We develop a Semantic Programming Ontology (SPrO; https://github.com/SemanticProgramming/SPrO) that is used for software programming. SPrO can be used like a programming language with which one can control a data-centric Semantic Web application by describing it within a corresponding source code ontology. With the terms from SPrO you can describe the graphical user interface (GUI), data representations, user interactions, and all workflow processes of a Semantic Web application. The Java Interpreter (https://github.com/SemanticProgramming/Interpreter) functions as an interpreter that dynamically interprets and executes the descriptions in a source code ontology by interpreting them as declarative specifications. This Interface provides the interface. It has been customized to meet the requirements for semantic Morph·D·Base (https://github.com/SemanticProgramming/SemMorphDBase).
Currently, the following general functions have been implemented:
- creation of all relevant HTML/CSS entities based on the design guidelines catalogue of semantic Morph·D·Base;
- automated generation of the GUI based on the specifications in the source code ontologies;
- message system: error and success messages from the WebSocket are displayed in the GUI;
- dynamic updating of the GUI based on user-actions and WebSocket triggers;
- data binding: changes in the GUI are send back to the WebSocket for validation and storage.
In addition to these general functions, the following tools have been developed, which will be used in the new module for formalized morphological descriptions in Morph·D·Base:
- partonomy tool: partonomy browser that not only allows describing an organism as the collection of its parts but also provides a navigation tree to the different sections of the description (see 2.3.4);
- text annotation tool: uses about 100 ontologies provided by the NCBO BioPortal (see http://bioportal.bioontology.org/) for automated text annotation;
- image annotation tool: bundles OpenLayers (https://openlayers.org/) and an image server tool developed at Hochschulbibliothekszentrum NRW (https://github.com/hbz/DeepZoomService) to allow users to define regions of interest for annotating high-res images.
Further information on the project is available at http://escience.biowikifarm.net - feel free to contact us at dev@morphdbase.de
This repository contains the Interface for Semantic Programming based on the Semantic Programming Ontology (SPrO). For Semantic Programming you also need the Semantic Programming Ontology (SPrO; https://github.com/SemanticProgramming/SPrO) and the Java Interpreter (https://github.com/SemanticProgramming/Interpreter). Basic functionalities are described in the SOCCOMAS source code ontology (SC-Basic; https://github.com/SemanticProgramming/SOCCOMAS) and can be re-used for your Semantic Web application.
Please be aware that this project is ongoing research! This code is for demonstration purposes only. Do not use in production environment!
We are using the MEAN stack:
- MongoDB, a NoSQL database
- Express.js, a web application framework that runs on Node.js
- Angular.js, a JavaScript MVC framework that runs in browser JavaScript engines
- Node.js, an execution environment for event-driven server-side and networking applications
Any platform with an up-to-date MEAN stack is fine. We mainly used Ubuntu 14.04 during development. All installing instructions for 3rd party software refers to this plattform. We recommend using a web server like nginx or apache to serve the Angular application in productive mode.
End users access the application using their web browser. To use all features a current browser is recommended:
- Chrome 62 or newer
- Firefox 57 or newer
- Safari 10 or newer
- Android 5 or newer
- iOS 9.3 or newer
- Microsoft Edge
- Internet Explorer 11 (depricated, not 100% supported for some CSS3)
We developed using the IntelliJ IDEA running on Ubuntu 14.04. Some information is specific for this ide an can be ignored if you prefere a different ide.
Clone via bash...
user@mdb:~$ git clone ssh://git@git.morphdbase.de:6020/sandra/MDB-Prototyp.git
Ubuntu 14 unfortunately comes with an outdated NodeJS version (0.1.x), so we have to update to a current version right after installation. Node 6.1.0 or higher is recommended.
user@mdb:~$ sudo apt-get install mongodb nodejs npm
user@mdb:~$ sudo npm cache clean -f
user@mdb:~$ sudo npm install -g n
user@mdb:~$ sudo n 4.4.2
user@mdb:~$ sudo service mongodb status
Might be depricated if you use "n" to install nodeJS ...
user@mdb:~$ sudo ln -sf /usr/local/n/versions/node/4.4.2/bin/node /usr/bin/node
During development nodemon is handy to launch the angular application as it restarts the application automatically if a file changes.
