diff --git a/lib/Doctrine/deploy/AddCertificationStatuses.php b/lib/Doctrine/deploy/AddCertificationStatuses.php
index a3e3307df..f931b79ac 100644
--- a/lib/Doctrine/deploy/AddCertificationStatuses.php
+++ b/lib/Doctrine/deploy/AddCertificationStatuses.php
@@ -1,24 +1,26 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
-/* AddNGIs.php: Loads a list of cert statuses from an XML file and inserts them into
- * the doctrine prototype.
- * XML format is the xml input format of the cert status seed data
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
+/* AddCertificationStatuses.php: Loads a list of cert statuses from
+ * an XML file and inserts them into the doctrine prototype.
+ * XML format is the xml input format of the cert status seed data.
  */
-$certStatsFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/CertificationStatuses.xml";
+$certStatsFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/CertificationStatuses.xml";
 $certStats = simplexml_load_file($certStatsFileName);
 
-foreach($certStats as $certStat) {
+foreach ($certStats as $certStat) {
     $doctrineCertStat = new CertificationStatus();
     $name = "";
-    foreach($certStat as $key => $value) {
-        if($key == "name") {
+    foreach ($certStat as $key => $value) {
+        if ($key == "name") {
             $name = (string) $value;
         }
     }
+
     $doctrineCertStat->setName($name);
     $entityManager->persist($doctrineCertStat);
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddCountries.php b/lib/Doctrine/deploy/AddCountries.php
index a43d33a74..f7dffc646 100644
--- a/lib/Doctrine/deploy/AddCountries.php
+++ b/lib/Doctrine/deploy/AddCountries.php
@@ -1,30 +1,33 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
-/* AddCountries.php: Loads a list of countries from an XML file and inserts them into
- * the doctrine prototype.
+/* AddCountries.php: Loads a list of countries from an XML file and
+ * inserts them into the doctrine prototype.
  */
 
-$countriesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/Countries.xml";
+$countriesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/Countries.xml";
 $countries = simplexml_load_file($countriesFileName);
 
-foreach($countries as $country) {
+foreach ($countries as $country) {
     $doctrineCountry = new Country();
     $code = "";
     $name = "";
-    foreach($country as $key => $value) {
-        if($key == "name") {
+    foreach ($country as $key => $value) {
+        if ($key == "name") {
             $code = (string) $value;
         }
-        if($key == "description") {
+
+        if ($key == "description") {
             $name = (string) $value;
         }
     }
+
     $doctrineCountry->setName($name);
     $doctrineCountry->setCode($code);
     $entityManager->persist($doctrineCountry);
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddDowntimes.php b/lib/Doctrine/deploy/AddDowntimes.php
index ac4075e8b..4e9f5c088 100644
--- a/lib/Doctrine/deploy/AddDowntimes.php
+++ b/lib/Doctrine/deploy/AddDowntimes.php
@@ -1,8 +1,8 @@
 <?php
 
 require_once __DIR__ . "/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
-require_once __DIR__.'/../entities/AlreadyLinkedException.php';
+require_once __DIR__ . "/AddUtils.php";
+require_once __DIR__ . "/../entities/AlreadyLinkedException.php";
 
 
 // For each of the hostnames below, GOCDB has two SRM services
@@ -17,69 +17,75 @@
 // this out.
 //
 // The duplicates are all SRM services apart from cert-ce-01 (CE) and
-// hyx.grid.icm.edu.pl (Unicore6.StorageManagement)  - something may be wrong with the
-// SRM service type the PROM GOCDB causing duplicate service eps
-// to be registered. Either that or there's a business reason
+// hyx.grid.icm.edu.pl (Unicore6.StorageManagement) - something may be
+// wrong with the SRM service type the PROM GOCDB causing duplicate
+// service eps to be registered. Either that or there's a business reason
 // for registering two.
 $duplicateSes = array ("se.reef.man.poznan.pl",  "lcg05.sinp.msu.ru",
-        "grid-se.ii.edu.mk",
-        "storage01.lcg.cscs.ch", "grid002.ics.forth.gr",
-        "eymir.grid.metu.edu.tr", "torik1.ulakbim.gov.tr",
-        "hyx.grid.icm.edu.pl", "cert-ce-01.cnaf.infn.it", // cert-ce-01 is a CE, not SRM
+        "grid-se.ii.edu.mk", "storage01.lcg.cscs.ch",
+        "grid002.ics.forth.gr", "eymir.grid.metu.edu.tr",
+        "torik1.ulakbim.gov.tr", "hyx.grid.icm.edu.pl",
+        "cert-ce-01.cnaf.infn.it", // cert-ce-01 is a CE, not SRM
         "se01.mosigrid.utcluj.ro");
 // Hack: the above SEs appear twice with the same service type. (nightmare)
 // However in most cases both SEs share the same downtimes...
 
-// AddDowntimes.php: Loads a list of downtimes  from an
+// AddDowntimes.php: Loads a list of downtimes from an
 // XML file and inserts them into the doctrine prototype.
-// XML format is the output from get_service_endpoints PI query.
-//
+// XML format is the output from get_downtime PI query.
 
 
 $allDowntimes = array();
-$downtimeFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/Downtimes.xml";
+$downtimeFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/Downtimes.xml";
 $downtimes = simplexml_load_file($downtimeFileName);
 $largestV4DowntimePK = 0;
 
 foreach ($downtimes as $downtimeXml) {
     // Each "downtimeXML" element is one SE's downtime.
     // If a single downtime affects many SEs, each
-    // SE will be named in a different $downtimeXml that will duplicate
-    // all the downtime specific fields.
+    // SE will be named in a different $downtimeXml that will
+    // duplicate all the downtime specific fields.
 
-    foreach($downtimeXml->attributes() as $key => $value) {
-        if((string) $key == "ID") {
+    foreach ($downtimeXml->attributes() as $key => $value) {
+        if ((string) $key == "ID") {
             $promId = (int) $value;
         }
     }
 
     $downtime = null;
     // See if we've already entered a downtime with this prom ID
-    if(isset($allDowntimes[$promId])) {
-        // load $downtime from db by $promId rather than loading from global array
-        // This assumes xml ID attribute (without 'G0' appended) is the same as
-        // xml PRIMARY_KEY attribute.
+    if (isset($allDowntimes[$promId])) {
+        // Load $downtime from db by $promId rather than loading from global
+        // array. This assumes xml ID attribute (without 'G0' appended) is
+        // the same as xml PRIMARY_KEY attribute.
         //
-        // $downtime = $entityManager->createQuery("select d FROM Downtime d WHERE d.primaryKey = ?1")
-        //   ->setParameter(1, (string) $promId.'G0')
-        //   ->getResult();
+        // $downtime = $entityManager->createQuery("select d FROM Downtime " .
+        //     "d WHERE d.primaryKey = ?1")
+        //                           ->setParameter(
+        //                               1,
+        //                               (string) $promId.'G0'
+        //                           )
+        //                           ->getResult();
         $downtime = $allDowntimes[$promId];
     }
 
-    if(!isset($downtime)) {
+    if (!isset($downtime)) {
         // Create a new downtime, add the SE to it
         $downtime = newDowntime($downtimeXml);
         // Finds one or more SEs by hostname and service type
-        $services = findSEs((string) $downtimeXml->HOSTNAME
-            , (string) $downtimeXml->SERVICE_TYPE);
+        $services = findSEs(
+            (string) $downtimeXml->HOSTNAME,
+            (string) $downtimeXml->SERVICE_TYPE
+        );
 
         // There are some edge cases where findSEs returns
-        // more than one SE (see the comment at the top of this file)
+        // more than one SE (see the comment at the top of this file).
         // However if the downtime isn't yet created we always
         // link to the first SE found.
-        if(!isset($services[0])) {
-            throw new Exception("No SE found with "
-                    . "hostname " . $downtimeXml->HOSTNAME . " ");
+        if (!isset($services[0])) {
+            throw new Exception("No SE found with hostname " .
+                $downtimeXml->HOSTNAME . " ");
         }
 
         // Bidirectional link the el and dt
@@ -91,33 +97,38 @@
         $GLOBALS['allDowntimes'][$promId] = $downtime;
     } else {
         // Find the SE and link it to the downtime
-        $services = findSEs((string) $downtimeXml->HOSTNAME
-                , (string) $downtimeXml->SERVICE_TYPE);
-
-        if(!isset($services[0])) {
-            throw new Exception("No SE found with "
-                    . "hostname " . $downtimeXml->HOSTNAME . " ");
+        $services = findSEs(
+            (string) $downtimeXml->HOSTNAME,
+            (string) $downtimeXml->SERVICE_TYPE
+        );
+
+        if (!isset($services[0])) {
+            throw new Exception("No SE found with hostname " .
+                $downtimeXml->HOSTNAME . " ");
         }
+
         try {
             // TODO? - We should probably iterate each el and try to link each
-            // to this DT. Will still need to throw alreadylinked exception when
-            // trying to link a SE that is already linked to the downtime
-            // in order to detect the SE duplicates. But iterating may only be necessary
-            // if it emerges that there are instances of more than 2 duplicate SEs
-            // (the duplicate SE count is tested for the expected 2 duplicates
-            // below in catch block).
+            // to this DT. Will still need to throw alreadylinked exception
+            // when trying to link a SE that is already linked to the downtime
+            // in order to detect the SE duplicates. But iterating may only be
+            // necessary if it emerges that there are instances of more than 2
+            // duplicate SEs (the duplicate SE count is tested for the expected
+            // 2 duplicates below in catch block).
             $els = $services[0]->getEndpointLocations();
-            if(count($els) > 1){
-                throw new LogicException('Coding error - there should only be one EL per Service');
+            if (count($els) > 1) {
+                throw new LogicException('Coding error - there should only ' .
+                    'be one EL per Service');
             }
 
