From 8c6db68f6f165b2d7e24e408bf59224e35346a92 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 21 Jun 2023 13:37:43 +0100 Subject: [PATCH 01/12] Update ci.yml --- .github/workflows/ci.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ccde8f478..b9be68979 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -71,10 +71,13 @@ jobs: uses: actions/checkout@v3 - name: JavaScript build, lint and test - working-directory: ./client + uses: actions/setup-node@v3 + with: + node-version: 18.x + - working-directory: ./client # hack the output from the linting steps to avoid these stopping the builds - we are not going to get # to a clean output without considerable effort, but it's useful to see the output - run: | + - run: | npm ci npm run build npm run test From 3650b4d6caa35db76b989ee3780f7532a735618c Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 21 Jun 2023 13:41:14 +0100 Subject: [PATCH 02/12] Fix JS build step --- .github/workflows/ci.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b9be68979..9e5a51a65 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -70,14 +70,15 @@ jobs: - name: Checkout code uses: actions/checkout@v3 - - name: JavaScript build, lint and test + - name: Use Node.js 18 uses: actions/setup-node@v3 with: node-version: 18.x - - working-directory: ./client + - name: JavaScript build, lint and test + working-directory: ./client # hack the output from the linting steps to avoid these stopping the builds - we are not going to get # to a clean output without considerable effort, but it's useful to see the output - - run: | + run: | npm ci npm run build npm run test From c299f878dc30bf7b86d265e23326060384650037 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 21 Jun 2023 13:43:35 +0100 Subject: [PATCH 03/12] Explicitly print out Node version in test step --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9e5a51a65..545e84fde 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -79,6 +79,7 @@ jobs: # hack the output from the linting steps to avoid these stopping the builds - we are not going to get # to a clean output without considerable effort, but it's useful to see the output run: | + node --version npm ci npm run build npm run test From bdab672ce59eb16e6350533bf12df52546fe407b Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 21 Jun 2023 15:08:53 +0100 Subject: [PATCH 04/12] Add engine version to package.json --- client/package.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/client/package.json b/client/package.json index b4508b362..a3b841721 100644 --- a/client/package.json +++ b/client/package.json @@ -105,5 +105,8 @@ "vue-router": "^3.4.3", "vuex": "^3.5.1", "zlibjs": "^0.1.7" + }, + "engines": { + "node": "^18.0.0" } } From f41563cb00b0977f2ab29ec9375337b81efd844d Mon Sep 17 00:00:00 2001 From: Mark W <24956497+ndg63276@users.noreply.github.com> Date: Wed, 5 Jul 2023 12:41:52 +0100 Subject: [PATCH 05/12] LIMS-858: Ignore containers with blank samplechangerlocation (#617) Co-authored-by: Mark Williams --- api/src/Page/Sample.php | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/api/src/Page/Sample.php b/api/src/Page/Sample.php index dd1abce22..a43884313 100644 --- a/api/src/Page/Sample.php +++ b/api/src/Page/Sample.php @@ -1054,7 +1054,7 @@ function _samples() else $info = $info[0]; - $where .= " AND d.dewarstatus='processing' AND c.beamlinelocation LIKE :" . (sizeof($args) + 1) . " AND c.samplechangerlocation is NOT NULL"; + $where .= " AND d.dewarstatus='processing' AND c.beamlinelocation LIKE :" . (sizeof($args) + 1) . " AND c.samplechangerlocation is NOT NULL AND c.samplechangerlocation != ''"; array_push($args, $info['BL']); } From abeb84122a1857bc3e20176b36a612f346dc6c53 Mon Sep 17 00:00:00 2001 From: Mark W <24956497+ndg63276@users.noreply.github.com> Date: Wed, 5 Jul 2023 12:42:21 +0100 Subject: [PATCH 06/12] LIMS-614: Use new XrayCentring/XrayCentringResults tables (#612) Co-authored-by: Mark Williams --- api/src/Database/Type/MySQL.php | 3 ++- api/src/Page/DC.php | 22 ---------------------- api/src/Page/Processing.php | 3 +-- 3 files changed, 3 insertions(+), 25 deletions(-) diff --git a/api/src/Database/Type/MySQL.php b/api/src/Database/Type/MySQL.php index d14a2a0d0..eb475396f 100644 --- a/api/src/Database/Type/MySQL.php +++ b/api/src/Database/Type/MySQL.php @@ -200,6 +200,7 @@ class MySQL extends DatabaseParent { 'PhasingProgramAttachment', // Xray Centring + 'XrayCentring', 'XrayCentringResult', 'BeamCalendar', @@ -551,4 +552,4 @@ function close() if ($this->conn) $this->conn->close(); } -} \ No newline at end of file +} diff --git a/api/src/Page/DC.php b/api/src/Page/DC.php index ed53921bc..1cfbd8a3c 100644 --- a/api/src/Page/DC.php +++ b/api/src/Page/DC.php @@ -47,7 +47,6 @@ class DC extends Page array('/chi', 'post', '_chk_image'), array('/imq/:id', 'get', '_image_qi'), array('/grid/:id', 'get', '_grid_info'), - array('/grid/xrc/:id', 'get', '_grid_xrc'), array('/grid/map', 'get', '_grid_map'), array('/ed/:id', 'get', '_edge', array('id' => '\d+'), 'edge'), array('/mca/:id', 'get', '_mca', array('id' => '\d+'), 'mca'), @@ -1476,27 +1475,6 @@ function _grid_map() } - # XRC - function _grid_xrc() - { - $info = $this->db->pq("SELECT dc.datacollectiongroupid, dc.datacollectionid, xrc.method, xrc.x, xrc.y - FROM gridinfo g - INNER JOIN datacollection dc ON dc.datacollectiongroupid = g.datacollectiongroupid - INNER JOIN xraycentringresult xrc ON xrc.gridinfoid = g.gridinfoid - WHERE dc.datacollectionid = :1 ", array($this->arg('id'))); - - if (!sizeof($info)) - $this->_output(array()); - else { - foreach ($info[0] as $k => &$v) { - if ($k == 'METHOD') - continue; - $v = floatval($v); - } - $this->_output($info[0]); - } - } - # ------------------------------------------------------------------------ # Fluorescence Map Info function _fluo_map() diff --git a/api/src/Page/Processing.php b/api/src/Page/Processing.php index 474907667..fd2996fa1 100644 --- a/api/src/Page/Processing.php +++ b/api/src/Page/Processing.php @@ -90,8 +90,7 @@ function _xrc_status($where, $ids) { "SELECT xrc.status as xrcstatus, dc.datacollectionid FROM datacollection dc INNER JOIN datacollectiongroup dcg ON dcg.datacollectiongroupid = dc.datacollectiongroupid - INNER JOIN gridinfo gr ON (gr.datacollectionid = dc.datacollectionid OR gr.datacollectiongroupid = dc.datacollectiongroupid) - LEFT OUTER JOIN xraycentringresult xrc ON xrc.gridinfoid = gr.gridinfoid + LEFT OUTER JOIN xraycentring xrc ON xrc.datacollectiongroupid = dc.datacollectiongroupid INNER JOIN blsession s ON s.sessionid = dcg.sessionid INNER JOIN proposal p ON p.proposalid = s.proposalid WHERE $where", From 2b1bd92e5e41e4f6013a1feb78737362ce149d66 Mon Sep 17 00:00:00 2001 From: John Holt Date: Tue, 11 Jul 2023 17:09:53 +0100 Subject: [PATCH 07/12] Check for invalid responses --- api/src/Authentication/Type/OIDC.php | 29 +++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/api/src/Authentication/Type/OIDC.php b/api/src/Authentication/Type/OIDC.php index cd0ddb519..269abbd73 100644 --- a/api/src/Authentication/Type/OIDC.php +++ b/api/src/Authentication/Type/OIDC.php @@ -19,16 +19,18 @@ function __construct() { curl_setopt($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) { + if(!$newProviderConfig + || !isset($newProviderConfig->userinfo_endpoint) + || !isset($newProviderConfig->authorization_endpoint) + || !isset($newProviderConfig->token_endpoint)) { error_log("OIDC Authentication provider replied with invalid JSON body"); return; } + $newProviderConfig->b64ClientCreds = base64_encode( + $oidc_client_id . ":" . $oidc_client_secret + ); $this->providerConfig = $newProviderConfig; } @@ -43,9 +45,12 @@ private function getUser($token) $response = curl_exec($ch); curl_close($ch); - $fedid = json_decode($response)->id; + $response_json = json_decode($response); + if (!