Usage:
nodemon server.js
user@mdb:~$ sudo npm install -g bower nodemon
Forever (re-)starts and monitors JavaScript applications. See start_stop.sh sample script (please change variables to meet your own needs).
Usage:
forever start --uid 'some_name_for_the_application' -a -w server.js" # Start application forever stop 'some_name_for_the_application' # Stop the application forever list # List all applications watched by forever forever stopall # Stop all applications watched by forever
user@mdb:~$ sudo npm install forever -g
Then, change directory to folder 'MDB-Prototyp' (same folder as package.json) and install NodeJS and Angular libraries:
user@mdb:~$ cd MDB-Prototyp/
user@mdb:~$ npm install
At this point the LESS configuration within the IntelliJ IDEA has to be configured, to compile our custom LESS File (mdb.less, includes bootstrap.less) to CSS
First, install LESS Plugins, if necessary:
IDEA --> Settings (STRG/ALT/S) --> Plugins
If no LESS Plugins are listed, go to "Browse repositories".
IDEA --> Settings (STRG/ALT/S) --> Other Settings --> LESS Profiles
- + new Profile
- LESS source directory: /home/.../MDB-Prototyp/less
- + new CSS Output Directory
- /home/.../MDB-Prototyp/public/css
x Compile automatically on save
=> APPLY!
git clone ssh://git@git.morphdbase.de:6020/sandra/MDB-Prototyp.git
sudo apt-get install mongodb # used for passport
sudo service mongodb status # check if mongodb is running
sudo apt-get install nodejs npm # install nodejs and node package manager
sudo ln -s /usr/bin/nodejs /usr/bin/node # create 'node' symlinc for legathy packages (depricated)
sudo npm install -g bower # install bower (global), the angular package manager
sudo npm install forever -g # CLI tool for ensuring that a given script runs continuously
sudo npm install -g nodemon # install nodemon (global), restarts server after changes automatically
npm install # install node packages
You need API keys to access certain 3rd party web services. Find the following strings and insert your own API keys:
- BioPortal API Key: https://data.bioontology.org/annotator?apikey=[YOUR BIOONTOLOGY API KEY]
user@mdb:~$ sudo service mongodb status
If not, start mongodb:
user@mdb:~$ mongod
or
user@mdb:~$ mongod --dbpath /srv/mongodb/ # custom db-path
user@mdb:~$ node server.js
... or by using Nodemon (restarts the server upon change):
user@mdb:~$ nodemon server.js
user@server:~$ forever stopall
user@server:~$ forever start --uid "mdb-proto" --minUptime 10000 --spinSleepTime 10000 -a -w server.js
user@ontology:~$ sh /home/smeid/mdb-prototype/start_proto.sh
bower_components/ --> install folder of bower paketmanager (angularjs modules)
node_modules/ --> install folder of npm paketmanager (nodejs modules)
less/ --> custom LESS files
public/ --> all of the files to be used in on the client side
bower/ --> several angular libs, copied from bower_components
css/ --> css files
app.css --> default stylesheet
mdb.css --> custom bootstrap css generated from less files
img/ --> image files
js/ --> javascript files
app.js --> declare top-level app module
controllers.js --> application controllers
directives.js --> custom angular directives
filters.js --> custom angular filters
services.js --> custom angular services
utilities.js --> custom mdb code snippets
server/
models/
user.js --> user model for mongodb
routes/
api.js --> route for login/logout/registration
index.js --> route for serving HTML pages and partials
unittests- -> unit testing
views/
index.html --> main page for app
partials/ --> angular view partials
index.html
entry.html
...
