├── .gitignore ├── AUTHORS ├── LICENSE ├── README.md ├── VERSION ├── client └── src │ ├── app │ ├── admin │ │ ├── admin-page.tpl.html │ │ ├── history-list-dir.js │ │ ├── history-list-service.js │ │ └── setting-list-controller.js │ ├── app.js │ ├── datasets │ │ ├── dataset-collection-create-panel.tpl.html │ │ ├── dataset-collection-list.tpl.html │ │ ├── dataset-irods-pull.tpl.html │ │ ├── dataset-list-controller.js │ │ ├── dataset-list-dir.js │ │ ├── dataset-list.tpl.html │ │ ├── dataset-selector-dialog.tpl.html │ │ └── dataset-upload.tpl.html │ ├── histories │ │ ├── history-list-controller.js │ │ ├── history-list-dir.js │ │ ├── history-list-service.js │ │ ├── history-list.tpl.html │ │ └── history-page.tpl.html │ ├── home │ │ └── home.tpl.html │ ├── users │ │ ├── user-session-controller.js │ │ ├── user-session-dir.js │ │ └── user-sign-in.tpl.html │ └── workflows │ │ ├── workflow-card-dir.js │ │ ├── workflow-card.tpl.html │ │ ├── workflow-detail.tpl.html │ │ ├── workflow-invocation-panel.tpl.html │ │ ├── workflow-invocation-toolbar.tpl.html │ │ ├── workflow-list-controller.js │ │ ├── workflow-list-dir.js │ │ ├── workflow-list-service.js │ │ ├── workflow-list.tpl.html │ │ ├── workflow-run-controller.js │ │ ├── workflow-run-dir.js │ │ ├── workflow-run-service.js │ │ ├── workflow-run-step.tpl.html │ │ └── workflow-run.tpl.html │ ├── common │ ├── resources │ │ ├── API-REQUEST-EXAMPLES.js │ │ ├── common.js │ │ └── error-message.tpl.html │ └── services │ │ └── toArrayFilter.js │ ├── css │ ├── angular-dialogs.min.css │ ├── bootstrap-dialogs.min.css │ ├── bootstrap-sortable.css │ ├── bootstrap.min.css │ ├── galaksio_logo.xcf │ ├── galaksio_logo_2.xcf │ ├── galaxy_logo.png │ ├── galaxy_logo2.png │ ├── home_back_science.png │ ├── invocation_error.png │ ├── invocation_new.png │ ├── invocation_sending.png │ ├── invocation_success.png │ ├── invocation_waiting.png │ ├── invocation_working.gif │ ├── invocation_working.png │ ├── main.css │ └── paintomics_white_300x66.png │ ├── favicon.ico │ ├── favicon.png │ ├── fonts │ ├── FontAwesome.otf │ ├── LICENSE.txt │ ├── OpenSans-Bold.ttf │ ├── OpenSans-BoldItalic.ttf │ ├── OpenSans-ExtraBold.ttf │ ├── OpenSans-ExtraBoldItalic.ttf │ ├── OpenSans-Italic.ttf │ ├── OpenSans-Light.ttf │ ├── OpenSans-LightItalic.ttf │ ├── OpenSans-Regular.ttf │ ├── OpenSans-Semibold.ttf │ ├── OpenSans-SemiboldItalic.ttf │ ├── font-awesome.min.css │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ ├── fontawesome-webfont.woff │ ├── fontawesome-webfont.woff2 │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ ├── glyphicons-halflings-regular.woff │ └── glyphicons-halflings-regular.woff2 │ ├── index.html │ ├── install.html │ └── lib │ ├── angular-backtop.min.js │ ├── angular-dialogs.min.js │ ├── angular-draganddrop.min.js │ ├── angular-sanitize.min.js │ ├── angular-scrollspy.min.js │ ├── angular-ui-router.min.js │ ├── angular.min.js │ ├── bootstrap-extensions.js │ ├── bootstrap-sortable.js │ ├── bootstrap.min.js │ ├── dagre.min.js │ ├── jquery.min.js │ ├── js.cookie.js │ ├── sigma.customEdgeShapes.min.js │ ├── sigma.customShapes.min.js │ ├── sigma.min.js │ ├── sigma.plugins.min.js │ └── ui-bootstrap-tpls-1.3.2.min.js ├── docker ├── Dockerfile ├── LICENSE ├── README.md ├── configs │ ├── entrypoint.sh │ ├── galaksio.wsgi │ └── httpd.conf ├── docker-compose-template-with-galaxy.yml ├── docker-compose-template.yml ├── docker-compose-with-galaxy.yml └── docker-compose.yml ├── docs ├── 1_1_galaxy.md ├── 1_1_galaxy │ ├── galaksio_logo.png │ ├── galaksio_screenshot.png │ └── galaxy_screenshot.png ├── 1_2_concepts.md ├── 1_2_concepts │ ├── galaksio_logo.png │ ├── galaxy_histories.png │ └── galaxy_workflows.png ├── 1_3_install.md ├── 1_3_install │ └── galaksio_logo.png ├── 1_4_quick_start.md ├── 1_4_quick_start │ ├── galaksio_logo.png │ └── video.png ├── 2_1_users.md ├── 2_1_users │ ├── galaksio_logo.png │ ├── galaksio_users_1.png │ └── galaksio_users_2.png ├── 3_1_histories.md ├── 3_1_histories │ ├── galaksio_logo.png │ └── histories_1.png ├── 3_2_histories.md ├── 3_2_histories │ ├── galaksio_logo.png │ └── histories_2.png ├── 3_3_histories.md ├── 3_3_histories │ ├── galaksio_logo.png │ ├── histories_3.png │ ├── histories_4.png │ ├── histories_5.png │ └── histories_6.png ├── 4_1_workflows.md ├── 4_1_workflows │ ├── galaksio_logo.png │ ├── workflows1.png │ └── workflows2.png ├── 4_2_workflows.md ├── 4_2_workflows │ ├── galaksio_logo.png │ ├── worflows1.png │ ├── worflows2.png │ ├── worflows3.png │ ├── worflows4.png │ ├── worflows5.png │ └── worflows6.png ├── 5_use_case.md ├── 5_use_case │ └── galaksio_logo.png ├── 6_license.md ├── 6_license │ ├── ECH2020.png │ ├── galaksio_logo.png │ ├── gplv3-127x51.png │ └── logoB3Africa400x300.jpg ├── ECH2020.png ├── galaksio_logo.png ├── index.md ├── index │ ├── ECH2020.png │ ├── galaksio_logo.png │ └── logoB3Africa400x300.jpg └── logoB3Africa400x300.jpg ├── mkdocs.yml ├── server ├── __init__.py ├── conf │ └── .dummy ├── launch_server.py ├── log │ └── .dummy ├── resources │ ├── __init__.py │ ├── example_serverconf.cfg │ └── logging.cfg ├── run.sh ├── server.py └── servlets │ ├── AdminFunctions.py │ ├── GalaxyAPI.py │ └── __init__.py └── setup.cfg /.gitignore: -------------------------------------------------------------------------------- 1 | server/venv 2 | server/.idea 3 | server/log/application.log 4 | server/conf/__init__.py 5 | server/conf/logging.cfg 6 | server/conf/server.cfg 7 | server/conf/server.cfg_back 8 | *.pyc 9 | .idea 10 | server/launch_server.pid 11 | -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- 1 | Galaksio has been developed as part of the B3Africa Project (http://www.b3africa.org/), which has received funding from the European Union’s Horizon 2020 research and innovation programme. The project’s 2 | consortium consists of 11 European and African partners. 3 | 4 | Galaksio is a web application which simplifies the usage of the Galaxy bioinformatics platform (https://usegalaxy.org/). 5 | 6 | - SVERIGES LANTBRUKSUNIVERSITET (SLU); Sweden 7 | - BIOBANKING AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC); Austria 8 | - KAROLINSKA INSTITUTET (KI); Sweden 9 | - INSTITUTE OF HUMAN VIROLOGY NIGERIA; Nigeria 10 | - INTERNATIONAL LIVESTOCK RESEARCH INSTITUTE (ILRI); Kenya 11 | - INTERNATIONAL AGENCY FOR RESEARCH ON CANCER (IARC); France 12 | - MAKERERE UNIVERSITY (MAK); Uganda 13 | - MEDIZINISCHE UNIVERSITÄT GRAZ; Austria 14 | - STELLENBOSCH UNIVERSITY (SUN); South Africa 15 | - UNIVERSITY OF THE WESTERN CAPE (UWT); South Africa 16 | - UPPSALA UNIVERSITY (UU); Sweden 17 | 18 | Contributors: 19 | 20 | - Dr. Erik Bongcam-Rudloff (SLU), Project coordinator. 21 | - Tomas Klingström (SLU), coordinator for WP-4 [Bioinformatics]. 22 | - Rafael Hernández (SLU), main developer for WP-4. 23 | - Oskar Danielsson (SLU), developer WP-4 24 | 25 | Other contributors: 26 | - Gerrit Botha (UCT); South Africa 27 | - Zipho Mashologu (SANBI); South Africa 28 | - Peter van Heusden (SANBI); South Africa 29 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |
2 | 3 |
4 | 5 | > An easy to use GUI for running Galaxy workflows. 6 | 7 | Galaksio is a web application that simplifies the usage of the Galaxy bioinformatics platform (https://usegalaxy.eu/). 8 | Galaksio provides a simple but complete UI for using Galaxy for biologists that require bioinformatics workflows to complete their research. 9 | Using the application, users can run any workflow implemented in the associated Galaxy instance in just few *clicks*. 10 | Besides, the rich user interface allows customizing the execution, uploading the necessary files, downloading the results, and executing several workflows simultaneously in the background. 11 | 12 | ![](./docs/1_1_galaxy/galaksio_screenshot.png) 13 | 14 | ### Quick start 15 | First install all dependencies. For example, the instructions for an Ubuntu 16.04 server would be: 16 | ```bash 17 | apt-get update 18 | apt-get install -y python-pip unzip wget 19 | pip install requests bioblend flask fpdf 20 | ``` 21 | 22 | Download and extract the [latest version](https://github.com/fikipollo/galaksio.git) of Galaksio from the GitHub repository. 23 | ```bash 24 | wget https://github.com/sgbc/galaksio/archive/master.zip 25 | unzip galaksio-latest.zip 26 | ``` 27 | 28 | Launch the Flask server. Your new Galaksio instance will be listening to port 8081. 29 | ```bash 30 | galaksio-latest/server/run.sh --start 31 | ``` 32 | 33 | By default Galaksio is configured to work with the official [Galaxy](https://usegalaxy.eu) instance.This and other options can be customized through the web application. The first time that you access to your Galaksio instance you will need to configure some of the main settings. 34 | 35 | ## Documentation 36 | Documentation for the project, including installation instructions, can be found at the ReadTheDocs platform: [http://galaksio.readthedocs.io/en/latest/](http://galaksio.readthedocs.io/en/latest/). 37 | 38 | ## Docker for Galaksio 39 | The Galaksio Docker Image is an easy distributable full-fledged Galaksio installation. 40 | The docker image for Galaksio can be found in the [docker hub](https://hub.docker.com/r/fikipollo/galaksio/). However, you can download the Dockerfile and other files from the [Github repository](https://github.com/fikipollo/galaksio-docker) 41 | 42 | ## About 43 | Galaksio has been developed by the [SLU Global Bioinformatics Centre](http://sgbc.slu.se/) at the Sveriges lantbruksuniversitet (Swedish University of Agricultural Sciences). 44 | This project is part of the B3Africa Project [http://www.b3africa.org/](http://www.b3africa.org/), which has received funding under grant agreement nr 654404 from the European Union’s Horizon 2020 research and innovation programme. 45 | **Galaksio** application is distributed under **GNU General Public License, Version 3.**. 46 | 47 | 48 | -------------------------------------------------------------------------------- /VERSION: -------------------------------------------------------------------------------- 1 | Galaksio v0.3.1 September 2017 2 | 3 | ## Version Log 4 | 5 | ** VERSION 0.3.1 September 2017 ** 6 | - Visual improvements. 7 | 8 | ** VERSION 0.3 September 2017 ** 9 | - Adding some error control logic and forcing the reload of the page after sign-out (will cancel automatically all the 10 | pending requests) to avoid error messages after signing out (Issue #2). 11 | - Now the panel showing the current invocation state shows also the state for each step in the workflow. Besides 12 | the results for the workflow execution are always shown even if the workflow failed. 13 | Additionally, the user can get more details for each step in the workflow and see the used parameters and other useful 14 | information (Issue #13 and #28). 15 | - Added a more developed method for form validation. Now erroneous fields are indicated at the top of the form and at 16 | the right of each invalid input with a red exclamation symbol. Besides, the application will autofocus the first 17 | invalid field (Issue #10 and #14). 18 | - Added support for "section" data types (Issue #11) 19 | - Upgraded the version of "AngularJS dialogs" library to support the Report button handler (Issue #12). 20 | - Added settings to configure a SMTP server in Galaksio and send the error report via email to the developers account. 21 | Alternatively, if not SMTP settings are provided, the report is forwarded to a main Galaksio server which will send 22 | the report by email (Issue #12). 23 | - Fixed some visual issues (Issue #17). 24 | - Display step name (if any) in data and data collection inputs (Issue #16). 25 | - Added +/- zoom button in workflow diagram, now mouse wheel is used only for scrolling (Issue #18). 26 | - Added affix support to history list, now the left panel scrolls down following the window (Issue #20). 27 | - Replaced yes/no checkboxes by 2 state button (Issue #22). 28 | - Replaced radio buttons by a drop-down menu (Issue #23). 29 | - Replaced multi-select fields by list of checkboxes (Issue #24). 30 | - Fixed to aggressive warning during input data (Issue #25) 31 | - Fixed issues with workflow execution state (erroneous "Finished" state after sending) (Issue #26 and #27) 32 | - Forced to recreate the forms when going back to step 2 during Workflow execution (Issue #31 and #29) 33 | - Added a "Read more" button in workflow description (workflow card) when description is too long (Issue #30). 34 | - Added tools for filtering the list of invocations. Besides, we have improved the performance when retrieving the 35 | list of invocations and their state (reduce the number of requests, avoid repeating requests,...). 36 | -------------------------------------------------------------------------------- /client/src/app/admin/history-list-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - history-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('histories.directives.history-list', []); 27 | 28 | /***************************************************************************/ 29 | /*DIRECTIVES ***************************************************************/ 30 | /***************************************************************************/ 31 | 32 | app.directive("historyListPanel", function() { 33 | return { 34 | restrict: 'E', 35 | templateUrl: 'app/histories/history-list.tpl.html' 36 | }; 37 | }); 38 | 39 | })(); 40 | -------------------------------------------------------------------------------- /client/src/app/admin/history-list-service.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - histories.services.history-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('histories.services.history-list', []); 27 | 28 | app.factory("HistoryList", ['$rootScope', function($rootScope) { 29 | var histories = []; 30 | 31 | return { 32 | getHistories: function() { 33 | return histories; 34 | }, 35 | setHistories: function(_histories) { 36 | histories = _histories; 37 | return this; 38 | }, 39 | getHistory: function(history_id) { 40 | for(var i in histories){ 41 | if(histories[i].id === history_id){ 42 | return histories[i]; 43 | } 44 | } 45 | return null; 46 | }, 47 | }; 48 | }]); 49 | })(); 50 | -------------------------------------------------------------------------------- /client/src/app/admin/setting-list-controller.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - AdminController 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('admin.controllers.setting-list', [ 27 | 'ui.bootstrap', 28 | 'ang-dialogs', 29 | 'ui.router' 30 | ]); 31 | 32 | /****************************************************************************** 33 | * _____ ____ _ _ _______ _____ ____ _ _ ______ _____ _____ 34 | * / ____/ __ \| \ | |__ __| __ \ / __ \| | | | | ____| __ \ / ____| 35 | * | | | | | | \| | | | | |__) | | | | | | | | |__ | |__) | (___ 36 | * | | | | | | . ` | | | | _ /| | | | | | | | __| | _ / \___ \ 37 | * | |___| |__| | |\ | | | | | \ \| |__| | |____| |____| |____| | \ \ ____) | 38 | * \_____\____/|_| \_| |_| |_| \_\\____/|______|______|______|_| \_\_____/ 39 | * 40 | ******************************************************************************/ 41 | app.controller('AdminController', function($state, $rootScope, $scope, $http, $uibModal, $dialogs, APP_EVENTS){ 42 | /****************************************************************************** 43 | * ___ ___ _ _ _____ ___ ___ _ _ ___ ___ 44 | * / __/ _ \| \| |_ _| _ \/ _ \| | | | | __| _ \ 45 | * | (_| (_) | .` | | | | / (_) | |__| |__| _|| / 46 | * \___\___/|_|\_| |_|_|_|_\\___/|____|____|___|_|_\ 47 | * | __| | | | \| |/ __|_ _|_ _/ _ \| \| / __| 48 | * | _|| |_| | .` | (__ | | | | (_) | .` \__ \ 49 | * |_| \___/|_|\_|\___| |_| |___\___/|_|\_|___/ 50 | * 51 | ******************************************************************************/ 52 | 53 | /** 54 | * This function retrieves the current settings for the application. 55 | * 56 | * @chainable 57 | * @return {Object} the controller. 58 | */ 59 | this.retrieveSettings = function(){ 60 | //GET THE EXTRA INFORMATION FOR THE HISTORY (datasets) 61 | $http($rootScope.getHttpRequestConfig("GET", "setting-list")).then( 62 | function successCallback(response){ 63 | $scope.settings = response.data.settings; 64 | var regInteger = /^\d+$/; 65 | 66 | for(var i in $scope.settings){ 67 | //TRY TO PARSE AS A NUMBER 68 | if(regInteger.test($scope.settings[i])){ 69 | $scope.settings[i] = Number.parseInt($scope.settings[i]); 70 | }else if($scope.settings[i].toLowerCase && ($scope.settings[i].toLowerCase() === "true" || $scope.settings[i].toLowerCase() === "false")){ 71 | $scope.settings[i] = $scope.settings[i].toLowerCase() === "true"; 72 | } 73 | } 74 | 75 | if($scope.settings["AUTO_INSTALL"]){ 76 | me.updateSettingsHandler(); 77 | } 78 | }, 79 | function errorCallback(response){ 80 | debugger; 81 | var message = "Failed when retrieving the list of settings."; 82 | $dialogs.showErrorDialog(message, { 83 | logMessage : message + " at AdminController:retrieveSettings." 84 | }); 85 | console.error(response.data); 86 | document.location.replace("/"); 87 | } 88 | ); 89 | return this; 90 | }; 91 | 92 | /****************************************************************************** 93 | * _____ _____ _ _ _____ 94 | * | __\ \ / / __| \| |_ _| 95 | * | _| \ V /| _|| .` | | | 96 | * _ _ |___| \_/_|___|_|\_| |_| ___ ___ 97 | * | || | /_\ | \| | \| | | __| _ \/ __| 98 | * | __ |/ _ \| .` | |) | |__| _|| /\__ \ 99 | * |_||_/_/ \_\_|\_|___/|____|___|_|_\|___/ 100 | * 101 | ******************************************************************************/ 102 | 103 | /** 104 | * This function updates the settings for the server 105 | * 106 | * @chainable 107 | * @return {Object} the controller. 108 | */ 109 | this.updateSettingsHandler = function(){ 110 | $scope.isLoading = true; 111 | if(!($scope.settings.ADMIN_ACCOUNTS instanceof Array)){ 112 | $scope.settings.ADMIN_ACCOUNTS = $scope.settings.ADMIN_ACCOUNTS.replace(/ /g, "").split(","); 113 | } 114 | 115 | $http($rootScope.getHttpRequestConfig("POST", "setting-update", {data: $scope.settings})).then( 116 | function successCallback(response){ 117 | $dialogs.showSuccessDialog("Settings successfully updated. You may need to restart the server to apply the changes.", { 118 | logMessage : "Settings updated at AdminController:retrieveHistoryData.", 119 | callback : function(){ 120 | $rootScope.$broadcast(APP_EVENTS.logoutRequired); 121 | } 122 | }); 123 | $scope.isLoading = false; 124 | }, 125 | function errorCallback(response){ 126 | $scope.isLoading = false; 127 | 128 | debugger; 129 | var message = "Failed when updating the settings."; 130 | $dialogs.showErrorDialog(message, { 131 | logMessage : message + " at AdminController:updateSettings." 132 | }); 133 | console.error(response.data); 134 | } 135 | ); 136 | return this; 137 | }; 138 | 139 | /****************************************************************************** 140 | * ___ _ _ ___ _____ ___ _ _ ___ ____ _ _____ ___ ___ _ _ 141 | * |_ _| \| |_ _|_ _|_ _| /_\ | | |_ _|_ / /_\_ _|_ _/ _ \| \| | 142 | * | || .` || | | | | | / _ \| |__ | | / / / _ \| | | | (_) | .` | 143 | * |___|_|\_|___| |_| |___/_/ \_\____|___/___/_/ \_\_| |___\___/|_|\_| 144 | * 145 | ******************************************************************************/ 146 | var me = this; 147 | setTimeout(function(){ 148 | me.retrieveSettings(); 149 | },4000); 150 | 151 | 152 | });//end controller 153 | })();//end wrapper 154 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-collection-list.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |
3 | 4 | 5 | Collection name 6 | Type 7 |
8 |
9 | 10 | 11 | Loading collections... 12 | 13 | 14 | 15 | No data 16 | 17 |
20 | {{$index + 1}} 21 | 22 | {{dataset.name}} 23 | {{getCollectionType(dataset)}} 24 |
25 | 26 | 27 | Loading collections... 28 | 29 | 30 |
31 | 32 | {{element.element_identifier}}: 33 | {{element.element_index + 1}}. 34 | {{element.object.name}} 35 | 36 | 37 | Pair {{element.element_identifier}}: 38 |
39 | {{subelement.element_identifier}}: {{subelement.object.name}} 40 |
41 | 42 |
43 |
44 |
45 |
46 | 47 |

