  * @method void setProducerDefinition(string $producerDefinition)
  */

From 83faecd89ed75d4beed8513f1a936364849a457a Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Sun, 31 Jul 2016 20:18:26 +0000
Subject: [PATCH 09/20] Set producer level fields from producer definition

---
 .../tracker/controllers/components/ApiComponent.php | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 41c6e66e0..b91499136 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -358,9 +358,6 @@ public function submissionValidate($args)
         }
 
         if (isset($args['producerConfig'])) {
-            // At the current time, we are looking for the producerConfig,
-            // validating it, and logging a warning with any violations, we
-            // are not saving the producerConfig.
             $producerConfig = $args['producerConfig'];
             $refResolver = new JsonSchema\RefResolver(new JsonSchema\Uri\UriRetriever(), new JsonSchema\Uri\UriResolver());
             $schemaPath = BASE_PATH.'/modules/tracker/schema/producer.json';
@@ -401,6 +398,16 @@ public function submissionValidate($args)
 
                 // Save the producer definition to the producer.
                 $producerDao->setProducerDefinition($producerConfig);
+                // Update top level fields on the producer based on the definition.
+                if (isset($producerDefinition->histogram_max_x)) {
+                    $producerDao->setHistogramMaxX($producerDefinition->histogram_max_x);
+                }
+                if (isset($producerDefinition->grid_across_metric_groups)) {
+                    $producerDao->setGridAcrossMetricGroups($producerDefinition->grid_across_metric_groups);
+                }
+                if (isset($producerDefinition->histogram_number_of_bins)) {
+                    $producerDao->setHistogramNumberOfBins($producerDefinition->histogram_number_of_bins);
+                }
                 $producerModel->save($producerDao);
 
                 $defaults = $producerDefinition->defaults;

From 7bccc72983fa3ce90eef1320abb0df54c93ca9dd Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Sun, 31 Jul 2016 20:20:20 +0000
Subject: [PATCH 10/20] Add document to submission model

---
 modules/tracker/database/mysql/2.0.4.sql            | 1 +
 modules/tracker/database/upgrade/2.0.4.php          | 4 ++++
 modules/tracker/models/base/SubmissionModelBase.php | 1 +
 modules/tracker/models/dao/SubmissionDao.php        | 2 ++
 4 files changed, 8 insertions(+)

diff --git a/modules/tracker/database/mysql/2.0.4.sql b/modules/tracker/database/mysql/2.0.4.sql
index 2ac28096c..3eb8d9f45 100644
--- a/modules/tracker/database/mysql/2.0.4.sql
+++ b/modules/tracker/database/mysql/2.0.4.sql
@@ -41,6 +41,7 @@ CREATE TABLE IF NOT EXISTS `tracker_submission` (
     `branch` varchar(255) NOT NULL DEFAULT '',
     `extra_urls` text,
     `reproduction_command` text,
+    `document` text,
     PRIMARY KEY (`submission_id`),
     UNIQUE KEY (`uuid`),
     KEY (`user_id`),
diff --git a/modules/tracker/database/upgrade/2.0.4.php b/modules/tracker/database/upgrade/2.0.4.php
index 16211dfff..e95506f6f 100644
--- a/modules/tracker/database/upgrade/2.0.4.php
+++ b/modules/tracker/database/upgrade/2.0.4.php
@@ -35,5 +35,9 @@ public function mysql()
             '   ADD COLUMN `min` double,'.
             '   ADD COLUMN `lower_is_better` tinyint(4) NOT NULL DEFAULT 0;'
         );
+        $this->db->query(
+            'ALTER TABLE `tracker_submission` '.
+            '   ADD COLUMN `document` text;'
+        );
     }
 }
diff --git a/modules/tracker/models/base/SubmissionModelBase.php b/modules/tracker/models/base/SubmissionModelBase.php
index 755a1d2e8..f87217369 100644
--- a/modules/tracker/models/base/SubmissionModelBase.php
+++ b/modules/tracker/models/base/SubmissionModelBase.php
@@ -42,6 +42,7 @@ public function __construct()
             'extra_urls' => array('type' => MIDAS_DATA),
             'branch' => array('type' => MIDAS_DATA),
             'producer_revision' => array('type' => MIDAS_DATA),
+            'document' => array('type' => MIDAS_DATA),
             'reproduction_command' => array('type' => MIDAS_DATA),
             'producer' => array(
                 'type' => MIDAS_MANY_TO_ONE,
diff --git a/modules/tracker/models/dao/SubmissionDao.php b/modules/tracker/models/dao/SubmissionDao.php
index 9f0c61983..e99158e1a 100644
--- a/modules/tracker/models/dao/SubmissionDao.php
+++ b/modules/tracker/models/dao/SubmissionDao.php
@@ -49,6 +49,8 @@
  * @method void setProducerRevision(string $producerRevision)
  * @method string getReproductionCommand()
  * @method void setReproductionCommand(string $reproductionCommand)
+ * @method string getDocument()
+ * @method void setDocument(string $document)
  */
 class Tracker_SubmissionDao extends Tracker_AppDao
 {