package.json --> set up and configure node packages (npm install)
bower.json --> set up and configure angular packages (bower install)
server.js --> app config
Unit tests are located at [project_root]/unittests. Use InteliJ to run Karma unit tests or start from terminal:
user@mdb:~$ [project_root]/node_modules/karma/bin/karma --configFile=[project_root]/karma.conf.js start
“Well, I’ll just launch the app and see if everything works. We’ve never had any problem doing that.” – No one ever
The Angular team at Google provides two tools for testing Angular applications:
-
Karma, a test runner for unit testing, and http://karma-runner.github.io/0.12/intro/installation.html
-
Protractor, a test framework for writing end-to-end (E2E) tests.
- https://blog.logentries.com/2015/01/unit-testing-with-karma-and-jasmine-for-angularjs/
- http://karma-runner.github.io/0.10/index.html
- https://www.airpair.com/angularjs/posts/testing-angular-with-karma
- http://jasmine.github.io/edge/introduction.html
- https://www.npmjs.com/package/karma-detect-browsers
- http://www.sitepoint.com/unit-testing-angularjs-services-controllers-providers/
- http://andyshora.com/unit-testing-best-practices-angularjs.html
- http://www.smashingmagazine.com/2014/10/07/introduction-to-unit-testing-in-angularjs/
- https://bardevblog.wordpress.com/2013/07/28/setting-up-angularjs-angular-seed-node-js-and-karma/
The recommended approach is to install Karma (and all the plugins your project needs) locally in the project's directory.
# Install Karma:
user@mdb:~$ npm install karma --save-dev
# Install plugins that your project needs:
user@mdb:~$ npm install karma-jasmine karma-chrome-launcher karma-phantomjs-launcher --save-dev
-
configure your karma.conf.js file using this guide:
http://karma-runner.github.io/0.12/intro/configuration.html
smeid@hulk:~/Git/mdb-nodeangular$ karma init Which testing framework do you want to use ? Press tab to list possible options. Enter to move to the next question. > jasmine Do you want to use Require.js ? This will add Require.js plugin. Press tab to list possible options. Enter to move to the next question. > no Do you want to capture any browsers automatically ? Press tab to list possible options. Enter empty string to move to the next question. > Firefox > Chrome > Safari > Opera > What is the location of your source and test files ? You can use glob patterns, eg. "js/*.js" or "test/**/*Spec.js". Enter empty string to move to the next question. > public/js/*.js > unittests/*.js > Should any of the files included by the previous patterns be excluded ? You can use glob patterns, eg. "**/*.swp". Enter empty string to move to the next question. > Do you want Karma to watch all the files and run the tests on change ? Press tab to list possible options. > yes Config file generated at "/home/smeid/Git/mdb-nodeangular/karma.conf.js". -
Karma runner plugin for detecting all browsers installed on the current system. Adds all found browsers to the browser array in the karma config file:
user@mdb:~$ ./node_modules/karma/bin/karma start
or by IntelliJ IDEA.
Typing ./node_modules/karma/bin/karma start sucks and so you might find it useful to install karma-cli globally.
user@mdb:~$ npm install -g karma-cli
Then, you can run Karma simply by karma from anywhere and it will always run the local version.
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.3.16/angular-mocks.js"></script>
Jasmine - "Jasmine is a behavior-driven development framework for testing JavaScript code."
describe("A suite", function() {
it("contains spec with an expectation", function() {
expect(true).toBe(true);
});
});
Alternatives:
- Mocha - "The fun, simple, flexible JavaScript test framework."
- QUnit - "A JavaScript Unit Testing framework, used by jQuery."