Found {{filtered.length}} collections

48 |
49 | 50 | Show {{displayedHistory.content.length - maxDatasets}} more datasets. 51 | 52 |
53 |
54 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-irods-pull.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |

Not implemented yet...

3 |
4 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-list-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - datasets.services.dataset-upload 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('datasets.dataset-list', []); 27 | 28 | app.directive("datasetListPanel", function() { 29 | return { 30 | restrict: 'E', 31 | templateUrl: 'app/datasets/dataset-list.tpl.html' 32 | }; 33 | }); 34 | 35 | app.directive("datasetCollectionListPanel", function() { 36 | return { 37 | restrict: 'E', 38 | templateUrl: 'app/datasets/dataset-collection-list.tpl.html' 39 | }; 40 | }); 41 | 42 | app.directive("datasetCollectionCreatePanel", function() { 43 | return { 44 | restrict: 'E', 45 | templateUrl: 'app/datasets/dataset-collection-create-panel.tpl.html' 46 | }; 47 | }); 48 | 49 | app.directive("datasetListInput", function() { 50 | return { 51 | restrict: 'E', 52 | replace: true, 53 | controller: 'DatasetListController', 54 | template: 55 | '' 61 | }; 62 | }); 63 | 64 | app.directive("datasetCollectionListInput", function() { 65 | return { 66 | restrict: 'E', 67 | replace: true, 68 | controller: 'DatasetListController', 69 | template: 70 | '' 76 | }; 77 | }); 78 | 79 | app.directive("datasetUploadPanel", function() { 80 | return { 81 | restrict: 'E', 82 | templateUrl: 'app/datasets/dataset-upload.tpl.html' 83 | }; 84 | }); 85 | 86 | app.directive('fileModel', ['$parse', function ($parse) { 87 | return { 88 | restrict: 'A', 89 | link: function($scope, element, attrs) { 90 | element.bind('change', function(){ 91 | $scope.$apply(function(){ 92 | if(element[0].files instanceof FileList){ 93 | for(var i=0; i < element[0].files.length; i++){ 94 | element[0].files[i].state="pending" 95 | $scope.files.push(element[0].files[i]); 96 | } 97 | }else{ 98 | element[0].files[0].state="pending" 99 | $scope.files.push(element[0].files[0]); 100 | } 101 | }); 102 | }); 103 | } 104 | }; 105 | }]); 106 | 107 | app.directive("datasetIrodsPullPanel", function() { 108 | return { 109 | restrict: 'E', 110 | templateUrl: 'app/datasets/dataset-irods-pull.tpl.html' 111 | }; 112 | }); 113 | })(); 114 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-list.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 16 | 17 | 18 | 19 | 20 | 23 | 24 | 25 | 26 | 37 | 38 | 39 |
File nameExtensionOptions
14 | Loading datasets... 15 |
No data
{{$index + 1}}{{dataset.name}}{{dataset.extension}} 27 | 28 | Download 29 | 30 | 31 | Delete 32 | 33 | 34 | Undelete 35 | 36 |
40 |
41 | 44 |
45 |
46 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-selector-dialog.tpl.html: -------------------------------------------------------------------------------- 1 | 2 |
3 |

Choose the input file

4 |
5 |
6 | 7 | 8 |
9 |
10 | 13 |

Current history name: {{displayedHistory.name}}

14 |
15 | 16 |
17 |
18 |
19 | 20 | 21 |
22 |
23 | 26 |

Current history name: {{displayedHistory.name}}

27 |
28 | 29 |
30 |
31 |
32 | 33 | 34 | 37 | 38 | 39 | 40 | 43 | 44 | 45 | 51 | 52 |
53 |
54 | 55 | 56 |
57 | 58 | -------------------------------------------------------------------------------- /client/src/app/datasets/dataset-upload.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |
3 | Please note that max allowed size for files is {{MAX_CONTENT_LENGTH}} MB. 4 |
5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 29 | 34 | 35 | 36 |
File nameSizeTypeStatus
No files selected, use the options below to load data
{{file.name}}{{adaptFileSize(file.size)}}{{file.type}} 24 | {{file.state}} 25 | {{file.state}} 26 | {{file.state}} 27 | {{file.state}} 28 | 30 | 31 | 32 | 33 |
37 | 38 | Upload files 39 | Choose local file 40 |
41 | -------------------------------------------------------------------------------- /client/src/app/histories/history-list-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - history-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('histories.directives.history-list', []); 27 | 28 | /***************************************************************************/ 29 | /*DIRECTIVES ***************************************************************/ 30 | /***************************************************************************/ 31 | 32 | app.directive("historyListPanel", function() { 33 | return { 34 | restrict: 'E', 35 | templateUrl: 'app/histories/history-list.tpl.html' 36 | }; 37 | }); 38 | 39 | })(); 40 | -------------------------------------------------------------------------------- /client/src/app/histories/history-list-service.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - histories.services.history-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('histories.services.history-list', []); 27 | 28 | app.factory("HistoryList", ['$rootScope', function($rootScope) { 29 | var histories = []; 30 | 31 | return { 32 | getHistories: function() { 33 | return histories; 34 | }, 35 | setHistories: function(_histories) { 36 | histories = _histories; 37 | return this; 38 | }, 39 | getHistory: function(history_id) { 40 | for(var i in histories){ 41 | if(histories[i].id === history_id){ 42 | return histories[i]; 43 | } 44 | } 45 | return null; 46 | }, 47 | }; 48 | }]); 49 | })(); 50 | -------------------------------------------------------------------------------- /client/src/app/histories/history-list.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |
3 | 4 |
5 |
6 |

About histories

7 |

8 | When data is uploaded from your computer or analysis is done on existing data using Galaxy, each output from those steps generates a dataset. These datasets (and the output datasets from later analysis on them) are stored by Galaxy in Histories. 9 |

10 | Learn more about histories 11 |
12 |
13 |
14 | 15 | Refresh 16 | 17 | 18 | New history 19 | 20 | 21 | Switch to this history 22 | 23 | 24 |

Click on one history name to get more details.

25 | 26 | 27 |
28 | 29 | 30 |
31 | 32 |
33 |
34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 48 | 49 | 50 | 51 | 55 | 59 | 62 | 63 | 64 |
History nameCreation dateLast updatedCurrent
46 | Loading histories... 47 |
{{history.name}} 52 | 53 | {{history.create_time | date:'dd/MM/yyyy HH:mm'}} 54 | 56 | 57 | {{history.update_time | date:'dd/MM/yyyy HH:mm'}} 58 | 60 | 61 |
65 |
66 |
67 |
68 |
69 |
70 |
71 | 72 | Upload new files 73 | 74 | 75 | Manage collections 76 | 77 |

History name: {{displayedHistory.name}}

78 | 79 | 80 |

Show hidden and deleted datasets

81 | 82 | 83 | 84 |

Show hidden and deleted collections

85 | 86 | 87 |
88 |
89 | 90 | 95 |
96 | -------------------------------------------------------------------------------- /client/src/app/histories/history-page.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 5 | 6 |
7 | -------------------------------------------------------------------------------- /client/src/app/home/home.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 5 |
6 |
7 |
8 |

Welcome to Galaksio!

9 |

A simple but effective way to use Galaxy.

