diff --git a/.github/issue_template.md b/.github/issue_template.md
new file mode 100644
index 00000000..cafd7d7e
--- /dev/null
+++ b/.github/issue_template.md
@@ -0,0 +1,20 @@
+
+## Description
+
+
+## Steps to Reproduce
+
+
+## Expected Behaviour
+
+
+## Actual Behaviour
+
+
+## Settings
+
+- OS:
+
+## Screenshots
+
+
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
new file mode 100644
index 00000000..0e863f63
--- /dev/null
+++ b/.github/pull_request_template.md
@@ -0,0 +1,12 @@
+## Description
+Describe the changes made and why they were made.
+
+## Related issues and discussion
+#{Issue Number}
+
+## Screenshots, if any
+
+## Checklist
+Please make sure these boxes are checked before submitting your pull request - thanks!
+
+- [ ] Run the tests
diff --git a/.gitignore b/.gitignore
index fa6345ea..e6e95e72 100644
--- a/.gitignore
+++ b/.gitignore
@@ -63,4 +63,7 @@ typings/
.env
# next.js build output
-.next
\ No newline at end of file
+.next
+
+# public directory
+public/
\ No newline at end of file
diff --git a/BUILD.md b/BUILD.md
deleted file mode 100644
index 72951318..00000000
--- a/BUILD.md
+++ /dev/null
@@ -1,12 +0,0 @@
-## HOW TO BUILD
-
-``` bash
-# Install the project dependencies
-npm install
-
-# Run the tests
-npm test
-
-# Use npm start to launch the gulp default tasks (CSS, JS, Vendor, Images, Json Configs, ...) + Run the server
-npm start
-```
\ No newline at end of file
diff --git a/README.md b/README.md
index 02f40927..81837bc4 100644
--- a/README.md
+++ b/README.md
@@ -1,28 +1,28 @@
# InterMine Data Browser
-
Build Status (Travis CI):
-
+
Build Status (Travis CI):
+
-The goal of this project, is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine. without the requirement of having an extensive knowledge of the data model.
+The goal of this project is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine without the requirement of having an extensive knowledge of the data model.
-For the project organization, please refer to [https://github.com/intermine](https://github.com/intermine)
+For the project organization, please refer to [InterMine](https://github.com/intermine)
-Please note that development is very early on and the project is not ready to use yet.
+_Please note that the development is very early on and the project is not ready to use yet._
## DEPLOYMENT
-Try it out with the Heroku deployment (automatic deployment, may have some delay): [http://im-browser-prototype.herokuapp.com/](http://im-browser-prototype.herokuapp.com/)
+Try it out with the Heroku deployment [here](http://im-browser-prototype.herokuapp.com/) (automatic deployment, may have some delay)
-## DEPENDENCIES
+## GETTING STARTED
-Check [package.json](package.json)
+Please visit [Getting Started](getting-started.md)
-## BUILDING
+## DEPENDENCIES
-See [BUILD.md](BUILD.md)
+Check [package.json file](package.json)
## DOCUMENTATION
-Apart from the in-line comments in the code, documentation generated with documentation.js is available in [https://adrianbzg.github.io/InterMine-Data-Browser-Tool/](https://adrianbzg.github.io/InterMine-Data-Browser-Tool/). To update the documentation, the 'gulp documentation' is available.
+Apart from the in-line comments in the code, documentation generated with _documentation.js_ can be accessed [here](https://adrianbzg.github.io/InterMine-Data-Browser-Tool/). To update the documentation, the 'gulp documentation' is available.
## REQUIRED ONTOLOGY CONCEPTS (PER MINE) FOR EACH FILTER
@@ -40,18 +40,35 @@ Apart from the in-line comments in the code, documentation generated with docume
| Interactions | interactions.participant2.symbol + interactions.details.type + interactions.details.dataSets.name |
| Expression | atlasExpression.pValue + atlasExpression.tStatistic + atlasExpression.expression + atlasExpression.dataSets.name |
-## CONTRIBUTING
+## CONTRIBUTING GUIDELINES
1. Find a thing to fix/implement in [Issues](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues?direction=desc&sort=created&state=open) or come up with your own idea, [create a discussion issue](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues/new) for it and get a feedback.
-2. [Fork the repo](https://help.github.com/articles/fork-a-repo)
-3. Create your feature branch (`git checkout -b my-new-feature`)
-4. Commit your changes (`git commit -am 'Add some feature'`)
-5. Push to the branch (`git push origin my-new-feature`)
-6. [Create new Pull Request](https://help.github.com/articles/using-pull-requests)
+
+2. [Fork](https://help.github.com/articles/fork-a-repo) the repository.
+
+3. Create your new feature branch.
+
+ ``` bash
+ git checkout -b my-new-feature
+ ```
+
+4. Commit your changes.
+
+ ``` bash
+ git commit -am 'Add some feature
+ ```
+
+5. Push to the newly created feature branch.
+
+ ``` bash
+ git push origin my-new-feature
+ ```
+
+6. Create a new [Pull Request](https://help.github.com/articles/using-pull-requests)
## CONTACT
-You can contact the developers by opening an issue in this repo.
+You can contact the developers by opening a new issue in this repository [here](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues/new).
## SCREENSHOTS
diff --git a/app.js b/app.js
index 2ff60d7a..7bf813cd 100644
--- a/app.js
+++ b/app.js
@@ -5,12 +5,6 @@ var cookieParser = require('cookie-parser');
var logger = require('morgan');
var indexRouter = require('./routes/index');
-var statisticsRouter = require('./routes/statistics');
-var fetchRouter = require('./routes/fetch');
-
-var http = require('http');
-var https = require('https');
-var fs = require('fs');
var app = express();
@@ -25,8 +19,6 @@ app.use(cookieParser());
app.use(express.static(path.join(__dirname, 'public')));
app.use('/', indexRouter); // Home page router, to render the views
-app.use('/statistics', statisticsRouter); // Statistics router, intended to be used as REST API
-app.use('/fetch', fetchRouter); // Statistics router, intended to be used as REST API
// Catch 404 and forward to error handler
app.use(function(req, res, next) {
diff --git a/bin/www b/bin/www
index a198fc4b..abf9b8fe 100644
--- a/bin/www
+++ b/bin/www
@@ -25,7 +25,7 @@ var server = http.createServer(app);
* Listen on provided port, on all network interfaces.
*/
-server.listen(port);
+server.listen(port, () => console.log(`Server started on http://localhost:${port}`));
server.on('error', onError);
server.on('listening', onListening);
diff --git a/getting-started.md b/getting-started.md
new file mode 100644
index 00000000..997e2a95
--- /dev/null
+++ b/getting-started.md
@@ -0,0 +1,59 @@
+# Getting Started with the InterMine Data Browser
+
+If you're setting up the Data Browser locally, perhaps to fix a bug or contribute a pull request, here's how you can do it.
+
+## Prerequisites
+
+A recent version of [node](https://nodejs.org/en/) and [npm](https://www.npmjs.com/)
+
+## Clone the repository to your host
+
+Head to the directory in your host machine where you want to clone/place the repository and then enter the following commands on your terminal window:
+
+``` bash
+# Clone the repository
+git clone https://github.com/intermine/InterMine-Data-Browser-Tool.git
+
+# Change present working directory
+cd InterMine-Data-Browser-Tool
+```
+
+## Install dependencies
+
+In a console, run this command from the Data Browser root folder to install all the project dependencies:
+
+``` bash
+npm install
+```
+
+## Run the tests
+
+To ensure that everything works correctly before or after some changes are made to the code base, run the tests from your console using the following command:
+
+``` bash
+npm test
+```
+
+If all the test cases run without failing then it means that you are now ready to make a pull request or can proceed further to the next step.
+
+## Launch GulpJs Tasks and Start the Data Browser server
+
+The Data Browser always runs Gulp tasks first ([gulpfile.js](gulpfile.js)) to generate all the required files related to the client-side and then runs the server. The following command needs to be entered for the same:
+
+``` bash
+# Launch the gulp default tasks (CSS, JS, Vendor, Images, Json Configs, ...) + Run the server
+npm start
+```
+If you visit [http://localhost:3000](http://localhost:3000) you should see your Data Browser running locally on your machine!
+
+## Launch GulpJs Tasks only
+
+You can run the Gulp tasks separately without running the server using the following command:
+
+``` bash
+gulp
+```
+
+Once it is completed, you can see the generated files stored inside of `public/` folder.
+
+_More information on Gulp can be obtained [here](https://gulpjs.com/)._
\ No newline at end of file
diff --git a/gulpfile.js b/gulpfile.js
index b43bf2fc..4d038911 100644
--- a/gulpfile.js
+++ b/gulpfile.js
@@ -1,140 +1,149 @@
var gulp = require('gulp');
var sass = require('gulp-sass');
-var header = require('gulp-header');
var cleanCSS = require('gulp-clean-css');
var rename = require("gulp-rename");
-var uglify = require('gulp-uglify');
-var pug = require('gulp-pug');
-var beautify = require('gulp-html-beautify');
var pkg = require('./package.json');
var browserSync = require('browser-sync').create();
var exec = require('child_process').exec;
-
+var open = require('open');
+var port = process.env.PORT || 3000;
/**
* Gulp task to copy third party libraries from /node_modules into /vendor
*/
-gulp.task('vendor', function() {
- // Bootstrap
- gulp.src([
- './node_modules/bootstrap/dist/**/*',
- '!./node_modules/bootstrap/dist/css/bootstrap-grid*',
- '!./node_modules/bootstrap/dist/css/bootstrap-reboot*'
- ])
- .pipe(gulp.dest('./public/vendor/bootstrap'))
- // ChartJS
- gulp.src([
- './node_modules/chart.js/dist/*.js'
- ])
- .pipe(gulp.dest('./public/vendor/chart.js'))
- // Font Awesome
- gulp.src([
- './node_modules/font-awesome/**/*',
- '!./node_modules/font-awesome/{less,less/*}',
- '!./node_modules/font-awesome/{scss,scss/*}',
- '!./node_modules/font-awesome/.*',
- '!./node_modules/font-awesome/*.{txt,json,md}'
- ])
- .pipe(gulp.dest('./public/vendor/font-awesome'))
- // jQuery
- gulp.src([
- './node_modules/jquery/dist/*',
- '!./node_modules/jquery/dist/core.js'
- ])
- .pipe(gulp.dest('./public/vendor/jquery'))
- // jQuery Easing
- gulp.src([
- './node_modules/jquery.easing/*.js'
- ])
- .pipe(gulp.dest('./public/vendor/jquery-easing'))
- // InterMineJS
- gulp.src([
- './node_modules/imjs/dist/*',
- ])
- .pipe(gulp.dest('./public/vendor/imjs'))
+gulp.task('vendor', function(done) {
+ // Bootstrap
+ gulp.src([
+ './node_modules/bootstrap/dist/**/*',
+ '!./node_modules/bootstrap/dist/css/bootstrap-grid*',
+ '!./node_modules/bootstrap/dist/css/bootstrap-reboot*'
+ ])
+ .pipe(gulp.dest('./public/vendor/bootstrap'))
+ // ChartJS
+ gulp.src([
+ './node_modules/chart.js/dist/*.js'
+ ])
+ .pipe(gulp.dest('./public/vendor/chart.js'))