             // Check this endpoint isn't already linked to downtime.
             // The els have already been persisted/flushed against
             // the DB and so already have IDs.
-            foreach($downtime->getEndpointLocations() as $existingEL) {
-                if($existingEL == $els[0]) { // their Ids will be the same
-                    throw new AlreadyLinkedException("Downtime {$downtime->getId()} is already "
-                    . "linked to el {$existingEL->getId()}");
+            foreach ($downtime->getEndpointLocations() as $existingEL) {
+                if ($existingEL == $els[0]) { // their Ids will be the same
+                    throw new AlreadyLinkedException("Downtime " .
+                        "{$downtime->getId()} is already linked to el " .
+                        "{$existingEL->getId()}");
                 }
             }
 
@@ -126,43 +137,46 @@
             //$downtime->addService($services[0]);
 
         } catch (Exception $e) {
-            if($e instanceof AlreadyLinkedException) {
+            if ($e instanceof AlreadyLinkedException) {
                 // Downtime is already linked to this SE
 
                 // Check whether this exception is caused by a known issue
                 // with duplicate SEs (see comment at the top of the file).
                 // Issue is known if two SEs are found and the hostname is
-                // a known duplicate
+                // a known duplicate.
                 $twoSes = false;
-                if(count($services) == 2) {
+                if (count($services) == 2) {
                     $twoSes = true;
                 } else {
                     // we will have to deal with this case and link the
-                    throw new Exception("More than duplicate 2 SEs found: ".$services[0]->getHostName());
+                    throw new Exception("More than duplicate 2 SEs found: " .
+                        $services[0]->getHostName());
                 }
 
                 $knownDup = false;
-                foreach($duplicateSes as $dup) {
-                    if($dup == $services[0]->getHostName()) {
+                foreach ($duplicateSes as $dup) {
+                    if ($dup == $services[0]->getHostName()) {
                         $knownDup = true;
                     }
                 }
 
-                // If the above two tests are true then we've hit an edge case
-                // where a downtime currently links to one SE that's a known
-                // duplicate and it needs to link to the other (duplicated) SE.
-                // The other SE will always be the second result in $services ([1])
-                if($twoSes && $knownDup) {
+                // If the above two tests are true then we've hit an edge
+                // case where a downtime currently links to one SE that's
+                // a known duplicate and it needs to link to the other
+                // (duplicated) SE. The other SE will always be the second
+                // result in $services ([1])
+                if ($twoSes && $knownDup) {
                     //$downtime->addService($services[1]);
                     $els = $services[1]->getEndpointLocations();
 
 
         // Check this SE isn't already registered
-        //foreach($downtime->getEndpointLocations() as $existingEL) {
-        //	if($existingEL == $els[0]) {
-        //		throw new AlreadyLinkedException("Downtime {$downtime->getId()} is already "
-        //		. "linked to el {$existingEL->getId()}");
-        //	}
+        //foreach ($downtime->getEndpointLocations() as $existingEL) {
+        //    if ($existingEL == $els[0]) {
+        //        throw new AlreadyLinkedException("Downtime " .
+        //            "{$downtime->getId()} is already linked to el " .
+        //            "{$existingEL->getId()}");
+        //    }
         //}
 
                     // Bidirectional link the el and dt
@@ -173,7 +187,7 @@
     }
 }
 
-foreach($allDowntimes as $downtime) {
+foreach ($allDowntimes as $downtime) {
     $GLOBALS['entityManager']->persist($downtime);
 }
 
@@ -183,11 +197,11 @@
     print_r($e);
 }
 
-// Creates a new Doctrine downtime entity from the output of a get_downtime
-// SimpleXML element.
+// Creates a new Doctrine downtime entity from the output of a
+// get_downtime SimpleXML element.
 function newDowntime($downtimeXml) {
     $downtime = new Downtime();
-    foreach($downtimeXml->attributes() as $key => $value) {
+    foreach ($downtimeXml->attributes() as $key => $value) {
         switch($key) {
             case "ID":
                 $promId = (int) $value;
@@ -201,10 +215,10 @@ function newDowntime($downtimeXml) {
         }
     }
 
-    // Get the largest v4 downtime PK which is an integer appended by the string 'G0'
-    // slice off the 'G0' and get the integer value.
+    // Get the largest v4 downtime PK which is an integer appended by
+    // the string 'G0' slice off the 'G0' and get the integer value.
     $v4pk = (int)substr($primaryKey, 0, strlen($primaryKey)-2);
-    if($v4pk > $GLOBALS['largestV4DowntimePK']){
+    if ($v4pk > $GLOBALS['largestV4DowntimePK']) {
         $GLOBALS['largestV4DowntimePK'] = $v4pk;
     }
 
diff --git a/lib/Doctrine/deploy/AddInfrastructures.php b/lib/Doctrine/deploy/AddInfrastructures.php
index 71a618056..f28e7dd6a 100644
--- a/lib/Doctrine/deploy/AddInfrastructures.php
+++ b/lib/Doctrine/deploy/AddInfrastructures.php
@@ -1,25 +1,27 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
-/* AddNGIs.php: Loads a list of infrastructures from an XML file and inserts them into
- * the doctrine prototype.
+/* AddInfrastructures.php: Loads a list of infrastructures from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the xml input production status format.
  */
-$infrastructureFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/Infrastructures.xml";
+$infrastructureFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/Infrastructures.xml";
 $infs = simplexml_load_file($infrastructureFileName);
 
-foreach($infs as $xmlInf) {
+foreach ($infs as $xmlInf) {
     $doctrineInf = new Infrastructure();
     $name = "";
-    foreach($xmlInf as $key => $value) {
-        if($key == "name") {
+    foreach ($xmlInf as $key => $value) {
+        if ($key == "name") {
             $name = (string) $value;
         }
     }
+
     $doctrineInf->setName($name);
     $entityManager->persist($doctrineInf);
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddNGIRoles.php b/lib/Doctrine/deploy/AddNGIRoles.php
index 4b9de7882..d21f103f8 100644
--- a/lib/Doctrine/deploy/AddNGIRoles.php
+++ b/lib/Doctrine/deploy/AddNGIRoles.php
@@ -1,15 +1,16 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
-$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/UsersAndRoles.xml";
+$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/UsersAndRoles.xml";
 $usersRoles = simplexml_load_file($usersRolesFileName);
 
-foreach($usersRoles as $user) {
-    foreach($user->USER_ROLE as $role) {
+foreach ($usersRoles as $user) {
+    foreach ($user->USER_ROLE as $role) {
         // Check for blank role, skip if it's blank
-        if((string) $role->USER_ROLE == "") {
+        if ((string) $role->USER_ROLE == "") {
             continue;
         }
 
@@ -18,72 +19,101 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
-                                     ->setParameter(':roleType', (string) $role->USER_ROLE)
-                                     ->getResult();
+                                   ->setParameter(
+                                       ':roleType',
+                                       (string) $role->USER_ROLE
+                                   )
+                                   ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
-         // * one role type*/
-        if(count($roleTypes) !== 1) {
-            throw new Exception(count($roleTypes) . " role types found with name: " .
-                $role->USER_ROLE);
+         // * one role type */
+        if (count($roleTypes) !== 1) {
+            throw new Exception(count($roleTypes) . " role types found " .
+                "with name: " . $role->USER_ROLE);
         }
-        foreach($roleTypes as $result) {
+
+        foreach ($roleTypes as $result) {
             $roleType = $result;
         }
 
         // Get user entity
-        $dql = "SELECT u FROM User u JOIN u.userIdentifiers up WHERE up.keyValue = :keyValue";
+        $dql = "SELECT u FROM User u JOIN u.userIdentifiers " .
+            "up WHERE up.keyValue = :keyValue";
         $users = $entityManager->createQuery($dql)
-                  ->setParameter('keyValue', trim((string) $user->CERTDN))
-                  ->getResult();
+                               ->setParameter(
+                                   'keyValue',
+                                   trim((string) $user->CERTDN)
+                               )
+                               ->getResult();
 
         // /* Error checking: ensure each "user" refers to exactly
          // * one user */
-        if(count($users) !== 1) {
+        if (count($users) !== 1) {
             throw new Exception(count($users) . " users found with DN: " .
                 $user->CERTDN);
         }
-        foreach($users as $doctrineUser) {
+
+        foreach ($users as $doctrineUser) {
             $doctrineUser = $doctrineUser;
         }
 
-        // Check for invalid NGIs and skip
-        // typically these are decomissioned ROCs
-        if($role->ON_ENTITY == 'GridIreland' || $role->ON_ENTITY == 'NGS'
-            || $role->ON_ENTITY == 'LondonT2' || $role->ON_ENTITY == 'Tier1A'
-            || $role->ON_ENTITY == 'Tier1A') {
+        // Check for invalid NGIs and skip.
+        // Typically these are decomissioned ROCs.
+        if (
+            $role->ON_ENTITY == 'GridIreland'
+            || $role->ON_ENTITY == 'NGS'
+            || $role->ON_ENTITY == 'LondonT2'
+            || $role->ON_ENTITY == 'Tier1A'
+            || $role->ON_ENTITY == 'Tier1A'
+        ) {
             continue;
         }
 
-        // get ngi entity
+        // Get ngi entity
         $ngiName = (string) $role->ON_ENTITY;
         $dql = "SELECT n FROM NGI n WHERE n.name = :ngi";
         $ngis = $entityManager->createQuery($dql)
-                                     ->setParameter('ngi', $ngiName)
-                                     ->getResult();
+                              ->setParameter(
+                                  'ngi',
+                                  $ngiName
+                              )
+                              ->getResult();
+
         // /* Error checking: ensure each "ngi" refers to exactly
          // * one ngi */
-        if(count($ngis) !== 1) {
+        if (count($ngis) !== 1) {
             throw new Exception(count($ngis) . " ngis found name: " .
                 $ngiName);
         }
-        foreach($ngis as $ngi) {
+
+        foreach ($ngis as $ngi) {
             $ngi = $ngi;
         }
 