From a11b9914fd0e564d394c9e050cec061555ed540b Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Sun, 31 Jul 2016 20:20:40 +0000
Subject: [PATCH 11/20] Save document to submission model in API

---
 .../controllers/components/ApiComponent.php   | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index b91499136..77ec8e378 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -442,9 +442,6 @@ public function submissionValidate($args)
         }
 
         if (isset($args['submissionDocument'])) {
-            // At the current time, we are looking for the submissionDocument,
-            // validating it, and logging a warning with any violations, we
-            // are not saving the producerConfig.
             $submissionDocument = $args['submissionDocument'];
             $refResolver = new JsonSchema\RefResolver(new JsonSchema\Uri\UriRetriever(), new JsonSchema\Uri\UriResolver());
             $schemaPath = BASE_PATH.'/modules/tracker/schema/submission.json';
@@ -460,7 +457,21 @@ public function submissionValidate($args)
                 }
             } else {
                 $this->getLogger()->info('The supplied submissionDocument JSON for uuid '.$uuid.' is valid.');
-            }
+
+                /** @var Tracker_ProducerModel $producerModel */
+                $producerModel = MidasLoader::loadModel('Producer', 'tracker');
+                /** @var Tracker_ProducerDao $producerDao */
+                $producerDao = $submissionDao->getProducer();
+                if (!$producerModel->policyCheck(
+                    $producerDao,
+                    $user,
+                    MIDAS_POLICY_WRITE
+                )) {
+                    throw new Exception('Write permission on the producer required', 403);
+                }
+                $submissionDao->setDocument($submissionDocument);
+                $submissionModel->save($submissionDao);
+              }
         }
     }
 

From 62f21205603754182f4bbaccfc745d2a20a1b07d Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Mon, 1 Aug 2016 22:25:56 -0400
Subject: [PATCH 12/20] Applied fixes from StyleCI

---
 modules/tracker/controllers/components/ApiComponent.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 77ec8e378..5902f7e11 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -471,7 +471,7 @@ public function submissionValidate($args)
                 }
                 $submissionDao->setDocument($submissionDocument);
                 $submissionModel->save($submissionDao);
-              }
+            }
         }
     }
 

From ea56b9e8b24f05bc9179734e777504a70cddb368 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 22:32:37 +0000
Subject: [PATCH 13/20] Add min and lower_is_better fields to aggregate metric
 spec model

---
 modules/tracker/database/mysql/2.0.4.sql                     | 2 ++
 modules/tracker/database/upgrade/2.0.4.php                   | 5 +++++
 modules/tracker/models/base/AggregateMetricSpecModelBase.php | 2 ++
 modules/tracker/models/dao/AggregateMetricSpecDao.php        | 4 ++++
 4 files changed, 13 insertions(+)