+ // Font Awesome
+ gulp.src([
+ './node_modules/font-awesome/**/*',
+ '!./node_modules/font-awesome/{less,less/*}',
+ '!./node_modules/font-awesome/{scss,scss/*}',
+ '!./node_modules/font-awesome/.*',
+ '!./node_modules/font-awesome/*.{txt,json,md}'
+ ])
+ .pipe(gulp.dest('./public/vendor/font-awesome'))
+ // jQuery
+ gulp.src([
+ './node_modules/jquery/dist/*',
+ '!./node_modules/jquery/dist/core.js'
+ ])
+ .pipe(gulp.dest('./public/vendor/jquery'))
+ // jQuery Easing
+ gulp.src([
+ './node_modules/jquery.easing/*.js'
+ ])
+ .pipe(gulp.dest('./public/vendor/jquery-easing'))
+ // InterMineJS
+ gulp.src([
+ './node_modules/imjs/dist/*',
+ ])
+ .pipe(gulp.dest('./public/vendor/imjs'))
+
+ // Signals completion of the task
+ done();
});
/**
* Gulp task to move the images in the src folder to the public folder
*/
gulp.task('images', function() {
- gulp.src([
- './src/img/*'
- ])
- .pipe(gulp.dest('./public/img/'))
+ return gulp.src([
+ './src/img/*'
+ ])
+ .pipe(gulp.dest('./public/img/'))
});
/**
* Gulp task to move the JSON mine configs in the src folder to the public folder
*/
gulp.task('mine_configs', function() {
- gulp.src([
- './src/mine_configs/*'
- ])
- .pipe(gulp.dest('./public/mine_configs/'))
+ return gulp.src([
+ './src/mine_configs/*'
+ ])
+ .pipe(gulp.dest('./public/mine_configs/'))
});
/**
* Gulp task to compile SCSS
*/
gulp.task('css:compile', function() {
- return gulp.src('./src/scss/**/*.scss')
- .pipe(sass.sync({
- outputStyle: 'expanded'
- }).on('error', sass.logError))
- .pipe(gulp.dest('./public/stylesheets'))
+ return gulp.src('./src/scss/**/*.scss')
+ .pipe(sass.sync({
+ outputStyle: 'expanded'
+ }).on('error', sass.logError))
+ .pipe(gulp.dest('./public/stylesheets'))
});
/**
* Gulp task to minify CSS
*/
-gulp.task('css:minify', ['css:compile'], function() {
- return gulp.src([
- './src/css/*.css',
- '!./src/css/*.min.css'
- ])
- .pipe(cleanCSS())
- .pipe(rename({
- suffix: '.min'
- }))
- .pipe(gulp.dest('./public/stylesheets'))
- .pipe(browserSync.stream());
+gulp.task('css:minify', function() {
+ return gulp.src([
+ './src/css/*.css',
+ '!./src/css/*.min.css'
+ ])
+ .pipe(cleanCSS())
+ .pipe(rename({
+ suffix: '.min'
+ }))
+ .pipe(gulp.dest('./public/stylesheets'))
+ .pipe(browserSync.stream());
});
/**
* Gulp task for CSS
*/
-gulp.task('css', ['css:compile', 'css:minify']);
+gulp.task('css', gulp.series('css:compile', 'css:minify'));
/**
* Gulp task to minify JavaScript
*/
gulp.task('js:minify', function() {
- return gulp.src([
- './src/js/*.js',
- '!./src/js/*.min.js'
- ])
- //.pipe(uglify())
- .pipe(rename({
- suffix: '.min'
- }))
- .pipe(gulp.dest('./public/javascripts'))
- .pipe(browserSync.stream());
+ return gulp.src([
+ './src/js/*.js',
+ '!./src/js/*.min.js'
+ ])
+ //.pipe(uglify())
+ .pipe(rename({
+ suffix: '.min'
+ }))
+ .pipe(gulp.dest('./public/javascripts'))
+ .pipe(browserSync.stream());
});
/**
* Gulp task for JS
*/
-gulp.task('js', ['js:minify']);
+gulp.task('js', gulp.series('js:minify'));
/**
* Gulp task for launching the documentation on src/ files and save it as HTML in the docs folder
*/
-gulp.task('documentation', function (cb) {
- exec('documentation build src/** -f html -o docs', function (err, stdout, stderr) {
- });
+gulp.task('documentation', function(cb) {
+ exec('documentation build src/** -f html -o docs', function(err, stdout, stderr) {});
+})
+
+/**
+ * Gulp task for launching browser with server url
+ */
+gulp.task('browser', function(cb) {
+ console.log("Launching Browser");
+ open(`http://localhost:${port}`);
+ console.log("Browser Launched");
+ return cb();
})
/**
* Gulp default task: CSS + JS + Vendor + images
*/
-gulp.task('default', ['css', 'js', 'vendor', 'images', 'mine_configs']);
+gulp.task('default', gulp.series(gulp.parallel('css', 'js', 'vendor', 'images', 'mine_configs'), 'browser'));
diff --git a/package.json b/package.json
index 5167a2fe..83c2ba67 100644
--- a/package.json
+++ b/package.json
@@ -1,56 +1,62 @@
{
- "title": "InterMine Data Brpwser",
- "name": "intermine-data-browser",
- "version": "1.0.8",
- "description": "A web-based data browser for InterMine",
- "homepage": "https://github.com/AdrianBZG/InterMine-Data-Browser-Tool",
- "bugs": {
- "url": "https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues",
- "email": "adrianrodriguezbazaga@gmail.com"
- },
- "scripts": {
- "start": "gulp & node ./bin/www",
- "dev": "gulp && webpack --config webpack.config.js",
- "test": "mocha --timeout 100000"
- },
- "author": "Adrian Rodriguez-Bazaga",
- "contributors": [
- "Yo Yehudi",
- "Rachel Lyne"
- ],
- "repository": {
- "type": "git",
- "url": "https://github.com/AdrianBZG/InterMine-Data-Browser-Tool"
- },
- "dependencies": {
- "bootstrap": "4.1.2",
- "browser-sync": "2.23.6",
- "chart.js": "2.7.1",
- "cookie-parser": "~1.4.3",
- "datatables.net-bs4": "1.10.16",
- "debug": "~2.6.9",
- "express": "^4.16.3",
- "font-awesome": "4.7.0",
- "gulp-clean-css": "3.9.2",
- "gulp-header": "2.0.1",
- "gulp-html-beautify": "^1.0.1",
- "gulp-pug": "^3.3.0",
- "gulp-rename": "^1.2.2",
- "gulp-sass": "^3.1.0",
- "gulp-uglify": "3.0.0",
- "http-errors": "~1.6.2",
- "jquery": "3.3.1",
- "jquery.easing": "^1.4.1",
- "jsdom": "^11.11.0",
- "morgan": "~1.9.0",
- "pug": "2.0.0-beta11",
- "gulp": "^3.9.1",
- "imjs": "^3.15.1"
- },
- "devDependencies": {
- "browser-sync": "2.23.6",
- "chai": "^4.1.2",
- "chai-http": "^4.0.0",
- "mocha": "^5.2.0"
- }
+ "title": "InterMine Data Brpwser",
+ "name": "intermine-data-browser",
+ "version": "1.1.0",
+ "description": "A web-based data browser for InterMine",
+ "homepage": "https://github.com/InterMine/InterMine-Data-Browser-Tool",
+ "bugs": {
+ "url": "https://github.com/InterMine/InterMine-Data-Browser-Tool/issues",
+ "email": "adrianrodriguezbazaga@gmail.com"
+ },
+ "scripts": {
+ "start": "gulp & node ./bin/www",
+ "dev": "gulp && webpack --config webpack.config.js",
+ "test": "mocha --timeout 100000"
+ },
+ "author": "Adrian Rodriguez-Bazaga",
+ "contributors": [
+ "Yo Yehudi",
+ "Rachel Lyne",
+ "LarkhSingla",
+ "Divyanshu Mahajan",
+ "Ankit Kumar",
+ "Nikhil Vats",
+ "Himanshu Singh",
+ "Varun Bhandia",
+ "holloh",
+ "himanshuc3"
+ ],
+ "repository": {
+ "type": "git",
+ "url": "https://github.com/InterMine/InterMine-Data-Browser-Tool"
+ },
+ "dependencies": {
+ "JSONStream": "^1.3.5",
+ "bootstrap": "^4.4.1",
+ "chart.js": "^2.9.3",
+ "cookie-parser": "~1.4.3",
+ "datatables.net-bs4": "1.10.16",
+ "debug": "~2.6.9",
+ "es6-promise": "^4.2.8",
+ "express": "^4.16.3",
+ "font-awesome": "4.7.0",
+ "gulp": "^4.0.2",
+ "gulp-clean-css": "^4.2.0",
+ "gulp-rename": "^1.2.2",
+ "gulp-sass": "^3.1.0",
+ "http-errors": "~1.6.2",
+ "imjs": "^3.18.1",
+ "jquery": "^3.4.1",
+ "jquery.easing": "^1.4.1",
+ "jsdom": "^11.11.0",
+ "morgan": "~1.9.0",
+ "open": "^7.0.2",
+ "pug": "^2.0.4"
+ },
+ "devDependencies": {
+ "browser-sync": "^2.26.7",
+ "chai": "^4.1.2",
+ "chai-http": "^4.0.0",
+ "mocha": "^5.2.0"
+ }
}
diff --git a/public/img/favicon.ico b/public/img/favicon.ico
deleted file mode 100644
index e5fa3ee0..00000000
Binary files a/public/img/favicon.ico and /dev/null differ
diff --git a/public/img/intermine-logo.png b/public/img/intermine-logo.png
deleted file mode 100644
index d729e394..00000000
Binary files a/public/img/intermine-logo.png and /dev/null differ
diff --git a/public/javascripts/common.min.js b/public/javascripts/common.min.js
deleted file mode 100644
index 494e0287..00000000
--- a/public/javascripts/common.min.js
+++ /dev/null
@@ -1,2060 +0,0 @@
-$(document).ready(function() {
- initializeStartupConfiguration();
-});
-
-/**
- * This method initialies the global variables used for the filters, reads the JSON filters config
- * and handles the default mine view.
- */
-function initializeStartupConfiguration() {
- window.imTableConstraint = {
- "goAnnotation" : [],
- "datasetName" : [],
- "pathwayName" : [],
- "proteinDomainName" : [],
- "diseaseName" : [],
- "organism" : [],
- "savedList": null
- }; // 0 = GO annotation, 1 = Dataset Name, 2 = Pathway Name, 3 = Protein Domain Name, 4 = Disease Name
-
- window.interminesHashMap = null;
- window.locationFilter = null;
- window.interactionsFilter = null;
- window.clinVarFilter = null;
- window.expressionFilter = null;
- window.organismFilterLetters = ["A","B","C","D","E","F","G","H","I","J"];
- window.organismFilter = null;
- window.organismColorsMap = {}
- window.proteinLocalisationFilter = null;
- window.currentClassViewFilter = null;
- window.pieChartObject = null;
- window.geneLengthChartObject = null;
-
- window.minesConfigs = null;
- window.minesPreferredOrganisms = null;
-
- readTextFile("./mine_configs/mines_config.json", function(text) {
- window.minesConfigs = JSON.parse(text);
- });
-
- readTextFile("./mine_configs/mines_preferred_organisms.json", function(text) {
- window.minesPreferredOrganisms = JSON.parse(text);
- });
-
- // Initial mine service url (HumanMine), name and view
- window.mineUrl = "httpCOLONSLASHSLASHwww.humanmine.orgSLASHhumanmineSLASHservice";
- window.selectedMineName = "HumanMine";
- if(!sessionStorage.getItem('currentClassView')) {
- sessionStorage.setItem('currentClassView', 'Gene');
- }
-
- // Check if there is a saved mine in LocalStorage
- if (typeof(Storage) !== "undefined") {
- if (localStorage.getItem("selectedMineName") && localStorage.getItem("mineUrl")) {
- window.mineUrl = localStorage.getItem("mineUrl");
- window.selectedMineName = localStorage.getItem("selectedMineName");
- }
- }
-
- // Handle the API Keys manager buttons
- $("#apiKeyManagerButton").click(function() {
- // Update the key manager structures
- initializeKeyManager();
-
- // Show the window
- $('#apiKeyManagerModal').appendTo("body").modal('show');
- });
-
- $("#apiKeyManagerSaveButton").click(function() {
- var newApiKeysObject = [];
-
- var anyError = false; // We will use this variable to check for errors
-
- // Iterate through the elements in the div containing the keys and update the LocalStorage object
- $('#apiKeyManagerModalKeysDiv').children('div').each(function () {
- var mineName = $(this).children("label").text();
- var mineAPIkey = $(this).children("input").val();
-
- // Sanity check: if the API key is valid, we save it, otherwise, warn the user
- if(mineAPIkey != "") {
- $.ajax({
- url: findElementJSONarray(window.interminesHashMap, "mine", mineName).mineurl + '/user/whoami?token=' + mineAPIkey,
- type: 'GET',
- async: false,
- success: function(data) {
- newApiKeysObject.push({ "mine" : mineName, "apikey" : mineAPIkey });
- },
- error: function(e) {
- anyError = true;
-
- // Show error
- if ($("#invalidAPIkeyAlert").length == 0) {
- $("#navbarResponsive").prepend("
×Error: API key provided for " + mineName + " is not a valid API key - please check you have entered it correctly.