An Introduction to MongoDB: https://scotch.io/tutorials/an-introduction-to-mongodb
user@ws:~$ sudo apt-get install mongodb
Set password
user@mdb:~$ mongo
$ use admin
$ db.createUser({ user: "admin", pwd: "SECRET_PASSWORD", roles: [{ role: "userAdminAnyDatabase", db: "admin" }] })
Enable authentication (add 'auth = true')
user@mdb:~$ sudo vi /etc/mongodb.conf
user@mdb:~$ sudo service mongod restart
jSi328SjfeuASkf)d
user@ws:~$ mongod
With our MongoDB service running, we just have to connect to it. While mongod starts MongoDB, the command to connect to it is:
user@ws:~$ mongo
db.auth("admin", "SECRET_PASSWORD")
$ show dbs
MongoDB will not create a database unless you insert information into that database. The trick is you don’t have to worry about explicitly creating a database! You can just use a database (even if it’s not created), create a collection and document, and everything will automatically be made for you!
$ db
$ use db_name
// save one user
user@mdb:~$ db.users.save({ name: 'Chris' });
// save multiple users
user@mdb:~$ db.users.save([{ name: 'Chris'}, { name: 'Holly' }]);
// show all users
user@mdb:~$ db.users.find();
// find a specific user
user@mdb:~$ db.users.find({ name: 'Holly' });
user@mdb:~$ db.users.update({ name: 'Holly' }, { name: 'Holly Lloyd' });
// remove all
user@mdb:~$ db.users.remove({});
// remove one
user@mdb:~$ db.users.remove({ name: 'Holly' });
Robomongo - http://robomongo.org/
Ubuntu 14.04 ships with the outdated MongoDB 2.4.x. This is ok, but the performance of MongoDB 3.x is much better. To upgrade to the current version, use the MongoDB.org repository:
user@mdb:~$ sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927
user@mdb:~$ echo "deb http://repo.mongodb.org/apt/ubuntu trusty/mongodb-org/3.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.2.list
user@mdb:~$ sudo apt-get update
user@mdb:~$ sudo apt-get install -y mongodb-org
user@mdb:~$ sudo apt-get autoremove
user@mdb:~$ sudo apt-get install libkrb5-dev
user@mdb:~$ sudo npm install -g mongodb
http://dochub.mongodb.org/core/startingandstoppingmongo
Start mongod Processes
By default, MongoDB stores data in the /data/db directory. On Windows, MongoDB stores data in C:\data\db. On all platforms, MongoDB listens for connections from clients on port 27017.
Specify a Data Directory
If you want mongod to store data files at a path other than /data/db you can specify a dbPath. The dbPath must exist before you start mongod. If it does not exist, create the directory and the permissions so that mongod can read and write data to this path. For more information on permissions, see the security operations documentation. To specify a dbPath for mongod to use as a data directory, use the --dbpath option. The following invocation will start a mongod instance and store data in the /srv/mongodb path
user@mdb:~$ mongod --dbpath /srv/mongodb/
user@mdb:~$ sudo mongod --dbpath /home/smeid/mongodb/
user@mdb:~$ sudo killall mongod
user@mdb:~$ sudo mongod --dbpath /home/smeid/mongodb/
user@mdb:~$ echo -n "The current installed npm version is " && npm --version
user@mdb:~$ sudo npm update -g npm
user@mdb:~$ echo -n "The new version is " && npm --version
user@mdb:~$ sudo npm update -g grunt-cli
user@mdb:~$ echo -n "The current installed bower version is " && bower --version
user@mdb:~$ sudo npm update -g bower
user@mdb:~$ echo -n "The new version is " && bower --version
Install "n" for the installation of node, if not already installed:
user@mdb:~$ sudo npm cache clean -f
user@mdb:~$ sudo npm install -g n
Update node using n:
user@mdb:~$ echo -n "The current installed node version is " && node --version
user@mdb:~$ sudo n 4.4.4
user@mdb:~$ sudo ln -sf /usr/local/n/versions/node/4.4.4/bin/node /usr/bin/node
user@mdb:~$ echo -n "The new version is " && node --version
Set node as an alias for nodejs if you use nodejs in stead of node
https://github.com/creationix/nvm