$response_json || !isset($response_json->id)) { + return false; + } - return $fedid; + return $response_json->id; } function authenticate($login, $password) @@ -92,8 +97,14 @@ function authenticateByCode($code) curl_setopt($ch, CURLOPT_HTTPHEADER, array('Authorization: Basic ' . $this->providerConfig->b64ClientCreds)); $response = curl_exec($ch); curl_close($ch); - - $token = json_decode($response)->access_token; + + $response_json = json_decode($response); + if (!$response_json || !isset($response_json->access_token)) { + error_log("Invalid authentication attempt, provider returned invalid response"); + return false; + } + + $token = $response_json->access_token; if(!$token) { error_log("Invalid authentication attempt, provider returned no access token"); From fcfbe4cdbdca6f64501996483504d93d9d469e49 Mon Sep 17 00:00:00 2001 From: Mark W <24956497+ndg63276@users.noreply.github.com> Date: Fri, 14 Jul 2023 12:22:40 +0100 Subject: [PATCH 08/12] LIMS-871: Fix wrong number of dewar uses for staff (#626) Co-authored-by: Mark Williams --- api/src/Page/Shipment.php | 2 +- client/src/js/modules/shipment/views/regdewar.js | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/api/src/Page/Shipment.php b/api/src/Page/Shipment.php index 4bc483eae..ebc31ec33 100644 --- a/api/src/Page/Shipment.php +++ b/api/src/Page/Shipment.php @@ -568,7 +568,7 @@ function _dewar_registry() $args = array($this->proposalid); $where = 'p.proposalid=:1'; - $fields = "r.dewarregistryid, max(CONCAT(p.proposalcode, p.proposalnumber)) as prop, r.facilitycode, TO_CHAR(r.purchasedate, 'DD-MM-YYYY') as purchasedate, ROUND(TIMESTAMPDIFF('DAY',r.purchasedate, CURRENT_TIMESTAMP)/30.42,1) as age, r.labcontactid, count(d.dewarid) as dewars, GROUP_CONCAT(distinct CONCAT(p.proposalcode,p.proposalnumber) SEPARATOR ', ') as proposals, r.bltimestamp, TO_CHAR(max(d.bltimestamp),'DD-MM-YYYY') as lastuse, count(dr.dewarreportid) as reports"; + $fields = "r.dewarregistryid, max(CONCAT(p.proposalcode, p.proposalnumber)) as prop, r.facilitycode, TO_CHAR(r.purchasedate, 'DD-MM-YYYY') as purchasedate, ROUND(TIMESTAMPDIFF('DAY',r.purchasedate, CURRENT_TIMESTAMP)/30.42,1) as age, r.labcontactid, count(distinct d.dewarid) as dewars, GROUP_CONCAT(distinct CONCAT(p.proposalcode,p.proposalnumber) SEPARATOR ', ') as proposals, r.bltimestamp, TO_CHAR(max(d.bltimestamp),'DD-MM-YYYY') as lastuse, count(dr.dewarreportid) as reports"; $group = "r.facilitycode"; if ($this->has_arg('all') && $this->staff) { diff --git a/client/src/js/modules/shipment/views/regdewar.js b/client/src/js/modules/shipment/views/regdewar.js index d302f12b8..0dbb529f5 100644 --- a/client/src/js/modules/shipment/views/regdewar.js +++ b/client/src/js/modules/shipment/views/regdewar.js @@ -96,6 +96,7 @@ define(['marionette', }) this.dewars = new Dewars(null, { FACILITYCODE: this.model.get('FACILITYCODE') }) + this.dewars.queryParams.all = 1 this.dewars.fetch().done(this.getHistory.bind(this)) var columns = [ @@ -199,4 +200,4 @@ define(['marionette', }) -}) \ No newline at end of file +}) From adcff10fc776f646fa49ac8b14ac8d55d05df498 Mon Sep 17 00:00:00 2001 From: Mark W <24956497+ndg63276@users.noreply.github.com> Date: Wed, 19 Jul 2023 14:18:07 +0100 Subject: [PATCH 09/12] Let P beamlines show autoprocessing (#602) Co-authored-by: Jacob Filik --- client/src/js/app/store/modules/store.menus.js | 2 ++ client/src/js/modules/dc/components/dc-wrapper.vue | 2 ++ 2 files changed, 4 insertions(+) diff --git a/client/src/js/app/store/modules/store.menus.js b/client/src/js/app/store/modules/store.menus.js index 95972e63b..33f8776d7 100644 --- a/client/src/js/app/store/modules/store.menus.js +++ b/client/src/js/app/store/modules/store.menus.js @@ -43,6 +43,8 @@ const menuStore = { 'b22': GenProcMenu, 'b23': GenProcMenu, 'i21': GenProcMenu, + 'p99': GenProcMenu, + 'p45': GenProcMenu, } }), diff --git a/client/src/js/modules/dc/components/dc-wrapper.vue b/client/src/js/modules/dc/components/dc-wrapper.vue index b2b22e696..ad30b5154 100644 --- a/client/src/js/modules/dc/components/dc-wrapper.vue +++ b/client/src/js/modules/dc/components/dc-wrapper.vue @@ -72,6 +72,8 @@ let dc_views = { b22: GenProcDCList, b23: GenProcDCList, i21: GenProcDCList, + p99: GenProcDCList, + p45: GenProcDCList, } export default { From 211a08c689d44e104d3dac4d7966e571bc3a6dae Mon Sep 17 00:00:00 2001 From: Mark W <24956497+ndg63276@users.noreply.github.com> Date: Thu, 20 Jul 2023 16:42:33 +0100 Subject: [PATCH 10/12] LIMS-899: Null path to blobs causes errors (#632) Co-authored-by: Mark Williams --- api/src/Downstream/Type/Dimple.php | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/api/src/Downstream/Type/Dimple.php b/api/src/Downstream/Type/Dimple.php index a180d85a5..932487436 100644 --- a/api/src/Downstream/Type/Dimple.php +++ b/api/src/Downstream/Type/Dimple.php @@ -16,7 +16,8 @@ function _get_blobs() { return $this->db->pq( "SELECT view1, view2, view3, filepath FROM mxmrrunblob - WHERE mxmrrunid = :1", + WHERE mxmrrunid = :1 + AND filepath is not NULL", array($this->_mrrun["MXMRRUNID"]) ); } From e0c07640694f722fa79805c06828b843ef6f9aca Mon Sep 17 00:00:00 2001 From: NKatti2011 <108797920+NKatti2011@users.noreply.github.com> Date: Tue, 25 Jul 2023 10:44:54 +0100 Subject: [PATCH 11/12] LIMS-116: Summary page revamp (#606) * updating .gitignore * adding frontend files and building backend * adding front end files and router files * create sidebar, filter options added, routes added * add routing to page,search bar and column selector * adding pagination continutation * adding csv, all columns, rest of filters * added descending and ascending * sidebar dropdown&changed data structure&hide row * cleaning up fixing jump bug * refactored backend mapped data * added expanding row * refactored favourites * refactored orderby filter * cleaned up code, added comments * added all params to watcher * added summary db connection * add routes to summary * add backend changes summarypage * changes to expandable sidebar, cleaning up fronte * clean up, add functions to get data * front end changes, group concat backend * remove summarypage code * fix pagination, timeout * delete old summary file * changed pagination in summary.php * changed backend to not include tot * fix refined cell c column * added ifsets to avoid undefined offset error * delete offset for output * change order of operands * change filters, fix operands * fix csv button * changed prop to propid * format beamlinename * change al,be,gamma * add selected columns summary * additional changes for selected columns * add multiple selections change expandable sidebar * redo routing, keep alive summary * fixes, change routing, results display, orderby * fixes to selected columns * format page to allow for customisation * area for potential formatting and fix to querypara * changes to regex, combobox multiple, and fomat * column select fix, resize pill fix, format inputs * Update api/src/Database/DatabaseConnectionFactory.php Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/sp/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/saxs/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/pow/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/mx/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/em/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/app/components/combo-box.vue Co-authored-by: Guilherme Francisco * Update api/src/Database/DatabaseFactory.php Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> * Update api/src/TemplateParser.php Co-authored-by: Guilherme Francisco * Code review changes: database conns, code tidy * add get started button --------- Co-authored-by: Guilherme Francisco Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> --- api/config_sample.php | 5 + api/index.php | 12 +- .../Database/DatabaseConnectionFactory.php | 11 + api/src/Database/DatabaseFactory.php | 27 +- api/src/Database/Type/PureMySQL.php | 262 + api/src/Page/Summary.php | 423 + api/src/TemplateParser.php | 1 + client/package-lock.json | 13522 ++++++++++++++++ client/src/css/main.scss | 2 + client/src/css/partials/_summary.scss | 248 + client/src/js/app/components/combo-box.vue | 165 +- .../js/app/components/expandable-sidebar.vue | 106 + client/src/js/app/components/navbar.vue | 13 + client/src/js/app/layouts/main.vue | 4 +- client/src/js/app/router/router.js | 2 + client/src/js/app/store/store.js | 3 + .../summary/collections/summaryresults.js | 23 + .../modules/summary/models/summaryresult.js | 13 + client/src/js/modules/summary/routes.js | 14 + client/src/js/modules/summary/utils/utils.js | 28 + .../src/js/modules/summary/views/summary.vue | 1484 ++ client/src/js/modules/types/gen/menu.js | 1 + 22 files changed, 16352 insertions(+), 17 deletions(-) create mode 100644 api/src/Database/Type/PureMySQL.php create mode 100644 api/src/Page/Summary.php create mode 100644 client/src/css/partials/_summary.scss create mode 100644 client/src/js/app/components/expandable-sidebar.vue create mode 100644 client/src/js/modules/summary/collections/summaryresults.js create mode 100644 client/src/js/modules/summary/models/summaryresult.js create mode 100644 client/src/js/modules/summary/routes.js create mode 100644 client/src/js/modules/summary/utils/utils.js create mode 100644 client/src/js/modules/summary/views/summary.vue diff --git a/api/config_sample.php b/api/config_sample.php index 8278c5a03..1727e9025 100644 --- a/api/config_sample.php +++ b/api/config_sample.php @@ -13,6 +13,11 @@ $isb = array('user' => 'user', 'pass' => 'pass', 'db' => 'localhost/ispyb'); $dbtype = 'mysql'; + # Summary Database credentials + ######### DELETE if not using connection. + $summarydbconfig = array('user' => 'user', 'pass' => 'pass', 'db' => 'localhost/ispyb'); + $ifsummary = true; + # Encoded JWT key, used to sign and check validaty of jwt tokens # - Create one of these using /api/authenticate/key # This can be changed to invalidate all currently active tokens diff --git a/api/index.php b/api/index.php index c12ab0dc4..c95874ef7 100644 --- a/api/index.php +++ b/api/index.php @@ -69,7 +69,7 @@ function setupApplication($mode): Slim 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; + $valid_components, $enabled_container_types, $ifsummary; $app->contentType('application/json'); $app->response()->body(json_encode(array( 'motd' => $motd, @@ -87,7 +87,8 @@ function setupApplication($mode): Slim 'preset_proposal' => $preset_proposal, 'timezone' => $timezone, 'valid_components' => $valid_components, - 'enabled_container_types' => $enabled_container_types + 'enabled_container_types' => $enabled_container_types, + 'ifsummary' => $ifsummary ))); }); return $app; @@ -102,6 +103,13 @@ function setupDependencyInjectionContainer($app) return $db; }); + $app->container->singleton('dbsummary', function () use ($app): DatabaseParent { + $dbFactory = new DatabaseFactory(new DatabaseConnectionFactory()); + $db = $dbFactory->get("summary"); + $db->set_app($app); + return $db; + }); + $app->container->singleton('authData', function () use ($app) { return new AuthenticationData($app->container['db']); }); diff --git a/api/src/Database/DatabaseConnectionFactory.php b/api/src/Database/DatabaseConnectionFactory.php index 0889645f9..0afb84363 100644 --- a/api/src/Database/DatabaseConnectionFactory.php +++ b/api/src/Database/DatabaseConnectionFactory.php @@ -9,6 +9,7 @@ class DatabaseConnectionFactory public function get($databaseType) { global $isb; + global $summarydbconfig; if (!$databaseType) { error_log('Database type variable, dbtype, is not specified in config.php - defaulting to MySql.'); @@ -24,6 +25,16 @@ public function get($databaseType) $conn = new \mysqli($host, $isb['user'], $isb['pass'], $dbn, $port); $conn->set_charset("utf8mb4"); } + elseif ($databaseType == 'PureMySQL') { + $port = array_key_exists('port', $summarydbconfig) ? $summarydbconfig['port'] : null; + if (!$port) { + $port = ini_get("mysqli.default_port"); + } + list($host, $dbn) = explode('/', $summarydbconfig['db']); + $conn = new \mysqli($host, $summarydbconfig['user'], $summarydbconfig['pass'], $dbn, $port); + $conn->set_charset("utf8mb4"); + } + if ($conn == null) { Utils::returnError("Database Configuration Error", "Database connection for type '$databaseType' does not exist."); diff --git a/api/src/Database/DatabaseFactory.php b/api/src/Database/DatabaseFactory.php index 70a124454..8edcb1b23 100644 --- a/api/src/Database/DatabaseFactory.php +++ b/api/src/Database/DatabaseFactory.php @@ -9,7 +9,8 @@ class DatabaseFactory // Value is class name in SynchWeb\Database\Type namespace. // Key is lower case representation of class name. public $database_types = array( - 'mysql' => 'MySQL' + 'mysql' => ["dbClassName" =>'MySQL', "dataConnectionName" => 'MySQL'], + 'summary' => ["dbClassName" =>'PureMySQL', "dataConnectionName" => 'PureMySQL'] ); function __construct($databaseConnectionFactory) @@ -19,25 +20,27 @@ function __construct($databaseConnectionFactory) private $databaseConnectionFactory; - public function get() - { - // Global variable is named $dbtype in config.php. - global $dbtype; - $database_type = $dbtype; + public function get($databaseType = null) + { + if ( $databaseType == null) { + // Global variable is named $dbtype in config.php. + global $dbtype; + $databaseType = $dbtype; + } - if (!$database_type) { + if (!$databaseType) { error_log('Database type variable, dbtype, is not specified in config.php - defaulting to MySql.'); $database_type = 'MySQL'; } // Determine fully-qualified class name of database class corresponding to $database_type. - if (key_exists(strtolower($database_type), $this->database_types)) { - $dbClassName = $this->database_types[strtolower($database_type)]; + if (key_exists(strtolower($databaseType), $this->database_types)) { + $dbType = $this->database_types[strtolower($databaseType)]; - $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbClassName; + $full_class_name = 'SynchWeb\\Database\\Type\\' . $dbType["dbClassName"];; if (class_exists($full_class_name)) { - $conn = $this->databaseConnectionFactory->get($dbClassName); + $conn = $this->databaseConnectionFactory->get($dbType["dataConnectionName"]); return new $full_class_name($conn); } else { @@ -46,7 +49,7 @@ public function get() } else { - error_log("Database type '$database_type' not configured."); + error_log("Database type '$databaseType' not configured."); } return null; } diff --git a/api/src/Database/Type/PureMySQL.php b/api/src/Database/Type/PureMySQL.php new file mode 100644 index 000000000..8ab7d786b --- /dev/null +++ b/api/src/Database/Type/PureMySQL.php @@ -0,0 +1,262 @@ +error('There was an error connecting to MySQL: ', htmlentities(mysqli_connect_errno())); + } + } + + // wsrep_sync_wait waits for cluster replication on a mariadb cluster + function wait_rep_sync($state = false) + { + # Empty - DatabaseFactory checks this exists + } + + function start_transaction() + { + $this->transaction = True; + $this->conn->autocommit(False); + } + + function end_transaction() + { + if ($this->errors > 0) + $this->conn->rollback(); + else + $this->conn->commit(); + + $this->conn->autocommit(True); + $this->transaction = False; + + if ($this->errors > 0) + $this->error('There was an error with MySQL', $this->conn->error . __LINE__); + $this->errors = 0; + } + + function paginate($query, $args = array()) + { + // MySQL is Limit Start Row, Number + // Oracle subselect is Start Row, End Row + if (sizeof($args)) + $args[sizeof($args) - 1] = $args[sizeof($args) - 1] - $args[sizeof($args) - 2]; + return $this->pq("$query LIMIT ?,?", $args); + } + + + + // return the last SQL query executed in fully expanded form (i.e. including binded params) - this is mainly for testing purposes (so ideally would not be part of the actual class...) + function getLastQuery() + { + echo '