");
-
- $("#closeInvalidAPIkeyAlert").click(function() {
- $("#invalidAPIkeyAlert").hide();
- });
- } else {
- $("#invalidAPIkeyAlert").show();
- }
- }.bind(this, anyError) // Bind to this environment, so local variable is accesible from inside
- });
- } else {
- newApiKeysObject.push({ "mine" : mineName, "apikey" : mineAPIkey });
- }
- }).promise().done( function(){
- if(!anyError) {
- // Save to Local Storage and reload
- localStorage.setItem("api-keys", JSON.stringify(newApiKeysObject));
- location.reload();
- }
-
- // Hide the window
- $('#apiKeyManagerModal').modal('toggle');
- });
- });
-
-
- $("#listManagerButton").click(function() {
- initializeSavedLists();
- $("#listManagerModal").modal("show");
- })
-
- $("#viewConstraintsButton").click(function() {
- initializeConstraintsList();
- $("#constraintsModal").modal("show");
- })
-
- // Handle the view manager buttons
- $("#viewManagerButton").click(function() {
- // Update the key manager structures
- initializeViewManager();
-
- // Show the window
- $('#viewManagerModal').appendTo("body").modal('show');
- });
-
- $("#resetAllButton").click(function() {
- location.reload();
- });
-
- // Update organism short name filter
- updateOrganismsSidebarFilter();
- createSidebarEvents();
-}
-
-/**
- * Method to initialize the constraint list from the IM table
- */
-
-function initializeConstraintsList() {
- var tableConstraints = window.imTable.query.constraints;
- if(tableConstraints.length > 0) {
- var listHtml = "";
- for(var i = 0; i < tableConstraints.length; i++) {
- if(tableConstraints[i].value) {
- listHtml += "
');
- }
-
- $.when(getDatasetNamesInClass()).done(function(result) {
- if (!window.datasetNamesLoaded) {
- var availableDatasetNames = [];
-
- for (var i = 0; i < result.results.length; i++) {
- if (result.results[i]["item"] != null) {
- if (result.results[i]["item"] == "KEGG pathways data set" || result.results[i]["item"] == "HGNC identifiers" || result.results[i]["item"] == "BioGRID interaction data set" || result.results[i]["item"] == "IntAct interactions data set" || result.results[i]["item"] == "ClinVar data set" || result.results[i]["item"] == "OMIM diseases") {
- continue;
- }
- availableDatasetNames.push({
- label: result.results[i]["item"] + " (" + result.results[i]["count"] + ")",
- value: result.results[i]["item"]
- });
- }
- }
-
- // First remove the form-check elements
- $('#datasetsSelector').empty();
-
- var resultantElementsNumber = result.results.length;
- var resultantElementsArray = [];
-
- for (var i = 0; i < availableDatasetNames.length; i++) {
- resultantElementsArray.push(availableDatasetNames[i]["value"]);
- }
-
- resultantElementsArray.sort();
-
- // At most, 3 elements, which are ordered (top 3)
- if (resultantElementsNumber > 3) {
- resultantElementsNumber = 3;
- }
-
- // Fill the organism short name dropdown with top 5 organisms according to count
- for (var i = 0; i < resultantElementsNumber; i++) {
- var datasetName = resultantElementsArray[i];
- //var datasetCount = "(" + result.results[i]["count"] + ")";
- $("#datasetsSelector").append(
- '');
-
- $('#' + datasetName.replace(/[^a-zA-Z0-9]/g, '')).change(function() {
- if ($(this).is(":checked")) {
- var checkboxValue = $(this).val();
- window.imTableConstraint["datasetName"].push(checkboxValue);
- } else {
- var checkboxValue = $(this).val();
- remove(window.imTableConstraint["datasetName"], checkboxValue);
- }
- updateTableWithConstraints();
- });
- }
-
- window.datasetNamesLoaded = true;
- }
-
- });
- } catch (err) {
- $("#datasetFilterLi").remove();
- console.log(err);
- }
-}
-
-function createPathwaysNameFilter() {
- try {
- $.when(getPathwayNamesInClass()).done(function(result) {
-
- var availablePathwayNames = [];
-
- for (var i = 0; i < result.results.length; i++) {
- if (result.results[i]["item"] != null) {
- availablePathwayNames.push({
- label: result.results[i]["item"] + " (" + result.results[i]["count"] + ")",
- value: result.results[i]["item"]
- });
- }
- }
-
- $("#pathwayNameSearchInput").autocomplete({
- minLength: 3,
- source: function(request, response) {
- var results = $.ui.autocomplete.filter(availablePathwayNames, request.term);
- response(results.slice(0, 15));
- },
- select: function(event, ui) {
- event.preventDefault();
- $("#pathwayNameSearchInput").val(ui.item.value);
-
- // Filter the table
- window.imTableConstraint["pathwayName"].push(ui.item.value);
- updateTableWithConstraints();
-
- var buttonId = ui.item.value.replace(/[^a-zA-Z0-9]/g, '') + "button";
-
- $("#pathwayFilterList").append(
- '
');
-
- $("#" + buttonId).click(function() {
- remove(window.imTableConstraint["pathwayName"], ui.item.value);
- updateTableWithConstraints();
- $("#" + ui.item.value.replace(/[^a-zA-Z0-9]/g, '')).remove();
- });
- },
- focus: function(event, ui) {
- event.preventDefault();
- $("#pathwayNameSearchInput").val(ui.item.value);
- }
- });
-
- });
- } catch (err) {
- $("#pathwayNameFilterLi").remove();
- console.log(err);
- }
-}
-
-/**
- * Method to add the default filters for all mines
- */
-function addDefaultFilters() {
- createPathwaysNameFilter();
- createGoAnnotationFilter();
-}
-
-/**
- * Method to fill the mine selector and add the proper event handling
- */
-function fillMineSelector() {
- if ($('#mineSelector option').length == 0) {
- var windowUrl = new URL(window.location.href);
-
- $.when(getIntermines()).done(function(result) {
- //$('#mineSelector').find('option').remove().end().append('').val('httpCOLONSLASHSLASHwww.humanmine.orgSLASHhumanmineSLASHservice');
-
- // Need to store current mine to append it at the end, or there are some problems with selector events
- var currentMineNameTemp;
- var currentMineUrlTemp;
- for (var i = 0; i < result.instances.length; i++) {
- if (result.instances[i].url.startsWith("https")) continue;
-
- // Temporarily skiping mines with missing concepts for the default filters
- if (result.instances[i].name == "GrapeMine" || result.instances[i].name == "RepetDB" || result.instances[i].name == "Wheat3BMine" || result.instances[i].name == "WormMine" || result.instances[i].name == "XenMine" || result.instances[i].name == "PlanMine") continue;
-
- // Mines giving error when querying the API or not responding
- if (result.instances[i].name == "ModMine" || result.instances[i].name == "MitoMiner") continue;
-
- var mineUrl = result.instances[i].url;
-
- // Check for mines not requiring to format the URL
- if (mineUrl[mineUrl.length - 1] == "/") {
- mineUrl += "service";
- } else {
- mineUrl += "/service";
- }
-
- mineUrl = formatMineURL(mineUrl);
-
- if(result.instances[i].name === window.selectedMineName) {
- currentMineNameTemp = result.instances[i].name;
- currentMineUrlTemp = mineUrl;
- } else {
- $('#mineSelector').append('').val(mineUrl);
- }
-
- // In case that the user gave a mine to be rendered, set it here
- if (windowUrl.searchParams.get("givenMine") && result.instances[i].name == windowUrl.searchParams.get("givenMine")) {
- window.mineUrl = mineUrl;
- window.selectedMineName = result.instances[i].name;
- sessionStorage.setItem('currentClassView', 'Gene');
-
- // Update the imTable
- clearCustomFilters();
- updateElements(window.imTable.history.currentQuery.constraints, "PieChart");
- updateGeneLengthChart(window.imTable.history.currentQuery.constraints, "GeneLengthChart");
- }
-
- }
-
- $('#mineSelector').append('').val(mineUrl);
- $("#mineSelector option[value='" + currentMineUrlTemp + "']").attr("selected","selected");
-
- // Event handling
- $("#mineSelector").change(function(e) {
- // Sanity check
-
- if(!e.eventPhase) return false;
-
- var sanity = true;
- var selectedOption = $("#mineSelector option:selected").text();
- var selectedOptionUrl = $(this).val();
-
- $.ajax({
- 'url': escapeMineURL(selectedOptionUrl),
- data: {},
- async: false,
- error: function(xhr, status) {
- // Check for error and cancel mine switching if an error appeared
-
- // Server or Client errors
- if ((xhr.status >= 500 && xhr.status <= 511) || (xhr.status >= 400 && xhr.status <= 431)) {
- // Show error
- if ($("#unavailableMineAlert").length == 0) {
- $("#navbarResponsive").prepend("
×Sorry, it looks like the " + selectedOption + " server is having problems right now. You can try coming back later, or try browsing a different mine using the mine selector in the top-left corner.
");
-
- $("#closeUnavailableMineAlert").click(function() {
- $("#unavailableMineAlert").hide();
- });
- } else {
- $("#unavailableMineAlert").show();
-}
-
- // Handle error
- sanity = false;
- e.preventDefault();
- e.stopPropagation();
- e.stopImmediatePropagation();
- return false;
- }
- }
- });
-
- if (sanity) {
- // Update settings
- window.mineUrl = selectedOptionUrl;
- window.selectedMineName = selectedOption;
- sessionStorage.setItem('currentClassView', 'Gene');
- window.datasetNamesLoaded = false;
- window.CustomFiltersAdded = false;
-
- // Update LocalStorage if its available
- if (typeof(Storage) !== "undefined") {
- localStorage.setItem("mineUrl", window.mineUrl);
- localStorage.setItem("selectedMineName", window.selectedMineName);
- }
-
- location.reload();
- }
- });
-
- // And now fire change event for the dropdown
- $('#mineSelector').trigger('change');
-
- });
- }
-}
-
-/**
- * Method to handle the Custom filters available in the current selected mine
- */
-function handleCustomFilters() {
- if (!window.CustomFiltersAdded) {
- var mineData = window.minesConfigs.filter(function(v){
- return v.mineName===window.selectedMineName;
- });
-
- if (mineData.length > 0) {
- addCustomFilters();
- setDynamicExpressionDatasetSelectorEvents();
- window.CustomFiltersAdded = true;
- } else {
- // Dataset filter should be the last one
- createDatasetFilter();
- }
- }
-}
-
-function setDynamicExpressionDatasetSelectorEvents() {
- $('body').on('change','#expressionDatasetSelector',function(){
- var selectedDataset = $('#expressionDatasetSelector').val();
-
- if(selectedDataset == "E-MTAB-513") {
- $("#expressionExpressionSelector").hide();
- $("#expressionPvalueSearchInput").hide();
- $("#expressionTstatisticSearchInput").hide();
- $("#expressionTissueSearchInput").show();
- $("#expressionFPKMSearchInput").show();
- } else {
- $("#expressionExpressionSelector").show();
- $("#expressionPvalueSearchInput").show();
- $("#expressionTstatisticSearchInput").show();
- $("#expressionTissueSearchInput").hide();
- $("#expressionFPKMSearchInput").hide();
- }
- });
-}
-
-/**
- * Method updates the piechart and sidebar elements according to the received constraints
- * @param {string} constraints: the new constraints that the im-table is using
- * @param {string} pieChartID: the div id of the pie chart, in order to update it
- */
-function updateElements(constraints, pieChartID) {
- fillMineSelector();
- addDefaultFilters();
- handleCustomFilters();
- initializeKeyManager();
- initializeViewManager();
- addViewManagerSelectOptions();
-
- $.when(getItemsInClass(constraints)).done(function(result) {
- createSidebarEvents();
- updatePieChart(result, pieChartID);
- });
-}
-
-/**
- * Method that initializes and manages the key manager keys using LocalStorage and
- * fills the Key Manager modal accordingly
- */
-function initializeKeyManager() {
- // Check if LocalStorage is available
- if (typeof(Storage) !== "undefined") {
- window.interminesHashMap = [];
- $.when(getIntermines()).done(function(result) {
- // First get the mines
- for (var i = 0; i < result.instances.length; i++) {
- if (result.instances[i].url.startsWith("https")) continue;
-
- // Temporarily skiping mines with missing concepts for the default filters
- if (result.instances[i].name == "GrapeMine" || result.instances[i].name == "RepetDB" || result.instances[i].name == "Wheat3BMine" || result.instances[i].name == "WormMine" || result.instances[i].name == "XenMine" || result.instances[i].name == "PlanMine") continue;
-
- // Mines giving error when querying the API or not responding
- if (result.instances[i].name == "ModMine" || result.instances[i].name == "MitoMiner") continue;
-
- var mineName = result.instances[i].name;
-
- var mineUrl = result.instances[i].url;
-
- // Check for mines not requiring to format the URL
- if (mineUrl[mineUrl.length - 1] == "/") {
- mineUrl += "service";
- } else {
- mineUrl += "/service";
- }
-
- window.interminesHashMap.push({ "mine" : mineName, "mineurl" : mineUrl, "apikey" : "Paste your API key here" });
- }
-
- // Now check that the API keys in LocalStorage are up-to-date
- if (localStorage.getItem("api-keys")) {
- // Maybe there is a new mine since last update, so let's check
- var currentApiKeysObject = JSON.parse(localStorage.getItem("api-keys"));
- for (var i = 0; i < window.interminesHashMap.length; i++) {
- if(!findElementJSONarray(currentApiKeysObject, "mine", window.interminesHashMap[i].mine)) {
- currentApiKeysObject.push({ "mine" : window.interminesHashMap[i].mine, "apikey" : "Paste your API key here" });
- }
- }
- localStorage.setItem("api-keys", JSON.stringify(currentApiKeysObject));
- } else {
- localStorage.setItem("api-keys", JSON.stringify(window.interminesHashMap));
- }
-
- // Finally, feed the API manager modal
- $("#apiKeyManagerModalKeysDiv").html("");
- var uptodateAPIkeysArray = JSON.parse(localStorage.getItem("api-keys"));
- for (var i = 0; i < uptodateAPIkeysArray.length; i++) {
- var htmlToAdd = '
';
-
- if(uptodateAPIkeysArray[i].apikey != "Paste your API key here" && uptodateAPIkeysArray[i].apikey != "") {
- htmlToAdd += '
';
- } else {
- htmlToAdd += '';
- }
-
- $("#apiKeyManagerModalKeysDiv").append(htmlToAdd);
- }
- });
- }
-}
-
-/**
- * Method that initializes and manages the view manager using LocalStorage and
- * fills the view manager modal accordingly
- */
-function initializeViewManager() {
- // First check if LocalStorage is available
- if (typeof(Storage) !== "undefined") {
- // Is the view manager object in Local Storage?
- var currentViewManagerObject;
- if (!localStorage.getItem("view-manager")) {
- localStorage.setItem("view-manager", "[]");
- }
-
- currentViewManagerObject = JSON.parse(localStorage.getItem("view-manager"));
-
-
- // Handle the current views display
- var currentMineViewManagerSettings;
-
- $("#viewManagerModalCurrentViewsDiv").html("");
-
- if(findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName)) {
- currentMineViewManagerSettings = findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName);
- if(currentMineViewManagerSettings.viewNames) {
- var currentMineAndViewSettingsValues = currentMineViewManagerSettings.viewNames.split(",");
- for (var i = 0; i < currentMineAndViewSettingsValues.length; i++) {
- // Add the HTML
- var htmlToAdd = '
';
- htmlToAdd += '
';
- $("#viewManagerModalCurrentViewsDiv").append(htmlToAdd);
-
- // Now handle the remove button
- $("#viewManager" + currentMineAndViewSettingsValues[i] + "RemoveButton").click(function() {
- // Get view name from the label
- var labelViewName = $(this).closest("div").find("label").text();
-
- // Get the current view config
- var currentMineSettings = findElementJSONarray(JSON.parse(localStorage.getItem("view-manager")), "mine", window.selectedMineName);
-
- // Remove the correct one
- var newViewConfig = currentMineSettings.viewNames.split(",");
- remove(newViewConfig, labelViewName);
- newViewConfig = newViewConfig.join(",");
-
- // Update in structure
- currentMineSettings.viewNames = newViewConfig;
-
- // Update in Local Storage
- localStorage.setItem("view-manager", JSON.stringify([currentMineSettings]));
-
- // Remove from list
- $("#viewManager" + labelViewName + "Div").remove();
-
- // Remove from main view
- $("#" + labelViewName + "Button").remove();
-
- // Is list now empty?
