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| # EditorConfig helps developers define and maintain consistent | ||
| # coding styles between different editors and IDEs | ||
| # editorconfig.org | ||
|
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| root = true | ||
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| [*] | ||
|
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| # Change these settings to your own preference | ||
| indent_style = space | ||
| indent_size = 2 | ||
|
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| # We recommend you to keep these unchanged | ||
| end_of_line = lf | ||
| charset = utf-8 | ||
| trim_trailing_whitespace = true | ||
| insert_final_newline = true | ||
|
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| [*.md] | ||
| trim_trailing_whitespace = false |
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| *.less text | ||
| *.styl text | ||
| *.js text | ||
| *.ts text | ||
| *.coffee text | ||
| *.json text | ||
| *.htm text | ||
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| *.log | ||
| *.pot | ||
| *.pyc | ||
| *.swp | ||
| *.lock | ||
| /.tscache | ||
| /.idea | ||
| /build/ | ||
| /dist/ | ||
| node_modules/ | ||
| /src/**/*.js | ||
| /tests/**/*.js | ||
| *.map | ||
| *.css | ||
| *.js | ||
| *.log |
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| @@ -0,0 +1,39 @@ | ||
| language: python | ||
| sudo: required | ||
| env: | ||
| - TOXENV=py27 | ||
| - TOXENV=py34 | ||
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| node_js: | ||
| - 6 | ||
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| before_install: | ||
| - export DISPLAY=:99.0 | ||
| - sh -e /etc/init.d/xvfb start | ||
| - nvm install 6 | ||
| - if [[ `npm -v` != 3* ]]; then npm i -g npm@3; fi | ||
|
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| install: | ||
| - npm install | ||
| - sudo apt-get install cython | ||
| - pip install -r requirements_dev.txt | ||
| - pip install -r requirements.txt | ||
|
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| script: npm run dist | ||
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| deploy: | ||
| provider: releases | ||
| api_key: | ||
| secure: 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 | ||
| file_glob: true | ||
| file: | ||
| - dist/targid2*.egg | ||
| - dist/targid2.tar.gz | ||
| on: | ||
| tags: true | ||
|
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| notifications: | ||
| slack: | ||
| secure: LH7fnnRykIAmW6H1qwuq0v6om7FeMUbcXTw5Y3jxavXXIlqVMFPCqz8ymBaLze1n0X6dtg1YLHV5M6XJozHr0ApGEdq9fIW8RimUtjHjDZ04hiZJdiIQwNIJHecRT7DbCJwOV67h9MekmMA1GRA6k/KUB9wGYy8FX7Hz9+XoV6K+/6tuIiMULApaJO3p5vhl1IGfmsU9Y2eWcx4Z3FuZdVhfB2TNjtmempiQvEUtj7BI3gkH5nX7yxxXV+aW1aiFLSWHYlzlYHLT03A22xSfrSdBXMxc/ESWMO/zUP3VE07DDssPnwdK4nmPU+f1rW8OzQBECqp8gloMP41kss0SFDn7ZhVnMbVxABR/F9Qd9/7gFI+/FJdZFwsA8em8PUFPPzsD/6cXUhuVksRVfax5fCe/NLNS20XDwpMSE4xkzkL2ZG0lT1XMv7uCgpMAlv2g+qtfBq7/D0rluzx3CCDODclWsx/avUFeFz98P0I573BpSYJFjTYJdF0jLd0Szev4MPqy1UqAqI5Dg49IdCYvxUGWvXdTqeFX5OIijr6WvgpxO6/swOzAa+i0kEV8PmC1Sa72jHoG2rJhvbZqxWLsyvNCtZU76osZuUr+efvAhFWmAKKpuhM19Dzt8xlanITm/r/a1MBoFU2D20DBE4jU/Ji2peuhJkMVv95656mYNa0= | ||
| on_success: change | ||
| on_failure: change |
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| { | ||
| "generator-phovea": { | ||
| "type": "app-server", | ||
| "name": "targid2", | ||
| "author": "The Caleydo Team", | ||
| "githubAccount": "phovea", | ||
| "modules": [ | ||
| "phovea_clue", | ||
| "phovea_vis_lineup", | ||
| "phovea_data_mongo", | ||
| "phovea_data_redis" | ||
| ], | ||
| "extensions": [ | ||
| { | ||
| "type": "application", | ||
| "id": "targid2", | ||
| "module": "", | ||
| "extras": { | ||
| "name": "Target Discovery Platform" | ||
| } | ||
| }, | ||
| { | ||
| "type": "targidView", | ||
| "id": "startMenu", | ||
| "module": "StartMenu", | ||
| "extras": { | ||
| "name": "startMenu", | ||
| "factory": "create", | ||
| "idtype": "none", | ||
| "selection": "none" | ||
| } | ||
| }, | ||
| { | ||
| "type": "targidView", | ||
| "id": "login_first", | ||
| "module": "LoginFirstView", | ||
| "extras": { | ||
| "name": "Login First", | ||
| "factory": "create", | ||
| "idtype": "none", | ||
| "selection": "none" | ||
| } | ||
| }, | ||
| { | ||
| "type": "targidView", | ||
| "id": "welcome", | ||
| "module": "WelcomeView", | ||
| "extras": { | ||
| "name": "Welcome", | ||
| "factory": "create", | ||
| "idtype": "none", | ||
| "selection": "none" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionFactory", | ||
| "id": "targid2", | ||
| "module": "Targid", | ||
| "extras": { | ||
| "factory": "createCmd", | ||
| "creates": "(targidCreateView|targidRemoveView|targidReplaceView)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionFactory", | ||
| "id": "targid2", | ||
| "module": "LineUpCommands", | ||
| "extras": { | ||
| "factory": "createCmd", | ||
| "creates": "(lineupAddRanking|lineupSetRankingSortCriteria|lineupSetColumn|lineupAddColumn)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionCompressor", | ||
| "id": "targidCreateRemoveCompressor", | ||
| "module": "Targid", | ||
| "extras": { | ||
| "factory": "compressCreateRemove", | ||
| "matches": "(targidCreateView|targidRemoveView|targidReplaceView)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionFactory", | ||
| "id": "targid2", | ||
| "module": "View", | ||
| "extras": { | ||
| "factory": "createCmd", | ||
| "creates": "(targidSetParameter|targidSetSelection)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionCompressor", | ||
| "id": "targidCompressSetParameter", | ||
| "module": "View", | ||
| "extras": { | ||
| "factory": "compressSetParameter", | ||
| "matches": "(targidSetParameter)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "actionCompressor", | ||
| "id": "targidCompressSetSelection", | ||
| "module": "View", | ||
| "extras": { | ||
| "factory": "compressSetSelection", | ||
| "matches": "(targidSetSelection)" | ||
| } | ||
| }, | ||
| { | ||
| "type": "targidStartSession", | ||
| "id": "targid_session_start", | ||
| "module": "SessionList", | ||
| "extras": { | ||
| "name": "Last Sessions", | ||
| "factory": "createStartFactory", | ||
| "idtype": "none", | ||
| "selection": "none" | ||
| } | ||
| } | ||
| ], | ||
| "sextensions": [ | ||
| { | ||
| "type": "namespace", | ||
| "id": "targid2", | ||
| "module": "proxy", | ||
| "extras": { | ||
| "namespace": "/api/targid/proxy" | ||
| } | ||
| }, | ||
| { | ||
| "type": "namespace", | ||
| "id": "db_connector", | ||
| "module": "sql", | ||
| "extras": { | ||
| "namespace": "/api/targid/db" | ||
| } | ||
| }, | ||
| { | ||
| "type": "namespace", | ||
| "id": "targid_storage", | ||
| "module": "storage", | ||
| "extras": { | ||
| "namespace": "/api/targid/storage" | ||
| } | ||
| }, | ||
| { | ||
| "type": "namespace", | ||
| "id": "processing", | ||
| "module": "processing", | ||
| "extras": { | ||
| "namespace": "/api/targid/processing" | ||
| } | ||
| }, | ||
| { | ||
| "type": "processing-task", | ||
| "id": "targid_tasks", | ||
| "module": "tasks", | ||
| "extras": {} | ||
| } | ||
| ], | ||
| "libraries": [ | ||
| "d3", | ||
| "lineupjs" | ||
| ], | ||
| "unknown": { | ||
| "requirements": [ | ||
| "requests==2.2.1", | ||
| "SQLAlchemy==1.0.12" | ||
| ], | ||
| "debianPackages": [], | ||
| "redhatPackages": [] | ||
| }, | ||
| "app": "", | ||
| "entries": { | ||
| "app": "./src/index.ts" | ||
| }, | ||
| "libraryAliases": { | ||
| "d3": "d3/d3" | ||
| }, | ||
| "libraryExternals": [ | ||
| "d3", | ||
| "lineupjs", | ||
| "marked", | ||
| "marked", | ||
| "lineupjs", | ||
| "d3", | ||
| "font-awesome" | ||
| ], | ||
| "ignores": [], | ||
| "today": "Sun, 06 Nov 2016 15:02:36 GMT" | ||
| } | ||
| } |
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| Copyright (c) 2014, The Caleydo Team | ||
| Copyright (c) 2016, The Caleydo Team | ||
| All rights reserved. | ||
|
|
||
| Redistribution and use in source and binary forms, with or without | ||
| modification, are permitted provided that the following conditions are met: | ||
| Redistribution and use in source and binary forms, with or without modification, | ||
| are permitted provided that the following conditions are met: | ||
|
|
||
| * Redistributions of source code must retain the above copyright notice, this | ||
| list of conditions and the following disclaimer. | ||
| Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. | ||
|
|
||
| * Redistributions in binary form must reproduce the above copyright notice, | ||
| this list of conditions and the following disclaimer in the documentation | ||
| and/or other materials provided with the distribution. | ||
| Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. | ||
|
|
||
| * Neither the name of the {organization} nor the names of its | ||
| contributors may be used to endorse or promote products derived from | ||
| this software without specific prior written permission. | ||
|
|
||
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
| DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE | ||
| FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
| DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | ||
| SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | ||
| CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | ||
| OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| Neither the name of the Caleydo Software nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. | ||
|
|
||
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND | ||
| ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED | ||
| WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
| DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR | ||
| ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES | ||
| (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; | ||
| LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON | ||
| ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
| (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS | ||
| SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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| Caleydo Target Discovery Platform  | ||
| =================== | ||
| targid2 [![Phovea][phovea-image]][phovea-url] [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Dependency Status][daviddm-image]][daviddm-url] | ||
| ===================== | ||
|
|
||
| Target discovery platform for exploring rankings of genes, disease models, and other entities. | ||
|
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| Installation | ||
| ------------ | ||
|
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| [Set up a virtual machine using Vagrant](http://www.caleydo.org/documentation/vagrant/) and run these commands inside the virtual machine: | ||
| ``` | ||
| git clone https://github.com/phovea/targid2.git | ||
| cd targid2 | ||
| npm install | ||
| ``` | ||
|
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| Testing | ||
| ------- | ||
|
|
||
| ```bash | ||
| ./manage.sh clone Caleydo/targid2 | ||
| ./manage.sh resolve | ||
| ``` | ||
| npm run test | ||
| ``` | ||
|
|
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| Building | ||
| -------- | ||
|
|
||
| ``` | ||
| npm run build | ||
| ``` | ||
|
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|
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|
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| *** | ||
|
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| <a href="https://caleydo.org"><img src="http://caleydo.org/assets/images/logos/caleydo.svg" align="left" width="200px" hspace="10" vspace="6"></a> | ||
| This repository is part of **[Caleydo Web](http://caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/). | ||
| This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/). | ||
|
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||
|
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| [phovea-image]: https://img.shields.io/badge/Phovea-Client%20Plugin-F47D20.svg | ||
| [phovea-url]: https://phovea.caleydo.org | ||
| [npm-image]: https://badge.fury.io/js/targid2.svg | ||
| [npm-url]: https://npmjs.org/package/targid2 | ||
| [travis-image]: https://travis-ci.org/phovea/targid2.svg?branch=master | ||
| [travis-url]: https://travis-ci.org/phovea/targid2 | ||
| [daviddm-image]: https://david-dm.org/phovea/targid2.svg?theme=shields.io | ||
| [daviddm-url]: https://david-dm.org/phovea/targid2 |
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