'; + $sql = $this->lastQuery; + for ($i = 1; $i < count($this->lastArgs); $i++) + { + $val = $this->lastArgs[$i]; + if (is_string($val)) + { + $val = "'" . $val . "'"; + } + else if (is_null($val)) + { + $val = 'null'; + } + $sql = preg_replace('/\?/', $val, $sql, 1); + } + $sql = preg_replace('/\\n/', '', $sql); // replace newlines + return preg_replace('/\s\s+/', ' ', $sql); // remove excess spaces + } + + function pq($query, $args = array(), $upperCaseKeys = true) + { + + if ($this->debug) + { + print '

MySQL Debug

'; + print SqlFormatter::format($query); + echo '
'; + } + + $stmt = $this->conn->prepare($query); + + if (!$stmt) + { + if ($this->transaction) + $this->errors++; + else + { + $err = mysqli_error($this->conn); + $this->error('There was an error with MySQL', $err); + return; + } + } + + if (sizeof($args)) + { + $vtypes = array('NULL' => 'i', 'integer' => 'i', 'double' => 'd', 'string' => 's'); + + $strfs = ''; + foreach ($args as $a) + { + $t = gettype($a); + $strfs .= $vtypes[$t]; + } + + array_unshift($args, $strfs); + call_user_func_array(array(&$stmt, 'bind_param'), $this->refs($args)); + } + + $this->lastQuery = $query; + $this->lastArgs = $args; + if ($this->debug) + { + print_r("Full SQL query: " . $this->getLastQuery()); + } + + if (!$stmt->execute()) + { + if ($this->transaction) + $this->errors++; + else + { + $err = mysqli_error($this->conn); + $this->error('There was an error with MySQL', $err); + return; + } + } + + $data = array(); + if (strpos($query, 'SELECT') !== false) + { + $result = $stmt->get_result(); + if ($result) + { + if ($result->num_rows > 0) + { + while ($row = $result->fetch_assoc()) + { + $c = array(); + // oracle inheritance ;( + foreach ($row as $key => $val) + { + if ($val !== null) + { + if (gettype($val) == gettype(0.1)) + $val = round($val, 5); + $val = strval($val); + } + if ($upperCaseKeys) + { + $key = strtoupper($key); + } + $c[$key] = $val; + } + array_push($data, $c); + } + } + } + } + + if ($this->debug) + { + echo '
'; + print_r('row count: ' . sizeof($data)); + echo '
'; + } + + // Need mysqlnd for this :( + // $result = $stmt->get_result(); + + // $data = array(); + + // if ($result) { + // if($result->num_rows > 0) { + // while($row = $result->fetch_assoc()) { + // array_push($data, array_change_key_case($row, CASE_UPPER)); + // } + // } + // } + + $stmt->close(); + + return $data; + } + + // Union multiple queries that take the same arguments and return the same columns + // Query can optionally be wrapped, where :QUERY will be replaced with the inner query: + // $wrapper = 'SELECT * FROM (:QUERY) GROUP BY id'; + function union($queries, $args, $all = false, $wrapper = null) + { + $nargs = sizeof($args); + $all_args = array(); + $union_kw = $all ? 'UNION ALL' : 'UNION'; + foreach ($queries as $i => &$query) + { + $offset = $i * $nargs; + $query = preg_replace_callback('/\:(\d+)/', + function ($mat) use ($offset) + { + return ':' . (intval($mat[1]) + $offset); + }, + $query); + $all_args = array_merge($all_args, $args); + } + + $union = implode("\n$union_kw\n", $queries); + if ($wrapper) + { + $union = preg_replace('/:QUERY/', $union, $wrapper); + } + + return $this->pq($union, $all_args); + } + + private function refs($arr) + { + $refs = array(); + foreach ($arr as $key => $value) + { + $refs[$key] = & $arr[$key]; + } + return $refs; + } + + function read($field) + { + return $field; + } + + function id() + { + return mysqli_insert_id($this->conn); + } + + function close() + { + if ($this->conn) + $this->conn->close(); + } +} \ No newline at end of file diff --git a/api/src/Page/Summary.php b/api/src/Page/Summary.php new file mode 100644 index 000000000..7b34bc8d7 --- /dev/null +++ b/api/src/Page/Summary.php @@ -0,0 +1,423 @@ + '(\w|\s|\-|\(|\))+', + 'propid' => '(.*)', + + // visit + 'com' => '(\[[^\ \]]*\],(asc|desc))', //comment + 'PROPOSALID' => '(\[[^\ \]]*\],(asc|desc))', + + 'BEAMLINENAME' => '(\[[^\ \]]*\],(asc|desc))', + // 'VISITNUMBER' => '(\[[^\ \]]*\],(asc|desc))', + + // Filter Parameters - array of parameter orders e.g. ascending, descending and the comparison value + 'sample' => '(^(\w+),(asc|desc|)+$)', //sample name + 'filetemp' => '(^(\w+),(asc|desc|)+$)', //file template + // 'dcid' => '(.*)', //data collection id + 'pp' => '(\[[^\ \]]*\],(asc|desc|))', // processing programs + 'sg' => '(\[[^\ \]]*\],(asc|desc|))', // space group + + + // Filter Parameters - array of parameter operands and orders such as greater than, equal to, between, less than, like, ascending, descending and the comparison value. + 'STARTDATE' => '(.*)', // visit start date + 'rca' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type a + 'rcb' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type b + 'rcc' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type c + 'rcal' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type alpha + 'rcbe' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type beta + 'rcga' => '(^(\d+),(.+),(asc|desc|)+$)', // refined cell type gamma + 'rlho' => '(^(\d+),(.+),(asc|desc|)+$)', // resolution limit high outer + 'rmpmi' => '(^(\d+),(.+),(asc|desc|)+$)', // rmeaswithiniplusiminus inner + 'riso' => '(^(\d+),(.+),(asc|desc|)+$)', // resioversigi2 overall + 'cci' => '(^(\d+),(.+),(asc|desc|)+$)', // ccanomalous inner + 'cco' => '(^(\d+),(.+),(asc|desc|)+$)', // ccanomalous overall + 'rfsi' => '(^(\d+),(.+),(asc|desc|)+$)', // rfreevaluestart inner + 'rfei' => '(^(\d+),(.+),(asc|desc|)+$)', // rfreevalueend inner + 'nobi' => '(^(\d+),(.+),(asc|desc|)+$)', // noofblobs inner + + + ); + + public static $dispatch = array( + array('/results', 'get', '_get_results'), + array('/proposal', 'get', '_get_proposal'), + array('/spacegroup', 'get', '_get_spacegroup'), + array('/procprogram', 'get', '_get_processingprogram'), + array('/bl', 'get', '_get_beamline') + ); + + public $string_arg_types = array( + 'pp' => ["order" =>'ppt.processingPrograms ', "where" => 'lower(ppt.processingPrograms) = lower( ? ) '], + 'sg' => ["order" =>'sgt.spaceGroup ', "where" => 'lower(sgt.spaceGroup) = lower( ? ) '], + 'BEAMLINENAME' => ["order" =>'vt.beamLineName ', "where" => 'lower(vt.beamLineName) LIKE lower( ? ) '] + ); + + + public $val_arg_types = array( + 'rca' => ["arg" => 'sf.refinedCell_a '], + 'rcb' => ["arg" => 'sf.refinedCell_b '], + 'rcc' => ["arg" => 'sf.refinedCell_c '], + 'rcal' => ["arg" => 'sf.refinedCell_alpha '], + 'rcbe' => ["arg" => 'sf.refinedCell_beta '], + 'rcga' => ["arg" => 'sf.refinedCell_gamma '], + 'rlho' => ["arg" => 'sf.resolutionLimitHighOuter '], + 'rmpmi' => ["arg" => 'sf.rMeasWithinIPlusIMinusInner '], + 'riso' => ["arg" => 'sf.resIOverSigI2Overall '], + 'cci' => ["arg" => 'sf.ccAnomalousInner '], + 'cco' => ["arg" => 'sf.ccAnomalousOverall '], + 'rfsi' => ["arg" => 'sf.rFreeValueStartInner '], + 'rfei' => ["arg" => 'sf.rFreeValueEndInner '], + 'nobi' => ["arg" => 'sf.noofblobs '] + + ); + + + private $summarydb; + + + function __construct(Slim $app, $db, $user) + { + global $summarydbconfig; + + parent::__construct($app, $db, $user); + + if ($summarydbconfig) { + $dbFactory = new DatabaseFactory(new DatabaseConnectionFactory()); + $db = $dbFactory->get("summary"); + $this->summarydb = $db; + } + + } + + private function error_on_no_summary_db(){ + global $summarydbconfig; + if (!