diff --git a/modules/tracker/database/mysql/2.0.4.sql b/modules/tracker/database/mysql/2.0.4.sql
index 3eb8d9f45..5956be60f 100644
--- a/modules/tracker/database/mysql/2.0.4.sql
+++ b/modules/tracker/database/mysql/2.0.4.sql
@@ -139,7 +139,9 @@ CREATE TABLE IF NOT EXISTS `tracker_aggregate_metric_spec` (
     `abbreviation` varchar(255) NOT NULL DEFAULT '',
     `warning` double,
     `fail` double,
+    `min` double,
     `max` double,
+    `lower_is_better` tinyint(4) NOT NULL DEFAULT '0',
     PRIMARY KEY (`aggregate_metric_spec_id`),
     KEY (`producer_id`)
 ) DEFAULT CHARSET=utf8;
diff --git a/modules/tracker/database/upgrade/2.0.4.php b/modules/tracker/database/upgrade/2.0.4.php
index e95506f6f..650827c91 100644
--- a/modules/tracker/database/upgrade/2.0.4.php
+++ b/modules/tracker/database/upgrade/2.0.4.php
@@ -39,5 +39,10 @@ public function mysql()
             'ALTER TABLE `tracker_submission` '.
             '   ADD COLUMN `document` text;'
         );
+        $this->db->query(
+            'ALTER TABLE `tracker_aggregate_metric_spec` '.
+            '   ADD COLUMN `min` double,'.
+            '   ADD COLUMN `lower_is_better` tinyint(4) NOT NULL DEFAULT 0;'
+        );
     }
 }
diff --git a/modules/tracker/models/base/AggregateMetricSpecModelBase.php b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
index 9ef9a36b2..8f2eb1794 100644
--- a/modules/tracker/models/base/AggregateMetricSpecModelBase.php
+++ b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
@@ -38,7 +38,9 @@ public function __construct()
             'abbreviation' => array('type' => MIDAS_DATA),
             'warning' => array('type' => MIDAS_DATA),
             'fail' => array('type' => MIDAS_DATA),
+            'min' => array('type' => MIDAS_DATA),
             'max' => array('type' => MIDAS_DATA),
+            'lower_is_better' => array('type' => MIDAS_DATA),
             'producer' => array(
                 'type' => MIDAS_MANY_TO_ONE,
                 'model' => 'Producer',
diff --git a/modules/tracker/models/dao/AggregateMetricSpecDao.php b/modules/tracker/models/dao/AggregateMetricSpecDao.php
index 869f5ab1b..e4d0666df 100644
--- a/modules/tracker/models/dao/AggregateMetricSpecDao.php
+++ b/modules/tracker/models/dao/AggregateMetricSpecDao.php
@@ -37,8 +37,12 @@
  * @method void setWarning(float $warning)
  * @method float getFail()
  * @method void setFail(float $fail)
+ * @method float getMin()
+ * @method void setMin(float $min)
  * @method float getMax()
  * @method void setMax(float $max)
+ * @method bool getLowerIsBetter()
+ * @method void setLowerIsBetter(boolean $lowerIsBetter)
  * @method Tracker_ProducerDao getProducer()
  * @method void setProducer(Tracker_ProducerDao $producerDao)
  */

From 532a0ae952676dad8a5d72f1f71e07437a694b06 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 22:33:12 +0000
Subject: [PATCH 14/20] Set producer and metric name on created TrendThresholds

---
 modules/tracker/models/pdo/TrendThresholdModel.php | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/tracker/models/pdo/TrendThresholdModel.php b/modules/tracker/models/pdo/TrendThresholdModel.php
index d8e668234..77c15515b 100644
--- a/modules/tracker/models/pdo/TrendThresholdModel.php
+++ b/modules/tracker/models/pdo/TrendThresholdModel.php
@@ -52,10 +52,12 @@ public function upsert(
          $sql = $this->database->select()->setIntegrityCheck(false)
             ->where('producer_id = ?', $producerDao->getProducerId())
             ->where('metric_name = ?', $metricName);
-        /** @var Tracker_TrendThresholdDao $trendThresholdDao */
-        $trendThresholdDao = $this->initDao('TrendThreshold', $this->database->fetchRow($sql), $this->moduleName);
+         /** @var Tracker_TrendThresholdDao $trendThresholdDao */
+         $trendThresholdDao = $this->initDao('TrendThreshold', $this->database->fetchRow($sql), $this->moduleName);
          if ($trendThresholdDao === false) {
              $trendThresholdDao = MidasLoader::newDao('TrendThresholdDao', $this->moduleName);
+             $trendThresholdDao->setProducerId($producerDao->getProducerId());
+             $trendThresholdDao->setMetricName($metricName);
          }
          if ($abbreviation !== false) {
              $trendThresholdDao->setAbbreviation($abbreviation);

From 94a8e251f625876322069422e9ecccdbc49fc4c9 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 22:33:57 +0000
Subject: [PATCH 15/20] Add upsert to AggregateMetricSpec model

---
 .../base/AggregateMetricSpecModelBase.php     | 28 ++++++++
 .../models/pdo/AggregateMetricSpecModel.php   | 68 +++++++++++++++++++
 2 files changed, 96 insertions(+)

diff --git a/modules/tracker/models/base/AggregateMetricSpecModelBase.php b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
index 8f2eb1794..8833714ca 100644
--- a/modules/tracker/models/base/AggregateMetricSpecModelBase.php
+++ b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
@@ -83,6 +83,34 @@ public function createAggregateMetricSpec($producerDao, $name, $spec, $descripti
         return $aggregateMetricSpecDao;
     }
 
