Merge pull request #636 from DiamondLightSource/pre-release/2023-R3.2

Pre release/2023 r3.2
DiamondLightSource · Jul 26, 2023 · 20eba26 · 20eba26
2 parents 9814675 + 0dbfe03
commit 20eba26
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Showing 39 changed files with 264 additions and 160 deletions.
diff --git a/api/composer.json b/api/composer.json
@@ -19,7 +19,6 @@
     "firebase/php-jwt": "2.2.0",
     "jdorn/sql-formatter": "1.2.9",
     "mpdf/mpdf": "8.1.2",
-    "phpxmlrpc/phpxmlrpc": "3.1.2",
     "ralouphie/getallheaders": "2.0.5",
     "slim/slim": "2.6.2",
     "stomp-php/stomp-php": "3.0.6",

diff --git a/api/config_sample.php b/api/config_sample.php
@@ -27,11 +27,12 @@
 
     # Follow CAS SSO
     $cas_sso = true;
+    $sso_url = "sso.server.ac.uk";
 
-    // OIDC (or OAuth2) client ID and secret. Only useful if authentication_type is set to OIDC
+    # OIDC (or OAuth2) client ID and secret. Only useful if authentication_type is set to OIDC
     $oidc_client_id = "oidcClientId";
     $oidc_client_secret = "oidcClientSecret";
-    // Cookie key used for SSO/cookie based authentication
+    # Cookie key used for SSO/cookie based authentication
     $cookie_key = "synchweb-auth";
 
     # CAS CA Cert (for SSO)
@@ -58,6 +59,9 @@
     # Timezone
     $timezone = 'Europe/London';
 
+    # URL to access the PV archiver
+    $archive_url = '';
+
     # Valid Components
     #   Denotes that only staff may create proteins, otherwise they must come from replication 
     #   with a valid `externalid`, users may still clone proteins
@@ -150,6 +154,13 @@
     # and for shipment booked,
     $shipbooked_email = '[email protected]';
 
+    # dewar back in storage (complete)
+    $dewar_complete_email = '';
+
+    # Send a 'visit finished' email when a dewar moves from this beamline to this (regex) location
+    $dewar_complete_email_locations = array('i03' => '/tray-\w+/',
+                                           );
+
     # Industrial Contacts
     # - Industrial users get a personalised email with in contact details,
     #   template in assets/emails/dewar-stores-in-in.html

diff --git a/api/index.php b/api/index.php
@@ -66,7 +66,7 @@ function setupApplication($mode): Slim
     });
 
     $app->get('/options', function () use ($app) {
-        global $motd, $authentication_type, $cas_url, $cas_sso, $package_description,
+        global $motd, $authentication_type, $cas_url, $cas_sso, $sso_url, $package_description,
             $facility_courier_countries, $facility_courier_countries_nde,
             $dhl_enable, $dhl_link, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types;
@@ -76,6 +76,7 @@ function setupApplication($mode): Slim
             'authentication_type' => $authentication_type,
             'cas_url' => $cas_url,
             'cas_sso' => $cas_sso,
+            'sso_url' => $sso_url,
             'package_description' => $package_description,
             'facility_courier_countries' => $facility_courier_countries,
             'facility_courier_countries_nde' => $facility_courier_countries_nde,

diff --git a/api/src/Authentication/AuthenticationTypeFactory.php b/api/src/Authentication/AuthenticationTypeFactory.php
@@ -12,7 +12,8 @@ class AuthenticationTypeFactory {
         'dummy' => 'Dummy',
         'ldap' => 'LDAP',
         'simple' => 'Simple',
-        'oidc' => 'OIDC'
+        'oidc' => 'OIDC',
+        'combined' => 'Combined',
     );
 
     // Return instance of authentication class corresponding to $authentication_type.

diff --git a/api/src/Authentication/Type/Combined.php b/api/src/Authentication/Type/Combined.php
@@ -0,0 +1,39 @@
+<?php
+
+namespace SynchWeb\Authentication\Type;
+
+use SynchWeb\Authentication\AuthenticationInterface;
+use SynchWeb\Authentication\AuthenticationParent;
+
+/**
+ * Combined OIDC and CAS login to allow current api users to use the authentiate api
+ *  endpoint with username and password
+ */
+class Combined extends AuthenticationParent implements AuthenticationInterface
+{
+    private $CASAuth;
+    private $OIDCAuth;
+
+    function __construct() {
+        $this->CASAuth = new CAS();
+        $this->OIDCAuth = new OIDC();
+    }
+
+
+    public function authenticate($login, $password)
+    {
+        return $this->CASAuth->authenticate($login, $password);
+    }
+
+    public function check() {
+        return $this->OIDCAuth->check();
+    }
+
+    public function authorise() {
+        return $this->OIDCAuth->authorise();
+    }
+
+    public function authenticateByCode($code){
+        return $this->OIDCAuth->authenticateByCode($code);
+    }
+}
diff --git a/api/src/Authentication/Type/OIDC.php b/api/src/Authentication/Type/OIDC.php
@@ -2,7 +2,6 @@
 
 namespace SynchWeb\Authentication\Type;
 