- if(currentMineSettings.viewNames.split(",")[0] === "") {
- $("#viewManagerModalCurrentViewsDiv").html("You have not added any custom view for this mine.");
- }
- });
- }
- } else {
- $("#viewManagerModalCurrentViewsDiv").html("You have not added any custom view for this mine.");
- }
- } else {
- $("#viewManagerModalCurrentViewsDiv").html("You have not added any custom view for this mine.");
- }
-
- // Handle the add buton
- $("#viewManagerAddViewButton").click(function() {
- var e = document.getElementById("addViewDropDown");
- var inputViewName = e.options[e.selectedIndex].value;
-
- currentMineViewManagerSettings = findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName)
-
- if(!currentMineViewManagerSettings) {
- currentViewManagerObject.push({ "mine" : window.selectedMineName, "viewNames" : "" });
- currentMineViewManagerSettings = findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName)
- }
-
- var currentViewConfig = currentMineViewManagerSettings.viewNames.split(",");
- if(inputViewName != "Gene" && inputViewName != "Protein" && !currentViewConfig.includes(inputViewName)) {
- currentViewConfig.push(inputViewName);
-
- if(currentViewConfig[0] === "") {
- currentMineViewManagerSettings.viewNames = currentViewConfig[1];
- } else {
- currentMineViewManagerSettings.viewNames = currentViewConfig.join(",");
- }
-
- // Save in LS and reload
- localStorage.setItem("view-manager", JSON.stringify([currentMineViewManagerSettings]));
- location.reload();
- }
- });
- }
-}
-
-/**
- * Method that updates the gene length chart
- * @param {string} geneLengthChartID: the div id of the gene length chart, in order to update it
- */
-function updateGeneLengthChart(constraints, geneLengthChartID) {
- $.when(getGeneLengthsInClass(constraints)).done(function(result) {
- if (window.geneLengthChartObject) {
- window.geneLengthChartObject.destroy();
- }
-
- var ctx = document.getElementById(geneLengthChartID);
-
- var countData = [];
- var labelsData = [];
- var onHoverLabel = [];
- var colorsData = Array(result['results'].length).fill("#337ab7");
-
- // Statistical values
- var uniqueValues = result['uniqueValues'];
- var minimumValue = result['results'][0]['min'];
- var maximumValue = result['results'][0]['max'];
- var averageValue = parseFloat(result['results'][0]['average']).toFixed(3);
- var elementsPerBucket = (maximumValue - minimumValue) / (result['results'][0].buckets);
- var stdevValue = parseFloat(result['results'][0]['stdev']).toFixed(3);
- var chartTitle = "Distribution of " + uniqueValues + " Gene Lengths";
- var chartSubTitle = "Min: " + minimumValue + ". Max: " + maximumValue + ". Avg: " + averageValue + ". Stdev: " + stdevValue;
-
- for (var i = 0; i < result['results'].length - 1; i++) {
- // Lower and upper limits for each bucket
- var lowerLimit = Math.round(minimumValue + (elementsPerBucket * i));
- var upperLimit = Math.round(minimumValue + (elementsPerBucket * (i+1)));
- countData.push(Math.log2(result['results'][i]['count']) + 1);
- labelsData.push(lowerLimit + " to " + upperLimit);
- onHoverLabel.push(lowerLimit + " to " + upperLimit + ": " + result['results'][i]['count'] + " values");
- }
-
- // Plot
- var barChartOptions = {
- responsive: true,
- maintainAspectRatio: false,
- //Boolean - Whether the scale should start at zero, or an order of magnitude down from the lowest value
- scaleBeginAtZero : true,
- elements: {
- center: {
- text: '90%',
- color: '#FF6384', // Default is #000000
- fontStyle: 'Arial', // Default is Arial
- sidePadding: 20 // Default is 20 (as a percentage)
- }
- },
- legend: {
- display: false,
- position: 'top',
- onClick: function(e) {
- e.stopPropagation();
- }
- },
- hover: {
- mode: 'nearest',
- intersect: true,
- },
- title: {
- display: true,
- text: [chartTitle, chartSubTitle],
- position: 'bottom'
- },
- scales: {
- xAxes: [{
- ticks: {
- beginAtZero: false,
- autoSkip: false,
- maxRotation: 90,
- minRotation: 90
- }
- }],
- yAxes: [{
- ticks: {
- beginAtZero: true,
- min: 0,
- display: false
- }
- }]
- },
- tooltips: {
- callbacks: {
- label: function(tooltipItem, data) {
- return onHoverLabel[tooltipItem.index];
- }
- },
- custom: function(tooltip) {
- if (!tooltip.opacity) {
- document.getElementById(geneLengthChartID).style.cursor = 'default';
- return;
- }
- }
- }
- };
-
- window.geneLengthChartObject = new Chart(ctx, {
- type: 'bar',
- data: {
- labels: labelsData,
- datasets: [{
- data: countData,
- backgroundColor: colorsData,
- }],
- },
- options: barChartOptions
- });
- });
-}
diff --git a/public/javascripts/main-view.min.js b/public/javascripts/main-view.min.js
deleted file mode 100644
index 63a63daa..00000000
--- a/public/javascripts/main-view.min.js
+++ /dev/null
@@ -1,278 +0,0 @@
-$(document).ready(function() {
-
- if(!sessionStorage.getItem('currentClassView')) {
- sessionStorage.setItem('currentClassView', 'Gene');
- }
-
- var currentClassView = sessionStorage.getItem('currentClassView');
-
- checkForHTTPS();
- initializeViewButtons();
- handleResponsiveness();
- handleCurrentClassFilter(currentClassView);
-
- window.tableConstraintLogic = "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (Y AND Z AND W AND X)";
-
- document.title = currentClassView + " in HumanMine";
- $("#proteinsButton").removeClass("btn-primary").addClass("btn-default");
- $("#genesButton").removeClass("btn-default").addClass("btn-primary");
- var mineUrl = window.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- // Remove Graphs box if class is not currently Gene or Protein (issue #39)
- if(!["Gene", "Protein"].includes(currentClassView)) {
- $("#graphsBoxBody").hide();
- }
-
- // Instantiate the im-table with all the data available in Gene from HumanMine
- var selector = '#dataTable';
- var service = {
- root: mineUrl,
- token: getSessionToken()
- };
- var query = {
- constraintLogic: window.tableConstraintLogic,
- select: ['*'],
- //select: ['*','goAnnotation.ontologyTerm.name','pathways.name'],
- from: currentClassView
- };
-
- imtables.configure({
- TableCell: {
- PreviewTrigger: 'click'
- }
- });
-
- imtables.configure('TableResults.CacheFactor', 20);
-
- var imtable = imtables.loadDash(
- selector, {
- "start": 0,
- "size": 25
- }, {
- service: service,
- query: query
- }
- ).then(
- function(table) {
- table.children.table.on("rendered", function(changeDetail) {
- document.title = sessionStorage.getItem('currentClassView') + " in " + window.selectedMineName;
- updateElements(table.history.currentQuery.constraints, "PieChart");
- updateGeneLengthChart(table.history.currentQuery.constraints, "GeneLengthChart");
- });
-
- window.imTable = table.children.table;
- },
- function(error) {
- console.error('Could not load table', error);
- }
- );
-});
-
-/**
- * Method that dynamically adds a IN, NOT IN and LOOKUP filter based on the current class to the left sidebar
- * @param {string} currentClassView: the current class being viewed
- */
-function handleCurrentClassFilter(currentClassView) {
- // Add the element to the sidebar
- $("#sidebarUl").prepend(
- '
');
-
- // Handle the events
- $('#' + currentClassView + 'SearchButton').click(function() {
- if (window.currentClassViewFilter) clearCurrentClassViewConstraint();
-
- var currentClassViewInput = $('#' + currentClassView + 'SearchInput').val();
- var currentClassViewSearchType = $('#' + currentClassView + 'SearchTypeSelector').val();
-
- window.currentClassViewFilter = [];
-
- // Any input given?
- if(currentClassViewInput) {
- // LOOKUP, IN or NOTIN ?
- if(currentClassViewSearchType === "LOOKUP") {
- window.imTable.query.addConstraint({
- "path": currentClassView,
- "op": "LOOKUP",
- "value": currentClassViewInput,
- "extraValue": ""
- });
-
- window.currentClassViewFilter.push(window.imTable.query.constraints[window.imTable.query.constraints.length - 1]);
- }
-
- if(currentClassViewSearchType === "IN") {
- window.imTable.query.addConstraint({
- "path": currentClassView,
- "op": "IN",
- "value": currentClassViewInput
- });
-
- window.currentClassViewFilter.push(window.imTable.query.constraints[window.imTable.query.constraints.length - 1]);
- }
-
- if(currentClassViewSearchType === "NOTIN") {
- window.imTable.query.addConstraint({
- "path": currentClassView,
- "op": "NOT IN",
- "value": currentClassViewInput
- });
-
- window.currentClassViewFilter.push(window.imTable.query.constraints[window.imTable.query.constraints.length - 1]);
- }
- }
- });
-
- $('#' + currentClassView + 'ResetButton').click(function() {
- if (window.currentClassViewFilter) clearCurrentClassViewConstraint();
- $("#" + currentClassView + "SearchInput").val('');
- });
-}
-
-/**
- * This method initializes the default view buttons and adds others depending on the mine and user-specific configuration
- */
-function initializeViewButtons() {
- var currentClassView = sessionStorage.getItem('currentClassView');
- var defaultViews = ['Gene','Protein'];
-
- // Add default views
- for (var i = 0; i < defaultViews.length; i++) {
- if(currentClassView === defaultViews[i]) {
- $("#headerButtons").append(
- '');
- } else {
- $("#headerButtons").append(
- '');
- }
-
- $('#' + defaultViews[i] + 'Button').click(function(event) {
- sessionStorage.setItem('currentClassView', String(this.id).split('Button')[0]);
- location.reload();
- });
- }
-
- // Add classes with preferredBagType tag for the current mine
- var mineURL = escapeMineURL(window.mineUrl);
-
- if(mineURL.slice(-1) != "/") {
- mineURL += "/";
- }
-
- mineURL += "model?format=json";
-
- $.when(getMineModel(mineURL)).done(function(result) {
- var mineClasses = JSON.parse(JSON.stringify(result.model.classes));
- var mineClassesArray = [];
- for(var x in mineClasses){
- mineClassesArray.push(mineClasses[x]);
- }
-
- for (var i = 0; i < mineClassesArray.length; i++) {
- if(mineClassesArray[i].tags.includes("im:preferredBagType") && !defaultViews.includes(mineClassesArray[i].name)) {
- if(currentClassView === mineClassesArray[i].name) {
- $("#headerButtons").append(
- '');
- } else {
- $("#headerButtons").append(
- '');
- }
-
- $('#' + mineClassesArray[i].name + 'Button').click(function(event) {
- sessionStorage.setItem('currentClassView', String(this.id).split('Button')[0]);
- location.reload();
- });
- }
- }
- });
-
- // Add custom views
- if (!localStorage.getItem("view-manager")) {
- localStorage.setItem("view-manager", "[]");
- }
-
- var currentViewManagerObject = JSON.parse(localStorage.getItem("view-manager"));
- if(findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName)) {
- var currentMineViewManagerSettings = findElementJSONarray(currentViewManagerObject, "mine", window.selectedMineName);
- if(currentMineViewManagerSettings.viewNames) {
- var currentMineAndViewSettingsValues = currentMineViewManagerSettings.viewNames.split(",");
- for (var i = 0; i < currentMineAndViewSettingsValues.length; i++) {
- // Add the HTML
- if(currentClassView === currentMineAndViewSettingsValues[i]) {
- $("#headerButtons").append(
- '');
- } else {
- $("#headerButtons").append(
- '');
- }
-
- $('#' + currentMineAndViewSettingsValues[i] + 'Button').click(function(event) {
- sessionStorage.setItem('currentClassView', String(this.id).split('Button')[0]);
- location.reload();
- });
- }
- }
- }
-}
-
-/**
- * This method checks if there has been any window resize event to change the navbar padding accordingly
- */
-function handleResponsiveness() {
- var width = $(window).width();
-
- // Initial sizing
- if (width < 992) {
- var navbarHeight = $("#navbarResponsive").height();
- if (width < 770) {
- $("body.fixed-nav").css("padding-top", navbarHeight + 75);
- } else {
- $("body.fixed-nav").css("padding-top", navbarHeight + 56);
- }
- } else {
- $("body.fixed-nav").css("padding-top", "56px");
- }
-
- // Event handling
- $(window).on('resize', function() {
- if ($(this).width() != width) {
- width = $(this).width();
- // Regular device
- if (width < 992) {
- var navbarHeight = $("#navbarResponsive").height();
- if (width < 770) {
- $("body.fixed-nav").css("padding-top", navbarHeight + 75);
- } else {
- $("body.fixed-nav").css("padding-top", navbarHeight + 56);
- }
- }
- // Small device
- else {
- $("body.fixed-nav").css("padding-top", "56px");
- }
- }
- });
-}
-
-/**
- * This method removes any constraint that has been applied to the current class view filter
- */
-function clearCurrentClassViewConstraint() {
- for(var i = 0; i < window.currentClassViewFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.currentClassViewFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.currentClassViewFilter = null;
-}
-
-/**
- * This method checks if the user is using HTTPS protocol to access the browser in order to show an informative warning
- */
-function checkForHTTPS() {
- if (window.location.protocol.includes("https")) {
- $("#navbarResponsive").prepend("
You are currently viewing the HTTPS website. Due to security limitations, we are unable to show results from HTTP-only InterMines. You may be able to see more results if you reload this site via HTTP, and/or allow unsafe scripts to run.
");
- }
-}
diff --git a/public/javascripts/piechart-events.min.js b/public/javascripts/piechart-events.min.js
deleted file mode 100644
index ce69f4a1..00000000
--- a/public/javascripts/piechart-events.min.js
+++ /dev/null
@@ -1 +0,0 @@
-function formatChartClickedSegmentAsConstraintForFilter(r){var t=[[],[]];return t[0].push({path:"organism.shortName",op:"=",value:r.trim(),code:"A"}),t[1].push("A"),1 1) {
- result[1] = result[1].join(" or ");
- } else {
- result[1] = result[1].join("");
- }
-
- return result;
-}
-
-/**
- * This method adds the event handling to the sidebar
- */
-function createSidebarEvents() {
- $('#organismshortnamelist li').click(function() {
- if ($(this).hasClass("checked")) {
- $(this).removeClass("checked");
- $(this).addClass("unchecked");
- } else {
- $(this).addClass("checked");
- $(this).removeClass("unchecked");
- }
-
- var selectedOrganismsArray = $('.checked a p').filter(".float-md-left").toArray();
-
- if(selectedOrganismsArray.length > 0) {
- if(window.organismFilter) clearOrganismConstraint();
-
- window.imTableConstraint["organism"] = [];
-
- for(var i = 0; i < selectedOrganismsArray.length; i++) {
- window.imTableConstraint["organism"].push(selectedOrganismsArray[i].innerHTML);
- }
- } else {
- window.imTableConstraint["organism"] = []
- if(window.organismFilter) clearOrganismConstraint();
- }
-
- updateTableWithConstraints();
- });
-
- $('#btnDatasetViewMore').click(function() {
- if (!window.showingMoreDatasets) {
- window.showingMoreDatasets = true;
- showMoreDatasetNames();
- $('#btnDatasetViewMore').remove();
- }
- });
-}
-
-/**
- * This method removes any constraint that has been applied to the Protein Localisation filter
- */
-function clearProteinLocalisationFilterConstraint() {
- for(var i = 0; i < window.proteinLocalisationFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.proteinLocalisationFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.expressionFilter = null;
-}
-
-/**
- * This method removes any constraint that has been applied to the Expression filter
- */
-function clearExpressionFilterConstraint() {
- for(var i = 0; i < window.expressionFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.expressionFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.expressionFilter = null;
-}
-
-/**
- * This method removes any constraint that has been applied to the Locations filter
- */
-function clearLocationConstraint() {
- for(var i = 0; i < window.locationFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.locationFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.locationFilter = null;
-}
-
-/**
- * This method removes any constraint that has been applied to the Interactions filter
- */
-function clearInteractionsConstraint() {
- for(var i = 0; i < window.interactionsFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.interactionsFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.interactionsFilter = null;
-}
-
-/**
- * This method removes any constraint that has been applied to the Organism filter
- */
-function clearOrganismConstraint() {
- for(var i = 0; i < window.organismFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.organismFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.organismFilter = null;
-}
-
-/**
- * This method removes any constraint that has been applied to the ClinVar filter
- */
-function clearClinVarConstraint() {
- for(var i = 0; i < window.clinVarFilter.length; i++) {
- try {
- window.imTable.query.removeConstraint(window.clinVarFilter[i]);
- }
- catch(err) {
- continue;
- }
- }
- window.clinVarFilter = null;
-}
-
-/**
- * This method adds a dataset constraint to the im-table.
- * @param {string} input the dataset name to be added as a filter
- */
-function addDatasetConstraint(datasetName) {
- // Filter by the selected dataset name
- window.imTable.query.addConstraint({
- "path": "dataSets.name",
- "op": "==",
- "value": datasetName,
- "code": datasetName.replace(/ /g, '')
- });
-}
\ No newline at end of file
diff --git a/public/javascripts/utils.min.js b/public/javascripts/utils.min.js
deleted file mode 100644
index 2a42f1c0..00000000
--- a/public/javascripts/utils.min.js
+++ /dev/null
@@ -1,107 +0,0 @@
-function findElementJSONarray(arr, propName, propValue) {
- for (var i=0; i < arr.length; i++)
- if (arr[i][propName] == propValue)
- return arr[i];
-}
-
-/**
- * Method that escapes a mine URL (to not valid URL format)
- * @param {string} mineURL: the mine URL
- * @returns {string} the escapped mine URL
- */
-function formatMineURL(mineURL) {
- return mineURL.replace(/:/g, "COLON").replace(/\//g, "SLASH");
-}
-
-/**
- * Method that escapes a mine URL (to valid URL format)
- * @param {string} mineURL: the mine URL
- * @returns {string} the formatted mine URL
- */
-function escapeMineURL(mineURL) {
- return mineURL.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-}
-
-/**
- * Method to read a json file from a given location
- */
-function readTextFile(file, callback) {
- var rawFile = new XMLHttpRequest();
- rawFile.overrideMimeType("application/json");
- rawFile.open("GET", file, true);
- rawFile.onreadystatechange = function() {
- if (rawFile.readyState === 4 && rawFile.status == "200") {
- callback(rawFile.responseText);
- }
- }
- rawFile.send(null);
-}
-
-/**
- * Auxiliary function to remove an element from an array
- */
-function remove(arr, what) {
- var found = arr.indexOf(what);
-
- while (found !== -1) {
- arr.splice(found, 1);
- found = arr.indexOf(what);
- }
-}
-
-/**
- * Auxiliary function to flatten an array
- * @param {array} arr: the array to be flattened
- * @returns {array} the flattened array
- */
-function flatten(arr) {
- return arr.reduce(function(flat, toFlatten) {
- return flat.concat(Array.isArray(toFlatten) ? flatten(toFlatten) : toFlatten);
- }, []);
-}
-
-/**
- * This method is used to get an array of hexadecimal colors, following the rainbow pattern, with the given size (useful for plots)
- * @param {number} input the size of the array of colors
- * @returns {array} an array of hexadecimal colors with the specific size, following a rainbow pattern
- */
-function getColorsArray(size) {
- var rainbow = [
- "#fbb735", "#e98931", "#eb403b", "#b32E37", "#6c2a6a",
- "#5c4399", "#274389", "#1f5ea8", "#227FB0", "#2ab0c5",
- "#39c0b3", '#b3cae5', '#dbdde4', '#e4e3e4', '#f7ddbb', '#efcab2',
- '#bccacc', '#c7d8d6', '#d9ebe0', '#ebf9e3', '#f4f8d0',
- '#5e7fb1', '#dce8f7', '#eff1f4', '#fce1a8', '#f7ec86',
- '#8fb8ee', '#cbe2f4', '#dbe5eb', '#f9d3b8', '#e0b2a3',
- '#a2e0f9', '#cef5fc', '#eafaeb', '#fefcd3', '#fdf4ba',
- '#6bafd2', '#a4c8dc', '#d6cbca', '#eabc96', '#db8876',
- '#b4ced8', '#d7e5d4', '#e2e8c9', '#f1e5b9', '#edd7ac',
- '#29153e', '#657489', '#bfb6aa', '#ead79d', '#f2ebda',
- '#20202f', '#273550', '#416081', '#adacb2', '#eac3a2',
- '#555351', '#555351', '#8d7b6c', '#cc9d7a', '#fff9aa',
- '#171c33', '#525f83', '#848896', '#bb9d78', '#f6e183',
- '#ffe3c8', '#efad9e', '#c79797', '#a78a92', '#857d8d',
- '#6f749e', '#9a8daf', '#d0a8b9', '#f8bbb1', '#fde6b1',
- '#536a97', '#8087ad', '#bca391', '#bd968a', '#a38b8a',
- '#325176', '#7b9ea7', '#9baf93', '#dbaf81', '#fbdf73',
- '#727288', '#8e889b', '#d3c2bd', '#f9d89a', '#f8c785',
- '#506e90', '#7695aa', '#a7bdb8', '#e2e2b8', '#fdf998',
- '#634b5f', '#868080', '#b7b29b', '#dfd6a4', '#e9f3a2',
- '#7e74b2', '#b3a2c2', '#e2cdbe', '#f6cf97', '#f4a77a',
- '#34a4ca', '#59d7dd', '#a8f2f0', '#d0f8ef', '#d6f6e1',
- '#7696cd', '#8fb2e4', '#b0cff0', '#d7e5ec', '#dee0e7',
- '#8dd6c3', '#c5e5e2', '#eafaeb', '#f9f7ca', '#fceea1',
- '#4e72c7', '#6d9ed7', '#a4c8d5', '#b4d9e1', '#c4d9d6',
- '#47565f', '#5b625a', '#947461', '#f98056', '#f7ec86',
- '#95b3bf', '#c6cdd3', '#e5d8d9', '#f1e1d9', '#f3e1cd',
- '#4c86ab', '#95a5bc', '#bfcdc9', '#dcd6c9', '#edd9c7',
- '#0f124a', '#1b2360', '#515b80', '#758391', '#e5e3b0',
- '#889db6', '#a5b8ce', '#c1cfdd', '#dee1e4', '#d5d1cf',
- '#74bddb', '#a8d1eb', '#cddbf5', '#e4e6fb', '#f6f4f8',
- '#a7d3cb', '#bcc1c4', '#e5cab3', '#fee6c5', '#fdecd0',
- '#325571', '#8e9fa4', '#decab2', '#f2d580', '#ffa642',
- '#c5d4d7', '#d6b98d', '#c99262', '#8c5962', '#43577e'
- ];
-
- return rainbow;
-}
\ No newline at end of file
diff --git a/public/mine_configs/mines_config.json b/public/mine_configs/mines_config.json
deleted file mode 100644
index 601bd092..00000000
--- a/public/mine_configs/mines_config.json
+++ /dev/null
@@ -1,108 +0,0 @@
-[
- {
- "mineName": "HumanMine",
- "customFilters": [
- {
- "filterQuery": [{
- "path": "alleles.type",
- "op": "==",
- "value": "AAA",
- "code": "O"
- },
- {
- "path": "alleles.clinicalSignificance",
- "op": "==",
- "value": "BBB",
- "code": "S"
- }
- ],
- "filterName": "CLINVAR"
- },
- {
- "filterQuery": [{
- "path": "diseases.name",
- "op": "ONE OF",
- "values": "AAA",
- "code": "P"
- }
- ],
- "filterName": "Diseases"
- },
- {
- "filterQuery": [{
- "path": "proteins.proteinDomainRegions.proteinDomain.name",
- "op": "ONE OF",
- "values": "AAA",
- "code": "Q"
- }
- ],
- "filterName": "Protein-Domain"
- },
- {
- "filterQuery": [{
- "path": "interactions.participant2.symbol",
- "op": "==",
- "value": "AAA",
- "code": "T"
- },
- {
- "path": "interactions.details.type",
- "op": "==",
- "value": "BBB",
- "code": "U"
- },
- {
- "path": "interactions.details.dataSets.name",
- "op": "==",
- "value": "CCC",
- "code": "V"
- }
- ],
- "filterName": "Interactions"
- },
- {
- "filterQuery": [{
- "path": "atlasExpression.pValue",
- "op": ">=",
- "value": "AAA",
- "code": "W"
- },
- {
- "path": "atlasExpression.tStatistic",
- "op": ">=",
- "value": "BBB",
- "code": "X"
- },
- {
- "path": "atlasExpression.expression",
- "op": ">=",
- "value": "CCC",
- "code": "Y"
- },
- {
- "path": "atlasExpression.dataSets.name",
- "op": "==",
- "value": "DDD",
- "code": "Z"
- },
- {
- "path": "atlasExpression.condition",
- "op": "==",
- "value": "BBB",
- "code": "X"
- }
- ],
- "filterName": "Expression"
- },
- {
- "filterQuery": [{
- "path": "diseases.hpoAnnotations.hpoTerm.name",
- "op": "ONE OF",
- "values": "AAA",
- "code": "R"
- }],
- "filterName": "Phenotype"
- }
- ]
- }
-]
\ No newline at end of file
diff --git a/public/mine_configs/mines_preferred_organisms.json b/public/mine_configs/mines_preferred_organisms.json
deleted file mode 100644
index ab122643..00000000
--- a/public/mine_configs/mines_preferred_organisms.json
+++ /dev/null
@@ -1,6 +0,0 @@
-[
- {
- "mineName": "FlyMine",
- "preferredOrganisms": ["D. persimilis", "D. sechellia", "D. yakuba", "D. ananassae", "D. grimshawi", "D. simulans", "D. virilis", "D. erecta", "D. rerio", "D. melanogaster", "D. pseudoobscura", "D. willistoni", "D. mojavensis"]
- }
-]
\ No newline at end of file
diff --git a/public/stylesheets/data-browser-style-main.css b/public/stylesheets/data-browser-style-main.css
deleted file mode 100644
index ec2bf2f7..00000000
--- a/public/stylesheets/data-browser-style-main.css
+++ /dev/null
@@ -1,706 +0,0 @@
-/* The alert message box */
-.alert {
- background-color: #f44336;
- /* Red */
- color: white;
- position: absolute;
- top: 100px;
- left: 50%;
- margin-left: -300px;
- width: 600px;
- transform: translateY(-50%);
- z-index: 1000;
-}
-
-/* The close button */
-.closebtn {
- margin-left: 15px;
- color: white;
- font-weight: bold;
- float: right;
- font-size: 22px;
- line-height: 20px;
- cursor: pointer;
- transition: 0.3s;
-}
-
-/* When moving the mouse over the close button */
-.closebtn:hover {
- color: black;
-}
-
-.ui-autocomplete {
- position: absolute;
- top: 100%;
- left: 0;
- z-index: 1000;
- display: none;
- float: left;
- min-width: 160px;
- padding: 5px 0;
- margin: 2px 0 0;
- list-style: none;
- font-size: 14px;
- text-align: left;
- background-color: #ffffff;
- border: 1px solid #cccccc;
- border: 1px solid rgba(0, 0, 0, 0.15);
- border-radius: 4px;
- -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
- box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
- background-clip: padding-box;
-}
-
-.centeredSelect {
- display: block;
- margin: 0 auto;
-}
-
-.ui-autocomplete > li > div {
- display: block;
- padding: 3px 20px;
- clear: both;
- font-weight: normal;
- line-height: 1.42857143;
- color: #333333;
- white-space: nowrap;
-}
-
-.ui-state-hover,
-.ui-state-active,
-.ui-state-focus {
- text-decoration: none;
- color: #262626;
- background-color: #f5f5f5;
- cursor: pointer;
-}
-
-.ui-helper-hidden-accessible {
- border: 0;
- clip: rect(0 0 0 0);
- height: 1px;
- margin: -1px;
- overflow: hidden;
- padding: 0;
- position: absolute;
- width: 1px;
-}
-
-html {
- position: relative;
- min-height: 100%;
-}
-
-body {
- overflow-x: hidden;
-}
-
-body.sticky-footer {
- margin-bottom: 56px;
-}
-
-body.sticky-footer .content-wrapper {
- min-height: calc(100vh - 56px - 56px);
-}
-
-.checked {
- background-color: #a4eafc;
-}
-
-body.fixed-nav {
- padding-top: 56px;
-}
-
-@media screen and (max-width: 991px) {
- body.fixed-nav {
- padding-top: calc(56px * 8.5);
- }
-}
-
-.content-wrapper {
- min-height: calc(100vh - 56px);
- padding-top: 1rem;
-}
-
-.scroll-to-top {
- position: fixed;
- right: 15px;
- bottom: 3px;
- display: none;
- width: 50px;
- height: 50px;
- text-align: center;
- color: white;
- background: rgba(52, 58, 64, 0.5);
- line-height: 45px;
-}
-
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diff --git a/public/stylesheets/hmb-style-main.css b/public/stylesheets/hmb-style-main.css
deleted file mode 100644
index 7da2a1c4..00000000
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diff --git a/public/stylesheets/hmb-style-main.min.css b/public/stylesheets/hmb-style-main.min.css
deleted file mode 100644
index bc0179e5..00000000
--- a/public/stylesheets/hmb-style-main.min.css
+++ /dev/null
@@ -1 +0,0 @@