+    /**
+     * Create or update a Tracker AggregateMetricSpec, matching on the Producer
+     * and spec fields.
+     *
+     * @param Tracker_ProducerDao $producerDao
+     * @param string $name name of the aggregate metric
+     * @param string $spec the spec for the aggregate metric spec
+     * @param false|string $abbreviation name abbreviation for the threshold
+     * @param false|string $description the description for the aggregate metric spec
+     * @param false|float $warning warning value for this threshold
+     * @param false|float $fail fail value for this threshold
+     * @param false|float $min min value for display of this threshold
+     * @param false|float $max max value for display of this threshold
+     * @param false|bool $lowerIsBetter whether lower values are better for this threshold
+     * @return false|Tracker_AggregateMetricSpecDao created from inputs
+     */
+    abstract public function upsert(
+        $producerDao,
+        $name,
+        $spec,
+        $abbreviation = false,
+        $description,
+        $warning = false,
+        $fail = false,
+        $min = false,
+        $max = false,
+        $lowerIsBetter = false);
+
     /**
      * Return all AggregateMetricSpecDaos tied to the producer.
      *
diff --git a/modules/tracker/models/pdo/AggregateMetricSpecModel.php b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
index be0e34d4a..649f3c9d7 100644
--- a/modules/tracker/models/pdo/AggregateMetricSpecModel.php
+++ b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
@@ -24,6 +24,74 @@
 class Tracker_AggregateMetricSpecModel extends Tracker_AggregateMetricSpecModelBase
 {
     /**
+     * Create or update a Tracker AggregateMetricSpec, matching on the Producer
+     * and spec fields.
+     *
+     * @param Tracker_ProducerDao $producerDao
+     * @param string $name name of the aggregate metric
+     * @param string $spec the spec for the aggregate metric spec
+     * @param false|string $abbreviation name abbreviation for the threshold
+     * @param false|string $description the description for the aggregate metric spec
+     * @param false|float $warning warning value for this threshold
+     * @param false|float $fail fail value for this threshold
+     * @param false|float $min min value for display of this threshold
+     * @param false|float $max max value for display of this threshold
+     * @param false|bool $lowerIsBetter whether lower values are better for this threshold
+     * @return false|Tracker_AggregateMetricSpecDao created from inputs
+     */
+    public function upsert(
+        $producerDao,
+        $name,
+        $spec,
+        $abbreviation = false,
+        $description,
+        $warning = false,
+        $fail = false,
+        $min = false,
+        $max = false,
+        $lowerIsBetter = false)
+     {
+         if (is_null($producerDao) || $producerDao === false) {
+             return false;
+         }
+         $sql = $this->database->select()->setIntegrityCheck(false)
+            ->where('producer_id = ?', $producerDao->getProducerId())
+            ->where('spec = ?', $spec);
+         /** @var Tracker_AggregateMetricSpecDao $aggregateMetricSpecDao */
+         $aggregateMetricSpecDao = $this->initDao('AggregateMetricSpec', $this->database->fetchRow($sql), $this->moduleName);
+         if ($aggregateMetricSpecDao === false) {
+             $aggregateMetricSpecDao = MidasLoader::newDao('AggregateMetricSpecDao', $this->moduleName);
+             $aggregateMetricSpecDao->setProducerId($producerDao->getProducerId());
+             $aggregateMetricSpecDao->setSpec($spec);
+         }
+         $aggregateMetricSpecDao->setName($name);
+         if ($abbreviation !== false) {
+             $aggregateMetricSpecDao->setAbbreviation($abbreviation);
+         }
+         if ($description !== false) {
+             $aggregateMetricSpecDao->setDescription($description);
+         }
+         if ($warning !== false) {
+             $aggregateMetricSpecDao->setWarning($warning);
+         }
+         if ($fail !== false) {
+             $aggregateMetricSpecDao->setFail($fail);
+         }
+         if ($min !== false) {
+             $aggregateMetricSpecDao->setMin($min);
+         }
+         if ($max !== false) {
+             $aggregateMetricSpecDao->setMax($max);
+         }
+         if ($lowerIsBetter !== false) {
+             $aggregateMetricSpecDao->setLowerIsBetter($lowerIsBetter);
+         }
+         $this->save($aggregateMetricSpecDao);
+
+         return $aggregateMetricSpecDao;
+     }
+
+     /**
      * Delete the given aggregate metric spec, any metrics calculated based on that spec,
      * and any associated notifications.
      *

From 372f56df996dc1cc8285e4ecb48554ab762f93d3 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 22:35:01 +0000
Subject: [PATCH 16/20] Update aggregate metrics, thresholds and notifications
 upon producer definition submission