-use phpCAS;
 use SynchWeb\Authentication\AuthenticationInterface;
 use SynchWeb\Authentication\AuthenticationParent;
 use SynchWeb\Utils;
@@ -12,16 +11,19 @@ class OIDC extends AuthenticationParent implements AuthenticationInterface
     private $providerConfig = array();
 
     function __construct() {
-        global $cas_url;
+        global $sso_url, $oidc_client_id, $oidc_client_secret;
 
         $ch = curl_init();
-        curl_setopt($ch, CURLOPT_URL, 'https://' . $cas_url . '/.well-known/openid-configuration');
+        curl_setopt($ch, CURLOPT_URL, 'https://' . $sso_url . '/.well-known/openid-configuration');
         curl_setopt($ch, CURLOPT_HEADER, 0);
         curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
         $response = curl_exec($ch);
         curl_close($ch);
 
         $newProviderConfig = json_decode($response);
+        $newProviderConfig->b64ClientCreds = base64_encode(
+            $oidc_client_id . ":" . $oidc_client_secret
+        );
 
         if($newProviderConfig == null) {
             error_log("OIDC Authentication provider replied with invalid JSON body");
@@ -32,9 +34,7 @@ function __construct() {
     }
 
     private function getUser($token)
-    {
-        global $cas_url, $cacert;
-
+    {        
         $ch = curl_init();
         curl_setopt($ch, CURLOPT_URL, $this->providerConfig->userinfo_endpoint);
         curl_setopt($ch, CURLOPT_HEADER, 0);
@@ -56,7 +56,12 @@ function authenticate($login, $password)
     function check()
     {
         global $cookie_key;
-        return($this->getUser($_COOKIE[$cookie_key]));
+
+        if (array_key_exists($cookie_key, $_COOKIE)) {
+            return($this->getUser($_COOKIE[$cookie_key]));
+        }
+
+        return false;
     }
 
     function authorise() 
@@ -72,21 +77,19 @@ function authorise()
 
     function authenticateByCode($code) 
     {   
-        global $cas_url, $cacert, $oidc_client_secret, $oidc_client_id, $cookie_key;
+        global $cacert, $oidc_client_secret, $oidc_client_id, $cookie_key;
 
         $redirect_url = Utils::filterParamFromUrl($_SERVER["HTTP_REFERER"], "code");
 
         $ch = curl_init();
         curl_setopt($ch, CURLOPT_URL, $this->providerConfig->token_endpoint . 
             '?grant_type=authorization_code&redirect_uri=' . 
             $redirect_url . 
-            "&code=" . $code . 
-            '&client_secret=' . $oidc_client_secret . 
-            '&client_id=' . $oidc_client_id
+            "&code=" . $code
         );
         curl_setopt($ch, CURLOPT_HEADER, 0);
-        curl_setopt($ch, CURLOPT_CAINFO, $cacert);
         curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
+        curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->providerConfig->b64ClientCreds));
         $response = curl_exec($ch);
         curl_close($ch);
 

diff --git a/api/src/Page.php b/api/src/Page.php
@@ -8,9 +8,6 @@
 use ReflectionClass;
 use Slim\Slim;
 use SynchWeb\Database\DatabaseParent;
-use xmlrpc_client;
-use xmlrpcmsg;
-use xmlrpcval;
 
 use SynchWeb\Queue;
 use SynchWeb\Utils;
@@ -948,47 +945,43 @@ function _ldap_search($search, $email = False)
 
     # ------------------------------------------------------------------------
     # Talk to channel archiver to get a pv
-    function _get_archive($pv, $s, $e, $n = 100)
+    function _get_archive($pv, $s, $e)
     {
         global $timezone;
+        global $archive_url;
 
-        $m = new xmlrpcmsg('archiver.values', array(
-            new xmlrpcval(1000, 'int'),
-            new xmlrpcval(array(new xmlrpcval($pv, 'string')), 'array'),
-            new xmlrpcval($s, 'int'),
-            new xmlrpcval(0, 'int'),
-            new xmlrpcval($e, 'int'),
-            new xmlrpcval(0, 'int'),
-            new xmlrpcval($n, 'int'),
-            new xmlrpcval(0, 'int'),
-        ));
-        $c = new xmlrpc_client("/archive/cgi/ArchiveDataServer.cgi", "archiver.pri.diamond.ac.uk", 80);
-
-        $r = $c->send($m);
-        $val = $r->value();
+        if (empty($archive_url))
+            return array();
+
+        $parameters = array(
+            'pv' => $pv,
+            'from' => date("Y-m-d\TH:i:s", $s).'Z',
+            'to' => date("Y-m-d\TH:i:s", $e).'Z',
+        );
+
+        $ret = array();
+        $url_query = http_build_query($parameters);
+        $archive_query_url = $archive_url . "?". $url_query;
+        $val = file_get_contents($archive_query_url);
 
         if ($val)
         {
-            $str = $val->arrayMem(0);
-            $vals = $str->structMem('values');
+            $str = json_decode($val)[0];
+            $vals = $str->data;
 