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.navbar-nav>.nav-item.dropdown>.nav-link:after{float:right;width:auto;content:'\f105';border:none;font-family:FontAwesome}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link .indicator{position:absolute;top:5px;left:21px;font-size:10px}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown.show>.nav-link:after{content:'\f107'}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown .dropdown-menu>.dropdown-item>.dropdown-message{overflow:hidden;max-width:none;text-overflow:ellipsis}@media (min-width:992px){#mainNav .navbar-brand{width:250px}#mainNav .navbar-collapse{overflow:visible;max-height:none}#mainNav .navbar-collapse .navbar-sidenav{position:absolute;top:0;left:0;-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column;margin-top:56px}#mainNav .navbar-collapse .navbar-sidenav>.nav-item{width:250px;padding:0}#mainNav .navbar-collapse .navbar-sidenav>.nav-item>.nav-link{padding:1em}#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level,#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level{padding-left:0;list-style:none}#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li,#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li{width:250px}#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a,#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a{padding:1em}#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a{padding-left:2.75em}#mainNav .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a{padding-left:3.75em}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link{min-width:0}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link:after{width:24px;text-align:center}#mainNav .navbar-collapse .navbar-nav>.nav-item.dropdown .dropdown-menu>.dropdown-item>.dropdown-message{max-width:300px}}#mainNav.fixed-top 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#mainNav.fixed-top #sidenavToggler i{-webkit-transform:scaleX(-1);-moz-transform:scaleX(-1);-o-transform:scaleX(-1);transform:scaleX(-1);filter:FlipH;-ms-filter:FlipH}#mainNav.static-top .sidenav-toggler{display:none}@media (min-width:992px){#mainNav.static-top .sidenav-toggler{display:flex}}body.sidenav-toggled #mainNav.static-top #sidenavToggler i{-webkit-transform:scaleX(-1);-moz-transform:scaleX(-1);-o-transform:scaleX(-1);transform:scaleX(-1);filter:FlipH;-ms-filter:FlipH}.content-wrapper{overflow-x:hidden;background:#fff}@media (min-width:992px){.content-wrapper{margin-left:250px}}#sidenavToggler i{font-weight:800}.navbar-sidenav-tooltip.show{display:none}@media (min-width:992px){body.sidenav-toggled .content-wrapper{margin-left:55px}}body.sidenav-toggled .navbar-sidenav{width:55px}body.sidenav-toggled .navbar-sidenav .nav-link-text{display:none}body.sidenav-toggled .navbar-sidenav .nav-item,body.sidenav-toggled .navbar-sidenav .nav-link{width:55px!important}body.sidenav-toggled .navbar-sidenav .nav-item:after,body.sidenav-toggled .navbar-sidenav .nav-link:after{display:none}body.sidenav-toggled .navbar-sidenav .nav-item{white-space:nowrap}body.sidenav-toggled .navbar-sidenav-tooltip.show{display:flex}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav .nav-link-collapse:after{color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item>.nav-link{color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item>.nav-link:hover{color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a{color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:focus,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:hover,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:focus,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:hover{color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link:after{color:#e9ecef}@media (min-width:992px){#mainNav.navbar-dark .navbar-collapse .navbar-sidenav{background:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav li.active a{color:#fff!important;background-color:#e9ecef}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav li.active a:focus,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav li.active a:hover{color:#fff}#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level,#mainNav.navbar-dark .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level{background:#e9ecef}}#mainNav.navbar-light .navbar-collapse .navbar-sidenav .nav-link-collapse:after{color:rgba(0,0,0,.5)}#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item>.nav-link{color:rgba(0,0,0,.9)}#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item>.nav-link:hover{color:rgba(0,0,0,.4)}#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a,#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a{color:rgba(0,0,0,.9)}#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:focus,#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:hover,#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:focus,#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:hover{color:rgba(0,0,0,.4)}#mainNav.navbar-light .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link:after{color:rgba(253,126,20,.5)}@media (min-width:992px){#mainNav.navbar-light .navbar-collapse .navbar-sidenav{background:#e9ecef}#mainNav.navbar-light .navbar-collapse .navbar-sidenav li.active a{color:#e9ecef!important;background-color:#e9ecef}#mainNav.navbar-light .navbar-collapse .navbar-sidenav li.active a:focus,#mainNav.navbar-light .navbar-collapse .navbar-sidenav li.active a:hover{color:#e9ecef}#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level,#mainNav.navbar-light .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level{background:#e9ecef}}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav .nav-link-collapse:after{color:rgba(0,0,0,.5)}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item>.nav-link{color:rgba(0,0,0,.5)}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item>.nav-link:hover{color:rgba(0,0,0,.7)}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a{color:rgba(0,0,0,.5)}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:focus,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level>li>a:hover,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:focus,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level>li>a:hover{color:rgba(0,0,0,.7)}#mainNav.navbar-orange .navbar-collapse .navbar-nav>.nav-item.dropdown>.nav-link:after{color:rgba(0,0,0,.5)}@media (min-width:992px){#mainNav.navbar-orange .navbar-collapse .navbar-sidenav{background:#e9ecef}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav li.active a{color:#e9ecef!important;background-color:#e9ecef}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav li.active a:focus,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav li.active a:hover{color:#e9ecef}#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-second-level,#mainNav.navbar-orange .navbar-collapse .navbar-sidenav>.nav-item .sidenav-third-level{background:#e9ecef}}.card-body-icon{position:absolute;z-index:0;top:-25px;right:-25px;font-size:5rem;-webkit-transform:rotate(15deg);-ms-transform:rotate(15deg);transform:rotate(15deg)}@media (min-width:576px){.card-columns{column-count:1}}@media (min-width:768px){.card-columns{column-count:2}}@media (min-width:1200px){.card-columns{column-count:2}}.card-login{max-width:25rem}.card-register{max-width:40rem}footer.sticky-footer{position:absolute;right:0;bottom:0;width:100%;height:56px;background-color:#e9ecef;line-height:55px}@media (min-width:992px){footer.sticky-footer{width:calc(100% - 250px)}}@media (min-width:992px){body.sidenav-toggled footer.sticky-footer{width:calc(100% - 55px)}}#loader{position:absolute;left:50%;top:40%;z-index:1;width:150px;height:150px;margin:-75px 0 0 -75px;border:16px solid #f3f3f3;border-radius:50%;border-top:16px solid #3498db;width:120px;height:120px;-webkit-animation:spin 2s linear infinite;animation:spin 2s linear infinite}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0)}100%{-webkit-transform:rotate(360deg)}}@keyframes spin{0%{transform:rotate(0)}100%{transform:rotate(360deg)}}.animate-bottom{position:relative;-webkit-animation-name:animatebottom;-webkit-animation-duration:1s;animation-name:animatebottom;animation-duration:1s}@-webkit-keyframes animatebottom{from{bottom:-100px;opacity:0}to{bottom:0;opacity:1}}@keyframes animatebottom{from{bottom:-100px;opacity:0}to{bottom:0;opacity:1}}.badge{display:inline}#accordion .glyphicon{margin-right:0}.panel-collapse>.list-group .list-group-item:first-child{border-top-right-radius:0;border-top-left-radius:0}.panel-collapse>.list-group .list-group-item{border-width:1px 0}.panel-collapse>.list-group{margin-bottom:0}.panel-collapse .list-group-item{border-radius:0}.panel-collapse .list-group .list-group{margin:0;margin-top:30px}.panel-collapse .list-group-item li.list-group-item{margin:0 0;border-top:1px solid #ddd!important;border-bottom:0;padding-left:0}.panel-collapse .list-group-item li.list-group-item:last-child{padding-bottom:0}.panel-collapse div.list-group div.list-group{margin:0}.panel-collapse div.list-group .list-group a.list-group-item{border-top:1px solid #ddd!important;border-bottom:0;padding-left:0}.panel-collapse .list-group-item li.list-group-item{border-top:1px solid #ddd!important}.checkbox{padding-left:20px}.checkbox label{display:inline-block;vertical-align:middle;position:relative;padding-left:5px}.checkbox label::before{content:"";display:inline-block;position:absolute;width:17px;height:17px;left:0;margin-left:-20px;border:1px solid #ccc;border-radius:3px;background-color:#fff;-webkit-transition:border .15s ease-in-out,color .15s ease-in-out;-o-transition:border .15s ease-in-out,color .15s ease-in-out;transition:border .15s ease-in-out,color .15s ease-in-out}.checkbox 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label::after{display:inline-block;position:absolute;content:" ";width:11px;height:11px;left:3px;top:3px;margin-left:-20px;border-radius:50%;background-color:#555;-webkit-transform:scale(0,0);-ms-transform:scale(0,0);-o-transform:scale(0,0);transform:scale(0,0);-webkit-transition:-webkit-transform .1s cubic-bezier(.8,-.33,.2,1.33);-moz-transition:-moz-transform .1s cubic-bezier(.8,-.33,.2,1.33);-o-transition:-o-transform .1s cubic-bezier(.8,-.33,.2,1.33);transition:transform .1s cubic-bezier(.8,-.33,.2,1.33)}.radio input[type=radio]{opacity:0;z-index:1}.radio input[type=radio]:focus+label::before{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}.radio input[type=radio]:checked+label::after{-webkit-transform:scale(1,1);-ms-transform:scale(1,1);-o-transform:scale(1,1);transform:scale(1,1)}.radio input[type=radio]:disabled+label{opacity:.65}.radio input[type=radio]:disabled+label::before{cursor:not-allowed}.radio.radio-inline{margin-top:0}.radio-primary input[type=radio]+label::after{background-color:#428bca}.radio-primary input[type=radio]:checked+label::before{border-color:#428bca}.radio-primary input[type=radio]:checked+label::after{background-color:#428bca}.radio-danger input[type=radio]+label::after{background-color:#d9534f}.radio-danger input[type=radio]:checked+label::before{border-color:#d9534f}.radio-danger input[type=radio]:checked+label::after{background-color:#d9534f}.radio-info input[type=radio]+label::after{background-color:#5bc0de}.radio-info input[type=radio]:checked+label::before{border-color:#5bc0de}.radio-info input[type=radio]:checked+label::after{background-color:#5bc0de}.radio-warning input[type=radio]+label::after{background-color:#f0ad4e}.radio-warning input[type=radio]:checked+label::before{border-color:#f0ad4e}.radio-warning input[type=radio]:checked+label::after{background-color:#f0ad4e}.radio-success input[type=radio]+label::after{background-color:#5cb85c}.radio-success input[type=radio]:checked+label::before{border-color:#5cb85c}.radio-success input[type=radio]:checked+label::after{background-color:#5cb85c}.saved-list-item{overflow-x:scroll}
\ No newline at end of file
diff --git a/public/stylesheets/style.css b/public/stylesheets/style.css
deleted file mode 100644
index 9453385b..00000000
--- a/public/stylesheets/style.css
+++ /dev/null
@@ -1,8 +0,0 @@
-body {
- padding: 50px;
- font: 14px "Lucida Grande", Helvetica, Arial, sans-serif;
-}
-
-a {
- color: #00B7FF;
-}
diff --git a/routes/fetch.js b/routes/fetch.js
deleted file mode 100644
index 33c17b11..00000000
--- a/routes/fetch.js
+++ /dev/null
@@ -1,430 +0,0 @@
-var express = require('express');
-var imjs = require('imjs');
-var request = require('request');
-var router = express.Router();
-var jsdom = require("jsdom");
-const {
- JSDOM
-} = jsdom;
-const {
- document
-} = (new JSDOM('')).window;
-global.document = document;
-global.window = document.defaultView;
-var $ = require('jquery');
-
-/**
- * Method that formats a mine URL
- * @param {string} mineURL: the mine URL
-* @returns {string} the formatted mine URL
- */
-function formatMineURL(mineURL) {
- return mineURL.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-}
-
-/**
- * GET Pathway Names from HumanMine inside a class (parameter)
- */
-router.get('/pathways/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["pathways.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "pathways.name",
- "direction": "ASC"
- }]
- };
-
- var pathways = new imjs.Query(query, service),
- pathwaysPath = [query.from, query.select[0]].join('.');
- pathways.summarize(pathwaysPath).then(function(pathwaySummary) {
- //This returns the pathway name and the number of gene rows associated with the pathway
- res.json(pathwaySummary);
- });
-});
-
-/**
- * GET Protein Atlas Expression Tissue Names from HumanMine inside a class (parameter)
- */
-router.get('/proteinatlastissuenames/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["proteinAtlasExpression.tissue.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "proteinAtlasExpression.tissue.name",
- "direction": "ASC"
- }]
- };
-
- var theQuery = new imjs.Query(query, service),
- queryPath = [query.from, query.select[0]].join('.');
- theQuery.summarize(queryPath).then(function(querySummary) {
- res.json(querySummary);
- });
-});
-
-/**
- * GET Protein Atlas Expression Cell Types from HumanMine inside a class (parameter)
- */
-router.get('/proteinatlascelltypes/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["proteinAtlasExpression.cellType", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "proteinAtlasExpression.cellType",
- "direction": "ASC"
- }]
- };
-
- var theQuery = new imjs.Query(query, service),
- queryPath = [query.from, query.select[0]].join('.');
- theQuery.summarize(queryPath).then(function(querySummary) {
- res.json(querySummary);
- });
-});
-
-/**
- * GET Clinical Significance values from HumanMine inside a class (parameter)
- */
-router.get('/clinicalsignificance/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["alleles.clinicalSignificance", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "alleles.clinicalSignificance",
- "direction": "ASC"
- }]
- };
-
- var theQuery = new imjs.Query(query, service),