$summarydbconfig) { + $this->_error("Not valid when summary database not configured."); + } + } + + function _get_results() { + $this->error_on_no_summary_db(); + $where = ''; + $where_arr = array(); + $order = ''; + $order_arr = array(); + $args = array(); + + $op_array = array(">", "LIKE", "=", "<"); + + if (!$this->has_arg('propid')) $this->_error('No proposal defined'); + + // $propid_array = explode(',', $this->arg('propid')); + $propid_args = preg_split('/[,]+(?![^\[]*\])/', urldecode($this->arg('propid'))); + $propid_array = explode(',', implode(str_replace(array('[',']'),'', $propid_args))); + array_push($order_arr, 'sf.autoProcIntegrationId DESC'); + + + if (!$this->staff) { + $person_id = $this->user->personId; + + $where_propid_personid_array = array(); + + + // # check user can see selected proposals and get all available visits if so + foreach ($propid_array as $value) { + array_push($where_propid_personid_array, '(sf.personid = ?'); + array_push($where_propid_personid_array, 'AND pt.proposalid = ? )'); + array_push($args, $person_id); + array_push($args, $value); + }; + + array_push($where_arr, '('.implode(' OR ', $where_propid_personid_array).')'); + + + } else { + $where_propid_array = array(); + + foreach ($propid_array as $value) { + array_push($where_propid_array, 'pt.proposalid = ?'); + array_push($args, $value); + }; + + array_push($where_arr, '('.implode(' OR ', $where_propid_array).')'); + + } + + + // [VALUE, ORDER] + + if ($this->has_arg('sample')) { + $sample_args = explode(',', urldecode($this->arg('sample'))); + + array_push($args, $sample_args[0]); + array_push($where_arr, "lower(sf.name) LIKE lower(CONCAT(CONCAT('%',?),'%')) ESCAPE '$' "); + + if (isset($sample_args[1]) == 'desc' || isset($sample_args[1]) == 'asc') { + array_push($order_arr, 'sf.name '.$sample_args[2]); + } + + } + + + if ($this->has_arg('filetemp')) { + $filetemp_args = explode(',', urldecode($this->arg('filetemp'))); + + array_push($args, $filetemp_args[0]); + array_push($where_arr, "lower(sf.fileTemplate) LIKE lower(CONCAT(CONCAT('%',?),'%')) ESCAPE '$' "); + + if (isset($filetemp_args[1]) == 'desc' || isset($filetemp_args[1]) == 'asc') { + array_push($order_arr, 'sf.fileTemplate '.$filetemp_args[1]); + } + + } + + + foreach ($this->string_arg_types as $key => $value) { + + if ($this->has_arg($key)) { + + $temp_array = array(); + + $temp_args = preg_split('/[,]+(?![^\[]*\])/', urldecode($this->arg($key))); + + $temp_values = explode(',', str_replace(array('[',']'),'', $temp_args[0])); + + foreach ($temp_values as $temp_value) { + array_push($temp_array, $value['where']); + array_push($args, $temp_value); + } + + array_push($where_arr, '('.implode(" OR ", $temp_array).')'); + + if (isset($temp_args[1]) == 'desc' || isset($temp_args[1]) == 'asc') { + array_push($order_arr, $value['order'].$temp_args[1]); + } + } + } + + + // [VALUE, OPERAND, ORDER] + + foreach ($this->val_arg_types as $key => $value) { + + if ($this->has_arg($key)) { + $temp_args = explode(',', $this->arg($key)); + + array_push($args, $temp_args[0]); + + if (in_array($temp_args[1], $op_array) ) { + array_push($where_arr, $value['arg'].$temp_args[1].' ?'); + } + + + if (isset($temp_args[2]) == 'desc' || isset($temp_args[2]) == 'asc') { + array_push($order_arr, $value['arg'].$temp_args[2]); + } + + } + + } + + + // AND is the delimieter between seperate queries, converted to string + $where = implode(" AND ", $where_arr); + + if (count($order_arr) > 0) { + $order = implode(", ", $order_arr); + } + + + // add multiselect params to end of where clause. + // $where = $where.$pp_where.$sg_where.$BEAMLINENAME_where; + + // get tot query + $tot_args = $args; + + $tot = $this->summarydb->pq( + "SELECT COUNT(sf.autoProcIntegrationId) as TOT + FROM SummaryFact sf + JOIN ProposalDimension pt on pt.proposalDimId = sf.proposalDimId + JOIN VisitDimension vt on vt.sessionDimId = sf.sessionDimId + JOIN ProcessingProgramDimension ppt on ppt.processingProgramsDimId = sf.processingProgramsDimId + JOIN SpaceGroupDimension sgt on sgt.spaceGroupDimId = sgt.spaceGroupDimId + WHERE $where + GROUP BY sf.datacollectionId" + , $tot_args); + + $tot = sizeof($tot) ? intval($tot[0]['TOT']) : 0; + + // paginate + $pp = $this->has_arg('per_page') ? $this->arg('per_page') : 15; + $pg = $this->has_arg('page') ? $this->arg('page')-1 : 0; + $start = $pg*$pp; + $end = $pg*$pp+$pp; + + $st = sizeof($args)+1; + $en = $st + 1; + array_push($args, $start); + array_push($args, $end); + + $pgs = intval($tot/$pp); + if ($tot % $pp != 0) $pgs++; + + + $rows = $this->summarydb->paginate( + "SELECT + pt.prop, + sf.autoProcIntegrationId, + sf.dataCollectionId, + sf.personId, + sf.visit_number, + sf.startTime, + vt.beamLineName, + sf.comments, + GROUP_CONCAT(COALESCE(sf.fileTemplate, 'NULL')) as FILETEMPLATE, + GROUP_CONCAT(COALESCE(sf.name, 'NULL')) as SAMPLENAME, + GROUP_CONCAT(COALESCE(sgt.spaceGroup, 'NULL')) as SPACEGROUP, + GROUP_CONCAT(COALESCE(ppt.processingPrograms, 'NULL')) as PROCESSINGPROGRAMS, + GROUP_CONCAT(COALESCE(sf.refinedCell_a, 'NULL')) as REFINEDCELL_A, + GROUP_CONCAT(COALESCE(sf.refinedCell_b, 'NULL')) as REFINEDCELL_B, + GROUP_CONCAT(COALESCE(sf.refinedCell_c, 'NULL')) as REFINEDCELL_C, + GROUP_CONCAT(COALESCE(sf.refinedCell_alpha, 'NULL')) as REFINEDCELL_ALPHA, + GROUP_CONCAT(COALESCE(sf.refinedCell_beta, 'NULL')) as REFINEDCELL_BETA, + GROUP_CONCAT(COALESCE(sf.refinedCell_gamma, 'NULL')) as REFINEDCELL_GAMMA, + GROUP_CONCAT(COALESCE(sf.resolutionLimitHighOuter, 'NULL')) as RESOLUTIONLIMITHIGHOUTER, + GROUP_CONCAT(COALESCE(sf.rMeasWithinIPlusIMinusInner, 'NULL')) as RMEASWITHINIPLUSIMINUSINNER, + GROUP_CONCAT(COALESCE(sf.resIOverSigI2Overall, 'NULL')) as RESIOVERSIGI2OVERALL, + GROUP_CONCAT(COALESCE(sf.ccAnomalousInner, 'NULL')) as CCANOMALOUSINNER, + GROUP_CONCAT(COALESCE(sf.ccAnomalousOverall, 'NULL')) as CCANOMALOUSOVERALL, + GROUP_CONCAT(COALESCE(sf.rFreeValueStartInner, 'NULL')) as RFREEVALUESTARTINNER, + GROUP_CONCAT(COALESCE(sf.rFreeValueEndInner, 'NULL')) as RFREEVALUEENDINNER, + GROUP_CONCAT(COALESCE(sf.noofblobs, 'NULL')) as NOOFBLOBS + FROM SummaryFact sf + JOIN ProposalDimension pt on pt.proposalDimId = sf.proposalDimId + JOIN VisitDimension vt on vt.sessionDimId = sf.sessionDimId + JOIN ProcessingProgramDimension ppt on ppt.processingProgramsDimId = sf.processingProgramsDimId + JOIN SpaceGroupDimension sgt on sgt.spaceGroupDimId = sf.spaceGroupDimId + WHERE $where + GROUP BY sf.dataCollectionId + ORDER BY $order " + , $args); + + + if (!$rows) { + $this->_error($this->arg('TITLE') . ' could not be found anywhere!', 404); + } + + // sql query output + + // $this->_output(array('data' => $where, 'args' => $args)); + $this->_output(array('data' => $rows, 'total' => $tot )); + // $this->_output(array('data' => $rows, 'where' => $where, 'order' => $order, 'args' => $args)); + + + + } + + function _get_proposal() { + $this->error_on_no_summary_db(); + $args = array(); + $where = "WHERE 1=1"; + + if (!$this->staff) { + $person_id = $this->user->personId; + + // $person_id = 16565; + + $where_person = "sf.personId = ".