10 |
11 |
12 |
13 | 14 |
15 |
16 |
17 |

Resources

18 | 32 |
33 |
34 |
35 | 36 |
37 |
38 |
39 | 40 | Go to history 41 | 42 |

Current history

43 |

History name: {{displayedHistory.name}}

44 | 45 |
46 |
47 |
48 |
49 | -------------------------------------------------------------------------------- /client/src/app/users/user-session-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - workflow-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('users.directives.user-session', [ 27 | 'ui.bootstrap', 28 | 'users.controllers.user-session' 29 | ]); 30 | 31 | app.service('loginModal', function ($uibModal, $rootScope) { 32 | function assignCurrentUser (user) { 33 | $rootScope.currentUser = userF; 34 | return user; 35 | } 36 | 37 | return function() { 38 | var instance = $uibModal.open({ 39 | templateUrl: 'app/users/user-sign-in.tpl.html' 40 | }) 41 | 42 | return instance.result.then(assignCurrentUser); 43 | }; 44 | }); 45 | 46 | app.directive("sessionToolbar", function() { 47 | return { 48 | restrict: 'E', 49 | replace:true, 50 | template: 51 | '
' + 52 | '
' + 53 | ' ' + 57 | ' ' + 63 | '
' + 64 | '
' 65 | }; 66 | }); 67 | 68 | app.directive('ngPwcheck', [function () { 69 | return { 70 | require: 'ngModel', 71 | link: function (scope, elem, attrs, ctrl) { 72 | var firstPassword = '#' + attrs.ngPwcheck; 73 | elem.on('keyup', function () { 74 | scope.$apply(function () { 75 | var v = elem.val()===$(firstPassword).val(); 76 | ctrl.$setValidity('pwmatch', v); 77 | }); 78 | }); 79 | $(firstPassword).on('keyup', function () { 80 | scope.$apply(function () { 81 | var v = elem.val()===$(firstPassword).val(); 82 | ctrl.$setValidity('pwmatch', v); 83 | }); 84 | }); 85 | } 86 | } 87 | }]); 88 | 89 | app.directive("userSessionInfoPanel", function() { 90 | return { 91 | restrict: 'E', 92 | replace:true, 93 | template: 94 | '
' + 95 | '

Your account

' + 96 | '

Galaxy server:{{GALAXY_SERVER_URL}}

' + 97 | ' ' + 98 | ' Close session' + 99 | ' ' + 100 | '

Signed in as {{userInfo.email}}

' + 101 | '

Disk usage: {{userInfo.disk_usage || "Loading..."}}

' + 102 | '
' 103 | }; 104 | }); 105 | 106 | })(); 107 | -------------------------------------------------------------------------------- /client/src/app/users/user-sign-in.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 61 |
62 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-card-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - workflows.directives.workflow-card 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('workflows.directives.workflow-card', [ 27 | ]); 28 | 29 | /***************************************************************************/ 30 | /*DIRECTIVES ***************************************************************/ 31 | /***************************************************************************/ 32 | app.directive("workflowCard", function($timeout) { 33 | return { 34 | restrict: 'E', 35 | templateUrl: "app/workflows/workflow-card.tpl.html", 36 | link: function (scope, element, attrs) { 37 | //Execute the afterRender function (linked to a controller function) 38 | $timeout(scope.$eval(attrs.afterRender), 0); 39 | } 40 | }; 41 | }); 42 | 43 | app.directive('maxContentHeight',function(){ 44 | return { 45 | restrict: 'A', 46 | link: function($scope,$el,$attr) { 47 | $scope.$watch( 48 | function() { 49 | return $($el).height(); 50 | }, 51 | function(height) { 52 | $scope.showMore = height > ~~$attr['maxContentHeight']; 53 | } 54 | )} 55 | }; 56 | }); 57 | })(); 58 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-card.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |
3 | 4 | 5 | 6 |

{{workflow.name}}

7 |
8 | Loading details... 9 |
10 |
11 | 12 | 13 | 14 | [...] 15 | Read more 16 | Read more 17 | 18 | {{workflow.annotation}} 19 | 20 |

No description provided

21 |
22 |
23 | {{tag}} 24 |
25 |
26 |
27 | Created by {{workflow.owner}} 28 |
29 |
30 | Imported workflow 31 |
32 | 33 | Run workflow 34 | 35 | 36 | Import to my collection 37 | 38 | 39 | More details 40 | 41 |
42 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-detail.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 5 |
6 |

Workflow name: {{workflow.name}}

7 | 8 | 9 | 10 |
11 |

Details

12 |

Author: {{workflow.owner}}

13 |

Description: {{((workflow.annotation !== "" && workflow.annotation !== null)?workflow.annotation:"No description provided")}}

14 |
15 | 16 | 17 | 18 |
19 | Update diagram layout 20 |

Workflow overview

21 | 22 | Loading workflow details... 23 | 24 |
25 |
26 |
27 | 28 | 29 | 30 | 40 |
41 |
42 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-invocation-panel.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |

Workflow invocations 3 | 4 | Refresh 5 | Loading... 6 |

7 |
8 |
9 | 10 |
11 | 14 |
15 |
16 |
17 |
Show: 18 | 19 | 20 | 21 |
22 | 23 | 24 | 25 | 28 | 29 | 30 | 36 | 37 | 38 | 39 | 40 | 47 | 54 | 61 | 68 | 75 | 82 | 90 | 91 |
Workflow nameDateStateTools
26 | Loading invocations... 27 |
31 |
Whoops! Looks like there are no workflows in the queue.
32 | 35 |
{{invocation.workflow_title}}{{adaptInvocationDate(invocation.update_time)}} 41 | 42 | 43 | 44 | 45 | Done 46 | 48 | 49 | 50 | 51 | 52 | Sending 53 | 55 | 56 | 57 | 58 | 59 | Running 60 | 62 | 63 | 64 | 65 | 66 | Waiting 67 | 69 | 70 | 71 | 72 | 73 | Failed 74 | 76 | 77 | 78 | 79 | 80 | Unknown 81 | 83 | 84 | Recover 85 | 86 | 87 | Hide 88 | 89 |
92 |
93 | 96 | 99 |
100 |
101 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-invocation-toolbar.tpl.html: -------------------------------------------------------------------------------- 1 |
2 |
3 | 4 | 5 | 6 | 7 | 8 | {{running}} 9 | Running 10 | 11 | 12 | 13 | 14 | 15 | 16 | {{done}} 17 | Done 18 | 19 | 20 | 21 | 22 | 23 | 24 | {{waiting}} 25 | Waiting 26 | 27 | 28 | 29 | 30 | 31 | 32 | {{erroneous}} 33 | Failed 34 | 35 | 36 | 37 | 38 | 39 | 40 | Loading... 41 | 42 |
43 |
44 | 45 | 46 | 47 | 48 | 49 | 50 | 57 | 64 | 71 | 78 | 85 | 92 | 97 | 98 | 99 | 101 | 102 |
Workflow nameDateStateTools
No data
{{invocation.workflow_title}}{{adaptInvocationDate(invocation.update_time)}} 51 | 52 | 53 | 54 | 55 | Done 56 | 58 | 59 | 60 | 61 | 62 | Sending 63 | 65 | 66 | 67 | 68 | 69 | Running 70 | 72 | 73 | 74 | 75 | 76 | Waiting 77 | 79 | 80 | 81 | 82 | 83 | Failed 84 | 86 | 87 | 88 | 89 | 90 | Unknown 91 | 93 | 94 | Recover 95 | 96 |
100 | Show more invocations
103 |
104 |
105 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-list-dir.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - workflow-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('workflows.workflow-list', []); 27 | 28 | /***************************************************************************/ 29 | /*DIRECTIVES ***************************************************************/ 30 | /***************************************************************************/ 31 | 32 | })(); 33 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-list-service.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - workflows.services.workflow-list 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('workflows.services.workflow-list', []); 27 | 28 | app.factory("WorkflowList", ['$rootScope', function($rootScope) { 29 | var workflows = {}; 30 | var tags = []; 31 | var selectedTags = []; 32 | var filters = []; 33 | var tagColors = ['yellow', 'green', 'red', 'blue', 'purple', 'pink', 'yellow2', 'green2', 'red2', 'blue2', 'purple2', 'pink2'] 34 | var old = new Date(0); 35 | //http://stackoverflow.com/questions/18247130/how-to-store-the-data-to-local-storage 36 | return { 37 | getWorkflows: function() { 38 | return Object.values(workflows); 39 | }, 40 | setWorkflows: function(_workflows) { 41 | workflows = {}; 42 | var workflow; 43 | for(var i in _workflows){ 44 | workflow = _workflows[i]; 45 | if(workflow.name.search(/^imported: /) !== -1){ 46 | workflow.name = workflow.name.replace(/imported: /g, ""); 47 | workflow.imported = true; 48 | } 49 | 50 | workflows[workflow.id] = workflow; 51 | } 52 | 53 | old = new Date(); 54 | return this; 55 | }, 56 | updateWorkflows: function(_workflows) { 57 | var workflow; 58 | for(var i in _workflows){ 59 | workflow = _workflows[i]; 60 | if(workflow.name.search(/^imported: /) !== -1){ 61 | workflow.name = workflow.name.replace(/imported: /g, ""); 62 | workflow.imported = true; 63 | } 64 | workflows[workflow.id] = workflow; 65 | } 66 | 67 | return this; 68 | }, 69 | getWorkflow: function(workflow_id) { 70 | return workflows[workflow_id]; 71 | }, 72 | addWorkflow: function(workflow) { 73 | workflows[workflow.id] = workflow; 74 | return this; 75 | }, 76 | deleteWorkflow: function(workflow) { 77 | delete workflows[workflow.id]; 78 | return this; 79 | }, 80 | getTags: function() { 81 | return tags; 82 | }, 83 | getTag: function(_tag) { 84 | for(var i in tags){ 85 | if(tags[i].name === _tag){ 86 | return tags[i]; 87 | } 88 | } 89 | return null; 90 | }, 91 | setTags: function(_tags) { 92 | tags = _tags; 93 | return this; 94 | }, 95 | updateTags: function() { 96 | var tagsAux = {}, _tags; 97 | var _workflows = this.getWorkflows(); 98 | for(var i in _workflows){ 99 | _tags = _workflows[i].tags; 100 | for(var j in _tags){ 101 | tagsAux[_tags[j]] = { 102 | name: _tags[j], 103 | times: ((tagsAux[_tags[j]] === undefined)?1:tagsAux[_tags[j]].times + 1) 104 | } 105 | } 106 | } 107 | tags = Object.keys(tagsAux).map(function(k) { return tagsAux[k] }); 108 | 109 | for(var i in tags){ 110 | tags[i].color = tagColors[i%tagColors.length] 111 | } 112 | 113 | tags.push({name: "All", times: _workflows.length}) 114 | 115 | return this; 116 | }, 117 | selectTag: function(tag){ 118 | selectedTags.push(tag); 119 | return this; 120 | }, 121 | deselectTag: function(tag){ 122 | var pos = selectedTags.indexOf(tag); 123 | if(pos !== -1){ 124 | selectedTags.splice(pos,1); 125 | } 126 | return this; 127 | }, 128 | getSelectedTags: function(){ 129 | return selectedTags; 130 | }, 131 | removeAllSelectedTags(){ 132 | selectedTags = []; 133 | return this; 134 | }, 135 | getFilters: function() { 136 | return filters; 137 | }, 138 | setFilters: function(_filters) { 139 | filters = _filters; 140 | return this; 141 | }, 142 | removeFilter: function(_filter){ 143 | var pos = filters.indexOf(_filter); 144 | if(pos !== -1){ 145 | filters.splice(pos,1); 146 | } 147 | return this; 148 | }, 149 | removeAllFilters: function(){ 150 | filters = []; 151 | return this; 152 | }, 153 | getOld: function(){ 154 | return (new Date() - old)/120000; 155 | } 156 | }; 157 | }]); 158 | })(); 159 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-list.tpl.html: -------------------------------------------------------------------------------- 1 |
2 | 5 | 46 |
47 |
48 |
    49 |
  • 50 | 51 | 55 |
    • 56 |
57 |
    58 |
  • 59 | 60 | 64 |
    • 65 |
66 | 67 | Loading workflows... 68 | 69 | 70 | Showing results for {{ displaySearchWords }} 71 | 72 | 73 | Found {{filteredWorkflows}} workflows 74 | Refresh list 75 | 76 |
77 |
78 |
79 |
80 |

About workflows

81 |

82 | Workflows are analyses that are intended to be executed (one ore more times) with different user-provided input datasets. Workflow can be reused over and over, not only reducing tedious work, but enhancing reproducibility by applying the same exact methods to all of your data.
83 | From the perspective of Galaksio, workflows must be designed by skilled users (e.g. a bioinformatician) using the Galaxy tools for workflow edition. 84 |