- queryPath = [query.from, query.select[0]].join('.');
- theQuery.summarize(queryPath).then(function(querySummary) {
- //This returns the pathway name and the number of gene rows associated with the pathway
- res.json(querySummary);
- });
-});
-
-/**
- * GET Alleles Type values from HumanMine inside a class (parameter)
- */
-router.get('/allelestype/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["alleles.type", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "alleles.type",
- "direction": "ASC"
- }]
- };
-
- var theQuery = new imjs.Query(query, service),
- queryPath = [query.from, query.select[0]].join('.');
- theQuery.summarize(queryPath).then(function(querySummary) {
- //This returns the pathway name and the number of gene rows associated with the pathway
- res.json(querySummary);
- });
-});
-
-/**
- * GET Diseases Names from HumanMine inside a class (parameter)
- */
-router.get('/diseases/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["diseases.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "diseases.name",
- "direction": "ASC"
- }]
- };
-
- var diseases = new imjs.Query(query, service),
- diseasesPath = [query.from, query.select[0]].join('.');
- diseases.summarize(diseasesPath).then(function(diseasesSummary) {
- //This returns the pathway name and the number of gene rows associated with the pathway
- res.json(diseasesSummary);
- });
-});
-
-/**
- * GET Datasets Names from HumanMine inside a class (parameter)
- */
-router.get('/datasets/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["dataSets.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "dataSets.name",
- "direction": "ASC"
- }]
- };
-
- var datasets = new imjs.Query(query, service),
- datasetsPath = [query.from, query.select[0]].join('.');
- datasets.summarize(datasetsPath).then(function(datasetSummary) {
- res.json(datasetSummary);
- });
-});
-
-/**
- * GET Ontology Terms from HumanMine inside a class (parameter)
- */
-router.get('/ontologyterms/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- if (className == "Gene") {
- var query = {
- "from": className,
- "select": ["goAnnotation.ontologyTerm.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "goAnnotation.ontologyTerm.name",
- "direction": "ASC"
- }]
- };
-
- var goterms = new imjs.Query(query, service),
- gotermsPath = [query.from, query.select[0]].join('.');
- goterms.summarize(gotermsPath).then(function(gotermSummary) {
- res.json(gotermSummary);
- });
-
- }
-
- if (className == "Protein") {
- var query = {
- "from": className,
- "select": ["ontologyAnnotations.ontologyTerm.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "ontologyAnnotations.ontologyTerm.name",
- "direction": "ASC"
- }]
- };
-
- var goterms = new imjs.Query(query, service),
- gotermsPath = [query.from, query.select[0]].join('.');
- goterms.summarize(gotermsPath).then(function(gotermSummary) {
- res.json(gotermSummary);
- });
- }
-});
-
-/**
- * GET Protein Domain Name from HumanMine
- */
-router.get('/proteindomainname/:mineUrl', function(req, res, next) {
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
-
- var query = {
- "from": "Gene",
- "select": ["proteins.proteinDomainRegions.proteinDomain.name", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "proteins.proteinDomainRegions.proteinDomain.name",
- "direction": "ASC"
- }]
- };
-
- var protdomname = new imjs.Query(query, service),
- protdomnamePath = [query.from, query.select[0]].join('.');
- protdomname.summarize(protdomnamePath).then(function(protdomnameSummary) {
- res.json(protdomnameSummary);
- });
-
-
-});
-
-/**
- * GET Interaction Participant 2 Gene Symbol from HumanMine
- */
-router.get('/participant2genesymbols/:mineUrl', function(req, res, next) {
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": "Gene",
- "select": ["interactions.participant2.symbol"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "interactions.participant2.symbol",
- "direction": "ASC"
- }]
- };
-
- var part2genesymbol = new imjs.Query(query, service),
- part2genesymbolPath = [query.from, query.select[0]].join('.');
- part2genesymbol.summarize(part2genesymbolPath).then(function(part2genesymbolSummary) {
- res.json(part2genesymbolSummary);
- });
-
-
-});
-
-/**
- * GET Phenotype Names from HumanMine inside a class (parameter)
- */
-router.get('/phenotypes/:mineUrl', function(req, res, next) {
- var mineUrl = formatMineURL(req.params.mineUrl);
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": "Gene" ,
- "select": [
- "diseases.hpoAnnotations.hpoTerm.name",
- "primaryIdentifier"
- ],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "symbol",
- "direction": "ASC"
- }]
- };
-
- var pathways = new imjs.Query(query, service),
- pathwaysPath = [query.from, query.select[0]].join('.');
- pathways.summarize(pathwaysPath).then(function(pathwaySummary) {
- //This returns the pathway name and the number of gene rows associated with the pathway
- res.json(pathwaySummary);
- });
-});
-
-router.post('/lists/:mineUrl', function(req, res, next) {
- const mineUrl = formatMineURL(req.params.mineUrl);
- const { apiKey } = req.body;
- const token = apiKey || null;
- var service = new imjs.Service({
- root: mineUrl,
- token
- });
- service.fetchLists().then(lists => res.json(lists));
-});
-module.exports = router;
\ No newline at end of file
diff --git a/routes/statistics.js b/routes/statistics.js
deleted file mode 100644
index 38959fb9..00000000
--- a/routes/statistics.js
+++ /dev/null
@@ -1,257 +0,0 @@
-var express = require('express');
-var imjs = require('imjs');
-var request = require('request');
-var router = express.Router();
-
-/**
- * GET endpoint to retrieve the count of items per class in HumanMine.
- */
-router.get('/count/primary/:mineUrl', function(req, res, next) {
- var mineUrl = req.params.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- var result = []
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": 'Gene',
- "select": ['primaryIdentifier']
- };
-
- service.count(query).then(function(response) {
- result.push({
- "name": "Gene",
- "count": response
- });
- var query = {
- "from": 'Protein',
- "select": ['primaryIdentifier']
- };
- service.count(query).then(function(response) {
- result.push({
- "name": "Protein",
- "count": response
- });
- res.json(result);
- })
-
- })
-});
-
-/**
- * POST count of items inside a class (parameter) using custom constraints in HumanMine
- */
-router.post('/count/items/:mineUrl/:classname', function(req, res, next) {
- var constraints = req.body;
- var className = req.params.classname;
- var mineUrl = req.params.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var result = []
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- if (className == "Gene") {
- var query = {
- "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
- "from": 'Gene',
- "select": ['primaryIdentifier'],
- "model": {
- 'name': 'genomic'
- },
- "where": constraints
- };
-
- var q = new imjs.Query(query, service);
-
- q.summarize("Gene.organism.shortName", 50)
- .then(function(response) {
- result.push({
- "itemName": "Organism short name",
- "response": response
- });
- res.json(result);
- }).catch(function(error) {
- console.log('error');
- console.log(error.message);
- });
-
- }
-
- if (className == "Protein") {
- var query = {
- "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
- "from": 'Protein',
- "select": ['primaryIdentifier'],
- "model": {
- 'name': 'genomic'
- },
- "where": constraints
- };
-
- var q = new imjs.Query(query, service);
-
- q.summarize("Protein.organism.shortName", 10)
- .then(function(response) {
- result.push({
- "itemName": "Organism short name",
- "response": response
- });
- res.json(result);
- }).catch(function(error) {
- console.log('error');
- console.log(error.message);
- });
- }
-
-});
-
-/**
- * POST Gene Lengths summaries from a mine inside a class (parameter) using custom constraints
- */
-router.post('/genelength/:mineUrl/:classname', function(req, res, next) {
- var constraints = req.body;
- var className = req.params.classname;
- var mineUrl = req.params.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
- "from": className,
- "select": ["length", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "where": constraints,
- "orderBy": [{
- "path": "length",
- "direction": "ASC"
- }]
- };
-
- var genelengths = new imjs.Query(query, service),
- genelengthsPath = [query.from, query.select[0]].join('.');
- genelengths.summarize(genelengthsPath).then(function(genelengthsSummary) {
- //This returns the gene length and the number of gene rows associated with the gene length
- res.json(genelengthsSummary);
- });
-});
-
-/**
- * GET Gene Lengths summaries from a mine inside a class (parameter)
- */
-router.get('/genelength/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = req.params.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- var query = {
- "from": className,
- "select": ["length", "primaryIdentifier"],
- "model": {
- "name": "genomic"
- },
- "orderBy": [{
- "path": "length",
- "direction": "ASC"
- }]
- };
-
- var genelengths = new imjs.Query(query, service),
- genelengthsPath = [query.from, query.select[0]].join('.');
- genelengths.summarize(genelengthsPath).then(function(genelengthsSummary) {
- //This returns the gene length and the number of gene rows associated with the gene length
- res.json(genelengthsSummary);
- });
-});
-
-/**
- * GET count of items inside a class (parameter) in HumanMine
- */
-router.get('/count/items/:mineUrl/:classname', function(req, res, next) {
- var className = req.params.classname;
- var mineUrl = req.params.mineUrl.replace(/COLON/g, ":").replace(/SLASH/g, "/");
-
- if (className != "Protein" && className != "Gene") {
- res.status(500).send('You need to specify a valid class: Protein, Gene');
- }
-
- var result = []
-
- var service = new imjs.Service({
- root: mineUrl
- });
-
- if (className == "Gene") {
- var query = {
- "from": 'Gene',
- "select": ['primaryIdentifier'],
- "model": {
- 'name': 'genomic'
- }
- };
-
- var q = new imjs.Query(query, service);
-
- q.summarize("Gene.organism.shortName", 10)
- .then(function(response) {
- result.push({
- "itemName": "Organism short name",
- "response": response
- });
- res.json(result);
- }).catch(function(error) {
- console.log('error');
- console.log(error.message);
- });
-
- }
-
- if (className == "Protein") {
- var query = {
- "from": 'Protein',
- "select": ['primaryIdentifier'],
- "model": {
- 'name': 'genomic'
- }
- };
-
- var q = new imjs.Query(query, service);
-
- q.summarize("Protein.organism.shortName", 10)
- .then(function(response) {
- result.push({
- "itemName": "Organism short name",
- "response": response
- });
- res.json(result);
- }).catch(function(error) {
- console.log('error');
- console.log(error.message);
- });
- }
-
-});
-
-module.exports = router;
\ No newline at end of file
diff --git a/src/css/hmb-style-main.css b/src/css/hmb-style-main.css
index 941b5b01..b30849bd 100644
--- a/src/css/hmb-style-main.css
+++ b/src/css/hmb-style-main.css
@@ -143,13 +143,23 @@ body.fixed-nav {
text-overflow: ellipsis;
}
+#headerButtons {
+ display: flex;
+ flex-wrap: nowrap;
+ margin: 5px;
+}
+
@media (min-width: 992px) {
- #mainNav .navbar-brand {
- width: 250px;
+ #mainNav {
+ display: flex;
+ justify-content: space-between;
}
#mainNav .navbar-collapse {
overflow: visible;
max-height: none;
+ position: fixed;
+ top: 0;
+ left: 0;
}
#mainNav .navbar-collapse .navbar-sidenav {
position: absolute;
@@ -158,7 +168,7 @@ body.fixed-nav {
-webkit-flex-direction: column;
-ms-flex-direction: column;
flex-direction: column;
- margin-top: 56px;
+ margin-top: 63px;
}
#mainNav .navbar-collapse .navbar-sidenav > .nav-item {
width: 250px;
@@ -404,6 +414,7 @@ body.sidenav-toggled .navbar-sidenav-tooltip.show {
@media (min-width: 992px) {
#mainNav.navbar-light .navbar-collapse .navbar-sidenav {
background: #e9ecef;
+ min-height: calc(100vh - 61px);
}
#mainNav.navbar-light .navbar-collapse .navbar-sidenav li.active a {
color: #e9ecef !important;
diff --git a/src/js/api-requests.js b/src/js/api-requests.js
new file mode 100644
index 00000000..7c8d9bf8
--- /dev/null
+++ b/src/js/api-requests.js
@@ -0,0 +1,603 @@
+/**
+ * Method to get the different intermines names and URLs from the registry
+ * @returns {array} an array with the server response containing the different intermines with their URLs
+ */
+function getIntermines() {
+ return $.ajax({
+ url: 'https://registry.intermine.org/service/instances?mines=%27prod%27',
+ type: 'GET',
+ error: function(e) {
+ console.log(e);
+ },
+ success: function(data) {}
+ })
+}
+
+// Methods from old /fetch route
+
+
+/**
+ * Method to get the different pathway names inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different pathway names
+ */
+function getPathwayNamesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["pathways.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "pathways.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var pathways = new imjs.Query(query, service),
+ pathwaysPath = [query.from, query.select[0]].join('.');
+ pathways.summarize(pathwaysPath).then(function(pathwaySummary) {
+ //This returns the pathway name and the number of gene rows associated with the pathway
+ resolve(pathwaySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different ontology terms inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different ontology terms
+ */
+function getOntologyTermsInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ if (className == "Gene") {
+ var query = {
+ "from": className,
+ "select": ["goAnnotation.ontologyTerm.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "goAnnotation.ontologyTerm.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var goterms = new imjs.Query(query, service),
+ gotermsPath = [query.from, query.select[0]].join('.');
+ goterms.summarize(gotermsPath).then(function(gotermSummary) {
+ resolve(gotermSummary);
+ });
+
+ }
+
+ if (className == "Protein") {
+ var query = {
+ "from": className,
+ "select": ["ontologyAnnotations.ontologyTerm.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "ontologyAnnotations.ontologyTerm.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var goterms = new imjs.Query(query, service),
+ gotermsPath = [query.from, query.select[0]].join('.');
+ goterms.summarize(gotermsPath).then(function(gotermSummary) {