---
 .../controllers/components/ApiComponent.php   | 65 +++++++++++++++++--
 1 file changed, 61 insertions(+), 4 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 5902f7e11..7a5ec3937 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -415,15 +415,16 @@ public function submissionValidate($args)
                     // Provide a default for $defaults so the below ?: logic works.
                     $defaults = new stdClass();
                 }
+                // Add or update any key metrics and thresholds.
+                /** @var Tracker_TrendModel $trendModel */
+                $trendModel = MidasLoader::loadModel('Trend', 'tracker');
+                /** @var Tracker_TrendThresholdModel $trendThresholdModel */
+                $trendThresholdModel = MidasLoader::loadModel('TrendThreshold', 'tracker');
                 $keyMetrics = $producerDefinition->key_metrics;
                 /** @var stdClass $keyMetric */
                 foreach ($keyMetrics as $keyMetric) {
-                    /** @var Tracker_TrendModel $trendModel */
-                    $trendModel = MidasLoader::loadModel('Trend', 'tracker');
                     // Set any needed trends to be key_metrics.
                     $trendModel->setAggregatableTrendAsKeyMetrics($producerDao, $keyMetric->name);
-                    /** @var Tracker_TrendThresholdModel $trendThresholdModel */
-                    $trendThresholdModel = MidasLoader::loadModel('TrendThreshold', 'tracker');
                     $trendThresholdModel->upsert($producerDao, $keyMetric->name,
                         isset($keyMetric->abbreviation) ? $keyMetric->abbreviation : false,
                         isset($keyMetric->warning) ? $keyMetric->warning :
@@ -438,6 +439,62 @@ public function submissionValidate($args)
                             (isset($defaults->lower_is_better) ? $defaults->lower_is_better : false)
                     );
                 }
+                // Add or update any aggregate metrics and thresholds, based on matching
+                // the producer and spec.
+                $aggregateMetrics = $producerDefinition->aggregate_metrics;
+                /** @var Tracker_AggregateMetricSpecModel $aggregateMetricSpecModel */
+                $aggregateMetricSpecModel = MidasLoader::loadModel('AggregateMetricSpec', 'tracker');
+                /** @var Tracker_AggregateMetricNotificationModel $aggregateMetricNotificationModel */
+                $aggregateMetricNotificationModel = MidasLoader::loadModel('AggregateMetricNotification', 'tracker');
+                /** @var UserModel $userModel */
+                $userModel = MidasLoader::loadModel('User');
+                /** @var stdClass $aggregateMetric */
+                foreach ($aggregateMetrics as $aggregateMetric) {
+                    /** @var Tracker_AggregateMetricSpecDao $aggregateMetricSpecDao */
+                    $aggregateMetricSpecDao = $aggregateMetricSpecModel->upsert($producerDao, $aggregateMetric->name, $aggregateMetric->definition,
+                        isset($aggregateMetric->abbreviation) ? $aggregateMetric->abbreviation : false,
+                        // Set empty string for description.
+                        '',
+                        isset($aggregateMetric->warning) ? $aggregateMetric->warning :
+                            (isset($defaults->warning) ? $defaults->warning : false),
+                        isset($aggregateMetric->fail) ? $aggregateMetric->fail :
+                            (isset($defaults->fail) ? $defaults->fail : false),
+                        isset($aggregateMetric->min) ? $aggregateMetric->min :
+                            (isset($defaults->min) ? $defaults->min : false),
+                        isset($aggregateMetric->max) ? $aggregateMetric->max :
+                            (isset($defaults->max) ? $defaults->max : false),
+                        isset($aggregateMetric->lower_is_better) ? $aggregateMetric->lower_is_better :
+                            (isset($defaults->lower_is_better) ? $defaults->lower_is_better : false)
+                    );
+                    // Delete any notifications tied to this Aggregate Metric, and create any
+                    // as needed.
+                    $staleNotifications = $aggregateMetricNotificationModel->findBy('aggregate_metric_spec_id', $aggregateMetricSpecDao->getAggregateMetricSpecId());
+                    /** @var Tracker_AggregateMetricNotificationDao $staleNotification */
+                    foreach ($staleNotifications as $staleNotification) {
+                        $aggregateMetricNotificationModel->delete($staleNotification);
+                    }
+                    if (isset($aggregateMetric->notifications)) {
+                        /** @var stdClass $notification */
+                        foreach ($aggregateMetric->notifications as $notification) {
+                            /** @var Tracker_AggregateMetricNotificationDao $aggregateMetricNotificationDao */
+                            $aggregateMetricNotificationDao = MidasLoader::newDao('AggregateMetricNotificationDao', $this->moduleName);
+                            $aggregateMetricNotificationDao->setAggregateMetricSpecId($aggregateMetricSpecDao->getAggregateMetricSpecId());
+                            $aggregateMetricNotificationDao->setBranch($notification->branch);
+                            $aggregateMetricNotificationDao->setComparison($notification->comparison);
+                            $aggregateMetricNotificationDao->setValue($notification->value);
+                            $aggregateMetricNotificationModel->save($aggregateMetricNotificationDao);
+                            if (isset($notification->emails)) {
+                                foreach ($notification->emails as $email) {
+                                    // We can only add notifications for valid users.
+                                    $userDao = $userModel->getByEmail($email);
+                                    if ($userDao !== false) {
+                                        $aggregateMetricNotificationModel->createUserNotification($aggregateMetricNotificationDao, $userDao);
+                                    }
+                                }
+                            }
+                        }
+                    }
+               }
             }
         }
 

From b382262df2d03b656f0f4a50db461fb44f713e28 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 22:39:35 +0000
Subject: [PATCH 17/20] Add false as default for upsert description param

---
 modules/tracker/models/base/AggregateMetricSpecModelBase.php | 2 +-
 modules/tracker/models/pdo/AggregateMetricSpecModel.php      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/tracker/models/base/AggregateMetricSpecModelBase.php b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
index 8833714ca..ba0d69261 100644
--- a/modules/tracker/models/base/AggregateMetricSpecModelBase.php
+++ b/modules/tracker/models/base/AggregateMetricSpecModelBase.php
@@ -104,7 +104,7 @@ abstract public function upsert(
         $name,
         $spec,
         $abbreviation = false,
-        $description,
+        $description = false,
         $warning = false,
         $fail = false,
         $min = false,
diff --git a/modules/tracker/models/pdo/AggregateMetricSpecModel.php b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
index 649f3c9d7..1e8c80fe0 100644
--- a/modules/tracker/models/pdo/AggregateMetricSpecModel.php
+++ b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
@@ -44,7 +44,7 @@ public function upsert(
         $name,
         $spec,
         $abbreviation = false,
-        $description,
+        $description = false,
         $warning = false,
         $fail = false,
         $min = false,

From 73a7fd3aa63956e2c997c756a0f6ff3d3854c32c Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Tue, 2 Aug 2016 18:40:17 -0400
Subject: [PATCH 18/20] Applied fixes from StyleCI

---
 .../controllers/components/ApiComponent.php   |  2 +-
 .../models/pdo/AggregateMetricSpecModel.php   | 72 +++++++++----------
 2 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 7a5ec3937..4d7ab1ba2 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -494,7 +494,7 @@ public function submissionValidate($args)
                             }
                         }
                     }
-               }
+                }
             }
         }
 
diff --git a/modules/tracker/models/pdo/AggregateMetricSpecModel.php b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
index 1e8c80fe0..5b9cbb324 100644
--- a/modules/tracker/models/pdo/AggregateMetricSpecModel.php
+++ b/modules/tracker/models/pdo/AggregateMetricSpecModel.php
@@ -50,48 +50,48 @@ public function upsert(
         $min = false,
         $max = false,
         $lowerIsBetter = false)
-     {
-         if (is_null($producerDao) || $producerDao === false) {
-             return false;
-         }
-         $sql = $this->database->select()->setIntegrityCheck(false)
+    {
+        if (is_null($producerDao) || $producerDao === false) {
+            return false;
+        }
+        $sql = $this->database->select()->setIntegrityCheck(false)
             ->where('producer_id = ?', $producerDao->getProducerId())
             ->where('spec = ?', $spec);
          /** @var Tracker_AggregateMetricSpecDao $aggregateMetricSpecDao */
          $aggregateMetricSpecDao = $this->initDao('AggregateMetricSpec', $this->database->fetchRow($sql), $this->moduleName);
-         if ($aggregateMetricSpecDao === false) {
-             $aggregateMetricSpecDao = MidasLoader::newDao('AggregateMetricSpecDao', $this->moduleName);
-             $aggregateMetricSpecDao->setProducerId($producerDao->getProducerId());
-             $aggregateMetricSpecDao->setSpec($spec);
-         }
-         $aggregateMetricSpecDao->setName($name);
-         if ($abbreviation !== false) {
-             $aggregateMetricSpecDao->setAbbreviation($abbreviation);
-         }
-         if ($description !== false) {
-             $aggregateMetricSpecDao->setDescription($description);
-         }
-         if ($warning !== false) {
-             $aggregateMetricSpecDao->setWarning($warning);
-         }
-         if ($fail !== false) {
-             $aggregateMetricSpecDao->setFail($fail);
-         }
-         if ($min !== false) {
-             $aggregateMetricSpecDao->setMin($min);
-         }
-         if ($max !== false) {
-             $aggregateMetricSpecDao->setMax($max);
-         }
-         if ($lowerIsBetter !== false) {
-             $aggregateMetricSpecDao->setLowerIsBetter($lowerIsBetter);
-         }
-         $this->save($aggregateMetricSpecDao);
+        if ($aggregateMetricSpecDao === false) {
+            $aggregateMetricSpecDao = MidasLoader::newDao('AggregateMetricSpecDao', $this->moduleName);
+            $aggregateMetricSpecDao->setProducerId($producerDao->getProducerId());
+            $aggregateMetricSpecDao->setSpec($spec);
+        }
+        $aggregateMetricSpecDao->setName($name);
+        if ($abbreviation !== false) {
+            $aggregateMetricSpecDao->setAbbreviation($abbreviation);
+        }
+        if ($description !== false) {
+            $aggregateMetricSpecDao->setDescription($description);
+        }
+        if ($warning !== false) {
+            $aggregateMetricSpecDao->setWarning($warning);
+        }
+        if ($fail !== false) {
+            $aggregateMetricSpecDao->setFail($fail);
+        }
+        if ($min !== false) {
+            $aggregateMetricSpecDao->setMin($min);
+        }
+        if ($max !== false) {
+            $aggregateMetricSpecDao->setMax($max);
+        }
+        if ($lowerIsBetter !== false) {
+            $aggregateMetricSpecDao->setLowerIsBetter($lowerIsBetter);
+        }
+        $this->save($aggregateMetricSpecDao);
 