85 | Learn more about workflows 86 |
87 |

88 | Loading workflows list... 89 |

90 | 91 |
92 | 95 |
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97 | 103 |
104 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-run-service.js: -------------------------------------------------------------------------------- 1 | /* 2 | * (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | * (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | * 5 | * All rights reserved. This program and the accompanying materials 6 | * are made available under the terms of the GNU Lesser General Public License 7 | * (LGPL) version 3 which accompanies this distribution, and is available at 8 | * http://www.gnu.org/licenses/lgpl.html 9 | * 10 | * This library is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | * Lesser General Public License for more details. 14 | * 15 | * Contributors: 16 | * Rafael Hernandez de Diego 17 | * Tomas Klingström 18 | * Erik Bongcam-Rudloff 19 | * and others. 20 | * 21 | * THIS FILE CONTAINS THE FOLLOWING MODULE DECLARATION 22 | * - workflows.services.workflow-run 23 | * 24 | */ 25 | (function(){ 26 | var app = angular.module('workflows.services.workflow-run', []); 27 | 28 | app.factory("WorkflowInvocationList", function() { 29 | var invocations = {}; 30 | var _hasErrors = false; 31 | 32 | return { 33 | getInvocations: function() { 34 | return Object.values(invocations); 35 | }, 36 | setInvocations: function(_invocations) { 37 | invocations = _invocations; 38 | return this; 39 | }, 40 | saveInvocations: function() { 41 | sessionStorage.workflow_invocations = JSON.stringify(invocations); 42 | return this; 43 | }, 44 | loadInvocations: function() { 45 | try { 46 | invocations = JSON.parse(sessionStorage.workflow_invocations); 47 | } catch (e) { 48 | console.error("Unable to load the stored invocations."); 49 | invocations = {}; 50 | } 51 | return this; 52 | }, 53 | clearInvocations: function() { 54 | invocations = {}; 55 | return this; 56 | }, 57 | addInvocation: function(_invocation) { 58 | delete _invocation.checking; 59 | invocations[_invocation.id] = _invocation; 60 | return this; 61 | }, 62 | removeInvocation: function(_invocation) { 63 | delete invocations[_invocation.id]; 64 | return this; 65 | }, 66 | updateInvocation: function(_invocation) { 67 | delete invocations[_invocation.id].checking; 68 | delete _invocation.checking; 69 | for(var attr in _invocation){ 70 | invocations[_invocation.id][attr] = _invocation[attr]; 71 | } 72 | return this; 73 | }, 74 | getInvocation: function(invocation_id) { 75 | return invocations[invocation_id]; 76 | }, 77 | getNewInvocation: function() { 78 | return { 79 | id: '', 80 | workflow_id: '', 81 | workflow_title: '', 82 | current_step : 1 83 | }; 84 | }, 85 | setHasErrors: function(errors) { 86 | _hasErrors = (errors === true); 87 | }, 88 | hasErrors: function() { 89 | return _hasErrors === true; 90 | } 91 | }; 92 | }); 93 | })(); 94 | -------------------------------------------------------------------------------- /client/src/app/workflows/workflow-run-step.tpl.html: -------------------------------------------------------------------------------- 1 | 2 | 3 |
4 |
5 | Step {{step.id}} : {{step.name}} 6 | 7 | 8 | 9 | 10 |
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12 | Loading... 13 |
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18 | -------------------------------------------------------------------------------- /client/src/common/resources/API-REQUEST-EXAMPLES.js: -------------------------------------------------------------------------------- 1 | ////EXECUTE A JOB 2 | //data = JSON.stringify({ 3 | // "workflow_id": "b472e2eb553fa0d1", 4 | // "history": "history_id=7b668ee810f6cf46", 5 | // "ds_map": { 6 | // "0": {"src": "hda", "id": "72ad249754f05d26"} 7 | // }, 8 | // "parameters": { 9 | // "1" : { 10 | // "exp" : "asdsa", 11 | // "iterate" : true 12 | // } 13 | // } 14 | //}) 15 | // 16 | //$.ajax({ 17 | // type: "POST", contentType: 'application/json; charset=utf-8', 18 | // url : "http://192.168.0.99/galaxy/api/workflows/b472e2eb553fa0d1/invocations", 19 | // data:data 20 | //}); 21 | // 22 | ////GET HISTORY CONTENT 23 | //http://192.168.0.99/galaxy/api/histories/7b668ee810f6cf46/contents 24 | // 25 | ////GET WORKFLOW COTENTS 26 | //http://192.168.0.99/galaxy/api/workflows/b472e2eb553fa0d1/download 27 | //http://192.168.0.99/galaxy/api/workflows/b472e2eb553fa0d1/invocations 28 | -------------------------------------------------------------------------------- /client/src/common/resources/common.js: -------------------------------------------------------------------------------- 1 | function arrayUnique(array) { 2 | var a = array.concat(); 3 | for(var i=0; i "; 15 | }; 16 | Object.values = function (o) { 17 | return Object.keys(o).map(function (k) { 18 | return o[k]; 19 | }); 20 | }; 21 | 22 | function getPathname(){ 23 | var pathname = window.location.pathname.split("/"); 24 | if(pathname.length > 1 && pathname[1] !== "" && pathname[1].indexOf(".html") === -1){ 25 | pathname = pathname[1] + "/"; 26 | }else{ 27 | pathname = ""; 28 | } 29 | return pathname; 30 | } 31 | 32 | function randomIDgenerator(len){ 33 | var charSet ='ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789'; 34 | var randomString = ''; 35 | for (var i = 0; i < len; i++) { 36 | var randomPoz = Math.floor(Math.random() * charSet.length); 37 | randomString += charSet.substring(randomPoz,randomPoz+1); 38 | } 39 | return randomString; 40 | } 41 | -------------------------------------------------------------------------------- /client/src/common/resources/error-message.tpl.html: -------------------------------------------------------------------------------- 1 |
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12 | -------------------------------------------------------------------------------- /client/src/common/services/toArrayFilter.js: -------------------------------------------------------------------------------- 1 | (function(){ 2 | angular.module('angular-toArrayFilter', []) 3 | .filter('toArray', function () { 4 | return function (obj, addKey) { 5 | if (!angular.isObject(obj)) return obj; 6 | if ( addKey === false ) { 7 | return Object.keys(obj).map(function(key) { 8 | return obj[key]; 9 | }); 10 | } else { 11 | return Object.keys(obj).map(function (key) { 12 | var value = obj[key]; 13 | return angular.isObject(value) ? 14 | Object.defineProperty(value, '$key', { enumerable: false, value: key}) : 15 | { $key: key, $value: value }; 16 | }); 17 | } 18 | }; 19 | }); 20 | })(); 21 | -------------------------------------------------------------------------------- /client/src/css/angular-dialogs.min.css: -------------------------------------------------------------------------------- 1 | /*! Angular dialogs v0.93 | Rafael Hernandez | MIT license */ 2 | .modal-error .modal-header{background:#d2322d;color:#fff}.modal-error .modal-body{color:#a9211e}.modal-info .modal-header{background:#428bca;color:#fff}.modal-success .modal-header{background:#5cb85c;color:#fff}.modal-warn .modal-header{background:#f0ad4e;color:#fff}.modal-confirmation .modal-header{background:#286090;color:#fff}.glyphicon-spin{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0)}100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0)}100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0)}100%{-o-transform:rotate(359deg)}}@keyframes spin{0%{-webkit-transform:rotate(0);transform:rotate(0)}100%{-webkit-transform:rotate(359deg);transform:rotate(359deg)}} 3 | -------------------------------------------------------------------------------- /client/src/css/bootstrap-dialogs.min.css: -------------------------------------------------------------------------------- 1 | .dialog-header-error{background-color:#d2322d}.dialog-header-wait{background-color:#428bca}.dialog-header-notify{background-color:#eee}.dialog-header-confirm{background-color:#333}.dialog-header-confirm h4,.dialog-header-confirm span,.dialog-header-error h4,.dialog-header-error span,.dialog-header-wait h4,.dialog-header-wait span{color:#fff} -------------------------------------------------------------------------------- /client/src/css/bootstrap-sortable.css: -------------------------------------------------------------------------------- 1 | table.sortable span.sign { 2 | display: block; 3 | position: absolute; 4 | top: 50%; 5 | right: 5px; 6 | font-size: 12px; 7 | margin-top: -10px; 8 | color: #bfbfc1; 9 | } 10 | 11 | table.sortable th:after { 12 | display: block; 13 | position: absolute; 14 | top: 50%; 15 | right: 5px; 16 | font-size: 12px; 17 | margin-top: -10px; 18 | color: #bfbfc1; 19 | } 20 | 21 | table.sortable th.arrow:after { 22 | content: ''; 23 | } 24 | 25 | table.sortable span.arrow, span.reversed, th.arrow.down:after, th.reversedarrow.down:after, th.arrow.up:after, th.reversedarrow.up:after { 26 | border-style: solid; 27 | border-width: 5px; 28 | font-size: 0; 29 | border-color: #ccc transparent transparent transparent; 30 | line-height: 0; 31 | height: 0; 32 | width: 0; 33 | margin-top: -2px; 34 | } 35 | 36 | table.sortable span.arrow.up, th.arrow.up:after { 37 | border-color: transparent transparent #ccc transparent; 38 | margin-top: -7px; 39 | } 40 | 41 | table.sortable span.reversed, th.reversedarrow.down:after { 42 | border-color: transparent transparent #ccc transparent; 43 | margin-top: -7px; 44 | } 45 | 46 | table.sortable span.reversed.up, th.reversedarrow.up:after { 47 | border-color: #ccc transparent transparent transparent; 48 | margin-top: -2px; 49 | } 50 | 51 | table.sortable span.az:before, th.az.down:after { 52 | content: "a .. z"; 53 | } 54 | 55 | table.sortable span.az.up:before, th.az.up:after { 56 | content: "z .. a"; 57 | } 58 | 59 | table.sortable th.az.nosort:after, th.AZ.nosort:after, th._19.nosort:after, th.month.nosort:after { 60 | content: ".."; 61 | } 62 | 63 | table.sortable span.AZ:before, th.AZ.down:after { 64 | content: "A .. Z"; 65 | } 66 | 67 | table.sortable span.AZ.up:before, th.AZ.up:after { 68 | content: "Z .. A"; 69 | } 70 | 71 | table.sortable span._19:before, th._19.down:after { 72 | content: "1 .. 9"; 73 | } 74 | 75 | table.sortable span._19.up:before, th._19.up:after { 76 | content: "9 .. 1"; 77 | } 78 | 79 | table.sortable span.month:before, th.month.down:after { 80 | content: "jan .. dec"; 81 | } 82 | 83 | table.sortable span.month.up:before, th.month.up:after { 84 | content: "dec .. jan"; 85 | } 86 | 87 | table.sortable thead th:not([data-defaultsort=disabled]) { 88 | cursor: pointer; 89 | position: relative; 90 | top: 0; 91 | left: 0; 92 | } 93 | 94 | table.sortable thead th:hover:not([data-defaultsort=disabled]) { 95 | background: #efefef; 96 | } 97 | 98 | table.sortable thead th div.mozilla { 99 | position: relative; 100 | } 101 | -------------------------------------------------------------------------------- /client/src/css/galaksio_logo.xcf: -------------------------------------------------------------------------------- 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54 |
55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | -------------------------------------------------------------------------------- /client/src/lib/angular-backtop.min.js: -------------------------------------------------------------------------------- 1 | var backtop = angular.module('angular.backtop', []); 2 | 3 | backtop.directive('backTop', [function() { 4 | return { 5 | restrict: 'E', 6 | transclude: true, 7 | replace: true, 8 | template: ' {{text}}', 9 | scope: { 10 | text: "@buttonText", 11 | speed: "@scrollSpeed", 12 | theme: "@buttonTheme" 13 | }, 14 | link: function(scope, element) { 15 | 16 | scope.text = scope.text || 'Go top!'; 17 | scope.speed = parseInt(scope.speed, 10) || 300; 18 | scope.theme = (scope.theme || ''); 19 | 20 | var self = this; 21 | 22 | scope.currentYPosition = function() { 23 | if (self.pageYOffset) 24 | return self.pageYOffset; 25 | if (document.documentElement && document.documentElement.scrollTop) 26 | return document.documentElement.scrollTop; 27 | if (document.body.scrollTop) 28 | return document.body.scrollTop; 29 | return 0; 30 | }; 31 | 32 | scope.smoothScroll = function() { 33 | var startY = scope.currentYPosition(); 34 | var stopY = 0; 35 | var distance = stopY > startY ? stopY - startY : startY - stopY; 36 | if (distance < 100) { 37 | scrollTo(0, stopY); 38 | return; 39 | } 40 | var speed = Math.round(scope.speed / 100); 41 | var step = Math.round(distance / 25); 42 | var leapY = stopY > startY ? startY + step : startY - step; 43 | var timer = 0; 44 | if (stopY > startY) { 45 | for (var i = startY; i < stopY; i += step) { 46 | setTimeout("window.scrollTo(0, " + leapY + ")", timer * speed); 47 | leapY += step; 48 | if (leapY > stopY) leapY = stopY; 49 | timer++; 50 | } 51 | return; 52 | } 53 | for (var j = startY; j > stopY; j -= step) { 54 | setTimeout("window.scrollTo(0, " + leapY + ")", timer * speed); 55 | leapY -= step; 56 | if (leapY < stopY) leapY = stopY; 57 | timer++; 58 | } 59 | }; 60 | 61 | scope.a = element; 62 | element.addClass('hidden'); 63 | 64 | scope.a.on('click', function() { 65 | scope.smoothScroll(); 66 | element.addClass('hidden'); 67 | }); 68 | 69 | window.addEventListener('scroll', function() { 70 | if (window.pageYOffset > 0) { 71 | element.removeClass('hidden'); 72 | } else { 73 | element.addClass('hidden'); 74 | } 75 | }); 76 | } 77 | }; 78 | 79 | }]); 80 | -------------------------------------------------------------------------------- /client/src/lib/angular-dialogs.min.js: -------------------------------------------------------------------------------- 1 | /*! Angular dialogs v0.93 | Rafael Hernandez | MIT license */ 2 | (function(){var app=angular.module("ang-dialogs",["ui.bootstrap"]);app.service("$dialogs",["$uibModal","$templateCache","$log","$timeout","$interval",function($uibModal,$templateCache,$log,$timeout,$interval){var me=this;this.modals={};this.modalStack=[];this.getModalInstance=function(modalID){return this.modals[modalID]};this.showDefaultDialog=function(message,config){config=config||{};config.messageType="default";config.icon=config.icon||"glyphicon glyphicon-info-sign";return this.showMessage(message,config)};this.showInfoDialog=function(message,config){config=config||{};config.messageType="info";config.icon=config.icon||"glyphicon glyphicon-info-sign";return this.showMessage(message,config)};this.showConfirmationDialog=function(message,config){config=config||{};config.messageType="confirmation";config.icon=config.icon||"glyphicon glyphicon-question-sign";return this.showMessage(message,config)};this.showSuccessDialog=function(message,config){config=config||{};config.messageType="success";config.icon=config.icon||" glyphicon glyphicon-ok-circle";return this.showMessage(message,config)};this.showWarningDialog=function(message,config){config=config||{};config.messageType="warn";config.icon=config.icon||" glyphicon glyphicon-exclamation-sign";return this.showMessage(message,config)};this.showErrorDialog=function(message,config){config=config||{};config.messageType="error";config.icon=config.icon||"glyphicon glyphicon-remove-circle";return this.showMessage(message,config)};this.showWaitDialog=function(message,config){config=config||{};config.messageType="wait";config.icon=config.icon||"glyphicon glyphicon-time";config.button=config.button||false;config.spin=true;return this.showMessage(message,config)};this.showMessage=function(message,config){config={messageType:config.messageType||"info",title:config.title||"",message:message||"",callback:config.callback,logMessage:config.logMessage||(message||""),button:config.button!==false,reportButton:config.reportButton===true,reportButtonHandler:config.reportButtonHandler,buttonReportText:config.buttonReportText||"Send report",buttonOkText:config.buttonOkText||"Accept",buttonCancelText:config.buttonCancelText||"Cancel",buttonCloseText:config.buttonCloseText||"Close",spin:config.spin===true,icon:config.icon||"",closable:config.closable===true,closeTimeout:config.closeTimeout};this.log(config.logMessage,config.messageType);var modalInstance=$uibModal.open({template:$templateCache.get("angular.dialog.tpl.html"),backdrop:config.closable?true:"static",controller:["$scope","$uibModalInstance",function($scope,$uibModalInstance){$scope.config=config;this.sendReportButtonHandler=config.reportButtonHandler||function(){me.log("Not implemented","error")};this.okButtonHandler=function(){$uibModalInstance.close("ok")};this.cancelButtonHandler=function(){$uibModalInstance.close("cancel")};this.closeButtonHandler=function(){$uibModalInstance.dismiss("close")}}],controllerAs:"controller"});modalInstance.config=config;modalInstance.result.then(function(result){me.unregisterModal(modalInstance);if(config.callback){config.callback(result)}},function(reason){me.unregisterModal(modalInstance);if(config.callback){config.callback(reason)}});modalInstance.id=this.getNewModalID();this.modals[modalInstance.id]=modalInstance;this.modalStack.push(modalInstance);if(config.closeTimeout){$timeout(function(){me.log("Autoclosing dialog");me.closeDialog({modalID:modalInstance.id})},config.closeTimeout*1e3);$interval(function(){config.closeTimeout--},1e3,config.closeTimeout)}return modalInstance};this.closeDialog=function(params,modal){params=params||{};params.option=params.option||"ok";if(modal===undefined){if(params.modalID){modal=me.getModalInstance(params.modalID)}else if(params.type){for(var i in me.modalStack){if(me.modalStack[i].config.type===params.type){me.closeDialog(params,me.modalStack[i])}}return}else{modal=me.modalStack[me.modalStack.length-1]}}if(modal===undefined){return}var isOpened=modal.opened.$$state.status;if(isOpened===1){modal.close(params.option)}else{$timeout(function(){me.closeDialog(params,modal)},500)}};this.unregisterModal=function(modal){delete me.modals[modal.id];for(var i in me.modalStack){if(me.modalStack[i].id===modal.id){me.modalStack.splice(i,1);return}}};this.getNewModalID=function(){var newID=Math.random().toString(36).substring(2,15)+Math.random().toString(36).substring(2,15);if(this.modals[newID]!==undefined)return this.getNewModalID();return newID};this.log=function(message,messageType){if("warn error log debug".indexOf(messageType)<0){messageType="info"}$log[messageType]((new Date).toUTCString()+" > "+message)};$templateCache.put("angular.dialog.tpl.html",'
'+'
'+' "+'

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"+'
'+"

"+' '+" {{config.message}}"+"