+ resolve(gotermSummary);
+ });
+ }
+ })
+}
+
+/**
+ * Method to get the different alleles clinical significance inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different alleles clinical significances
+ */
+function getAllelesClinicalSignifanceInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["alleles.clinicalSignificance", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "alleles.clinicalSignificance",
+ "direction": "ASC"
+ }]
+ };
+
+ var theQuery = new imjs.Query(query, service),
+ queryPath = [query.from, query.select[0]].join('.');
+ theQuery.summarize(queryPath).then(function(querySummary) {
+ //This returns the pathway name and the number of gene rows associated with the pathway
+ resolve(querySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different protein atlas expression cell types inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different protein atlas expression cell types
+ */
+function getProteinAtlasExpressionCellTypesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["proteinAtlasExpression.cellType", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "proteinAtlasExpression.cellType",
+ "direction": "ASC"
+ }]
+ };
+
+ var theQuery = new imjs.Query(query, service),
+ queryPath = [query.from, query.select[0]].join('.');
+ theQuery.summarize(queryPath).then(function(querySummary) {
+ resolve(querySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different protein atlas expression tissue names inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different protein atlas expression tissue names
+ */
+function getProteinAtlasExpressionTissueNamesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["proteinAtlasExpression.tissue.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "proteinAtlasExpression.tissue.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var theQuery = new imjs.Query(query, service),
+ queryPath = [query.from, query.select[0]].join('.');
+ theQuery.summarize(queryPath).then(function(querySummary) {
+ resolve(querySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different alleles types inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different alleles types
+ */
+function getAllelesTypesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["alleles.type", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "alleles.type",
+ "direction": "ASC"
+ }]
+ };
+
+ var theQuery = new imjs.Query(query, service),
+ queryPath = [query.from, query.select[0]].join('.');
+ theQuery.summarize(queryPath).then(function(querySummary) {
+ //This returns the pathway name and the number of gene rows associated with the pathway
+ resolve(querySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different dataset names inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different dataset names
+ */
+function getDatasetNamesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["dataSets.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "dataSets.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var datasets = new imjs.Query(query, service),
+ datasetsPath = [query.from, query.select[0]].join('.');
+ datasets.summarize(datasetsPath).then(function(datasetSummary) {
+ resolve(datasetSummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different diseases names inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different diseases names
+ */
+function getDiseasesNamesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ if (className != "Protein" && className != "Gene") {
+ reject('You need to specify a valid class: Protein, Gene');
+ }
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": className,
+ "select": ["diseases.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "diseases.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var diseases = new imjs.Query(query, service),
+ diseasesPath = [query.from, query.select[0]].join('.');
+ diseases.summarize(diseasesPath).then(function(diseasesSummary) {
+ resolve(diseasesSummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different protein domain names inside a class in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different protein domain names
+ */
+function getProteinDomainNamesInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": "Gene",
+ "select": ["proteins.proteinDomainRegions.proteinDomain.name", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "proteins.proteinDomainRegions.proteinDomain.name",
+ "direction": "ASC"
+ }]
+ };
+
+ var protdomname = new imjs.Query(query, service),
+ protdomnamePath = [query.from, query.select[0]].join('.');
+ protdomname.summarize(protdomnamePath).then(function(protdomnameSummary) {
+ resolve(protdomnameSummary);
+ });
+ })
+}
+
+/**
+ * Method to get the different Participant 2 gene symbols in order to feed the typeahead
+ * @returns {array} an array with the server response containing the different participant 2 gene symbols in Interactions
+ */
+function getParticipant2SymbolsInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": "Gene",
+ "select": ["interactions.participant2.symbol"],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "interactions.participant2.symbol",
+ "direction": "ASC"
+ }]
+ };
+
+ var part2genesymbol = new imjs.Query(query, service),
+ part2genesymbolPath = [query.from, query.select[0]].join('.');
+ part2genesymbol.summarize(part2genesymbolPath).then(function(part2genesymbolSummary) {
+ resolve(part2genesymbolSummary);
+ });
+ })
+}
+
+function getPhenotypeNames(className, constraints) {
+ return new Promise((resolve, reject) => {
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "from": "Gene" ,
+ "select": [
+ "diseases.hpoAnnotations.hpoTerm.name",
+ "primaryIdentifier"
+ ],
+ "model": {
+ "name": "genomic"
+ },
+ "orderBy": [{
+ "path": "symbol",
+ "direction": "ASC"
+ }]
+ };
+
+ var pathways = new imjs.Query(query, service),
+ pathwaysPath = [query.from, query.select[0]].join('.');
+ pathways.summarize(pathwaysPath).then(function(pathwaySummary) {
+ //This returns the pathway name and the number of gene rows associated with the pathway
+ resolve(pathwaySummary);
+ });
+ })
+}
+
+/**
+ * Method to get the summary of gene length inside a class (in buckets) in order to feed the bar graph
+ * @param {array} constraints: the constraints for the endpoint call
+ * @returns {array} an array with the server response containing the summaries
+ */
+function getSavedLists() {
+ var hm = window.interminesHashMap;
+ var apiKey;
+ for(var i = 0; i < hm.length; ++i) {
+ var mineData = hm[i];
+ if(window.formatMineURL(mineData.mineurl) === window.mineUrl) {
+ var apiKeyArray = JSON.parse(localStorage.getItem('api-keys'));
+ for(var j = 0; j < apiKeyArray.length; ++j) {
+ if(mineData.mine === apiKeyArray[j].mine) {
+ apiKey = apiKeyArray[j].apikey;
+ break;
+ }
+ }
+ }
+ }
+
+
+ return new Promise((resolve, reject) => {
+ const token = apiKey || null;
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl),
+ token
+ });
+ service.fetchLists().then(lists => resolve(lists));
+ })
+}
+
+//
+
+/**
+* Method that returns a valid session API key for the current mine
+*/
+function getSessionToken() {
+
+ // Check if the user has a session token in Local Storage, for this mine
+ if (typeof(Storage) !== "undefined") {
+ if (localStorage.getItem("api-keys")) {
+ var apiKeysObject = JSON.parse(localStorage.getItem("api-keys"));
+ if(findElementJSONarray(apiKeysObject, "mine", window.selectedMineName)) {
+ var apiKeyForThisMine = findElementJSONarray(apiKeysObject, "mine", window.selectedMineName)["apikey"];
+ if(apiKeyForThisMine && apiKeyForThisMine != "" && apiKeyForThisMine != "Paste your API key here") {
+ // Change the added/not added API key icon
+ $("#APIKeyIconNotAdded").hide();
+ $("#APIKeyIconAdded").show();
+ return apiKeyForThisMine;
+ }
+ }
+ }
+ }
+
+ // Otherwise get a public one from the session route
+ var tokenUrl = escapeMineURL(window.mineUrl);
+ var tokenKey = "";
+
+ if(tokenUrl.slice(-1) == "/") {
+ tokenUrl += "session";
+ } else {
+ tokenUrl += "/session";
+ }
+
+ // Get token
+ $.ajax({
+ 'url': tokenUrl,
+ data: {},
+ async: false,
+ error: function(xhr, status) {},
+ success: function(data) {
+ tokenKey = data.token;
+ }
+ });
+
+ return tokenKey;
+}
+
+/**
+ * Method to get the model of a mine given its query service
+ * @returns {array} an array with the server response with the mine model
+ */
+function getMineModel(serviceUrl) {
+ return $.ajax({
+ url: serviceUrl,
+ type: 'GET',
+ contentType: "application/json; charset=utf-8",
+ dataType: "json",
+ error: function(e) {
+ console.log(e);
+ },
+ success: function(data) {}
+ })
+}
+
+/**
+ * Method to get the summary of gene length inside a class (in buckets) in order to feed the bar graph
+ * @param {array} constraints: the constraints for the endpoint call
+ * @returns {array} an array with the server response containing the summaries
+ */
+function getGeneLengthsInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ var query = {
+ "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
+ "from": className,
+ "select": ["length", "primaryIdentifier"],
+ "model": {
+ "name": "genomic"
+ },
+ "where": constraints,
+ "orderBy": [{
+ "path": "length",
+ "direction": "ASC"
+ }]
+ };
+
+ var genelengths = new imjs.Query(query, service),
+ genelengthsPath = [query.from, query.select[0]].join('.');
+ genelengths.summarize(genelengthsPath).then(function(genelengthsSummary) {
+ //This returns the gene length and the number of gene rows associated with the gene length
+ resolve(genelengthsSummary);
+ }).catch(function(error) {
+ reject(error.message);
+ });
+ });
+}
+
+/**
+ * Method to get the different items inside a class (count per organism) in order to feed the sidebar
+ * @param {array} constraints: the constraints for the endpoint call
+ * @returns {array} an array with the server response containing the different items in a class
+ */
+function getItemsInClass(className, constraints) {
+ return new Promise((resolve, reject) => {
+ var result = [];
+
+ var service = new imjs.Service({
+ root: escapeMineURL(window.mineUrl)
+ });
+
+ if (className == "Gene") {
+ var query = {
+ "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
+ "from": 'Gene',
+ "select": ['primaryIdentifier'],
+ "model": {
+ 'name': 'genomic'
+ },
+ "where": constraints
+ };
+
+ var q = new imjs.Query(query, service);
+
+ q.summarize("Gene.organism.shortName", 50)
+ .then(function(response) {
+ result.push({
+ "itemName": "Organism short name",
+ "response": response
+ });
+ resolve(result);
+ }).catch(function(error) {
+ reject(error.message);
+ });
+
+ }
+
+ if (className == "Protein") {
+ var query = {
+ "constraintLogic": "(A OR B OR C OR D OR E OR F OR G OR H OR I OR J) AND (K) AND (L) AND (M) AND (N) AND (O) AND (P) AND (Q) AND (R) AND (O AND S) AND (T AND U AND V) AND (W AND X AND Y AND Z)",
+ "from": 'Protein',
+ "select": ['primaryIdentifier'],
+ "model": {
+ 'name': 'genomic'
+ },
+ "where": constraints
+ };
+
+ var q = new imjs.Query(query, service);
+
+ q.summarize("Protein.organism.shortName", 10)
+ .then(function(response) {
+ result.push({
+ "itemName": "Organism short name",
+ "response": response
+ });
+ resolve(result);
+ }).catch(function(error) {
+ reject(error.message);
+ });
+ }
+ })
+}
\ No newline at end of file
diff --git a/src/js/common.js b/src/js/common.js
index 494e0287..1832e0ed 100644
--- a/src/js/common.js
+++ b/src/js/common.js
@@ -42,7 +42,7 @@ function initializeStartupConfiguration() {
});
// Initial mine service url (HumanMine), name and view
- window.mineUrl = "httpCOLONSLASHSLASHwww.humanmine.orgSLASHhumanmineSLASHservice";
+ window.mineUrl = "httpsCOLONSLASHSLASHwww.humanmine.orgSLASHhumanmineSLASHservice";
window.selectedMineName = "HumanMine";
if(!sessionStorage.getItem('currentClassView')) {
sessionStorage.setItem('currentClassView', 'Gene');
@@ -139,7 +139,11 @@ function initializeStartupConfiguration() {
});
// Update organism short name filter
- updateOrganismsSidebarFilter();
+ try {
+ updateOrganismsSidebarFilter();
+ } catch (err) {
+ console.log("There was an error updating the organism sidebar filter: ", err);
+ }
createSidebarEvents();
}
@@ -170,7 +174,7 @@ function initializeConstraintsList() {
function initializeSavedLists(){
if(window.savedListsInitialized) return;
- $.when(getSavedLists()).then(function(result) {
+ getSavedLists().then(function(result) {
var formElement = '';
var listElements = result.map(function(list) {
return "
" + list.title + "
"
@@ -385,7 +389,7 @@ function addViewManagerSelectOptions() {
* Method to expand the dataset names filter, showing the remaining ones and adding the appropriate event handling to them
*/
function showMoreDatasetNames() {
- $.when(getDatasetNamesInClass()).done(function(result) {
+ getDatasetNamesInClass(sessionStorage.getItem('currentClassView'), []).then(function(result) {
var availableDatasetNames = [];
for (var i = 0; i < result.results.length; i++) {
@@ -644,7 +648,7 @@ function addCustomFilters() {
$("#sidebarUl").append(
'
');
try {
- $.when(getPhenotypeNames()).done(function(result) {
+ getPhenotypeNames(sessionStorage.getItem('currentClassView'), []).then(function(result) {
var availablePhenotypeNames = [];
@@ -1172,8 +1176,9 @@ function addCustomFilters() {
* @param {string} results: the organism query results from the InterMine server
*/
function updateOrganismsSidebarFilter() {
+ var className = sessionStorage.getItem('currentClassView');
- $.when(getItemsInClass([])).done(function(result) {
+ getItemsInClass(className, []).then(function(result) {
// First remove the li elements
$('#organismshortnamelist').parent().find('li').remove();
@@ -1236,7 +1241,6 @@ function updateOrganismsSidebarFilter() {
* @param {string} results: the organism query results from the InterMine server
*/
function updatePieChart(result, pieChartID) {
-
// Update pie
if (window.pieChartObject) {
window.pieChartObject.destroy();
@@ -1419,7 +1423,7 @@ function updatePieChart(result, pieChartID) {
function createGoAnnotationFilter() {
try {
- $.when(getOntologyTermsInClass()).done(function(result) {
+ getOntologyTermsInClass(sessionStorage.getItem('currentClassView'), []).then(function(result) {
var availableGoTerms = [];
@@ -1479,7 +1483,7 @@ function createDatasetFilter() {
'