-        //check that the role is not a duplicate (v4 data contaisn duplicates)
+        // Check that the role is not a duplicate
+        // (v4 data contains duplicates)
         $ExistingUserRoles = $doctrineUser->getRoles();
         $thisIsADuplicateRole=false;
-        foreach($ExistingUserRoles as $role){
-            if($role->getRoleType() == $roleType and $role->getOwnedEntity() == $ngi and $role->getStatus() == 'STATUS_GRANTED'){
+        foreach ($ExistingUserRoles as $role) {
+            if (
+                $role->getRoleType() == $roleType
+                and $role->getOwnedEntity() == $ngi
+                and $role->getStatus() == 'STATUS_GRANTED'
+            ) {
                 $thisIsADuplicateRole = true;
             }
         }
 
-        if(!$thisIsADuplicateRole){
-            $doctrineRole = new Role($roleType, $doctrineUser, $ngi, 'STATUS_GRANTED');
+        if (!$thisIsADuplicateRole) {
+            $doctrineRole = new Role(
+                $roleType,
+                $doctrineUser,
+                $ngi,
+                'STATUS_GRANTED'
+            );
             $entityManager->persist($doctrineRole);
         }
     }
diff --git a/lib/Doctrine/deploy/AddNGIs.php b/lib/Doctrine/deploy/AddNGIs.php
index c690b8b29..30f02a7cc 100644
--- a/lib/Doctrine/deploy/AddNGIs.php
+++ b/lib/Doctrine/deploy/AddNGIs.php
@@ -1,11 +1,11 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
 /**
- * AddNGIs.php: Loads a list of NGIs from an XML file and inserts them into
- * the doctrine prototype.
+ * AddNGIs.php: Loads a list of NGIs from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the output from get_roc_list PI query.
  */
 
@@ -13,15 +13,19 @@
 $ngis = simplexml_load_file($ngisFileName);
 
 // Find the EGI project object
-$egiProject = $entityManager->getRepository('Project')->findOneBy(array("name" => "EGI"));
+$egiProject = $entityManager->getRepository('Project')
+                            ->findOneBy(array("name" => "EGI"));
 
-//Find the EGI scope tag
-$egiScope = $entityManager->getRepository('Scope')->findOneBy(array("name" => "EGI"));
+// Find the EGI scope tag
+$egiScope = $entityManager->getRepository('Scope')
+                          ->findOneBy(array("name" => "EGI"));
 
-//Add Local Scope so specified NGI is not part of EGI project
-$localScope = $entityManager->getRepository('Scope')->findOneBy(array("name" => "Local"));
+// Add Local Scope so that the specified NGI is
+// not part of the EGI project
+$localScope = $entityManager->getRepository('Scope')
+                            ->findOneBy(array("name" => "Local"));
 
-foreach($ngis as $xmlNgi) {
+foreach ($ngis as $xmlNgi) {
     $doctrineNgi = new NGI();
     $name = "";
     $email = "";
@@ -61,14 +65,20 @@
         }
 
         if ((string) $key == "CDATEON") {
-            // $cdateonString has the following format: '12-JAN-10 14.12.56.000000'
+            // $cdateonString has the following format:
+            // '12-JAN-10 14.12.56.000000'
             $cdateonString = (string) $value;
 
-            //convert to date time
-            $creationDate = DateTime::createFromFormat('d-M-y G.i.s.u', $cdateonString, new DateTimeZone('UTC'));
+            // Convert to date time
+            $creationDate = DateTime::createFromFormat(
+                'd-M-y G.i.s.u',
+                $cdateonString,
+                new DateTimeZone('UTC')
+            );
 
             if ($creationDate == false) {
-            throw new LogicException("Datetime in unexpected format. datetime: '" . $cdateonString . "'");
+                throw new LogicException("Datetime in unexpected " .
+                    "format. datetime: '" . $cdateonString . "'");
             }
         }
 
@@ -82,15 +92,15 @@
     $doctrineNgi->setSecurityEmail($securityEmail);
 
     // TODO
-    //if($cdateon == null) throw new Exception("CDATEON is null");
+    //if ($cdateon == null) throw new Exception("CDATEON is null");
     //$doctrineNgi->setCreationDate($cdateon);
 
-    // if the NGI has id 67518 (NGI_HU) do not add it to EGI Project
+    // If the NGI has id 67518 (NGI_HU) do not add it to EGI Project
     if ($objectID == "67518") {
         $doctrineNgi->addScope($localScope);
         $entityManager->persist($doctrineNgi);
     } else {
-        // add NGI to EGI project and give it EGI scope
+        // Add NGI to EGI project and give it EGI scope
         $egiProject->addNgi($doctrineNgi);
         $doctrineNgi->addScope($egiScope);
         $entityManager->persist($doctrineNgi);
@@ -98,6 +108,6 @@
 
 }
 
-// don't need to merge egiProject
-//$entityManager->merge($egiProject);
+// Don't need to merge egiProject
+// $entityManager->merge($egiProject);
 $entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddProjectRoles.php b/lib/Doctrine/deploy/AddProjectRoles.php
index 1a722d683..140d76bb3 100644
--- a/lib/Doctrine/deploy/AddProjectRoles.php
+++ b/lib/Doctrine/deploy/AddProjectRoles.php
@@ -1,10 +1,10 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
 /**
- * AddEgiRoles.php: Loads a list of roles from the get_user PI
+ * AddProjectRoles.php: Loads a list of roles from the get_user PI
  * query output (XML), finds what project entity the role is over,
  * if the project entity refers to exactly one project the role is
  * added to that project and inserted into the doctrine prototype.
@@ -12,13 +12,14 @@
  * project exists more than once, the role is not added to a project.
  */
 
-$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/UsersAndRoles.xml";
+$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/UsersAndRoles.xml";
 $usersRoles = simplexml_load_file($usersRolesFileName);
 
-foreach($usersRoles as $user) {
-    foreach($user->USER_ROLE as $role) {
+foreach ($usersRoles as $user) {
+    foreach ($user->USER_ROLE as $role) {
         // Check for blank role, skip if it's blank
-        if((string) $role->USER_ROLE == "") {
+        if ((string) $role->USER_ROLE == "") {
             continue;
         }
 
@@ -27,34 +28,44 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
-                                     ->setParameter(':roleType', (string) $role->USER_ROLE)
-                                     ->getResult();
+                                   ->setParameter(
+                                       ':roleType',
+                                       (string) $role->USER_ROLE
+                                   )
+                                   ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
-         // * one role type*/
-        if(count($roleTypes) !== 1) {
-            throw new Exception(count($roleTypes) . " role types found with name: " .
-                $role->USER_ROLE);
+         // * one role type */
+        if (count($roleTypes) !== 1) {
+            throw new Exception(count($roleTypes) . " role types found " .
+                "with name: " . $role->USER_ROLE);
         }
-        foreach($roleTypes as $result) {
+
+        foreach ($roleTypes as $result) {
             $roleType = $result;
         }
 
         // Get user entity
-        $dql = "SELECT u FROM User u JOIN u.userIdentifiers up WHERE up.keyValue = :keyValue";
+        $dql = "SELECT u FROM User u JOIN u.userIdentifiers up " .
+            "WHERE up.keyValue = :keyValue";
         $users = $entityManager->createQuery($dql)
-                  ->setParameter('keyValue', trim((string) $user->CERTDN))
-                  ->getResult();
+                               ->setParameter(
+                                   'keyValue',
+                                   trim((string) $user->CERTDN)
+                               )
+                               ->getResult();
 
         // /* Error checking: ensure each "user" refers to exactly
          // * one user */
-        if(count($users) !== 1) {
+        if (count($users) !== 1) {
             throw new Exception(count($users) . " users found with DN: " .
                 $user->CERTDN);
         }
-        foreach($users as $doctrineUser) {
+
+        foreach ($users as $doctrineUser) {
             $doctrineUser = $doctrineUser;
         }
 
@@ -64,18 +75,29 @@
         // Querying the project entity
         $dql = "SELECT p FROM Project p WHERE p.name = :project";
         $projects = $entityManager->createQuery($dql)
-                                     ->setParameter('project', $projectName)
-                                     ->getResult();
+                                  ->setParameter(
+                                      'project',
+                                      $projectName
+                                  )
+                                  ->getResult();
 
         // Error check: ensure each 'project' refers to exactly one project
         if (count($projects) !== 1) {
-            throw new Exception(count($projects) . " Projects found with name: " .
-                $projectName);
+            throw new Exception(count($projects) . " Projects found " .
+                "with name: " . $projectName);
         }
 
         // Finding the project object and adding the role to it
-        $getProject = $entityManager->getRepository('Project')->findOneBy(array("name" => $projectName));
-        $doctrineRole = new Role($roleType, $doctrineUser, $getProject, 'STATUS_GRANTED');
+        $getProject = $entityManager->getRepository('Project')
+                                    ->findOneBy(
+                                        array("name" => $projectName)
+                                    );
+        $doctrineRole = new Role(
+            $roleType,
+            $doctrineUser,
+            $getProject,
+            'STATUS_GRANTED'
+        );
         $entityManager->persist($doctrineRole);
     }
 }
diff --git a/lib/Doctrine/deploy/AddProjects.php b/lib/Doctrine/deploy/AddProjects.php
index b396a781c..a1e45d5ae 100644
--- a/lib/Doctrine/deploy/AddProjects.php
+++ b/lib/Doctrine/deploy/AddProjects.php
@@ -1,8 +1,8 @@
 <?php
-require_once __DIR__."/../bootstrap.php";
+require_once __DIR__ . "/../bootstrap.php";
 /* AddProjects.php: Manually inserts projects into
  * the doctrine prototype.
  */
 $proj = new Project("EGI");
 $entityManager->persist($proj);
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddRoleTypes.php b/lib/Doctrine/deploy/AddRoleTypes.php
index 143585843..3217bfa12 100644
--- a/lib/Doctrine/deploy/AddRoleTypes.php
+++ b/lib/Doctrine/deploy/AddRoleTypes.php
@@ -1,7 +1,7 @@
 <?php
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
-require_once __DIR__."/../../Gocdb_Services/RoleConstants.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
+require_once __DIR__ . "/../../Gocdb_Services/RoleConstants.php";
 /* AddRoleTypes.php: Manually inserts role types into
  * the doctrine prototype.
  */
@@ -30,7 +30,7 @@
     array("Regional Staff", "")
 );
 
