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DataSHIELD Interface Python

GitHub ActionsPyPI version

This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.

Configuration

The search path for the DataSHIELD configuration file is the following:

  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml

The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).

The format of the DataSHIELD configuration file is:

servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver

Each server entry in the list must have:

  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")

About

DataSHIELD Client Interface in Python

Resources

Readme
LGPL-2.1 license
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Custom properties

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2 stars

Watchers

1 watching

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0 forks
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} 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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DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
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0 forks
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Used by
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
DataSHIELD Interface Python
GitHub ActionsPyPI version
This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.
Configuration
The search path for the DataSHIELD configuration file is the following:
  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml
The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).
The format of the DataSHIELD configuration file is:
servers:
- name: server1url: https://opal-demo.obiba.orguser: dsuserpassword: P@ssw0rd
- name: server2url: https://opal.example.orgtoken: your-access-token-hereprofile: default
- name: server3url: https://study.example.org/opaluser: dsuserpassword: P@ssw0rdprofile: customdriver: datashield_opal.OpalDriver
Each server entry in the list must have:
  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")
About
DataSHIELD Client Interface in Python
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages