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README.md
README.md

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Neo4j

Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.

This repository contains following two sub-projects.

  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.

  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.

Prerequisites

To run the project you need to get the following prerequisites.

  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+

Installing

  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.

  • Download the latest source code by cloning the git repository.

git clone https://github.com/intermine/neo4j.git

  • Change the current directory to project directory. cd neo4j

intermine-neo4j

  • Change the current directory to project directory. cd intermine-neo4j

  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.

  • To build the project, run ./gradlew build

  • To see the list of all available taks and their description, run ./gradlew tasks --all.

  • To execute a particular task, run ./gradlew <taskName>

intermine-neo4jwebapp

  • Change the current directory to project directory. cd intermine-neo4jwebapp

  • To run a local instance of the server, run ./gradlew jettyRun

  • For Swagger documentation of the API, visit http://localhost:8080/.

  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.

Documentation

The project wiki contains detailed documentation of the code and the available gradle tasks.

About

Project to develop Neo4j as the backing store for InterMine

Topics

intermineneo4j

Resources

Readme
Activity
Custom properties

Stars

6 stars

Watchers

8 watching

Forks

9 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
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var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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README.md
README.md
Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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intermine-neo4j
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.editorconfig
.editorconfig
README.md
README.md
Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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intermine-neo4jwebapp
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.editorconfig
.editorconfig
README.md
README.md
Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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BranchesTags
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355 Commits
Folders and files
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intermine-neo4j
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.editorconfig
.editorconfig
README.md
README.md
Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
355 Commits
Folders and files
NameName
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intermine-neo4j
intermine-neo4j
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.editorconfig
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README.md
README.md
Repository files navigation
Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
Topics
intermineneo4j
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
8 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Neo4j
Project to develop Neo4j as the backing store for InterMine. Hosted at http://intermine-neo4jwebapp.herokuapp.com/.
This repository contains following two sub-projects.
  • intermine-neo4j contains the packages for Neo4j metadata management, PathQuery to Cypher conversion and data loaders for InterMine Neo4j database.
  • intermine-neo4jwebapp contains the web service API endpoint and servlets from which you can query InterMine Neo4j database.
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. We use gradle wrapper for building the project.
Prerequisites
To run the project you need to get the following prerequisites.
  • JDK 8
  • Neo4j Graph Database 3.2
  • Neo4j APOC 3+
Installing
  • Place the apoc-3.1.*.jar file to the plugins directory inside your local neo4j database directory. For example, inside /home/yourusername/neo4j-community-3.2.0/plugins.
  • Download the latest source code by cloning the git repository.
git clone https://github.com/intermine/neo4j.git
  • Change the current directory to project directory.
cd neo4j
intermine-neo4j
  • Change the current directory to project directory.
cd intermine-neo4j
  • Update your Neo4j Database URL, InterMine Service URL, credentials and other information in neo4jloader.properties file.
  • To build the project, run
./gradlew build
  • To see the list of all available taks and their description, run
./gradlew tasks --all.
  • To execute a particular task, run
./gradlew <taskName>
intermine-neo4jwebapp
  • Change the current directory to project directory.
cd intermine-neo4jwebapp
  • To run a local instance of the server, run
./gradlew jettyRun
  • For Swagger documentation of the API, visit http://localhost:8080/.
  • For testing PathQueryServlets, visit http://localhost:8080/servlet/.
Documentation
The project wiki contains detailed documentation of the code and the available gradle tasks.
About
Project to develop Neo4j as the backing store for InterMine
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