-foreach($roleTypeArray as $roleType) {
+foreach ($roleTypeArray as $roleType) {
     $rt = new RoleType($roleType[0], $roleType[1]);
     //$rt->setName($roleType[0]);
     //$rt->setClassification($roleType[1]);
@@ -42,9 +42,9 @@
 foreach ($roleTypeArray as $key => $value) {
     $rt = new RoleType($value);
     //echo $value;
-    if($value != RoleTypeName::GOCDB_ADMIN){
+    if ($value != RoleTypeName::GOCDB_ADMIN) {
         $entityManager->persist($rt);
     }
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddScopes.php b/lib/Doctrine/deploy/AddScopes.php
index 1a23abeac..9b20f53a4 100644
--- a/lib/Doctrine/deploy/AddScopes.php
+++ b/lib/Doctrine/deploy/AddScopes.php
@@ -1,32 +1,34 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
-/* AddNGIs.php: Loads a list of scopes from an XML file and inserts them into
- * the doctrine prototype.
+/* AddScopes.php: Loads a list of scopes from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the xml input format for scope data
  */
-$scopesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/Scopes.xml";
+$scopesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/Scopes.xml";
 $scopes = simplexml_load_file($scopesFileName);
 
-foreach($scopes as $scope) {
+foreach ($scopes as $scope) {
     $doctrineScope = new Scope();
     $name = "";
     $reserved = false;
-    foreach($scope as $key => $value) {
+    foreach ($scope as $key => $value) {
       switch ($key) {
         case "name":
           $name = (string) $value;
           break;
         case "reserved":
-          $reserved = ( $value == 1 );
+          $reserved = ($value == 1);
           break;
       }
     }
+
     $doctrineScope->setName($name);
     $doctrineScope->setReserved($reserved);
     $entityManager->persist($doctrineScope);
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddServiceEndpoints.php b/lib/Doctrine/deploy/AddServiceEndpoints.php
index 18cb4021e..d7827e489 100644
--- a/lib/Doctrine/deploy/AddServiceEndpoints.php
+++ b/lib/Doctrine/deploy/AddServiceEndpoints.php
@@ -1,67 +1,83 @@
 <?php
 
 require_once __DIR__ . "/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/AddUtils.php";
 
 /* Loads a list of SEs from an
  * XML file and inserts them into the doctrine prototype.
  * XML format is the output from get_service_endpoints PI query.
  */
-$seFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/ServiceEndpoints.xml";
+$seFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/ServiceEndpoints.xml";
 $ses = simplexml_load_file($seFileName);
 
 // Get EGI scope entity to join to later
 $dql = "SELECT s from Scope s WHERE s.name = 'EGI'";
-$scopes = $entityManager->createQuery($dql)->getResult();
+$scopes = $entityManager->createQuery($dql)
+                        ->getResult();
 /* Error checking: ensure we have the EGI scope */
 if (count($scopes) !== 1) {
-    throw new Exception(count($scopes) . " scopes found with short name: EGI");
+    throw new Exception(count($scopes) . " scopes found with " .
+        "short name: EGI");
 }
+
 foreach ($scopes as $egiScope) {
     $egiScope = $egiScope;
 }
 
 // Get local scope entity to join to later
 $dql = "SELECT s from Scope s WHERE s.name = 'Local'";
-$scopes = $entityManager->createQuery($dql)->getResult();
+$scopes = $entityManager->createQuery($dql)
+                        ->getResult();
 /* Error checking: ensure we have the local scope */
 if (count($scopes) !== 1) {
-    throw new Exception(count($scopes) . " scopes found with short name: Local");
+    throw new Exception(count($scopes) . " scopes found with " .
+        "short name: Local");
 }
+
 foreach ($scopes as $localScope) {
     $localScope = $localScope;
 }
 
 foreach ($ses as $xmlSe) {
     $doctrineSe = new Service();
-    // get the hosting site entity
+    // Get the hosting site entity
     $dql = "SELECT s from Site s WHERE s.shortName = ?1";
     $parentSites = $entityManager->createQuery($dql)
-            ->setParameter(1, (string) $xmlSe->SITENAME)
-            ->getResult();
+                                 ->setParameter(
+                                     1,
+                                     (string) $xmlSe->SITENAME
+                                 )
+                                 ->getResult();
 
     /* Error checking: ensure each SE's "parent site" refers to exactly
      * one ngi */
     if (count($parentSites) !== 1) {
-        throw new Exception(count($parentSites) . " sites found with short name: " .
-                $xmlSe->SITENAME . ". SE hostname is " . $xmlSe->HOSTNAME);
+        throw new Exception(count($parentSites) . " sites found " .
+            "with short name: " . $xmlSe->SITENAME .
+            ". SE hostname is " . $xmlSe->HOSTNAME);
     }
+
     foreach ($parentSites as $result) {
         $parentSite = $result;
     }
+
     $doctrineSe->setParentSiteDoJoin($parentSite);
 
-    // get the hosting service type
+    // Get the hosting service type
     $dql = "SELECT s from ServiceType s WHERE s.name = ?1";
     $sts = $entityManager->createQuery($dql)
-            ->setParameter(1, (string) $xmlSe->SERVICE_TYPE)
-            ->getResult();
+                         ->setParameter(
+                             1,
+                             (string) $xmlSe->SERVICE_TYPE
+                         )
+                         ->getResult();
 
     /* Error checking: ensure each SE's "SERVICE_TYPE" refers to exactly
      * one SERVICE_TYPE */
     if (count($sts) !== 1) {
-        throw new Exception(count($sts) . " SERVICE_TYPEs found with name: " .
-                $xmlSe->SERVICE_TYPE);
+        throw new Exception(count($sts) . " SERVICE_TYPEs found " .
+            "with name: " . $xmlSe->SERVICE_TYPE);
     }
 
     foreach ($sts as $st) {
@@ -94,13 +110,14 @@
     // Set the scope
     if ((string) $xmlSe->SCOPE == "EGI") {
         $doctrineSe->addScope($egiScope);
-    } else if ((String) $xmlSe->SCOPE == 'Local') {
+    } elseif ((string) $xmlSe->SCOPE == 'Local') {
         $doctrineSe->addScope($localScope);
     } else {
-        throw new Exception("Unknown scope " . $xmlSe->SCOPE . " for SE " . $xmlSe->HOSTNAME);
+        throw new Exception("Unknown scope " . $xmlSe->SCOPE .
+            " for SE " . $xmlSe->HOSTNAME);
     }
 
-    //set creation date
+    // Set creation date
     $creationDate = new \DateTime("now", new DateTimeZone('UTC'));
 
 
@@ -116,10 +133,12 @@
     $doctrineEndpointLocation = new EndpointLocation();
     $doctrineEndpointLocation->setUrl((string) $xmlSe->URL);
     $doctrineEndpointLocation->setName('sampleEndpoint');
-    $doctrineEndpointLocation->setInterfaceName((string)$doctrineSe->getServiceType()->getName());
+    $doctrineEndpointLocation->setInterfaceName((string)$doctrineSe
+                             ->getServiceType()->getName());
     $doctrineSe->addEndpointLocationDoJoin($doctrineEndpointLocation);
 
     $entityManager->persist($doctrineSe);
     $entityManager->persist($doctrineEndpointLocation);
 }
-$entityManager->flush();
\ No newline at end of file
+
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddServiceGroupRoles.php b/lib/Doctrine/deploy/AddServiceGroupRoles.php
index 0690473be..38a556f33 100644
--- a/lib/Doctrine/deploy/AddServiceGroupRoles.php
+++ b/lib/Doctrine/deploy/AddServiceGroupRoles.php
@@ -19,11 +19,14 @@
             continue;
         }
 
-        // get roletype entity
+        // Get roletype entity
         $userRole = (string) $role->USER_ROLE;
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = :roleType";
         $roleTypes = $entityManager->createQuery($dql)
-                                   ->setParameter(':roleType', $userRole)
+                                   ->setParameter(
+                                       ':roleType',
+                                       $userRole
+                                   )
                                    ->getResult();
 
         /*
@@ -44,7 +47,10 @@
         $dql = "SELECT u FROM User u JOIN u.userIdentifiers up " .
             "WHERE up.keyValue = :keyValue";
         $users = $entityManager->createQuery($dql)
-                               ->setParameter('keyValue', trim($userDN))
+                               ->setParameter(
+                                   'keyValue',
+                                   trim($userDN)
+                               )
                                ->getResult();
 
         /*
@@ -59,11 +65,15 @@
         // Set $doctrineUser as the first and only user in the users array
         $doctrineUser = $users[0];
 
-        // get serviceGroup entity
+        // Get serviceGroup entity
         $sgName = (string) $role->ON_ENTITY;
-        $dql = "SELECT sg FROM ServiceGroup sg WHERE sg.name = :service_group";
+        $dql = "SELECT sg FROM ServiceGroup sg WHERE " .
+            "sg.name = :service_group";
         $serviceGroups = $entityManager->createQuery($dql)
-                                       ->setParameter('service_group', $sgName)
+                                       ->setParameter(
+                                           'service_group',
+                                           $sgName
+                                       )
                                        ->getResult();
 