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"+'
'+' '+' "+' "+' "+"
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i(e){e.originalEvent&&(e.dataTransfer=e.originalEvent.dataTransfer),setTimeout(function(){d.unbind("$destroy",i)},0);var t=f.dragChannel||"defaultchannel";if(r.$broadcast("ANGULAR_DRAG_END",e,t),n(e),e.dataTransfer&&"none"!==e.dataTransfer.dropEffect){if(f.onDropSuccess){var s=a(f.onDropSuccess);o.$evalAsync(function(){s(o,{$event:e})})}}else if(e.dataTransfer&&"none"===e.dataTransfer.dropEffect&&f.onDropFailure){var l=a(f.onDropFailure);o.$evalAsync(function(){l(o,{$event:e})})}d.removeClass(c)}function s(n,r){var t;n.originalEvent&&(n.dataTransfer=n.originalEvent.dataTransfer),t=a(r),o.$apply(function(){var a,r=t(o,{$event:n});r&&e.isString(r)&&(a=document.getElementById(r),a&&n.dataTransfer.setDragImage(a,0,0))})}function l(n){n.originalEvent&&(n.dataTransfer=n.originalEvent.dataTransfer);var l=!v||u.classList.contains(g);if(l){var p=f.dragChannel||"defaultchannel",$="";f.drag&&($=o.$eval(f.drag));var m=f.dragImage||null;d.addClass(c),d.bind("$destroy",i);var 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'; secure' : '' 78 | ].join('')); 79 | } 80 | 81 | // Read 82 | 83 | if (!key) { 84 | result = {}; 85 | } 86 | 87 | // To prevent the for loop in the first place assign an empty array 88 | // in case there are no cookies at all. Also prevents odd result when 89 | // calling "get()" 90 | var cookies = document.cookie ? document.cookie.split('; ') : []; 91 | var rdecode = /(%[0-9A-Z]{2})+/g; 92 | var i = 0; 93 | 94 | for (; i < cookies.length; i++) { 95 | var parts = cookies[i].split('='); 96 | var cookie = parts.slice(1).join('='); 97 | 98 | if (cookie.charAt(0) === '"') { 99 | cookie = cookie.slice(1, -1); 100 | } 101 | 102 | try { 103 | var name = parts[0].replace(rdecode, decodeURIComponent); 104 | cookie = converter.read ? 105 | converter.read(cookie, name) : converter(cookie, name) || 106 | cookie.replace(rdecode, decodeURIComponent); 107 | 108 | if (this.json) { 109 | try { 110 | cookie = JSON.parse(cookie); 111 | } catch (e) {} 112 | } 113 | 114 | if (key === name) { 115 | result = cookie; 116 | break; 117 | } 118 | 119 | if (!key) { 120 | result[name] = cookie; 121 | } 122 | } catch (e) {} 123 | } 124 | 125 | return result; 126 | } 127 | 128 | api.set = api; 129 | api.get = function (key) { 130 | return api(key); 131 | }; 132 | api.getJSON = function () { 133 | return api.apply({ 134 | json: true 135 | }, [].slice.call(arguments)); 136 | }; 137 | api.defaults = {}; 138 | 139 | api.remove = function (key, attributes) { 140 | api(key, '', extend(attributes, { 141 | expires: -1 142 | })); 143 | }; 144 | 145 | api.withConverter = init; 146 | 147 | return api; 148 | } 149 | 150 | return init(function () {}); 151 | })); 152 | -------------------------------------------------------------------------------- /client/src/lib/sigma.customEdgeShapes.min.js: -------------------------------------------------------------------------------- 1 | !function(){"use strict";sigma.utils.pkg("sigma.canvas.edgehovers"),sigma.canvas.edgehovers.dashed=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),j=e("defaultNodeColor"),k=e("defaultEdgeColor");if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}f="edge"===e("edgeHoverColor")?a.hover_color||f:a.hover_color||e("defaultEdgeHoverColor")||f,h*=e("edgeHoverSizeRatio"),d.save(),d.setLineDash([8,3]),d.strokeStyle=f,d.lineWidth=h,d.beginPath(),d.moveTo(b[g+"x"],b[g+"y"]),d.lineTo(c[g+"x"],c[g+"y"]),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edgehovers"),sigma.canvas.edgehovers.dotted=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),j=e("defaultNodeColor"),k=e("defaultEdgeColor");if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}f="edge"===e("edgeHoverColor")?a.hover_color||f:a.hover_color||e("defaultEdgeHoverColor")||f,h*=e("edgeHoverSizeRatio"),d.save(),d.setLineDash([2]),d.strokeStyle=f,d.lineWidth=h,d.beginPath(),d.moveTo(b[g+"x"],b[g+"y"]),d.lineTo(c[g+"x"],c[g+"y"]),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edgehovers"),sigma.canvas.edgehovers.parallel=function(a,b,c,d,e){var f,g,h=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,i=e("prefix")||"",j=a[i+"size"]||1,k=e("edgeColor"),l=e("defaultNodeColor"),m=e("defaultEdgeColor"),n=b[i+"x"],o=b[i+"y"],p=c[i+"x"],q=c[i+"y"],r=sigma.utils.getDistance(n,o,p,q);if(!h)switch(k){case"source":h=b.color||l;break;case"target":h=c.color||l;break;default:h=m}h="edge"===e("edgeHoverColor")?a.hover_color||h:a.hover_color||e("defaultEdgeHoverColor")||h,j*=e("edgeHoverSizeRatio"),f=sigma.utils.getCircleIntersection(n,o,j,p,q,r),g=sigma.utils.getCircleIntersection(p,q,j,n,o,r),d.save(),d.strokeStyle=h,d.lineWidth=j,d.beginPath(),d.moveTo(f.xi,f.yi),d.lineTo(g.xi_prime,g.yi_prime),d.closePath(),d.stroke(),d.beginPath(),d.moveTo(f.xi_prime,f.yi_prime),d.lineTo(g.xi,g.yi),d.closePath(),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edgehovers"),sigma.canvas.edgehovers.tapered=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),g=e("prefix")||"",j=e("defaultNodeColor"),k=e("defaultEdgeColor"),l=b[g+"x"],m=b[g+"y"],n=c[g+"x"],o=c[g+"y"],p=sigma.utils.getDistance(l,m,n,o);if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}f="edge"===e("edgeHoverColor")?a.hover_color||f:a.hover_color||e("defaultEdgeHoverColor")||f,h*=e("edgeHoverSizeRatio");var q=sigma.utils.getCircleIntersection(l,m,h,n,o,p);d.save(),d.globalAlpha=.65,d.fillStyle=f,d.beginPath(),d.moveTo(n,o),d.lineTo(q.xi,q.yi),d.lineTo(q.xi_prime,q.yi_prime),d.closePath(),d.fill(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edges"),sigma.canvas.edges.dashed=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),j=e("defaultNodeColor"),k=e("defaultEdgeColor");if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}d.save(),d.strokeStyle=a.active?"edge"===e("edgeActiveColor")?f||k:e("defaultEdgeActiveColor"):f,d.setLineDash([8,3]),d.lineWidth=h,d.beginPath(),d.moveTo(b[g+"x"],b[g+"y"]),d.lineTo(c[g+"x"],c[g+"y"]),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edges"),sigma.canvas.edges.dotted=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),j=e("defaultNodeColor"),k=e("defaultEdgeColor");if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}d.save(),d.strokeStyle=a.active?"edge"===e("edgeActiveColor")?f||k:e("defaultEdgeActiveColor"):f,d.setLineDash([2]),d.lineWidth=h,d.beginPath(),d.moveTo(b[g+"x"],b[g+"y"]),d.lineTo(c[g+"x"],c[g+"y"]),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edges"),sigma.canvas.edges.parallel=function(a,b,c,d,e){var f,g,h=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,i=e("prefix")||"",j=a[i+"size"]||1,k=e("edgeColor"),l=e("defaultNodeColor"),m=e("defaultEdgeColor"),n=b[i+"x"],o=b[i+"y"],p=c[i+"x"],q=c[i+"y"],r=sigma.utils.getDistance(n,o,p,q);if(!h)switch(k){case"source":h=b.color||l;break;case"target":h=c.color||l;break;default:h=m}f=sigma.utils.getCircleIntersection(n,o,j,p,q,r),g=sigma.utils.getCircleIntersection(p,q,j,n,o,r),d.save(),d.strokeStyle=a.active?"edge"===e("edgeActiveColor")?h||m:e("defaultEdgeActiveColor"):h,d.lineWidth=j,d.beginPath(),d.moveTo(f.xi,f.yi),d.lineTo(g.xi_prime,g.yi_prime),d.closePath(),d.stroke(),d.beginPath(),d.moveTo(f.xi_prime,f.yi_prime),d.lineTo(g.xi,g.yi),d.closePath(),d.stroke(),d.restore()}}(),function(){"use strict";sigma.utils.pkg("sigma.canvas.edges"),sigma.canvas.edges.tapered=function(a,b,c,d,e){var f=a.active?a.active_color||e("defaultEdgeActiveColor"):a.color,g=e("prefix")||"",h=a[g+"size"]||1,i=e("edgeColor"),g=e("prefix")||"",j=e("defaultNodeColor"),k=e("defaultEdgeColor"),l=b[g+"x"],m=b[g+"y"],n=c[g+"x"],o=c[g+"y"],p=sigma.utils.getDistance(l,m,n,o);if(!f)switch(i){case"source":f=b.color||j;break;case"target":f=c.color||j;break;default:f=k}var q=sigma.utils.getCircleIntersection(l,m,h,n,o,p);d.save(),d.fillStyle=a.active?"edge"===e("edgeActiveColor")?f||k:e("defaultEdgeActiveColor"):f,d.globalAlpha=.65,d.beginPath(),d.moveTo(n,o),d.lineTo(q.xi,q.yi),d.lineTo(q.xi_prime,q.yi_prime),d.closePath(),d.fill(),d.restore()}}(); -------------------------------------------------------------------------------- /client/src/lib/sigma.customShapes.min.js: -------------------------------------------------------------------------------- 1 | (function(){"use strict";var a=[],b=function(b,c,d){a.push({name:b,drawShape:c,drawBorder:d})},c=function(){return a},d=function(a){return function(b,c,d,e,f,g){g.fillStyle=f,g.beginPath(),a(b,c,d,e,g),g.closePath(),g.fill()}},e=function(a){return function(b,c,d,e,f,g){g.strokeStyle=f,g.lineWidth=e/5,g.beginPath(),a(b,c,d,e,g),g.closePath(),g.stroke()}},f=function(a,b,c,d,e){var f=45*Math.PI/180;e.moveTo(b+d*Math.sin(f),c-d*Math.cos(f));for(var g=1;4>g;g++)e.lineTo(b+Math.sin(f+2*Math.PI*g/4)*d,c-Math.cos(f+2*Math.PI*g/4)*d)};b("square",d(f),e(f));var g=function(a,b,c,d,e){e.arc(b,c,d,0,2*Math.PI,!0)};b("circle",d(g),e(g));var h=function(a,b,c,d,e){e.moveTo(b-d,c),e.lineTo(b,c-d),e.lineTo(b+d,c),e.lineTo(b,c+d)};b("diamond",d(h),e(h));var i=function(a,b,c,d,e){var f=a.cross&&a.cross.lineWeight||5;e.moveTo(b-d,c-f),e.lineTo(b-d,c+f),e.lineTo(b-f,c+f),e.lineTo(b-f,c+d),e.lineTo(b+f,c+d),e.lineTo(b+f,c+f),e.lineTo(b+d,c+f),e.lineTo(b+d,c-f),e.lineTo(b+f,c-f),e.lineTo(b+f,c-d),e.lineTo(b-f,c-d),e.lineTo(b-f,c-f)};b("cross",d(i),e(i));var j=function(a,b,c,d,e){var f=a.equilateral&&a.equilateral.numPoints||5,g=(a.equilateral&&a.equilateral.rotate||0)*Math.PI/180,h=d;e.moveTo(b+h*Math.sin(g),c-h*Math.cos(g));for(var i=1;f>i;i++)e.lineTo(b+Math.sin(g+2*Math.PI*i/f)*h,c-Math.cos(g+2*Math.PI*i/f)*h)};b("equilateral",d(j),e(j));var k=function(a,b,c,d,e){var f=a.star&&a.star.numPoints||5,g=a.star&&a.star.innerRatio||.5,h=d,i=d*g,j=Math.PI/f;e.moveTo(b,c-d);for(var k=0;f>k;k++)e.lineTo(b+Math.sin(j+2*Math.PI*k/f)*i,c-Math.cos(j+2*Math.PI*k/f)*i),e.lineTo(b+Math.sin(2*Math.PI*(k+1)/f)*h,c-Math.cos(2*Math.PI*(k+1)/f)*h)};b("star",d(k),e(k));var l=function(a,b,c,d,e,f){f.fillStyle="yellow",f.beginPath(),f.arc(b,c,d,1.25*Math.PI,0,!1),f.arc(b,c,d,0,.75*Math.PI,!1),f.lineTo(b,c),f.closePath(),f.fill(),f.fillStyle="white",f.strokeStyle="black",f.beginPath(),f.arc(b+d/3,c-d/3,d/4,0,2*Math.PI,!1),f.closePath(),f.fill(),f.stroke(),f.fillStyle="black",f.beginPath(),f.arc(b+4*d/9,c-d/3,d/8,0,2*Math.PI,!1),f.closePath(),f.fill()};b("pacman",l,null),this.ShapeLibrary={enumerate:c,version:"0.1"}}).call(this),function(a){"use strict";if("undefined"==typeof sigma)throw"sigma is not declared";if("undefined"==typeof ShapeLibrary)throw"ShapeLibrary is not declared";sigma.utils.pkg("sigma.canvas.nodes"),sigma.utils.pkg("sigma.svg.nodes");var b=a,c={},d=function(a){b=a},e=function(a,d,e,f,g){if(b&&a.image&&a.image.url){var h=a.image.url,i=a.image.h||1,j=a.image.w||1,k=a.image.scale||1,l=a.image.clip||1,m=c[h];m||(m=document.createElement("IMG"),m.src=h,m.status="loading",m.onerror=function(){console.log("error loading",h),m.status="error"},m.onload=function(){console.log("redraw on image load",h),m.status="ok",b.refresh()},c[h]=m);var n=i>j?j/i:1,o=j>i?i/j:1,p=f*k;g.save(),g.beginPath(),g.arc(d,e,f*l,0,2*Math.PI,!0),g.closePath(),g.clip(),"ok"===m.status&&g.drawImage(m,d+Math.sin(-0.7855)*p*n,e-Math.cos(-0.7855)*p*o,p*n*2*Math.sin(-0.7855)*-1,p*o*2*Math.cos(-0.7855)),g.restore()}},f=function(a,c,d){if(b&&a.image&&a.image.url){{var e=document.createElementNS(d("xmlns"),"circle"),f=document.createElementNS(d("xmlns"),"clipPath"),g=d("classPrefix")+"-clip-path-"+a.id,h=document.createElementNS(d("xmlns"),"defs"),i=document.createElementNS(d("xmlns"),"image");a.image.url}f.setAttributeNS(null,"id",g),f.appendChild(e),h.appendChild(f);var j=/MSIE 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c.setAttributeNS(null,"class",b("classPrefix")+"-node-group"),c.setAttributeNS(null,"data-node-id",a.id),d.setAttributeNS(null,"data-node-id",a.id),d.setAttributeNS(null,"class",b("classPrefix")+"-node"),d.setAttributeNS(null,"fill",a.color||b("defaultNodeColor")),c.appendChild(d),f(a,c,b),c},update:function(a,b,c){for(var d=c("classPrefix"),e=a.image.clip||1,f=a.image.h||1,g=a.image.w||1,h=c("prefix")||"",i=a.image.scale||1,j=a[h+"size"],k=a[h+"x"],l=a[h+"y"],m=i*j,n=f>g?g/f:1,o=g>f?f/g:1,p=0,q=b.childNodes;p 11 | 12 | 13 | ################## BEGIN INSTALLATION ###################### 14 | #INSTALL THE DEPENDENCIES 15 | RUN apt-get update \ 16 | && apt-get install --no-install-recommends -y wget libapache2-mod-wsgi python-flask python-requests unzip python-pip \ 17 | && apt-get clean \ 18 | && pip install bioblend==0.10.0 \ 19 | && pip install fpdf 20 | 21 | #DOWNLOAD AND INSTALL THE APP CODE 22 | RUN wget -O /tmp/galaksio.zip https://github.com/sgbc/galaksio/archive/master.zip \ 23 | #RUN wget -O /tmp/galaksio.zip https://github.com/OskarSLU/galaksio/archive/v0.3.zip \ 24 | && unzip /tmp/galaksio.zip -d /tmp/galaksio \ 25 | && mv /tmp/galaksio/*/* /usr/local/apache2/htdocs/ \ 26 | && rm -r /tmp/galaksio/ \ 27 | && rm /tmp/galaksio.zip \ 28 | && sed -i 's/application\.launch/#application\.launch/' /usr/local/apache2/htdocs/server/launch_server.py \ 29 | && sed -i 's/isDocker = False/isDocker = True/' /usr/local/apache2/htdocs/server/launch_server.py \ 30 | && sed -i 's/8081/80/' /usr/local/apache2/htdocs/server/resources/example_serverconf.cfg 31 | 32 | COPY configs/entrypoint.sh /usr/bin/entrypoint.sh 33 | COPY configs/httpd.conf /usr/local/apache2/conf/httpd.conf 34 | COPY configs/galaksio.wsgi /usr/local/apache2/htdocs/galaksio.wsgi 35 | 36 | RUN chmod +x /usr/bin/entrypoint.sh \ 37 | && chown -R www-data:www-data /usr/local/apache2/htdocs/ 38 | 39 | ##################### INSTALLATION END ##################### 40 | 41 | VOLUME ["/usr/local/apache2/htdocs/server/conf/"] 42 | 43 | EXPOSE 80 44 | 45 | ENTRYPOINT ["/usr/bin/entrypoint.sh"] 46 | -------------------------------------------------------------------------------- /docker/LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2016 Rafa Hernandez 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /docker/README.md: -------------------------------------------------------------------------------- 1 | Galaksio Docker Image 2 | =================== 3 | The [Galaksio](https://github.com/tklingstrom/galaksio) [Docker](http://www.docker.io) Image is an easy distributable full-fledged Galaksio installation. 4 | 5 | Galaksio is a web application that simplifies the usage of the Galaxy bioinformatics platform (https://usegalaxy.eu/). 6 | Galaksio has been developed as part of the [B3Africa Project](http://www.b3africa.org/), which has received funding from the European Union’s Horizon 2020 research and innovation programme. 