-            $ret = array();
-            for ($i = 0; $i < $vals->arraySize(); $i++)
+            for ($i = 0; $i < sizeof($vals); $i++)
             {
-                $vs = $vals->arrayMem($i);
-                $v = $vs->structMem('value')->arrayMem(0)->scalarVal();
-                $t = $vs->structMem('secs')->scalarVal() - 3600;
-
+                $vs = $vals[$i];
+                $v = $vs->val;
+                $t = $vs->secs - 3600;
                 $inputTZ = new \DateTimeZone($timezone);
                 $transitions = $inputTZ->getTransitions($t, $t);
                 if ($transitions[0]['isdst'])
                     $t += 3600;
-
                 array_push($ret, array($t, $v));
             }
-
-            return $ret;
         }
+        return $ret;
     }
 
 

diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php
@@ -153,6 +153,11 @@ function _data_collections($single = null)
                         LEFT OUTER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
                         LEFT OUTER JOIN autoprocprogram app ON (app.autoprocprogramid = api.autoprocprogramid OR dc.datacollectionid = pj.datacollectionid)
                         INNER JOIN autoprocprogrammessage appm ON appm.autoprocprogramid = app.autoprocprogramid";
+            } else if ($this->arg('t') == "scrystal" || $this->arg('t') == "nscrystal") {
+                // Single crystal or explicitly non-single-crystal fields
+                $where = ($this->arg('t') == "nscrystal") ? ' AND NOT ' : ' AND ';
+                // This IS NOT NULL is not redundant; this condition always evalutes to TRUE with AND NOT without it
+                $where .= '(dcg.experimentType IS NOT NULL AND dcg.experimentType in ("OSC", "Diamond Anvil High Pressure"))';
             }
         }
 
@@ -986,8 +991,6 @@ function _data_collections($single = null)
 
                 if ($dc['DCT'] == 'Mesh')
                     $dc['DCT'] = 'Grid Scan';
-                if ($dc['DCT'] == 'OSC')
-                    $dc['DCT'] = 'Data Collection';
                 if ($dc['DCT'] != 'Serial Fixed' && $dc['DCT'] != 'Serial Jet' && $dc['AXISRANGE'] == 0 && $dc['NI'] > 1) {
                     $dc['TYPE'] = 'grid';
                 }

diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php
@@ -417,9 +417,9 @@ function _get_history()
     function _add_history()
     {
         global $in_contacts, $arrival_email;
-        global $dewar_complete_email; // Email list to cc if dewar back from beamline
+        global $dewar_complete_email, $dewar_complete_email_locations; // Email list to cc if dewar back from beamline
         # Flag to indicate we should e-mail users their dewar has returned from BL
-        $from_beamline = False;
+        $send_return_email = False;
 
         if (!$this->bcr())
             $this->_error('You need to be on the internal network to add history');
@@ -456,16 +456,12 @@ function _add_history()
             // We only add data to dewar history in lower case from this method.
             // If that ever changes, update this to become case insensitive search
             $last_location = $last_history['STORAGELOCATION'];
-
-            // Why don't we have beamline names in the database...?
-            // Currently grabbing them from the config object
-            // Not particularly efficient, but this is not a time critical operation so
-            // this approach covers all beamlines for future proofing.
-            // Stop/break if we find a match
-            $bls = $this->_get_beamlines_from_type('all');
-
-            if (in_array($last_location, $bls)) {
-                $from_beamline = True;
+            if (!isset($dewar_complete_email_locations) || !is_array($dewar_complete_email_locations)) {
+                $bls = $this->_get_beamlines_from_type('all');
+                $send_return_email = in_array($last_location, $bls);
+            } else if (array_key_exists($last_location, $dewar_complete_email_locations)) {
+                $email_location = $dewar_complete_email_locations[$last_location];
+                $send_return_email = preg_match($email_location, strtolower($this->arg('LOCATION')));
             }
         } else {
             // No history - could be a new dewar, so not necessarily an error...
@@ -525,10 +521,7 @@ function _add_history()
             $email->send($dew['LCRETEMAIL']);
         }
 
-        // Change this so it checks if the boolean flag "from_beamline" is set
-        // The old version assumed rack-<word>-from-bl
-        //if (preg_match('/rack-\w+-from-bl/', strtolower($this->arg('LOCATION'))) && $dew['LCRETEMAIL']) {
-        if ($from_beamline && $dew['LCRETEMAIL']) {
+        if ($dew['LCRETEMAIL'] && $send_return_email) {
             // Any data collections for this dewar's containers?
             // Note this counts data collection ids for containers and uses the DataCollection.SESSIONID to determine the session/visit
             // Should work for UDC (where container.sessionid is set) as well as any normal scheduled session (where container.sessionid is not set)