         /*
diff --git a/lib/Doctrine/deploy/AddServiceGroups.php b/lib/Doctrine/deploy/AddServiceGroups.php
index 715baf169..e5a87eec6 100644
--- a/lib/Doctrine/deploy/AddServiceGroups.php
+++ b/lib/Doctrine/deploy/AddServiceGroups.php
@@ -1,7 +1,7 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
 /* Loads a list of service types from an XML file and inserts them into
  * the doctrine prototype.
@@ -21,7 +21,7 @@
     exit;
 }
 
-foreach($sts as $st) {
+foreach ($sts as $st) {
     $instance = new ServiceGroup();
     $name = "";
     $desc = "";
diff --git a/lib/Doctrine/deploy/AddServiceTypes.php b/lib/Doctrine/deploy/AddServiceTypes.php
index 5b4de1503..b88ebab83 100644
--- a/lib/Doctrine/deploy/AddServiceTypes.php
+++ b/lib/Doctrine/deploy/AddServiceTypes.php
@@ -1,31 +1,32 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
-/* Loads a list of service types from an XML file and inserts them into
- * the doctrine prototype.
+/* Loads a list of service types from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the PROM GOCDB PI output for get_service_type
  */
 $stFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/ServiceTypes.xml";
 $sts = simplexml_load_file($stFileName);
 
-foreach($sts as $st) {
+foreach ($sts as $st) {
     $doctrineSt = new ServiceType();
     $name = "";
     $desc = "";
-    foreach($st as $key => $value) {
-        if($key == "SERVICE_TYPE_NAME") {
+    foreach ($st as $key => $value) {
+        if ($key == "SERVICE_TYPE_NAME") {
             $name = (string) $value;
         }
 
-        if($key == "SERVICE_TYPE_DESC") {
+        if ($key == "SERVICE_TYPE_DESC") {
             $desc = (string) $value;
         }
     }
+
     $doctrineSt->setName($name);
     $doctrineSt->setDescription($desc);
     $entityManager->persist($doctrineSt);
 }
 
-$entityManager->flush();
\ No newline at end of file
+$entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddSiteRoles.php b/lib/Doctrine/deploy/AddSiteRoles.php
index b8fc466b0..68fe495d2 100644
--- a/lib/Doctrine/deploy/AddSiteRoles.php
+++ b/lib/Doctrine/deploy/AddSiteRoles.php
@@ -1,105 +1,133 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
 
 /**
- * AddNGIs.php: Loads a list of Site roles from an XML file and inserts them into
- * the doctrine prototype.
+ * AddSiteRoles.php: Loads a list of Site roles from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the output from get_user_doctrine PI query.
  */
-$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/UsersAndRoles.xml";
+$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/UsersAndRoles.xml";
 $usersRoles = simplexml_load_file($usersRolesFileName);
 
-foreach($usersRoles as $user) {
-    foreach($user->USER_ROLE as $role) {
+foreach ($usersRoles as $user) {
+    foreach ($user->USER_ROLE as $role) {
         // Check for blank role, skip if it's blank
-        if((string) $role->USER_ROLE == "") {
+        if ((string) $role->USER_ROLE == "") {
             continue;
         }
 
         // Skip all non-site roles
-        if((string) $role->ENTITY_TYPE !== "site") {
+        if ((string) $role->ENTITY_TYPE !== "site") {
             continue;
         }
 
-        // Find the role type
-        // get the roletype entity
+        // Find the role type and get the roletype entity
         $dql = "SELECT rt FROM RoleType rt WHERE rt.name = ?1";
         $roleTypes = $entityManager->createQuery($dql)
-                                     ->setParameter(1, (string) $role->USER_ROLE)
-                                     ->getResult();
+                                   ->setParameter(
+                                       1,
+                                       (string) $role->USER_ROLE
+                                   )
+                                   ->getResult();
+
         // /* Error checking: ensure each role type refers to exactly
-         // * one role type*/
-        if(count($roleTypes) !== 1) {
-            throw new Exception(count($roleTypes) . " role types found with name: " .
-                $role->USER_ROLE);
+        //  * one role type */
+        if (count($roleTypes) !== 1) {
+            throw new Exception(count($roleTypes) . " role types found " .
+                "with name: " . $role->USER_ROLE);
         }
-        foreach($roleTypes as $result) {
+
+        foreach ($roleTypes as $result) {
             $roleType = $result;
         }
-        if(!($roleType instanceof RoleType)) {
+
+        if (!($roleType instanceof RoleType)) {
             throw new Exception("Not a doctrine role type");
         }
 
         // Get user entity
-        $dql = "SELECT u FROM User u JOIN u.userIdentifiers up WHERE up.keyValue = :keyValue";
+        $dql = "SELECT u FROM User u JOIN u.userIdentifiers up " .
+            "WHERE up.keyValue = :keyValue";
         $users = $entityManager->createQuery($dql)
-                  ->setParameter('keyValue', trim((string) $user->CERTDN))
-                  ->getResult();
+                               ->setParameter(
+                                   'keyValue',
+                                   trim((string) $user->CERTDN)
+                               )
+                               ->getResult();
 
         // /* Error checking: ensure each "user" refers to exactly
          // * one user */
-        if(count($users) !== 1) {
+        if (count($users) !== 1) {
             throw new Exception(count($users) . " users found with DN: " .
                 $user->CERTDN);
         }
 
-        foreach($users as $doctrineUser) {
+        foreach ($users as $doctrineUser) {
             $doctrineUser = $doctrineUser;
         }
 
-        if(!($doctrineUser instanceof User)) {
+        if (!($doctrineUser instanceof User)) {
             throw new Exception("Not a doctrine user");
         }
 
-        // Check for invalid sites and skip adding this role
-        // typically these sites don't have an NGI, country or production status
-        if(isBad((string) $role->ON_ENTITY)) {
+        // Check for invalid sites and skip adding this role.
+        // Typically these sites don't have an NGI,
+        // country or production status.
+        if (isBad((string) $role->ON_ENTITY)) {
             continue;
         }
 
-        // get the site entity
+        // Get the site entity
         $dql = "SELECT s FROM Site s WHERE s.shortName = ?1";
         $sites = $entityManager->createQuery($dql)
-                                     ->setParameter(1, (string) $role->ON_ENTITY)
-                                     ->getResult();
+                               ->setParameter(
+                                   1,
+                                   (string) $role->ON_ENTITY
+                               )
+                               ->getResult();
+
         // /* Error checking: ensure each "site" refers to exactly
          // * one site */
-        if(count($sites) !== 1) {
-            throw new Exception(count($sites) . " sites found with short name: " .
-                $role->ON_ENTITY);
+        if (count($sites) !== 1) {
+            throw new Exception(count($sites) . " sites found " .
+                "with short name: " . $role->ON_ENTITY);
         }
-        foreach($sites as $doctrineSite) {
+
+        foreach ($sites as $doctrineSite) {
             $doctrineSite = $doctrineSite;
         }
-        if(!($doctrineSite instanceof Site)) {
+
+        if (!($doctrineSite instanceof Site)) {
             throw new Exception("Not a doctrine site");
         }
 
-        //check that the role is not a duplicate (v4 data contaisn duplicates)
+        // Check that the role is not a duplicate
+        // (v4 data contains duplicates)
         $ExistingUserRoles = $doctrineUser->getRoles();
         $thisIsADuplicateRole=false;
-        foreach($ExistingUserRoles as $role){
-            if($role->getRoleType() == $roleType and $role->getOwnedEntity() == $doctrineSite and $role->getStatus() == 'STATUS_GRANTED'){
+        foreach ($ExistingUserRoles as $role) {
+            if (
+                $role->getRoleType() == $roleType
+                and $role->getOwnedEntity() == $doctrineSite
+                and $role->getStatus() == 'STATUS_GRANTED'
+            ) {
                 $thisIsADuplicateRole = true;
             }
         }
 
-        if(!$thisIsADuplicateRole){
-            $doctrineRole = new Role($roleType, $doctrineUser, $doctrineSite, 'STATUS_GRANTED');
+        if (!$thisIsADuplicateRole) {
+            $doctrineRole = new Role(
+                $roleType,
+                $doctrineUser,
+                $doctrineSite,
+                'STATUS_GRANTED'
+            );
             $entityManager->persist($doctrineRole);
         }
     }
 }
+
 $entityManager->flush();
diff --git a/lib/Doctrine/deploy/AddSites.php b/lib/Doctrine/deploy/AddSites.php
index c6640e32a..601e6f850 100644
--- a/lib/Doctrine/deploy/AddSites.php
+++ b/lib/Doctrine/deploy/AddSites.php
@@ -2,25 +2,27 @@
 require_once __DIR__ . "/../bootstrap.php";
 require_once __DIR__ . "/AddUtils.php";
 
-/* AddSites.php: Loads a list of sites from an XML file and inserts them into
- * the doctrine prototype.
+/* AddSites.php: Loads a list of sites from an XML file and
+ * inserts them into the doctrine prototype.
  * XML format is the output from get_site PI query.
  */
 $sitesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/Sites.xml";
 $sites = simplexml_load_file($sitesFileName);
 
-$xmlCertStatusChanges = simplexml_load_file( __DIR__ . "/" . $GLOBALS['dataDir'] . "/CertStatusChanges.xml");
-$xmlCertStatusLinkDates = simplexml_load_file(__DIR__ . "/" . $GLOBALS['dataDir'] . "/CertStatusDate.xml");
+$xmlCertStatusChanges = simplexml_load_file(__DIR__ . "/" .
+    $GLOBALS['dataDir'] . "/CertStatusChanges.xml");
+$xmlCertStatusLinkDates = simplexml_load_file(__DIR__ . "/" .
+    $GLOBALS['dataDir'] . "/CertStatusDate.xml");
 