-         return $aggregateMetricSpecDao;
-     }
+        return $aggregateMetricSpecDao;
+    }
 
-     /**
+    /**
      * Delete the given aggregate metric spec, any metrics calculated based on that spec,
      * and any associated notifications.
      *

From 29adfad2d00ab549369652d710d081f63b4a9578 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Wed, 3 Aug 2016 16:11:21 +0000
Subject: [PATCH 19/20] Replace double-ternary operators with helper function

---
 .../controllers/components/ApiComponent.php   | 90 +++++++++++++------
 1 file changed, 65 insertions(+), 25 deletions(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 4d7ab1ba2..40f820f0c 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -336,7 +336,9 @@ public function submissionAdd($args)
     }
 
     /**
-     * Validate documents tied to a submission.
+     * Validate the producer configuration and submission documents that are tied
+     * to a submission, updating the properties of the producer based off of
+     * the producer configuration.
      *
      * @param uuid The uuid of the submission to validate documents for
      * @param producerConfig (Optional) JSON object describing the pipeline
@@ -415,6 +417,47 @@ public function submissionValidate($args)
                     // Provide a default for $defaults so the below ?: logic works.
                     $defaults = new stdClass();
                 }
+
+                /**
+                 * Helper function to populate a metric based on the overall
+                 * metrics defaults, overriding any default values with any
+                 * specified in the metric itself, populating all properties with
+                 * some unassigned (false or null) value if no other value is found.
+                 * @param stdClass $metric the metric with specific values
+                 * @return array populated metric values
+                 */
+                $populateMetricValues = function ($metric) use ($defaults) {
+                    $populatedMetricUnassigned = array(
+                        'abbreviation' => false,
+                        'min' => false,
+                        'max' => false,
+                        'warning' => false,
+                        'fail' => false,
+                        // Special handling as false is meaningful in this case.
+                        'lower_is_better' => null,
+                    );
+                    $populatedMetric = array();
+                    /** @var string $key */
+                    /** @var mixed $unassignedValue */
+                    foreach ($populatedMetricUnassigned as $key => $unassignedValue) {
+                        if (isset($metric->$key)) {
+                            $populatedMetric[$key] = $metric->$key;
+                        } elseif(isset($defaults->$key)) {
+                            $populatedMetric[$key] = $defaults->$key;
+                        } else {
+                            $populatedMetric[$key] = $unassignedValue;
+                        }
+                    }
+                    if ($populatedMetric['lower_is_better'] === null &&
+                        $populatedMetric['warning'] !== false &&
+                        $populatedMetric['fail'] !== false) {
+                        // We can infer in this case.
+                        $populatedMetric['lower_is_better'] =
+                            $populatedMetric['warning'] < $populatedMetric['fail'];
+                    }
+                    return $populatedMetric;
+                };
+
                 // Add or update any key metrics and thresholds.
                 /** @var Tracker_TrendModel $trendModel */
                 $trendModel = MidasLoader::loadModel('Trend', 'tracker');
@@ -425,18 +468,16 @@ public function submissionValidate($args)
                 foreach ($keyMetrics as $keyMetric) {
                     // Set any needed trends to be key_metrics.
                     $trendModel->setAggregatableTrendAsKeyMetrics($producerDao, $keyMetric->name);
-                    $trendThresholdModel->upsert($producerDao, $keyMetric->name,
-                        isset($keyMetric->abbreviation) ? $keyMetric->abbreviation : false,
-                        isset($keyMetric->warning) ? $keyMetric->warning :
-                            (isset($defaults->warning) ? $defaults->warning : false),
-                        isset($keyMetric->fail) ? $keyMetric->fail :
-                            (isset($defaults->fail) ? $defaults->fail : false),
-                        isset($keyMetric->min) ? $keyMetric->min :
-                            (isset($defaults->min) ? $defaults->min : false),