7 | 8 | - Citation: 9 | > Klingström T, Hernández-de-Diego R, and Bongcam-Rudloff E. Galaksio, a user friendly workflow-centric front end for Galaxy. EMBnet.journal (in revision). 10 | 11 | 12 | # Build the image 13 | The docker image for Galaksio can be found in the [docker hub](https://hub.docker.com/r/tklingstrom/galaksio/). However, you can rebuild is manually by running **docker build**. 14 | 15 | ```sh 16 | sudo docker build -t galaksio . 17 | ``` 18 | Note that the current working directory must contain the Dockerfile file. 19 | 20 | ## Running the Container 21 | The recommended way for running your Galaksio docker is using the provided **docker-compose** script that resolves the dependencies and make easier to customize your instance. Alternatively you can run the docker manually. 22 | 23 | ## Quickstart 24 | This procedure starts Galaksio in a standard virtualised environment. 25 | 26 | - Install [docker](https://docs.docker.com/engine/installation/) for your system if not previously done. 27 | - `docker run -it -p 8081:80 tklingstrom/galaksio` 28 | - Galaksio will be available at [http://localhost:8081/](http://localhost:8081/) 29 | 30 | ## Using the docker-compose file 31 | Launching your Galaksio docker is really easy using docker-compose. Just download the *docker-compose.yml* file and customize the content according to your needs. There are few settings that should be change in the file, follow the instructions in the file to configure your container. 32 | To launch the container, type: 33 | ```sh 34 | sudo docker-compose up 35 | ``` 36 | Using the *-d* flag you can launch the containers in background. 37 | 38 | In case you do not have the Container stored locally, docker will download it for you. 39 | 40 | 41 | ## Run manually 42 | You can run manually your containers using the following commands: 43 | 44 | ```sh 45 | sudo docker run --name galaksio -v /your/data/location/galaksio-data:/usr/local/apache2/htdocs/server/conf/ -e ADMIN_ACCOUNTS=youradminuser -e GALAXY_SERVER=https://usegalaxy.eu -e GALAXY_SERVER_URL=https://usegalaxy.eu -p 8081:80 -d tklingstrom/galaksio 46 | ``` 47 | 48 | Please note that the name is likely to change as we move to an organizatio repo at Dockerhub hosted by SLU Global Bioinformatics Centre 49 | 50 | In case you do not have the Container stored locally, docker will download it for you. 51 | 52 | A short description of the parameters would be: 53 | - `docker run` will run the container for you. 54 | 55 | - `-p 8081:80` will make the port 80 (inside of the container) available on port 8081 on your host. 56 | Inside the container an Apache webserver is running on port 80 and that port can be bound to a local port on your host computer. 57 | 58 | - `tklingstrom/galaksio` is the Image name, which can be found in the [docker hub](https://hub.docker.com/r/tklingstrom/galaksio/). Please note that the name is likely to change as we move to an organizatio repo at Dockerhub hosted by SLU Global Bioinformatics Centre. 59 | 60 | - `-d` will start the docker container in daemon mode. 61 | 62 | - `-e VARIABLE_NAME=VALUE` changes the default value for a system variable. 63 | The Galaksio docker accepts the following variables that modify the behavior of the system in the docker. 64 | 65 | - **ADMIN_ACCOUNTS**, the email for the admin accounts. Using these accounts you can access to the admin page (e.g. [http://yourserver:8081/admin](http://yourserver:8081/admin)) and manipulate the settings for the system. 66 | - **GALAXY_SERVER**, the internal URL for the Galaxy server used by this Galaksio instance. 67 | - **GALAXY_SERVER_URL**, the external URL for the Galaxy server used by this Galaksio instance (usually be the same that above). 68 | - **MAX_CONTENT_LENGTH**, max size (in MB) for uploaded files (eg. a value of 300 will be 300MB). 69 | 70 | # First configuration for Galaksio 71 | By default Galaksio is configured to work with the official [Galaxy](https://usegalaxy.org) instance.This and other options can be customized through the web application. The first time that you access to your Galaksio instance you will need to configure some of the main settings. 72 | 73 | # Version log 74 | - v0.3 September 2017: First version of the docker. 75 | -------------------------------------------------------------------------------- /docker/configs/entrypoint.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Apache gets grumpy about PID files pre-existing 4 | rm -f /usr/local/apache2/logs/httpd.pid 5 | 6 | #Fix problems with mounted volumes ownership 7 | chown -R www-data:www-data /usr/local/apache2/htdocs/server/conf 8 | 9 | #Launch apache 10 | httpd -DFOREGROUND 11 | -------------------------------------------------------------------------------- /docker/configs/galaksio.wsgi: -------------------------------------------------------------------------------- 1 | import sys 2 | import os 3 | 4 | sys.path.insert(0, "/usr/local/apache2/htdocs") 5 | 6 | from server.launch_server import app as application 7 | 8 | -------------------------------------------------------------------------------- /docker/docker-compose-template-with-galaxy.yml: -------------------------------------------------------------------------------- 1 | ############################################################ 2 | # Launcher for Galaxy + Galaksio container 3 | # This is a template, the following values must be replaced: 4 | # - $${INSTANCE_NAME}, name for the instance 5 | # - $${INSTANCE_PORT_1}, port number for Galaxy instance 6 | # - $${INSTANCE_PORT_2}, port number for Galaksio instance 7 | # - $${MAX_CONTENT_LENGTH}, max size (in MB) for uploaded files (eg. a value of 300 will be 300MB) 8 | # - $${ADMIN_ACCOUNTS}, list of admin email accounts for Galaxy and Galaksio (emails separated by comma) 9 | # - $${GALAXY_INSTANCE_TITLE}, custom title for the Galaxy server (shown in home page) 10 | ############################################################ 11 | 12 | version: '2' 13 | services: 14 | 15 | $${INSTANCE_NAME}-galaxy: 16 | image: bgruening/galaxy-stable 17 | container_name: $${INSTANCE_NAME}-galaxy 18 | environment: 19 | - NONUSE=reports 20 | - GALAXY_CONFIG_ADMIN_USERS=$${ADMIN_ACCOUNTS} 21 | - GALAXY_CONFIG_BRAND="$${GALAXY_INSTANCE_TITLE}" 22 | depends_on: 23 | - $${INSTANCE_NAME}-galaksio-data 24 | volumes_from: 25 | - $${INSTANCE_NAME}-galaksio-data 26 | ports: 27 | - "$${INSTANCE_PORT_1}:80" 28 | 29 | $${INSTANCE_NAME}-galaksio: 30 | image: fikipollo/galaksio 31 | container_name: $${INSTANCE_NAME}-galaksio 32 | environment: 33 | - GALAXY_SERVER=http://galaxy_machine 34 | - GALAXY_SERVER_URL=http://localhost:8080 35 | - MAX_CONTENT_LENGTH=$${MAX_CONTENT_LENGTH} 36 | - ADMIN_ACCOUNTS=$${ADMIN_ACCOUNTS} 37 | links: 38 | - $${INSTANCE_NAME}-galaxy:galaxy_machine 39 | depends_on: 40 | - $${INSTANCE_NAME}-galaxy 41 | volumes_from: 42 | - $${INSTANCE_NAME}-galaksio-data 43 | ports: 44 | - "$${INSTANCE_PORT_2}:80" 45 | 46 | $${INSTANCE_NAME}-galaksio-data: 47 | image: busybox 48 | container_name: $${INSTANCE_NAME}-galaksio-data 49 | volumes: 50 | - /data/$${INSTANCE_NAME}-data/galaksio-data:/usr/local/apache2/htdocs/server/conf/ 51 | - /data/$${INSTANCE_NAME}-data/galaxy-data:/export 52 | - /data/$${INSTANCE_NAME}-data/galaxy-custom-tools/:/local_tools 53 | -------------------------------------------------------------------------------- /docker/docker-compose-template.yml: -------------------------------------------------------------------------------- 1 | ############################################################ 2 | # Launcher for Galaksio container 3 | # This is a template, the following values must be replaced: 4 | # - $${INSTANCE_NAME}, name for the instance 5 | # - $${INSTANCE_PORT_1}, port number for Galaksio instance 6 | # - $${GALAXY_SERVER}, internal URL for the Galaxy server used by this Galaksio instance. 7 | # - $${GALAXY_SERVER_URL}, external URL for the Galaxy server used by this Galaksio instance (usually be the same that above). 8 | # - $${MAX_CONTENT_LENGTH}, max size (in MB) for uploaded files (eg. a value of 300 will be 300MB) 9 | # - $${ADMIN_ACCOUNTS}, list of admin email accounts for Galaxy and Galaksio (emails separated by comma) 10 | ############################################################ 11 | 12 | version: '2' 13 | services: 14 | 15 | $${INSTANCE_NAME}-galaksio: 16 | image: fikipollo/galaksio 17 | container_name: $${INSTANCE_NAME}-galaksio 18 | environment: 19 | - GALAXY_SERVER=$${GALAXY_SERVER} 20 | - GALAXY_SERVER_URL=$${GALAXY_SERVER_URL} 21 | - MAX_CONTENT_LENGTH=$${MAX_CONTENT_LENGTH} 22 | - ADMIN_ACCOUNTS=$${ADMIN_ACCOUNTS} 23 | volumes_from: 24 | - $${INSTANCE_NAME}-galaksio-data 25 | ports: 26 | - "$${INSTANCE_PORT_1}:80" 27 | 28 | $${INSTANCE_NAME}-galaksio-data: 29 | image: busybox 30 | container_name: $${INSTANCE_NAME}-galaksio-data 31 | volumes: 32 | - /data/$${INSTANCE_NAME}-data/galaksio-data:/usr/local/apache2/htdocs/server/conf/ 33 | -------------------------------------------------------------------------------- /docker/docker-compose-with-galaxy.yml: -------------------------------------------------------------------------------- 1 | version: '2' 2 | services: 3 | 4 | instance1-galaxy: 5 | image: bgruening/galaxy-stable 6 | container_name: instance1-galaxy 7 | environment: 8 | - NONUSE=reports 9 | - GALAXY_CONFIG_ADMIN_USERS=myadmin@email.com 10 | - GALAXY_CONFIG_BRAND="My own Galaxy server" 11 | depends_on: 12 | - instance1-galaksio-data 13 | volumes_from: 14 | - instance1-galaksio-data 15 | ports: 16 | - "8080:80" 17 | 18 | instance1-galaksio: 19 | image: fikipollo/galaksio 20 | container_name: instance1-galaksio 21 | environment: 22 | - GALAXY_SERVER=http://galaxy_machine 23 | - GALAXY_SERVER_URL=http://localhost:8080 24 | - MAX_CONTENT_LENGTH=300 25 | - ADMIN_ACCOUNTS=myadmin@email.com 26 | links: 27 | - instance1-galaxy:galaxy_machine 28 | depends_on: 29 | - instance1-galaxy 30 | volumes_from: 31 | - instance1-galaksio-data 32 | ports: 33 | - "8081:80" 34 | 35 | instance1-galaksio-data: 36 | image: busybox 37 | container_name: instance1-galaksio-data 38 | volumes: 39 | - /data/instance1-data/galaksio-data:/usr/local/apache2/htdocs/server/conf/ 40 | - /data/instance1-data/galaxy-data:/export 41 | - /data/instance1-data/galaxy-custom-tools/:/local_tools 42 | -------------------------------------------------------------------------------- /docker/docker-compose.yml: -------------------------------------------------------------------------------- 1 | version: '2' 2 | services: 3 | 4 | instance1-galaksio: 5 | image: fikipollo/galaksio 6 | container_name: instance1-galaksio 7 | environment: 8 | - GALAXY_SERVER=https://usegalaxy.eu 9 | - GALAXY_SERVER_URL=https://usegalaxy.eu 10 | - MAX_CONTENT_LENGTH=300 11 | - ADMIN_ACCOUNTS=myadmin@email.com 12 | volumes_from: 13 | - instance1-galaksio-data 14 | ports: 15 | - "8081:80" 16 | 17 | instance1-galaksio-data: 18 | image: busybox 19 | container_name: instance1-galaksio-data 20 | volumes: 21 | - /data/instance1-data/galaksio-data:/usr/local/apache2/htdocs/server/conf/ 22 | -------------------------------------------------------------------------------- /docs/1_1_galaxy.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # The Galaxy project and Galaksio 7 | ## What is Galaxy? 8 | Galaxy is an open source, web-based platform for data intensive biomedical research. If you are new to Galaxy you can find several manuals and information [here](https://galaxyproject.org/tutorials/g101/). According to Galaxy's documentation, its goal is to develop and maintain a system that enables researchers without informatics expertise to perform computational analyses through the web. A user interacts with Galaxy through the web by uploading and analyzing the data. Galaxy interacts with underlying computational infrastructure (servers that run the analyses and disks that store the data) without exposing it to the user. 9 | 10 |
    11 | 12 |
    13 | 14 | ## What is Galaksio? 15 | Galaksio provides a workflow-centric graphical user interface for the Galaxy Workflow Management system in order to provide an accessible and automated interface for biologists and medical researchers completing routine tasks in bioinformatics. Galaksio reduce the workload of bioinformaticians as routine tasks can be performed with minimal training using verified procedures. The presentation of workflows also provides a comprehensive overview of necessary input data and a reporting tool to export the history or workflow for later evaluation or replication. 16 | 17 |
    18 | 19 |
    20 | -------------------------------------------------------------------------------- /docs/1_1_galaxy/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_1_galaxy/galaksio_logo.png -------------------------------------------------------------------------------- /docs/1_1_galaxy/galaksio_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_1_galaxy/galaksio_screenshot.png -------------------------------------------------------------------------------- /docs/1_1_galaxy/galaxy_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_1_galaxy/galaxy_screenshot.png -------------------------------------------------------------------------------- /docs/1_2_concepts.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # Some "must know" concepts 7 | - [What is a Workflow in Galaxy?](#what-is-a-workflow-in-galaxy) 8 | - [Datasets in Galaxy](#datasets-in-galaxy) 9 | - [Histories in Galaxy](#histories-in-galaxy) 10 | - [Dataset collections](#dataset-collections) 11 | 12 | Note: Part of this content has been Extracted from the [Galaxy project documentation](https://galaxyproject.org/learn). 13 | 14 | ## What is a Workflow in Galaxy? 15 | A workflow is a series of tools and dataset actions that run in sequence as a batch operation. Workflows are analyses that are intended to be executed (one ore more times) with different user-provided input datasets. Workflow can be reused over and over, not only reducing tedious work, but enhancing reproducibility by applying the same exact methods to all of your data. 16 | 17 | - Workflows can be created from scratch using the workflow editor. 18 | - Workflows can be annotated, viewed, shared, published, and imported - just like other Galaxy objects. 19 | - Any workflow that you have permissions to import, you can modify with the workflow editor. 20 | 21 | From the perspective of Galaksio, workflows must be designed by skilled users (e.g. a bioinformatician) using the Galaxy tools for workflow edition. 22 | 23 | [Learn more about workflows](https://galaxyproject.org/learn/advanced-workflow/). 24 | 25 |
    26 | 27 |