 $largestV4SitePk = 0;
-foreach($sites as $xmlSite) {
+foreach ($sites as $xmlSite) {
 
     // Check whether this site has a larger v4 primary key
     // than any other recorded so far
     $v4pkGO = trim((string) $xmlSite->PRIMARY_KEY);
-    // isolate just the number part (slice the 'GO' off the end)
-    $v4pk = (int)substr($v4pkGO, 0, strlen($v4pkGO)-2);
-    if($v4pk > $largestV4SitePk){
+    // Isolate just the number part (slice the 'GO' off the end)
+    $v4pk = (int) substr($v4pkGO, 0, strlen($v4pkGO)-2);
+    if ($v4pk > $largestV4SitePk) {
         $largestV4SitePk = $v4pk;
     }
 
@@ -35,11 +37,11 @@
     $doctrineSite->setTelephone((string) $xmlSite->CONTACT_TEL);
     $doctrineSite->setGiisUrl((string) $xmlSite->GIIS_URL);
     $doctrineSite->setTimezoneId((string) $xmlSite->TIMEZONE);
-    if(strlen((string)$xmlSite->LATITUDE) > 0){
-        $doctrineSite->setLatitude((float)$xmlSite->LATITUDE);
+    if (strlen((string) $xmlSite->LATITUDE) > 0) {
+        $doctrineSite->setLatitude((float) $xmlSite->LATITUDE);
     }
-    if(strlen((string)$xmlSite->LONGITUDE) > 0){
-        $doctrineSite->setLongitude((float)$xmlSite->LONGITUDE);
+    if (strlen((string) $xmlSite->LONGITUDE) > 0) {
+        $doctrineSite->setLongitude((float) $xmlSite->LONGITUDE);
     }
     $doctrineSite->setCsirtEmail((string) $xmlSite->CSIRT_EMAIL);
     $doctrineSite->setIpRange((string) $xmlSite->IP_RANGE);
@@ -51,97 +53,134 @@
     $doctrineSite->setAlarmEmail((string) $xmlSite->ALARM_EMAIL);
     $doctrineSite->setHelpdeskEmail((string) $xmlSite->HELPDESKEMAIL);
 
-    // get the parent NGI entity
+    // Get the parent NGI entity
     $dql = "SELECT n FROM NGI n WHERE n.name = ?1";
     $parentNgis = $entityManager->createQuery($dql)
-                                 ->setParameter(1, (string) $xmlSite->ROC)
-                                 ->getResult();
+                                ->setParameter(
+                                    1,
+                                    (string) $xmlSite->ROC
+                                )
+                                ->getResult();
+
     // /* Error checking: ensure each SE's "parent ngi" refers to exactly
-     // * one ngi */
-    if(count($parentNgis) !== 1) {
+    //  * one ngi */
+    if (count($parentNgis) !== 1) {
         throw new Exception(count($parentNgis) . " NGIs found with name: " .
             $xmlSite->ROC);
     }
-    foreach($parentNgis as $result) {
+
+    foreach ($parentNgis as $result) {
         $parentNgi = $result;
     }
+
     $doctrineSite->setNgiDoJoin($parentNgi);
 
-    // get the target infrastructure
+    // Get the target infrastructure
     $dql = "SELECT i FROM Infrastructure i WHERE i.name = :name";
     $infs = $entityManager->createQuery($dql)
-                                 ->setParameter('name', (string) $xmlSite->PRODUCTION_INFRASTRUCTURE)
-                                 ->getResult();
-    // /* Error checking: ensure each SE's "PRODUCTION_INFRASTRUCTURE" refers to exactly
-     // * one PRODUCTION_INFRASTRUCTURE */
-    if(count($infs) !== 1) {
-        throw new Exception(count($infs) . " Infrastructures found with name: " .
-            $xmlSite->PRODUCTION_INFRASTRUCTURE);
+                          ->setParameter(
+                              'name',
+                              (string) $xmlSite->PRODUCTION_INFRASTRUCTURE
+                          )
+                          ->getResult();
+
+    // /* Error checking: ensure each SE's "PRODUCTION_INFRASTRUCTURE"
+    //  * refers to exactly one PRODUCTION_INFRASTRUCTURE */
+    if (count($infs) !== 1) {
+        throw new Exception(count($infs) . " Infrastructures found " .
+            "with name: " . $xmlSite->PRODUCTION_INFRASTRUCTURE);
     }
-    foreach($infs as $inf) {
+
+    foreach ($infs as $inf) {
         $inf = $inf;
     }
+
     $doctrineSite->setInfrastructure($inf);
 
-    // get the cert status
+    // Get the cert status
     $dql = "SELECT c FROM CertificationStatus c WHERE c.name = ?1";
     $certStatuses = $entityManager->createQuery($dql)
-                                 ->setParameter(1, (string) $xmlSite->CERTIFICATION_STATUS)
-                                 ->getResult();
+                                  ->setParameter(
+                                      1,
+                                      (string) $xmlSite->CERTIFICATION_STATUS
+                                  )
+                                  ->getResult();
+
     /* Error checking: ensure each Site's "cert status" refers to exactly
      * one cert status */
-    if(count($certStatuses) !== 1) {
-        throw new Exception(count($certStatuses) . " cert statuses found with name: " .
-            $xmlSite->CERTIFICATION_STATUS);
+    if (count($certStatuses) !== 1) {
+        throw new Exception(count($certStatuses) . " cert statuses found " .
+            "with name: " . $xmlSite->CERTIFICATION_STATUS);
     }
-    foreach($certStatuses as $certStatus) {
+
+    foreach ($certStatuses as $certStatus) {
         $certStatus = $certStatus;
     }
+
     $doctrineSite->setCertificationStatus($certStatus);
 
-    $doctrineSite->addScope(getScope($entityManager, (string) $xmlSite->SCOPE));
+    $doctrineSite->addScope(
+        getScope(
+            $entityManager,
+            (string) $xmlSite->SCOPE
+        )
+    );
 
-    // get / set the country
+    // Get / set the country
     $dql = "SELECT c FROM Country c WHERE c.name = ?1";
     $countries = $entityManager->createQuery($dql)
-                                 ->setParameter(1, (string) $xmlSite->COUNTRY)
-                                 ->getResult();
+                               ->setParameter(
+                                   1,
+                                   (string) $xmlSite->COUNTRY
+                               )
+                               ->getResult();
+
     /* Error checking: ensure each country refers to exactly
      * one country */
-    if(count($countries) !== 1) {
-        throw new Exception(count($countries) . " country found with name: " .
-            $xmlSite->COUNTRY);
+    if (count($countries) !== 1) {
+        throw new Exception(count($countries) . " country found " .
+            "with name: " . $xmlSite->COUNTRY);
     }
-    foreach($countries as $country) {
+
+    foreach ($countries as $country) {
         $country = $country;
     }
+
     $doctrineSite->setCountry($country);
 
 
-    // get the Tier (optional value)
+    // Get the Tier (optional value)
     $dql = "SELECT t FROM Tier t WHERE t.name = ?1";
     $tiers = $entityManager->createQuery($dql)
-                                 ->setParameter(1, (string) $xmlSite->TIER)
-                                 ->getResult();
+                           ->setParameter(
+                               1,
+                               (string) $xmlSite->TIER
+                           )
+                           ->getResult();
+
     /* Error checking: ensure each tier refers to exactly
      * one TIER */
-    if(count($tiers) == 1) {
-        foreach($tiers as $tier) {
+    if (count($tiers) == 1) {
+        foreach ($tiers as $tier) {
             $tier = $tier;
         }
 
         $doctrineSite->setTier($tier);
     }
 
-    // get the SubGrid (optional value)
+    // Get the SubGrid (optional value)
     $dql = "SELECT s FROM SubGrid s WHERE s.name = ?1";
     $subGrids = $entityManager->createQuery($dql)
-        ->setParameter(1, (string) $xmlSite->SUBGRID)
-        ->getResult();
+                              ->setParameter(
+                                  1,
+                                  (string) $xmlSite->SUBGRID
+                              )
+                              ->getResult();
+
     /* Error checking: ensure each subgrid refers to exactly
      * one subgrid */
-    if(count($subGrids) == 1) {
-        foreach($subGrids as $subGrid) {
+    if (count($subGrids) == 1) {
+        foreach ($subGrids as $subGrid) {
             $subGrid = $subGrid;
         }
 
@@ -150,8 +189,11 @@
 
 
 
-    //set creation date
-    $creationDate = new \DateTime("now", new DateTimeZone('UTC'));
+    // Set creation date
+    $creationDate = new \DateTime(
+        "now",
+        new DateTimeZone('UTC')
+    );
 
     $doctrineSite->setCreationDate($creationDate);
 