$person_id; + + $rows = $this->summarydb->pq( + "SELECT pt.prop, pt.proposalid + FROM ProposalDimension pt + JOIN SummaryFact sf on pt.proposalDimId = sf.proposalDimId + WHERE $where_person + GROUP BY pt.proposalid"); + + $this->_output($rows); + + } else { + + $tot = $this->summarydb->pq( + "SELECT COUNT(proposalid) as TOT + FROM ProposalDimension pt + $where", $args); + + + $tot = sizeof($tot) ? intval($tot[0]['TOT']) : 0; + + // paginate + $pp = $this->has_arg('per_page') ? $this->arg('per_page') : 15; + $pg = $this->has_arg('page') ? $this->arg('page')-1 : 0; + $start = $pg*$pp; + $end = $pg*$pp+$pp; + + $st = sizeof($args)+1; + $en = $st + 1; + array_push($args, $start); + array_push($args, $end); + + $pgs = intval($tot/$pp); + if ($tot % $pp != 0) $pgs++; + + $order = 'p.proposalid DESC'; + + $rows = $this->summarydb->paginate( + "SELECT prop, proposalid + FROM ProposalDimension pt + $where", $args); + + $this->_output($rows); + + } + + + + } + + function _get_spacegroup() { + $this->error_on_no_summary_db(); + $rows = $this->summarydb->pq( + "SELECT spaceGroup + FROM SpaceGroupDimension sgt"); + + $this->_output($rows); + + } + + function _get_processingprogram() { + $this->error_on_no_summary_db(); + $rows = $this->summarydb->pq( + "SELECT processingPrograms + FROM ProcessingProgramDimension ppt"); + + $this->_output($rows); + + } + + function _get_beamline() { + $this->error_on_no_summary_db(); + $rows = $this->summarydb->pq( + "SELECT beamLineName + FROM VisitDimension vt"); + + $this->_output($rows); + + } + + + + +} + diff --git a/api/src/TemplateParser.php b/api/src/TemplateParser.php index ff3a32f39..bb52ffecf 100644 --- a/api/src/TemplateParser.php +++ b/api/src/TemplateParser.php @@ -20,6 +20,7 @@ class TemplateParser var $params = array(); function __construct($db) { + $this->db = $db; } diff --git a/client/package-lock.json b/client/package-lock.json index a87a11a4f..932359ebf 100644 --- a/client/package-lock.json +++ b/client/package-lock.json @@ -19078,5 +19078,13527 @@ "node": "*" } } + }, + "dependencies": { + "@achrinza/node-ipc": { + "version": "9.2.5", + "resolved": "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.5.tgz", + "integrity": "sha512-kBX7Ay911iXZ3VZ1pYltj3Rfu7Ow9H7sK4H4RSfWIfWR2JKNB40K808wppoRIEzE2j2hXLU+r6TJgCAliCGhyQ==", + "dev": true, + "requires": { + "@node-ipc/js-queue": "2.0.3", + "event-pubsub": "4.3.0", + "js-message": "1.0.7" + } + }, + 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center; + align-items: center; + display: flex; + position: fixed; + top: 20%; + left: 50%; +} + +.status { + height: 125px; + width: 75px; + justify-content: center; + align-items: center; + display: flex; + position: fixed; + top: 45%; + left: 50%; + color: rgb(111, 213, 111); +} + +.proposal-select { + color: black; + height: 10px; +} + + +.order-by { + cursor: pointer; + position: relative; + /* top: 60%; */ + content: ""; + width: 15px; + height: 20px; +} + + +.sidebar-button { + @apply tw-text-center tw-bg-content-active tw-border-content-active tw-text-xs tw-border-4 tw-text-black tw-py-1 tw-px-1 tw-rounded +} +.sidebar-button:hover { + @apply tw-border-teal-700 tw-bg-teal-700 +} + +.clear-button { + @apply tw-flex tw-text-black tw-text-center tw-text-xs tw-py-2 tw-px-1 tw-ml-2 +} + +.clear-button:focus { + @apply tw-text-content-active tw-text-content-active +} + +.filter-grid { + @apply tw-grid tw-grid-rows-1 tw-grid-cols-4 tw-grid-flow-col +} + +.filter-options-grid { + @apply tw-grid tw-grid-rows-6 tw-grid-cols-3 tw-grid-flow-col tw-mb-2 +} + +.format-options-grid { + @apply tw-grid tw-grid-rows-6 tw-grid-cols-1 tw-grid-flow-col tw-mb-2 + +} + +.select-column-button { + @apply tw-h-8 tw-rounded tw-text-xs tw-px-4 tw-text-center tw-inline-flex tw-items-center + tw-bg-content-sub-header-background tw-border-content-sub-header-background tw-border-4 + tw-text-black tw-py-1 tw-px-5 +} + +.select-columns-dropdown { + @apply tw-absolute tw-bg-white tw-rounded tw-shadow + tw-transition tw-ease-out tw-duration-100 +} + +.select-columns-dropdown-show{ + @apply tw-transform tw-opacity-100 tw-scale-100 tw-z-50 +} + +.select-columns-dropdown-hide { + z-index: -1; + @apply tw-transform tw-opacity-0 tw-scale-95 +} + +.select-columns-checkbox { + @apply tw-w-4 tw-h-4 tw-text-blue-600 tw-bg-gray-100 tw-rounded tw-border-gray-300 +} + +.download-file { + @apply tw-mt-10 tw-items-center tw-block tw-pt-1 tw-pl-5 tw-pr-5 tw-h-6 tw-ml-2 tw-mr-2 + tw-bg-content-sub-header-background tw-shadow tw-text-xs tw-rounded tw-shadow +} + +.simple-search { + @apply tw-pl-6 tw-px-4 tw-border +} + +.simple-search:focus { + @apply tw-outline-none tw-shadow-outline +} + +/* Tooltip container */ +.tooltip { + /* position: relative; + display: inline-block; */ + color: rgb(104, 104, 104); /* If you want dots under the hoverable text */ +} + +.add-white { + color: white; +} + +.add-gray { + color: rgb(104, 104, 104); +} + +.tooltip-position-relative { + position: relative; + display: inline-block; +} + +.tooltip-position-absolute { + position: absolute; +} + + +/* Tooltip text */ +.tooltip .tooltiptext { + font-family: Arial, Helvetica, sans-serif; + visibility: hidden; + opacity: 0.9; + width: 120px; + background-color: rgb(25, 24, 24); + color: #fff; + text-align: center; + padding: 5px 0; + border-radius: 6px; + + /* Position the tooltip text - see examples below! */ + position: absolute; + z-index: 1; +} + +/* Show the tooltip text when you mouse over the tooltip container */ +.tooltip:hover .tooltiptext { + visibility: visible; +} + +.description-options { + display:none; + position:absolute; + border:1px solid #828282; + font-family: Arial, Helvetica, sans-serif; + overflow-x:visible; + overflow-y:visible; + +} + +.tooltip:hover .description-options { + display:block; + min-width:100px; + min-height:50px; + background-color: white; + left:40%; + top: 50% +} + +.dc-nav { + position: absolute; + display: flex; +} + +.tiptext-preview { + position: absolute; + font-size:small; + cursor:pointer; +} + +.description { + display:none; + position:absolute; + left: 50%; + border:1px solid #000; + width:400px; + height:400px; +} + +.tiptext-preview:hover .description { + display:block; +} + +.param-options-wrapper { + display:flex; + margin-left: 65%; + margin-top: 5px; +} + + +.param-options-tooltip { + cursor:default; + font-size:12px; + font-weight: bold; + margin-top: 2px; + color: blue; + + &:hover .param-preview { + opacity:1; + display: inline; + transform: translateX(-50%) translateY(0) scale(1); + } + + &:hover { + box-shadow: 0 1px 5px rgba(0,0,0,.1); + border-color: #333; + } +} + +.param-preview { + display: none; + border-radius: 10px; + transition:.2s ease-in-out opacity, .2s ease-in-out transform; + opacity:0; + z-index: 1; + position:absolute; + box-shadow:0 1px 5px rgba(0,0,0,.5); + width:230px; + height:fit-content; + border:4px solid #fff; + background-color: #fff; + color: black; + font-weight: normal; + overflow-x:hidden; + overflow-y:auto; + transform-origin:center bottom; + transform: translateX(-50%) translateY(10px) scale(.9); + +// div { +// transform:scale(.2); +// transform-origin:0 0; +// } + +} \ No newline at end of file diff --git a/client/src/js/app/components/combo-box.vue b/client/src/js/app/components/combo-box.vue index 78ca2ac3a..01004048b 100644 --- a/client/src/js/app/components/combo-box.vue +++ b/client/src/js/app/components/combo-box.vue @@ -17,6 +17,7 @@ The v-closable takes an object as argumnt with properties: :data-testid="dataTestId" >
+ {{ searchArray.length==0 ? defaultText : '' }} +
+
+

{{ value[textField] }}

+ +
+
- No more data + No more data +

+
+
+ +
+
+
+ +
+
+
+ + {{ option[textField] }} + +
+
+ +