    Figure 1. Creating a workflow in Galaxy using the workflow editor.

    28 |
    29 | 30 | ## Datasets in Galaxy 31 | Datasets are the inputs and outputs of each step in an analysis project in Galaxy. The tracking information associated with Datasets in a History represent an experimental record of the methods, parameters, and other inputs. 32 | 33 | [More info](https://galaxyproject.org/learn/managing-datasets/) 34 | 35 | ## Histories in Galaxy 36 | When data is uploaded from your computer or analysis is done on existing data using Galaxy, each output from those steps generates a dataset. These datasets (and the output datasets from subsequent analysis on them) are stored by Galaxy in Histories. 37 | 38 | **The Current History** 39 | 40 | All users have one 'current' history, which can be thought of as a workspace or a current working directory in bioinformatics terms. You current history is displayed in the right hand side of the main 'Analyze Data' Galaxy interface in what is called the history panel. 41 | 42 | The history panel displays output datasets in the order in which they were created with the oldest/first shown at the bottom. As new analyses are done and new output datasets are generated, the newest datasets are added to the top of the history panel. In this way, the history panel displays the history of your analysis over time. 43 | 44 | Users that have registered an account and logged in can have many histories and the history panel allows switching between them and creating new ones. This can be useful to organize different analyses. 45 | 46 | [More info](https://galaxyproject.org/tutorials/histories/) 47 | 48 |
    49 | 50 |

    Figure 2. Galaxy history is simply the right panel of the interface.

    51 |
    52 | 53 | ## Dataset collections 54 | Collection are designed to simplify complex, multi-sample analyses. In Galaxy you perform data analyses and organize your data simply by clicking on things. In real-world analyses you never have just a few datasets, instead you have many (sometimes thousands) and Collections help manage your data to minimize the amount of clicking you have to do. 55 | 56 | [More info](https://galaxyproject.org/tutorials/collections/) 57 | -------------------------------------------------------------------------------- /docs/1_2_concepts/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_2_concepts/galaksio_logo.png -------------------------------------------------------------------------------- /docs/1_2_concepts/galaxy_histories.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_2_concepts/galaxy_histories.png -------------------------------------------------------------------------------- /docs/1_2_concepts/galaxy_workflows.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_2_concepts/galaxy_workflows.png -------------------------------------------------------------------------------- /docs/1_3_install/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_3_install/galaksio_logo.png -------------------------------------------------------------------------------- /docs/1_4_quick_start.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # General information 7 | **Galaksio** is a web tool that provides a simple but complete UI for using Galaxy for biologists that require bioinformatical workflows to complete their researching. Galaxy is an open source, web-based platform for data intensive biomedical research. A workflow in Galaxy is a series of tools and dataset actions that run in sequence as a batch operation. 8 | 9 | The major steps of workflow execution using Galaksio can be summarized as follows: 10 | 11 | * Log in the application using your Galaxy account or create a new one. 12 | * Upload your data to Galaksio to your Galaxy history and design your dataset collections. 13 | * Browse the publicly available workflows in Galaxy and import them to your collection. 14 | * Select a workflow to run and set the input files from your history. Optionally, customize the parameters for the tools in the workflow. 15 | * Launch the workflow execution and wait for results, or send the execution to background and continue working. 16 | * Evaluate and download the results. 17 | 18 | # Galaksio and Galaxy 19 | Galaksio is built to provide a more layered approach to Galaxy, providing a simplified user interface based on workflows and reducing the workload of bioinformaticians as routine tasks can be performed with minimal training. 20 | 21 | Galaksio uses the Galaxy API to run tools and manipulate the datasets, which means that every action in Galaksio is sent and executed in a Galaxy server. This also means that user accounts in Galaksio are the same than in Galaxy. Users can use their existing accounts in Galaxy to log in Galaksio, and new accounts created in Galaksio will be also available in the Galaxy server. By default, Galaksio will send the actions to the official Galaxy server running at [https://usegalaxy.org/](https://usegalaxy.org/). However, this option can be changed at any time by the administrator, using alternative Galaxy servers. 22 | 23 | # Galaksio or Galaxy? Target users for Galaksio 24 | Galaxy is a widely supported workflow management system that provides access to bioinformatics for experimentalists with limited expertise in programming. While researchers skilled enough in bioinformatics usually prefer command line tools, less advanced users are left on their own struggling to find and combine tools using the rich but unforgiving user interface provided by Galaxy. However, even for the most simplistic use of Galaxy, insights in bioinformatics are required in order to choose an optimal combination of tools, and set their parameters correctly. 25 | 26 | From the perspective of Galaksio, workflows implementation must be performed by skilled users (e.g. a bioinformatician) using the Galaxy tools for workflow edition. Implemented workflows are made public letting other users to reuse them. Less skilled users can access these public workflows at the "Workflows" section in Galaksio. Hence, a biologist that want to conduct his bioinformatics analysis, can search for a workflow that fullfills his requirements, and run it easily just choosing the input datasets. 27 | 28 | # What can I do with Galaksio? 29 | 30 | |Feature | Category | Implemented | Planned| | 31 | | --- | --- | :---: | :---: | 32 | |User sign-in/out | Users | X | | 33 | |User sign-up | Users | X | | 34 | |Workflow listing | Workflows | X | | 35 | |Workflow importing | Workflows | X | | 36 | |Workflow execution | Workflows | X | | 37 | |Workflow creation | Workflows | X | NO | 38 | |Simultaneous execution of workflows | Workflows | X | | 39 | |Recovering previous executions | Workflows | X | | 40 | |Help and description for tools in workflow | Workflows | X | | 41 | |Input selection and parameter configuration | Workflows | X | | 42 | |History selection | History | X | | 43 | |History creation | History | | YES | 44 | |History deletion | History | | YES | 45 | |Dataset uploading | Dataset manipulation | X | | 46 | |Dataset downloading | Dataset manipulation | X | | 47 | |Dataset deletion | Dataset manipulation | X | | 48 | |Dataset collection creation | Dataset manipulation | X | | 49 | |Dataset collection deletion | Dataset manipulation | | YES | 50 | |Tool execution | Tools | | YES | 51 | 52 | # A short use case of Galaksio 53 | Running a workflow in Galaksio 55 | -------------------------------------------------------------------------------- /docs/1_4_quick_start/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_4_quick_start/galaksio_logo.png -------------------------------------------------------------------------------- /docs/1_4_quick_start/video.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/1_4_quick_start/video.png -------------------------------------------------------------------------------- /docs/2_1_users.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # Users in Galaksio 7 | Galaksio has been designed to share the Galaxy user system. That means that if you already have a user account in the associated Galaxy server, you won't need to create a new account. Instead, you can easily sign-in Galaksio using your Galaxy credentials and all your data in Galaxy will be accessible from Galaksio. 8 | 9 |
    10 | 11 |

    Figure 1. Sign-in form in Galaksio.

    12 |
    13 | 14 | However, if you don't have an account in Galaxy, you can easily create a new account using the sign-up form. That will take you just few seconds! 15 | 16 |
    17 | 18 |

    Figure 2. Creating a new account in Galaksio/Galaxy.

    19 |
    20 | -------------------------------------------------------------------------------- /docs/2_1_users/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/2_1_users/galaksio_logo.png -------------------------------------------------------------------------------- /docs/2_1_users/galaksio_users_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/2_1_users/galaksio_users_1.png -------------------------------------------------------------------------------- /docs/2_1_users/galaksio_users_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/2_1_users/galaksio_users_2.png -------------------------------------------------------------------------------- /docs/3_1_histories.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | ## Histories in Galaksio 6 | As we've already seen, in Galaxy, when data is uploaded from your computer or an analysis is done, each output file generates a dataset that is stored by Galaxy in Histories. 7 | 8 | Galaksio provides multiple tools for easily manipulating your Histories and Datasets that are accessible by clicking at the *Histories* option in the left menu bar. The *Histories* section is divided in two panels (Figure 1). The first panel displays all the histories that are saved in your Galaxy account. The history panel allows switching between them, which can be useful to organize different analyses. The second panel displays the datasets and the collections that were added to a selected history. You can browse the contents of a history by clicking on the corresponding row in the Histories table. By default, the panel displays the contents of the current history. 9 | 10 |
    11 | 12 |

    Figure 1. Histories management in Galaksio.

    13 |
    14 | -------------------------------------------------------------------------------- /docs/3_1_histories/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_1_histories/galaksio_logo.png -------------------------------------------------------------------------------- /docs/3_1_histories/histories_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_1_histories/histories_1.png -------------------------------------------------------------------------------- /docs/3_2_histories.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | ### Managing datasets 6 | Datasets can be uploaded, downloaded or deleted from your history. Galaksio provides tools for uploading small-medium files (less than 2GB) from your disk. Use the tool "Upload new files" to open the dialog for file uploading. For bigger files you might want to use other options, such as FTP upload. 7 | 8 |
    9 | 10 |

    Figure 2. Uploading multiple files using the Galaksio interface.

    11 |
    12 | -------------------------------------------------------------------------------- /docs/3_2_histories/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_2_histories/galaksio_logo.png -------------------------------------------------------------------------------- /docs/3_2_histories/histories_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_2_histories/histories_2.png -------------------------------------------------------------------------------- /docs/3_3_histories.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | ## Managing dataset collections 6 | When you have just a few samples - clicking through them is easy. But once you've got hundreds - it becomes very annoying. Galaxy includes Dataset collections that allow you to combine numerous datasets in a single entity that can be easily manipulated. 7 | 8 | Figures 3-5 display the creation of a "Dataset list" collection. In order to create a new dataset collection, first we need to choose the type and a name for the new collection (Figure 3). In the next step, we choose the datasets that we want to include in our new collection (Figure 4). Once we've selected all the datasets, we can confirm the creation of the new collection (Figure 5). The new collection will be displayed in the current history. 9 | 10 |
    11 | 12 |

    Figure 3. First we need to choose the type and a name for the new collection.

    13 |
    14 | 15 |
    16 | 17 |

    Figure 4. Then, we choose the datasets that we want to include in our new collection.

    18 |
    19 | 20 |
    21 | 22 |

    Figure 5. Finally we confirm the creation of the new collection.

    23 |
    24 | 25 |
    26 | 27 |

    Figure 6. The new collection in the current history.

    28 |
    29 | -------------------------------------------------------------------------------- /docs/3_3_histories/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_3_histories/galaksio_logo.png -------------------------------------------------------------------------------- /docs/3_3_histories/histories_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_3_histories/histories_3.png -------------------------------------------------------------------------------- /docs/3_3_histories/histories_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_3_histories/histories_4.png -------------------------------------------------------------------------------- /docs/3_3_histories/histories_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_3_histories/histories_5.png -------------------------------------------------------------------------------- /docs/3_3_histories/histories_6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/3_3_histories/histories_6.png -------------------------------------------------------------------------------- /docs/4_1_workflows.md: -------------------------------------------------------------------------------- 1 | 2 |
    3 | 4 | 5 | # Browsing workflows 6 | A workflow is a series of tools and dataset actions that run in sequence as a batch operation. From the perspective of Galaksio, workflows are created from scratch by skilled users (e.g. a bioinformatician) using the workflow editor in Galaxy, and published allowing other users to import and reuse them. 7 | 8 | Your collection of imported workflows, as well as the published workflows are listed in Galaksio at the "Workflows" panel. By default, this panel displays your collection of workflows (Figure 1). However, you can easily browse all the published workflows by choosing the option "Show all public workflows" (Figure 2). This option will retrieve all the published workflows in the associated Galaxy instance. Workflows can be easily filtered by using the search tools. 9 | 10 | When a workflow does not belong to your collection, you will see that there are two options available. Using the option "More details", you can access to a more detailed view of the workflow that included an overview for the planned steps. Alternatively, you can use "Import to my collection" which will copy the selected workflow to our collection. 11 | 12 |
    13 | 14 |

    Figure 1. The collection of workflows.

    15 |
    16 | 17 |
    18 | 19 |

    Figure 2. Browsing all the published workflows.

    20 |
    21 | -------------------------------------------------------------------------------- /docs/4_1_workflows/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_1_workflows/galaksio_logo.png -------------------------------------------------------------------------------- /docs/4_1_workflows/workflows1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_1_workflows/workflows1.png -------------------------------------------------------------------------------- /docs/4_1_workflows/workflows2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_1_workflows/workflows2.png -------------------------------------------------------------------------------- /docs/4_2_workflows.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | # Running a workflow 6 | Workflows are analyses that are intended to be executed (one or more times) with different user-provided input Datasets. Workflow can be reused over and over, not only reducing tedious work, but enhancing reproducibility by applying the same exact methods to all of your data. 7 | 8 | Running a workflow is easy with Galaksio. At the "Workflows" panel, find the workflow that you want to run and click on the option "Run workflow". This option will open a more detailed view of the workflow. The first step in the process displays an overview of the workflow (Figure 1). Using the buttons located at the bottom we can easily configure our workflow execution. 9 | 10 |
    11 | 12 |

    Figure 1. Overview for the selected workflow.

    13 |
    14 | 15 | At the second step in the process we can choose the history that contains the files that will be used in the workflow. Additionally, we can upload new datasets or create new dataset collections (Figure 2). 16 | 17 |
    18 | 19 |

    Figure 2. In step 2, we can optionally choose the history that we want to use for the execution.

    20 |
    21 | 22 | The third step is probably the most important step in the process. At this step we need to choose the input datasets for the workflow (Figure 3). Input datasets (or dataset collections) can be selected from the current history. Make sure to select the correct files! 23 | 24 |
    25 | 26 |

    Figure 3. Choosing the input datasets for our example workflow.

    27 |
    28 | 29 | After selecting the input datasets, we can go to the next step. Step 4 displays all the steps that constitute the workflow. Due to the workflow was designed by an skilled user, we can assume that the default configuration for each step is valid for our analysis. Nevertheless, it is possible to customize the parameters for each step in the process. For example, figure 4 displays a custom configuration for the tool "Bowtie2". 30 | 31 |
    32 | 33 |

    Figure 4. Customizing the execution of the Bowtie2 tool.