@@ -159,50 +201,69 @@
     // The date of the CURRENT certStatus in v4 is recorded as
     // a link/linkType object using the dateOn property. For simplicity, we
     // store this date as an attribute on the Site.
-    foreach($xmlCertStatusLinkDates as $xmlCertStatusLinkDate){
-       $targetSiteName = (string) $xmlCertStatusLinkDate->name;
-       // only interested in the current site
-       if($targetSiteName == $doctrineSite->getShortName()){
-          // '01-JUL-13 11.09.10.000000 AM' which has the php datetime
-          // format of 'd-M-y H.i.s A' provided we trim off the '.000000' (millisecs)
-          // Note, '.000000' is present in all the <cert_date> elements.
-          $xmlLinkDateString = (string) $xmlCertStatusLinkDate->cert_date;
-          $xmlLinkDateString = preg_replace('/\.000000/', "", $xmlLinkDateString);
-          $linkDate =  \DateTime::createFromFormat('d-M-y H.i.s A', $xmlLinkDateString, new \DateTimeZone('UTC'));
-          if(!$linkDate) {
-              throw new Exception("Can't parse date/time  " . $xmlLinkDateString . " for site " .
-                      $doctrineSite->getShortName() . ". Correct format: 27-JUL-11 02.02.03 PM" );
-          }
+    foreach ($xmlCertStatusLinkDates as $xmlCertStatusLinkDate) {
+        $targetSiteName = (string) $xmlCertStatusLinkDate->name;
+        // Only interested in the current site
+        if ($targetSiteName == $doctrineSite->getShortName()) {
+            // '01-JUL-13 11.09.10.000000 AM' which has the php datetime
+            // format of 'd-M-y H.i.s A' provided we
+            // trim off the '.000000' (millisecs)
+            // Note, '.000000' is present in all the <cert_date> elements.
+            $xmlLinkDateString = (string) $xmlCertStatusLinkDate->cert_date;
+            $xmlLinkDateString = preg_replace(
+                '/\.000000/',
+                "",
+                $xmlLinkDateString
+            );
+            $linkDate =  \DateTime::createFromFormat(
+                'd-M-y H.i.s A',
+                $xmlLinkDateString,
+                new \DateTimeZone('UTC')
+            );
+            if (!$linkDate) {
+                throw new Exception("Can't parse date/time  " .
+                    $xmlLinkDateString . " for site " .
+                    $doctrineSite->getShortName() .
+                    ". Correct format: 27-JUL-11 02.02.03 PM");
+            }
 
           $doctrineSite->setCertificationStatusChangeDate($linkDate);
 
-       }
+        }
     }
 
 
     // Add the Site's certification status history/log.
-    // If the Site certStatus has never been updated from its initial state,
-    // then no changes will have occurred and the log will be empty for that Site.
+    // If the Site certStatus has never been updated from
+    // its initial state, then no changes will have occurred
+    // and the log will be empty for that Site.
     //
     // Importantly, because the v4 certStatus change log was added AFTER some
     // sites were already added to GOCDB4, the LAST AddedDate does NOT
     // necessarily correspond with the date of the CURRENT certification status.
     // Rather, the date of the CURRENT certStatus in v4 is recorded as
     // a link/linkType object using the dateOn property.
-    foreach($xmlCertStatusChanges as $xmlCertStatusChange){
-       $targetSiteName = (string) $xmlCertStatusChange->SITE;
-       // only interested in the current site
-       if($targetSiteName == $doctrineSite->getShortName()){
-           $doctrineCertStatusChangeLog = new \CertificationStatusLog();
-           $doctrineCertStatusChangeLog->setAddedBy((string) $xmlCertStatusChange->CHANGED_BY);
-           $doctrineCertStatusChangeLog->setOldStatus((string) $xmlCertStatusChange->OLD_STATUS);
-           $doctrineCertStatusChangeLog->setNewStatus((string) $xmlCertStatusChange->NEW_STATUS);
-           $doctrineCertStatusChangeLog->setReason((string) $xmlCertStatusChange->COMMENT);
-           $insertDate = new DateTime("@" . (string) $xmlCertStatusChange->UNIX_TIME);
-           $doctrineCertStatusChangeLog->setAddedDate($insertDate);
-           $entityManager->persist($doctrineCertStatusChangeLog);
-           $doctrineSite->addCertificationStatusLog($doctrineCertStatusChangeLog);
-       }
+    foreach ($xmlCertStatusChanges as $xmlCertStatusChange) {
+        $targetSiteName = (string) $xmlCertStatusChange->SITE;
+        // Only interested in the current site
+        if ($targetSiteName == $doctrineSite->getShortName()) {
+            $doctrineCertStatusChangeLog = new \CertificationStatusLog();
+            $doctrineCertStatusChangeLog->setAddedBy((string)
+                $xmlCertStatusChange->CHANGED_BY);
+            $doctrineCertStatusChangeLog->setOldStatus((string)
+                $xmlCertStatusChange->OLD_STATUS);
+            $doctrineCertStatusChangeLog->setNewStatus((string)
+                $xmlCertStatusChange->NEW_STATUS);
+            $doctrineCertStatusChangeLog->setReason((string)
+                $xmlCertStatusChange->COMMENT);
+            $insertDate = new DateTime("@" .
+                (string) $xmlCertStatusChange->UNIX_TIME);
+            $doctrineCertStatusChangeLog->setAddedDate($insertDate);
+            $entityManager->persist($doctrineCertStatusChangeLog);
+            $doctrineSite->addCertificationStatusLog(
+                $doctrineCertStatusChangeLog
+            );
+        }
     }
 
     $entityManager->persist($doctrineSite);
@@ -211,11 +272,11 @@
 
 // echo "\nPersisting Sites";
 // $i = 0;
-// foreach($allSites as $site) {
+// foreach ($allSites as $site) {
 //     $i++;
 //     $entityManager->persist($site);
 //     // Flush periodically to free memory.
-//     if($i % 10000 == 0) {
+//     if ($i % 10000 == 0) {
 //         echo ".";
 //         $entityManager->flush();
 //     }
diff --git a/lib/Doctrine/deploy/AddUsers.php b/lib/Doctrine/deploy/AddUsers.php
index 4df23c52e..e7227c535 100644
--- a/lib/Doctrine/deploy/AddUsers.php
+++ b/lib/Doctrine/deploy/AddUsers.php
@@ -1,13 +1,14 @@
 <?php
 
-require_once __DIR__."/../bootstrap.php";
-require_once __DIR__."/AddUtils.php";
-require __DIR__ . '/../../Gocdb_Services/Factory.php';
+require_once __DIR__ . "/../bootstrap.php";
+require_once __DIR__ . "/AddUtils.php";
+require __DIR__ . "/../../Gocdb_Services/Factory.php";
 
 $em = \Factory::getEntityManager();
 $serv = \Factory::getUserService();
 
-$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] . "/UsersAndRoles.xml";
+$usersRolesFileName = __DIR__ . "/" . $GLOBALS['dataDir'] .
+    "/UsersAndRoles.xml";
 $usersRoles = simplexml_load_file($usersRolesFileName);
 // Used to check for duplicates
 $idStrings = array();
@@ -26,6 +27,7 @@
         if (isset($idStrings[$idString])) {
             continue;
         }
+
         $idStrings[$idString] = true;
 
         $doctrineUser = new \User();
@@ -35,34 +37,48 @@
         $doctrineUser->setTitle((string) $user->TITLE);
         $doctrineUser->setEmail((string) $user->EMAIL);
         $doctrineUser->setTelephone((string) $user->TEL);
-        $doctrineUser->setWorkingHoursStart((string) $user->WORKING_HOURS_START);
-        $doctrineUser->setWorkingHoursEnd((string) $user->WORKING_HOURS_END);
+        $doctrineUser->setWorkingHoursStart((string)
+            $user->WORKING_HOURS_START);
+        $doctrineUser->setWorkingHoursEnd((string)
+            $user->WORKING_HOURS_END);
         $doctrineUser->setAdmin(false);
 
-        // Roughly half of users don't have a home site set
-        if ($user->HOMESITE !== "" &&  !isBad($user->HOMESITE)) {
+        // Check if users don't have a homesite set, or
+        // if the homesite is 'bad'.
+        if ($user->HOMESITE !== "" && !isBad($user->HOMESITE)) {
             // Get the home site entity
             $dql = "SELECT s from Site s WHERE s.shortName = ?1";
             $homeSites = $em->createQuery($dql)
-                    ->setParameter(1, (string) $user->HOMESITE)
-                    ->getResult();
+                            ->setParameter(
+                                1,
+                                (string) $user->HOMESITE
+                            )
+                            ->getResult();
 
             /* Error checking: ensure each "home site" refers to exactly
-            * one home site */
+             * one home site */
             if (count($homeSites) !== 1) {
-                throw new \Exception(count($homeSites) . " sites found with short name: " .
-                        $user->HOMESITE . ". user DN is  " . $user->CERTDN);
+                throw new \Exception(count($homeSites) . " sites found " .
+                    "with short name: " . $user->HOMESITE .
+                    ". user DN is  " . $user->CERTDN);
             }
+
             foreach ($homeSites as $result) {
                 $homeSite = $result;
             }
+
             $doctrineUser->setHomeSiteDoJoin($homeSite);
         }
 
         $em->persist($doctrineUser);
         $em->flush();
-        $serv->addUserIdentifier($doctrineUser, $identifierArr, $doctrineUser);
+        $serv->addUserIdentifier(
+            $doctrineUser,
+            $identifierArr,
+            $doctrineUser
+        );
     }
+
     $em->getConnection()->commit();
 } catch (\Exception $e) {
     $em->getConnection()->rollback();
diff --git a/lib/Doctrine/deploy/AddUtils.php b/lib/Doctrine/deploy/AddUtils.php
index a029702f6..6ec5c60c7 100644
--- a/lib/Doctrine/deploy/AddUtils.php
+++ b/lib/Doctrine/deploy/AddUtils.php
@@ -3,14 +3,15 @@
 
 // Finds one or more services by hostname and service type
 function findSEs($hostName, $serviceType) {
-    $dql = "SELECT s FROM Service s JOIN s.serviceType st"
-            . " WHERE s.hostName = :hostName AND st.name = :serviceType";
+    $dql = "SELECT s FROM Service s JOIN s.serviceType st " .
+        "WHERE s.hostName = :hostName AND " .
+        "st.name = :serviceType";
 
     $services = $GLOBALS['entityManager']
-    ->createQuery($dql)
-    ->setParameter(":hostName", $hostName)
-    ->setParameter(":serviceType", $serviceType)
-    ->getResult();
+        ->createQuery($dql)
+        ->setParameter(":hostName", $hostName)
+        ->setParameter(":serviceType", $serviceType)
+        ->getResult();
 
     return $services;
 }
@@ -18,35 +19,43 @@ function findSEs($hostName, $serviceType) {
 /* Is the passed site invalid?
  * Uses a list of known bad sites */
 function isBad($site) {
-    /* Roles over these sites are in the production data but can't be inserted
-     * into v5 because they don't have an NGI or a domain. v5 doesn't import sites without an NGI
-     * or domain
+    /* Roles over these sites are in the production data but can't be
+     * inserted into v5 because they don't have an NGI or a domain.
+     * v5 doesn't import sites without an NGI or domain
      *
      * Sites ignored becuase of no parent NGI:
-     * Australia-UNIMELB-LCG2, GUP-JKU,UNIBAS, FZK-PPS, MA-01-CNRST,  All sites under
-     * ROC_IGALC which was closed Apr-2013, all NGI_IE sites closed Jul-2013.
+     * Australia-UNIMELB-LCG2, GUP-JKU,UNIBAS, FZK-PPS, MA-01-CNRST,
+     * All sites under ROC_IGALC which was closed Apr-2013,
+     * all NGI_IE sites closed Jul-2013.
      * PPS-CNAF is a broken site with a production status of pps
-     * 15.08.13: Removed 'UFRJ-IF',  from this list as it appears to be fixed (??)
-     * 15.08.13: Removed 'EELA-UNLP',  from this list as it appears to be fixed (??)
-     * 15.08.13: Removed 'ULA-MERIDA', from this list as it appears to be fixed (??)
-     * 15.08.13: Removed 'ZA-MERAKA', 'ZA-WITS-CORE', 'ZA-UJ', 'ZA-CHPC' as NGI_ZA has been reinstated
+     * 15.08.13: Removed 'UFRJ-IF',  from this list as it
+     *     appears to be fixed (??)
+     * 15.08.13: Removed 'EELA-UNLP',  from this list as it
+     *     appears to be fixed (??)
+     * 15.08.13: Removed 'ULA-MERIDA', from this list as it
+     *     appears to be fixed (??)
+     * 15.08.13: Removed 'ZA-MERAKA', 'ZA-WITS-CORE', 'ZA-UJ',
+     *     'ZA-CHPC' as NGI_ZA has been reinstated
      */
-    $badSites = array('Australia-UNIMELB-LCG2', 'PPS-CNAF', 'GUP-JKU', 'UNIBAS', 'FZK-PPS'
-            , 'MA-01-CNRST', 'EELA-UC', 'CEFET-RJ', 'CMM-UChile', 'CPTEC-INPE'
-            , 'CUBAENERGIA', 'EPN', 'FING', 'GRID-CEDIA', 'GRyDs-USB'
-            , 'INCOR-HCFMUSP', 'UFCG-LSD', 'UIS-BUCARAMANGA',   'UTP-PANAMA', 'ITWM-PPS' , 'HU-BERLIN', 'SCAI-PPS'
-            , 'FZK-SC', 'FZK-Test', 'FZK-Test', 'GRIDOPS-GRIDVIEW', 'GSI-LCG2-PPS'
-            // next lot is from NGI_IE which was deleted.
-            , 'csTCDie', 'mpUCDie', 'giNUIMie', 'cpDIASie', 'csQUBuk', 'csUCCie'
-            , 'scgNUIGie', 'giITTAie', 'obsARMuk', 'giHECie', 'giRCSIie'
-            , 'giDCUie');
+    $badSites = array('Australia-UNIMELB-LCG2', 'PPS-CNAF', 'GUP-JKU',
+            'UNIBAS', 'FZK-PPS', 'MA-01-CNRST', 'EELA-UC', 'CEFET-RJ',
+            'CMM-UChile', 'CPTEC-INPE', 'CUBAENERGIA', 'EPN', 'FING',
+            'GRID-CEDIA', 'GRyDs-USB', 'INCOR-HCFMUSP', 'UFCG-LSD',
+            'UIS-BUCARAMANGA', 'UTP-PANAMA', 'ITWM-PPS' , 'HU-BERLIN',
+            'SCAI-PPS', 'FZK-SC', 'FZK-Test', 'FZK-Test',
+            'GRIDOPS-GRIDVIEW', 'GSI-LCG2-PPS',
+            // Next lot is from NGI_IE which was deleted.
+            'csTCDie', 'mpUCDie', 'giNUIMie', 'cpDIASie', 'csQUBuk',
+            'csUCCie', 'scgNUIGie', 'giITTAie', 'obsARMuk', 'giHECie',
+            'giRCSIie', 'giDCUie');
 
-    if(sizeof(array_intersect(array($site), $badSites)) == 0) {
+    if (sizeof(array_intersect(array($site), $badSites)) == 0) {
         return false;
     } else {
         return true;
     }
 }
+
 /**
  * Return a scope object given a scope name
  * @param EntityManager $entityManager
@@ -54,15 +63,17 @@ function isBad($site) {
  * @return \Scope
  */
 function getScope($entityManager, $scope) {
-    // get the scope
+    // Get the scope
     $dql = "SELECT s FROM Scope s WHERE s.name = ?1";
     $scopes = $entityManager->createQuery($dql)
-                                ->setParameter(1, $scope)
-                                ->getResult();
+                            ->setParameter(1, $scope)
+                            ->getResult();
+
     /* Error checking: ensure each Site's "SCOPE" refers to exactly
-    * one SCOPE */
-    if(count($scopes) !== 1) {
-        throw new Exception(count($scopes) . " SCOPEs found with name: " . $scope);
+     * one SCOPE */
+    if (count($scopes) !== 1) {
+        throw new Exception(count($scopes) . " SCOPEs found " .
+            "with name: " . $scope);
     }
 
     return $scopes[0];
diff --git a/lib/Doctrine/deploy/DeployRequiredDataRunner.php b/lib/Doctrine/deploy/DeployRequiredDataRunner.php
index 5b030a921..eee338d98 100644
--- a/lib/Doctrine/deploy/DeployRequiredDataRunner.php
+++ b/lib/Doctrine/deploy/DeployRequiredDataRunner.php
@@ -13,9 +13,9 @@
  * limitations under the License.
  */
 
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/AddUtils.php";
 
-if(isset($argv[1])) {
+if (isset($argv[1])) {
     $GLOBALS['dataDir'] = $argv[1];
 } else {
     die("Please specify your data directory (requiredData) \n");
@@ -23,17 +23,17 @@
 
 print_r("Deploying Required Lookup Data\n");
 
-require __DIR__."/AddInfrastructures.php";
+require __DIR__ . "/AddInfrastructures.php";
 echo "Added Infrastructures OK\n";
 
-require __DIR__."/AddCountries.php";
+require __DIR__ . "/AddCountries.php";
 echo "Added Countries OK\n";
 
-require __DIR__."/AddRoleTypes.php";
+require __DIR__ . "/AddRoleTypes.php";
 echo "Added Roles OK\n";
 
-require __DIR__."/AddCertificationStatuses.php";
+require __DIR__ . "/AddCertificationStatuses.php";
 echo "Added Certification Statuses OK\n";
 
-require __DIR__."/AddServiceTypes.php";
+require __DIR__ . "/AddServiceTypes.php";
 echo "Added Service Types OK\n";
diff --git a/lib/Doctrine/deploy/DeploySampleDataRunner.php b/lib/Doctrine/deploy/DeploySampleDataRunner.php
index 48f8a60e5..97d80a44f 100644
--- a/lib/Doctrine/deploy/DeploySampleDataRunner.php
+++ b/lib/Doctrine/deploy/DeploySampleDataRunner.php
@@ -14,44 +14,44 @@
  */
 
 
-require_once __DIR__."/AddUtils.php";
+require_once __DIR__ . "/AddUtils.php";
 
-if(isset($argv[1])) {
+if (isset($argv[1])) {
     $GLOBALS['dataDir'] = $argv[1];
 } else {
     die("Please specify your data directory (sampleData) \n");
 }
 
-print_r("Deploying Sample Data from ".$GLOBALS['dataDir']."\n");
+print_r("Deploying Sample Data from " . $GLOBALS['dataDir'] . "\n");
 
-require __DIR__."/AddProjects.php";
+require __DIR__ . "/AddProjects.php";
 echo "Added Projects OK\n";
 
-require __DIR__."/AddScopes.php";
+require __DIR__ . "/AddScopes.php";
 echo "Added Scopes OK\n";
 
-require __DIR__."/AddNGIs.php";
+require __DIR__ . "/AddNGIs.php";
 echo "Added NGIs OK\n";
 
-require __DIR__."/AddSites.php";
+require __DIR__ . "/AddSites.php";
 echo "Added Sites and JOINED to NGIs OK\n";
 
-require __DIR__."/AddServiceEndpoints.php";
+require __DIR__ . "/AddServiceEndpoints.php";
 echo "Added Services, EndpointLocations and JOINED associations OK\n";
 
-require __DIR__."/AddServiceGroups.php";
+require __DIR__ . "/AddServiceGroups.php";
 echo "Added Service Groups OK\n";
 
-require __DIR__."/AddUsers.php";
+require __DIR__ . "/AddUsers.php";
 echo "Added Users OK\n";
 
-require __DIR__."/AddSiteRoles.php";
+require __DIR__ . "/AddSiteRoles.php";
 echo "Added Site level Roles OK\n";
 
-require __DIR__."/AddNGIRoles.php";
+require __DIR__ . "/AddNGIRoles.php";
 echo "Added NGI level Roles OK\n";
 
-require __DIR__."/AddProjectRoles.php";
+require __DIR__ . "/AddProjectRoles.php";
 echo "Added EGI level Roles OK\n";
 
 require __DIR__ . "/AddServiceGroupRoles.php";