+ No more data

+ +
+
+
+ + +
@@ -123,6 +213,16 @@ export default { type: String, required: true }, + valueArray: { + type: Array, + default: () => ([]), + required: true + }, + searchArray: { + type: Array, + default: () => ([]), + required: true + }, defaultText: { type: String, default: 'Select an Item' @@ -160,6 +260,10 @@ export default { canCreateNewItem: { type: Boolean, default: true + }, + multiple: { + type: Boolean, + default: false } }, data() { @@ -247,6 +351,17 @@ export default { this.searching = false this.searchText = '' }, + selectMultipleOption(value, optionIndex) { + // The ref element will be stored in an array because of the way Vue 2 handles ref used in a v-for + const element = this.$refs[`selectOption${this.inputIndex}${optionIndex}`][0] + + // element.classList.toggle('item-multiple-selected') + + this.$emit('input', value) + this.addOptionArray(value) + this.searching = false + + }, closeComboBox(force = true) { // Loop through all the combobox elements and close every dropdown list const dropDownList = [] @@ -273,9 +388,24 @@ export default { } } } + }, + addOptionArray: function (val) { + + const index = this.valueArray.findIndex(item => item[this.valueField] == val[this.valueField]) + if (index >= 0) { + this.valueArray.splice(this.valueArray[index], 1) + + console.log('remove', this.valueArray) + } else { + this.valueArray.push(val) + console.log('add', this.valueArray) + } + + }, openOptionsList(event) { event.stopPropagation() + console.log('classlist', event.target.parentElement.previousElementSibling.classList) event.target.parentElement.previousElementSibling.classList.remove('select-hide') this.searching = true }, @@ -291,6 +421,9 @@ export default { }, createNewOption() { this.$emit('create-new-option', this.searchText) + }, + onInput(e) { + this.searchText=e.target.innerText } } } @@ -300,6 +433,10 @@ export default { .select-selected { @apply tw-bg-white tw-h-8 tw-rounded tw-border tw-border-content-dark-background tw-flex tw-items-center tw-cursor-pointer } + +.select-selected-multiple { + @apply tw-bg-white tw-h-8 tw-rounded tw-border tw-border-content-dark-background tw-flex tw-items-center tw-cursor-pointer +} .select-selected.disabled { @apply tw-bg-content-page-background } @@ -350,6 +487,9 @@ export default { .items-list > div { @apply tw-py-2 tw-px-2 tw-cursor-pointer tw-text-black; } +.items-list-multiple > div { + @apply tw-py-2 tw-px-2 tw-cursor-pointer tw-text-black; +} /* Style items (options): */ .select-items { @apply tw-absolute tw-bg-white; @@ -374,10 +514,31 @@ export default { .items-list .item:hover, .same-as-selected { @apply tw-bg-content-active tw-text-white; } + +.items-list-multiple .item-multiple:hover { + @apply tw-bg-content-active tw-text-white; +} + +.item-multiple-selected { + @apply tw-bg-content-active tw-text-white; +} .select-search-input.small { @apply tw-h-8; } .select-search-input { - @apply tw-h-10; + @apply tw-h-12; } + +.pill-input { + white-space: nowrap; + @apply tw-rounded-full tw-h-6 tw-max-w-xs tw-ml-1 tw-px-2 tw-py-1 tw-bg-content-active tw-text-sm +} + +::-webkit-scrollbar { + height: 2px; + width: 2px; + background-color: rgb(77, 118, 255); +} + + diff --git a/client/src/js/app/components/expandable-sidebar.vue b/client/src/js/app/components/expandable-sidebar.vue new file mode 100644 index 000000000..3d397a4f1 --- /dev/null +++ b/client/src/js/app/components/expandable-sidebar.vue @@ -0,0 +1,106 @@ + + + + + + + diff --git a/client/src/js/app/components/navbar.vue b/client/src/js/app/components/navbar.vue index 5a6701f5c..fba7d0302 100644 --- a/client/src/js/app/components/navbar.vue +++ b/client/src/js/app/components/navbar.vue @@ -10,6 +10,17 @@ class="tw-hidden tw-z-10 md:tw-flex md:flex-row tw-bg-sidebar-grad-end tw-justify-center tw-my-4 md:tw-mx-auto tw-border tw-border-gray-400 tw-divide-x tw-divide-gray-400" > + + + Summary + + + - + + + diff --git a/client/src/js/app/router/router.js b/client/src/js/app/router/router.js index d0d1e7aee..43d885ae2 100644 --- a/client/src/js/app/router/router.js +++ b/client/src/js/app/router/router.js @@ -40,6 +40,7 @@ import StatsRoutes from 'modules/stats/routes.js' import EMRoutes from 'modules/types/em/routes.js' import SubmissionRoutes from 'modules/submission/routes.js' import VisitsRoutes from 'modules/visits/routes.js' +import SummaryRoutes from 'modules/summary/routes.js' import { resolve } from 'promise' @@ -111,6 +112,7 @@ router.addRoutes(FaultRoutes) router.addRoutes(StatsRoutes) router.addRoutes(SubmissionRoutes) router.addRoutes(VisitsRoutes) +router.addRoutes(SummaryRoutes) // Hook the marionette navigation methods into vue-router methods diff --git a/client/src/js/app/store/store.js b/client/src/js/app/store/store.js index 2884f2146..6d851acab 100644 --- a/client/src/js/app/store/store.js +++ b/client/src/js/app/store/store.js @@ -43,6 +43,7 @@ const store = new Vuex.Store({ isLoading: false, motd: '', + ifsummary: false, help: false, // Global help flag used to denote if we should display inline help on pages skipHomePage: config.skipHome || false, models: {}, @@ -66,6 +67,8 @@ const store = new Vuex.Store({ state.motd = options.get('motd') || state.motd + state.ifsummary = options.get('ifsummary') || state.ifsummary + app.options = options }, setHelp(state, helpFlag) { diff --git a/client/src/js/modules/summary/collections/summaryresults.js b/client/src/js/modules/summary/collections/summaryresults.js new file mode 100644 index 000000000..95c6a87f6 --- /dev/null +++ b/client/src/js/modules/summary/collections/summaryresults.js @@ -0,0 +1,23 @@ +define(['backbone.paginator', 'modules/summary/models/summaryresult'], function(PageableCollection, SummaryResult) { + + return PageableCollection.extend({ + model: SummaryResult, + mode: 'server', + // url: '/summary/example', + url: '/summary/results', + + + state: { + pageSize: 15, + }, + + parseState: function(r, q, state, options) { + return { totalRecords: r.total } + }, + + parseRecords: function(r, options) { + return r.data + }, + + }) +}) \ No newline at end of file diff --git a/client/src/js/modules/summary/models/summaryresult.js b/client/src/js/modules/summary/models/summaryresult.js new file mode 100644 index 000000000..1a7ac52d2 --- /dev/null +++ b/client/src/js/modules/summary/models/summaryresult.js @@ -0,0 +1,13 @@ +define(['backbone'], function(Backbone) { + + return Backbone.Model.extend({ + idAttribute: 'proposalID', //change this + // urlRoot: '/summary/example', + urlRoot: '/summary/results', + + + + }) + + }) + \ No newline at end of file diff --git a/client/src/js/modules/summary/routes.js b/client/src/js/modules/summary/routes.js new file mode 100644 index 000000000..240c886a7 --- /dev/null +++ b/client/src/js/modules/summary/routes.js @@ -0,0 +1,14 @@ +const SummaryViewWrapper = () => import(/* webpackChunkName: "summary" */ 'modules/summary/views/summary.vue') + + +const routes = [ + // Root path has optional parameters so we need to deal with it first + // It doesn't play nicely with multiple child routes... + { + path: '/summary', + component: SummaryViewWrapper, + + } +] + +export default routes \ No newline at end of file diff --git a/client/src/js/modules/summary/utils/utils.js b/client/src/js/modules/summary/utils/utils.js new file mode 100644 index 000000000..cf7a39c34 --- /dev/null +++ b/client/src/js/modules/summary/utils/utils.js @@ -0,0 +1,28 @@ + + +export function convertToCSV(data) { + + const result = [ + // headers + Object.keys(data['0']), + // values + ...Object.values(data).map(item => Object.values(item)) + ] + .reduce((string, item) => { + string += item.join(',') + '\n'; + return string; + }, ''); + + return result; +} + +export function exportCSV(csv) { + + const anchor = document.createElement('a'); + anchor.href = 'data:text/csv;charset=utf-8,' + encodeURIComponent(csv); + anchor.target = '_blank'; + anchor.download = 'summary_export.csv'; + anchor.click(); + +} + diff --git a/client/src/js/modules/summary/views/summary.vue b/client/src/js/modules/summary/views/summary.vue new file mode 100644 index 000000000..32dd16c04 --- /dev/null +++ b/client/src/js/modules/summary/views/summary.vue @@ -0,0 +1,1484 @@ + + + + + + + + + diff --git a/client/src/js/modules/types/gen/menu.js b/client/src/js/modules/types/gen/menu.js index 183381b4f..f544cfa01 100644 --- a/client/src/js/modules/types/gen/menu.js +++ b/client/src/js/modules/types/gen/menu.js @@ -14,6 +14,7 @@ define([], function() { admin: { faults: { title: 'Fault Reports', icon: 'fa-tasks' }, + }, } From 8415438c1ac7ce197f81d957dfb3a4e07a0fb285 Mon Sep 17 00:00:00 2001 From: NKatti2011 <108797920+NKatti2011@users.noreply.github.com> Date: Fri, 28 Jul 2023 09:22:30 +0100 Subject: [PATCH 12/12] FIX: Prerelease merge for summary css fix (#641) * [LIMS-116] Fix: Summary page revamp, make css local (#639) * updating .gitignore * adding frontend files and building backend * adding front end files and router files * create sidebar, filter options added, routes added * add routing to page,search bar and column selector * adding pagination continutation * adding csv, all columns, rest of filters * added descending and ascending * sidebar dropdown&changed data structure&hide row * cleaning up fixing jump bug * refactored backend mapped data * added expanding row * refactored favourites * refactored orderby filter * cleaned up code, added comments * added all params to watcher * added summary db connection * add routes to summary * add backend changes summarypage * changes to expandable sidebar, cleaning up fronte * clean up, add functions to get data * front end changes, group concat backend * remove summarypage code * fix pagination, timeout * delete old summary file * changed pagination in summary.php * changed backend to not include tot * fix refined cell c column * added ifsets to avoid undefined offset error * delete offset for output * change order of operands * change filters, fix operands * fix csv button * changed prop to propid * format beamlinename * change al,be,gamma * add selected columns summary * additional changes for selected columns * add multiple selections change expandable sidebar * redo routing, keep alive summary * fixes, change routing, results display, orderby * fixes to selected columns * format page to allow for customisation * area for potential formatting and fix to querypara * changes to regex, combobox multiple, and fomat * column select fix, resize pill fix, format inputs * Update api/src/Database/DatabaseConnectionFactory.php Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/sp/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/saxs/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/pow/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/mx/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/em/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/app/components/combo-box.vue Co-authored-by: Guilherme Francisco * Update api/src/Database/DatabaseFactory.php Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> * Update api/src/TemplateParser.php Co-authored-by: Guilherme Francisco * Code review changes: database conns, code tidy * add get started button * Change styling to be local rather than global --------- Co-authored-by: Guilherme Francisco Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> * [LIMS-116] Fix: Summary page revamp, delete css global (#640) * updating .gitignore * adding frontend files and building backend * adding front end files and router files * create sidebar, filter options added, routes added * add routing to page,search bar and column selector * adding pagination continutation * adding csv, all columns, rest of filters * added descending and ascending * sidebar dropdown&changed data structure&hide row * cleaning up fixing jump bug * refactored backend mapped data * added expanding row * refactored favourites * refactored orderby filter * cleaned up code, added comments * added all params to watcher * added summary db connection * add routes to summary * add backend changes summarypage * changes to expandable sidebar, cleaning up fronte * clean up, add functions to get data * front end changes, group concat backend * remove summarypage code * fix pagination, timeout * delete old summary file * changed pagination in summary.php * changed backend to not include tot * fix refined cell c column * added ifsets to avoid undefined offset error * delete offset for output * change order of operands * change filters, fix operands * fix csv button * changed prop to propid * format beamlinename * change al,be,gamma * add selected columns summary * additional changes for selected columns * add multiple selections change expandable sidebar * redo routing, keep alive summary * fixes, change routing, results display, orderby * fixes to selected columns * format page to allow for customisation * area for potential formatting and fix to querypara * changes to regex, combobox multiple, and fomat * column select fix, resize pill fix, format inputs * Update api/src/Database/DatabaseConnectionFactory.php Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/sp/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/saxs/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/pow/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/mx/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/modules/types/em/menu.js Co-authored-by: Guilherme Francisco * Update client/src/js/app/components/combo-box.vue Co-authored-by: Guilherme Francisco * Update api/src/Database/DatabaseFactory.php Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> * Update api/src/TemplateParser.php Co-authored-by: Guilherme Francisco * Code review changes: database conns, code tidy * add get started button * Change styling to be local rather than global * delete summary css globals --------- Co-authored-by: Guilherme Francisco Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> --------- Co-authored-by: Guilherme Francisco Co-authored-by: John Holt <7570055+John-Holt-Tessella@users.noreply.github.com> --- client/src/css/main.scss | 2 +- .../modules/summary/styles}/_summary.scss | 0 client/src/js/modules/summary/views/summary.vue | 11 ++++++----- 3 files changed, 7 insertions(+), 6 deletions(-) rename client/src/{css/partials => js/modules/summary/styles}/_summary.scss (100%) diff --git a/client/src/css/main.scss b/client/src/css/main.scss index 3317ceaa2..28efbec82 100644 --- a/client/src/css/main.scss +++ b/client/src/css/main.scss @@ -23,7 +23,7 @@ @import "partials/_mc.scss"; @import "partials/_imaging.scss"; -@import "partials/_summary.scss"; + // Third-party diff --git a/client/src/css/partials/_summary.scss b/client/src/js/modules/summary/styles/_summary.scss similarity index 100% rename from client/src/css/partials/_summary.scss rename to client/src/js/modules/summary/styles/_summary.scss diff --git a/client/src/js/modules/summary/views/summary.vue b/client/src/js/modules/summary/views/summary.vue index 32dd16c04..e57f83fed 100644 --- a/client/src/js/modules/summary/views/summary.vue +++ b/client/src/js/modules/summary/views/summary.vue @@ -31,7 +31,7 @@ Filter
-

Select Proposals

+

Select Proposals

- +
-
+
-
- +
+ @@ -1351,6 +1351,7 @@ export default {