-                        isset($keyMetric->max) ? $keyMetric->max :
-                            (isset($defaults->max) ? $defaults->max : false),
-                        isset($keyMetric->lower_is_better) ? $keyMetric->lower_is_better :
-                            (isset($defaults->lower_is_better) ? $defaults->lower_is_better : false)
+                    $metricValues = $populateMetricValues($keyMetric);
+                    $trendThresholdModel->upsert(
+                        $producerDao,
+                        $keyMetric->name,
+                        $metricValues['abbreviation'],
+                        $metricValues['warning'],
+                        $metricValues['fail'],
+                        $metricValues['min'],
+                        $metricValues['max'],
+                        $metricValues['lower_is_better']
                     );
                 }
                 // Add or update any aggregate metrics and thresholds, based on matching
@@ -450,21 +491,20 @@ public function submissionValidate($args)
                 $userModel = MidasLoader::loadModel('User');
                 /** @var stdClass $aggregateMetric */
                 foreach ($aggregateMetrics as $aggregateMetric) {
+                    $metricValues = $populateMetricValues($aggregateMetric);
                     /** @var Tracker_AggregateMetricSpecDao $aggregateMetricSpecDao */
-                    $aggregateMetricSpecDao = $aggregateMetricSpecModel->upsert($producerDao, $aggregateMetric->name, $aggregateMetric->definition,
-                        isset($aggregateMetric->abbreviation) ? $aggregateMetric->abbreviation : false,
+                    $aggregateMetricSpecDao = $aggregateMetricSpecModel->upsert(
+                        $producerDao,
+                        $aggregateMetric->name,
+                        $aggregateMetric->definition,
+                        $metricValues['abbreviation'],
                         // Set empty string for description.
                         '',
-                        isset($aggregateMetric->warning) ? $aggregateMetric->warning :
-                            (isset($defaults->warning) ? $defaults->warning : false),
-                        isset($aggregateMetric->fail) ? $aggregateMetric->fail :
-                            (isset($defaults->fail) ? $defaults->fail : false),
-                        isset($aggregateMetric->min) ? $aggregateMetric->min :
-                            (isset($defaults->min) ? $defaults->min : false),
-                        isset($aggregateMetric->max) ? $aggregateMetric->max :
-                            (isset($defaults->max) ? $defaults->max : false),
-                        isset($aggregateMetric->lower_is_better) ? $aggregateMetric->lower_is_better :
-                            (isset($defaults->lower_is_better) ? $defaults->lower_is_better : false)
+                        $metricValues['warning'],
+                        $metricValues['fail'],
+                        $metricValues['min'],
+                        $metricValues['max'],
+                        $metricValues['lower_is_better']
                     );
                     // Delete any notifications tied to this Aggregate Metric, and create any
                     // as needed.

From 953bf4c2f6979fd6b7ead13f32dc50bd555c5e15 Mon Sep 17 00:00:00 2001
From: mgrauer <michael.grauer@kitware.com>
Date: Wed, 3 Aug 2016 12:14:06 -0400
Subject: [PATCH 20/20] Applied fixes from StyleCI

---
 modules/tracker/controllers/components/ApiComponent.php | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/tracker/controllers/components/ApiComponent.php b/modules/tracker/controllers/components/ApiComponent.php
index 40f820f0c..158ff1562 100644
--- a/modules/tracker/controllers/components/ApiComponent.php
+++ b/modules/tracker/controllers/components/ApiComponent.php
@@ -442,7 +442,7 @@ public function submissionValidate($args)
                     foreach ($populatedMetricUnassigned as $key => $unassignedValue) {
                         if (isset($metric->$key)) {
                             $populatedMetric[$key] = $metric->$key;
-                        } elseif(isset($defaults->$key)) {
+                        } elseif (isset($defaults->$key)) {
                             $populatedMetric[$key] = $defaults->$key;
                         } else {
                             $populatedMetric[$key] = $unassignedValue;
@@ -455,6 +455,7 @@ public function submissionValidate($args)
                         $populatedMetric['lower_is_better'] =
                             $populatedMetric['warning'] < $populatedMetric['fail'];
                     }
+
                     return $populatedMetric;
                 };