    34 |
    35 | 36 | Finally, the last step in the process displays an overview of the execution, including the selected input datasets and the custom options for the workflow steps (Figure 5). Now we are ready for launching our workflow! 37 | 38 |
    39 | 40 |

    Figure 5. The summary for our workflow execution. Now we are ready for launch!

    41 |
    42 | 43 | Using the option "Run workflow" we will notify Galaxy to start a new run of our customized workflow. Usually workflow execution can take a while to finish. Meanwhile, we can keep working on Galaksio as our worflows will be executed in background. Using the top toolbar we can get follow the current state of our executions and recover them as soon as they finish (Figure 6). 44 | 45 |
    46 | 47 |

    Figure 6. Workflows can be executed in background. In figure, the top bar displays the status for all the worflows (5 done and 1 running). This information is also available at the home panel, at the "Workflow invocations" section.

    48 |
    49 | 50 | When our workflow is done, we can recover them and access to the resulting datasets. All the results for our workflow can be downloaded and are stored in our current history. 51 | -------------------------------------------------------------------------------- /docs/4_2_workflows/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/galaksio_logo.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows1.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows2.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows3.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows4.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows5.png -------------------------------------------------------------------------------- /docs/4_2_workflows/worflows6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/4_2_workflows/worflows6.png -------------------------------------------------------------------------------- /docs/5_use_case.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # Use case 1. 7 | -------------------------------------------------------------------------------- /docs/5_use_case/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/5_use_case/galaksio_logo.png -------------------------------------------------------------------------------- /docs/6_license.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | # Galaksio, an easy to use GUI for running Galaxy workflows. 6 | 7 | **Galaksio** application is distributed under **GNU General Public License, Version 3.**. 8 | 9 |
    10 | 11 |
    12 | 13 | This program is **free software**; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. 14 | 15 | This program is distributed in the hope that it will be useful, but **WITHOUT ANY WARRANTY**; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 16 | 17 | You should have received a copy of the GNU General Public License along with this program. If not, see [http://www.gnu.org/licenses](http://www.gnu.org/licenses). 18 | 19 | Galaksio has been developed by the [SLU Global Bioinformatics Centre](http://sgbc.slu.se/) at the Sveriges lantbruksuniversitet (Swedish University of Agricultural Sciences). 20 | This project is part of the B3Africa Project [http://www.b3africa.org/](http://www.b3africa.org/), which has received funding from the European Union’s Horizon 2020 research and innovation programme. 21 | 22 | ## Contact 23 | 24 | ** Rafael Hernández de Diego, PhD Student **, Main Developer. 25 | 26 | ** Tomas Klingström, PhD Student **, B3Africa WP4 leader. 27 | 28 | ** Prof. Erik Bongcam-Rudloff **, Head Genomics of the SLU Global Bioinformatics Centre. 29 | 30 | For any question on Galaksio, you can mail us to [rafael.hernandez.de.diego@slu.se](mailto:rafael.hernandez.de.diego@slu.se). 31 | 32 | 33 |
    34 | 35 | 36 |
    37 | 38 | -------------------------------------------------------------------------------- /docs/6_license/ECH2020.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/6_license/ECH2020.png -------------------------------------------------------------------------------- /docs/6_license/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/6_license/galaksio_logo.png -------------------------------------------------------------------------------- /docs/6_license/gplv3-127x51.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/6_license/gplv3-127x51.png -------------------------------------------------------------------------------- /docs/6_license/logoB3Africa400x300.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/6_license/logoB3Africa400x300.jpg -------------------------------------------------------------------------------- /docs/ECH2020.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/ECH2020.png -------------------------------------------------------------------------------- /docs/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/galaksio_logo.png -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 |
    2 | 3 |
    4 | 5 | 6 | # Galaksio, an easy to use GUI for running Galaxy workflows. 7 | 8 | **Welcome to the Galaksio documentation.** 9 | 10 | **Galaksio** is a web tool that provides a simple but complete UI for using Galaxy for biologists that require bioinformatical workflows to complete their researching. 11 | 12 | Galaksio has been developed by the [SLU Global Bioinformatics Centre](http://sgbc.slu.se/) at the Sveriges lantbruksuniversitet (Swedish University of Agricultural Sciences). 13 | This project is part of the B3Africa Project [http://www.b3africa.org/](http://www.b3africa.org/), which has received funding from the European Union’s Horizon 2020 research and innovation programme. 14 | 15 | ## Contact 16 | 17 | ** Rafael Hernández de Diego, PhD Student **, Main Developer. 18 | 19 | ** Tomas Klingström, PhD Student **, B3Africa WP4 leader. 20 | 21 | ** Prof. Erik Bongcam-Rudloff **, Head Genomics of the SLU Global Bioinformatics Centre. 22 | 23 | For any question on Galaksio, you can mail us to [rafael.hernandez.de.diego@slu.se](mailto:rafael.hernandez.de.diego@slu.se). 24 | 25 |
    26 | 27 | 28 |
    29 | -------------------------------------------------------------------------------- /docs/index/ECH2020.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/index/ECH2020.png -------------------------------------------------------------------------------- /docs/index/galaksio_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/index/galaksio_logo.png -------------------------------------------------------------------------------- /docs/index/logoB3Africa400x300.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/index/logoB3Africa400x300.jpg -------------------------------------------------------------------------------- /docs/logoB3Africa400x300.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/docs/logoB3Africa400x300.jpg -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- 1 | site_name: Galaksio Documentation 2 | pages: 3 | - ['index.md', 'Home'] 4 | - ['1_1_galaxy.md', 'Getting start', 'The Galaxy project and Galaksio'] 5 | - ['1_2_concepts.md', 'Getting start', 'Must know concepts'] 6 | - ['1_3_install.md', 'Getting start', 'Installing Galaksio'] 7 | - ['1_4_quick_start.md', 'Getting start', 'Quick start'] 8 | - ['2_1_users.md', 'User system', 'Users in Galaksio'] 9 | - ['3_1_histories.md', 'Histories and datasets', 'Histories in Galaksio'] 10 | - ['3_2_histories.md', 'Histories and datasets', 'Managing datasets'] 11 | - ['3_3_histories.md', 'Histories and datasets', 'Managing dataset collections'] 12 | - ['4_1_workflows.md', 'Workflows', 'Browsing workflows'] 13 | - ['4_2_workflows.md', 'Workflows', 'Running a workflow'] 14 | - ['5_use_case.md', 'Use case', 'Example of use'] 15 | - ['6_license.md', 'About', 'License'] 16 | theme: readthedocs 17 | -------------------------------------------------------------------------------- /server/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/server/__init__.py -------------------------------------------------------------------------------- /server/conf/.dummy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/server/conf/.dummy -------------------------------------------------------------------------------- /server/launch_server.py: -------------------------------------------------------------------------------- 1 | import os 2 | import shutil 3 | 4 | from .server import Application 5 | 6 | isFirstLaunch = False 7 | isDocker = False 8 | 9 | if not os.path.isfile(os.path.dirname(os.path.realpath(__file__)) + "/conf/server.cfg"): 10 | print("Configuration not found, creating new settings file") 11 | conf_dir = os.path.dirname(os.path.realpath(__file__)) + "/conf/" 12 | res_dir = os.path.dirname(os.path.realpath(__file__)) + "/resources/" 13 | shutil.copyfile(res_dir + "__init__.py", conf_dir + "__init__.py") 14 | shutil.copyfile(res_dir + "example_serverconf.cfg", conf_dir + "server.cfg") 15 | shutil.copyfile(res_dir + "logging.cfg", conf_dir + "logging.cfg") 16 | isFirstLaunch = True 17 | else: 18 | print("Configuration found, launching application") 19 | 20 | application = Application() 21 | application.isFirstLaunch = isFirstLaunch 22 | application.isDocker = isDocker 23 | app = application.app 24 | 25 | application.launch() 26 | -------------------------------------------------------------------------------- /server/log/.dummy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/server/log/.dummy -------------------------------------------------------------------------------- /server/resources/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/server/resources/__init__.py -------------------------------------------------------------------------------- /server/resources/example_serverconf.cfg: -------------------------------------------------------------------------------- 1 | [server_settings] 2 | server_host_name = 0.0.0.0 3 | server_subdomain = 4 | server_port_number = 8081 5 | server_allow_debug = False 6 | safe_upload = True 7 | max_content_length = 300 8 | root_directory = 9 | tmp_directory = /tmp 10 | 11 | [galaxy_settings] 12 | galaxy_server = https://usegalaxy.eu 13 | galaxy_server_url = 14 | admin_accounts = myadmin@galaksio.com 15 | 16 | -------------------------------------------------------------------------------- /server/resources/logging.cfg: -------------------------------------------------------------------------------- 1 | [loggers] 2 | keys=root,errorLogger 3 | 4 | [handlers] 5 | keys=consoleHandler,fileHandler 6 | 7 | [formatters] 8 | keys=info 9 | 10 | [logger_root] 11 | level=DEBUG 12 | handlers=fileHandler, consoleHandler 13 | 14 | [logger_errorLogger] 15 | level=ERROR 16 | handlers=fileHandler, consoleHandler 17 | qualname=errorLogger 18 | 19 | [handler_consoleHandler] 20 | class=StreamHandler 21 | formatter=info 22 | args=(sys.stdout,) 23 | 24 | [handler_fileHandler] 25 | formatter=info 26 | class=handlers.RotatingFileHandler 27 | args=(os.path.join(sys.path[0], 'server/log/application.log'), 'a', 31457280, 15) 28 | 29 | [formatter_info] 30 | format=%(asctime)s - %(levelname)s - %(filename)s : %(funcName)s - %(message)s 31 | -------------------------------------------------------------------------------- /server/run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | DIR=$(dirname "$0") 4 | 5 | function printHelp { 6 | echo "Usage run.sh --start | --stop | --restart" 7 | echo "" 8 | } 9 | 10 | function start_service { 11 | cd $DIR/.. 12 | PYTHON=$(which python); 13 | $PYTHON -m server.launch_server & 14 | cd - 15 | disown %1; sleep 2 16 | pid=`ps -Af | grep 'launch_server.py' | grep -v "grep" | awk '{ print $2 }'` 17 | echo $pid > $DIR/launch_server.pid 18 | echo "Daemon started." 19 | } 20 | 21 | function stop_service { 22 | kill `cat $DIR/launch_server.pid` 23 | 24 | if [[ "$?" == "0" ]]; then 25 | rm $DIR/launch_server.pid 26 | echo "Success" 27 | else 28 | echo "Failed, daemon not stopped." 29 | fi 30 | } 31 | 32 | case "$1" in 33 | --start) 34 | start_service 35 | ;; 36 | --stop) 37 | stop_service 38 | ;; 39 | --restart) 40 | stop_service && sleep 2 && start_service 41 | ;; 42 | *) 43 | echo "Invalid option." 44 | printHelp 45 | ;; 46 | esac 47 | -------------------------------------------------------------------------------- /server/servlets/GalaxyAPI.py: -------------------------------------------------------------------------------- 1 | """ 2 | # (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU 3 | # (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/). 4 | # 5 | # All rights reserved. This program and the accompanying materials 6 | # are made available under the terms of the GNU Lesser General Public License 7 | # (LGPL) version 3 which accompanies this distribution, and is available at 8 | # http://www.gnu.org/licenses/lgpl.html 9 | # 10 | # This library is distributed in the hope that it will be useful, 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 | # Lesser General Public License for more details. 14 | # 15 | # Contributors: 16 | # Rafael Hernandez de Diego 17 | # Tomas Klingstrom 18 | # Erik Bongcam-Rudloff 19 | # and others. 20 | # 21 | """ 22 | from os import path as osPath 23 | 24 | from bioblend.galaxy import GalaxyInstance 25 | 26 | 27 | def generateWorkflowReport(request, settings): 28 | # Get the invocation and workflow data 29 | invocation = request.json.get("invocation") 30 | workflow = request.json.get("workflow") 31 | 32 | # Open a new connection with bioblend 33 | galaxy_key = request.values.get("key") 34 | gi = GalaxyInstance(settings.GALAXY_SERVER, galaxy_key) 35 | 36 | workflow_steps = {} 37 | for step in workflow.get("steps"): 38 | workflow_steps[step.get("uuid")] = step 39 | 40 | for step in invocation.get("steps"): 41 | workflow_step = workflow_steps[step.get("workflow_step_uuid")] 42 | workflow_step["state"] = step.get("state") 43 | workflow_step["job_id"] = step.get("job_id") 44 | workflow_step["job"] = gi.jobs.show_job(step.get("job_id")) 45 | 46 | # GENERATE THE HTML 47 | html_code = "" 48 | to_close_tags = [] 49 | 50 | html_code += addTag("h2", "Workflow details", "font-size: 30px; color:red") 51 | html_code += getEntryLine("Workflow name", workflow.get("name"), "font-size: 30px; color:red") 52 | html_code += openNewSection("div", "font-size: 20px;", to_close_tags) 53 | html_code += getEntryLine("Workflow name", workflow.get("name"), "font-size: 30px; color:red") 54 | html_code += getEntryLine("Owner", workflow.get("owner")) 55 | html_code += getEntryLine("Run date", invocation.get("update_time")) 56 | html_code += closeSection(to_close_tags) 57 | 58 | html_code += addTag("h2", "Steps details", "font-size: 30px; color:red") 59 | html_code += openNewSection("div", "font-size: 16px;", to_close_tags) 60 | 61 | for step in sorted(list(workflow_steps.values()), key=lambda k: k['id']): 62 | html_code += openNewSection("div", "font-size: 14px;", to_close_tags) 63 | html_code += addTag("h3", "Step" + str(step.get("id")) + ". " + step.get("name"), "font-size: 30px; color:red") 64 | html_code += addTag("b", "Inputs") 65 | 66 | if step.get("type") == "data_input": 67 | pass 68 | else: 69 | try: 70 | html_code += getEntryLine("Inputs", str(step.get("inputs"))) 71 | except Exception: 72 | pass 73 | 74 | html_code += addTag("b", "Params") 75 | try: 76 | html_code += getEntryLine("Inputs", str(step.get("job"))) 77 | except Exception: 78 | pass 79 | 80 | html_code += closeSection(to_close_tags) 81 | 82 | html_code += closeSection(to_close_tags) 83 | 84 | from fpdf import FPDF, HTMLMixin 85 | 86 | class MyFPDF(FPDF, HTMLMixin): 87 | pass 88 | 89 | pdf = MyFPDF() 90 | # First page 91 | pdf.add_page() 92 | pdf.write_html(html_code) 93 | tmp_path = osPath.join(settings.TMP_DIRECTORY, "report.pdf") 94 | pdf.output(tmp_path, 'F') 95 | 96 | return tmp_path 97 | 98 | 99 | def getEntryLine(label, value, style=""): 100 | return "

    " + label + ": " + value + "

    " 101 | 102 | 103 | def addTag(type, text, style=""): 104 | return "<" + type + " style='" + style + "'>" + text + "" 105 | 106 | 107 | def openNewSection(type, style, to_close_tags): 108 | to_close_tags.append(type) 109 | return "<" + type + " style='" + style + "'>" 110 | 111 | 112 | def closeSection(to_close_tags): 113 | tag = to_close_tags.pop() 114 | return "" 115 | -------------------------------------------------------------------------------- /server/servlets/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SGBC/galaksio/f783fd7a71c74a45b223033b6b102417e416bf6c/server/servlets/__init__.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [flake8] 2 | ignore = E501 3 | import-order-style = smarkets 4 | --------------------------------------------------------------------------------