@@ -0,0 +1,9 @@ | |||||
__pycache__ | |||||
*.pyc | |||||
node_modules | |||||
/frontend/dist/ | |||||
/backend/server.pem | |||||
/testdata/ | |||||
/backend/supervisord/supervisord.log | |||||
/dockerfiles/wba/files/wba/dist | |||||
/package-lock.json |
@@ -0,0 +1,77 @@ | |||||
import aiohttp | |||||
from aiohttp import web | |||||
from argparse import ArgumentParser | |||||
import ssl | |||||
import json | |||||
def options_fetch_blocks(request): | |||||
return web.Response(headers={ 'Access-Control-Allow-Origin': '*' }) | |||||
async def post_fetch_blocks(request): | |||||
body = await request.read() | |||||
body = json.loads(body) | |||||
proxy_host = body['keepProxyHost'] | |||||
arv_token = body['arvToken'] | |||||
segments = body['segments'] | |||||
use_ssl = body['useSsl'] \ | |||||
if 'useSsl' in body \ | |||||
else True | |||||
protocol = 'https://' \ | |||||
if use_ssl \ | |||||
else 'http://' | |||||
name = body['name'] \ | |||||
if 'name' in body \ | |||||
else None | |||||
content_type = body['contentType'] \ | |||||
if 'contentType' in body \ | |||||
else 'application/octet-stream' | |||||
res = web.StreamResponse() | |||||
res.content_type = content_type | |||||
if name: | |||||
res.headers['Content-Disposition'] = 'attachment; filename*=UTF-8\'\'"' + name + '"' | |||||
else: | |||||
res.headers['Content-Disposition'] = 'inline' | |||||
res.headers['Access-Control-Allow-Origin'] = '*' | |||||
await res.prepare(request) | |||||
async with aiohttp.ClientSession(connector=aiohttp.TCPConnector(verify_ssl=False)) as session: | |||||
for seg in segments: | |||||
url = protocol + proxy_host + '/' + seg[0] | |||||
async with session.get(url, headers={ 'Authorization': 'OAuth2 ' + arv_token }) as response: | |||||
block = await response.read() | |||||
block = block[seg[1]:seg[2]] | |||||
await res.write(block) | |||||
return res | |||||
def get_index(request): | |||||
return web.Response(text='Use /fetch-blocks to stream files from Keep') | |||||
def create_parser(): | |||||
parser = ArgumentParser() | |||||
parser.add_argument('--port', type=int, default=50080) | |||||
parser.add_argument('--ssl-cert', type=str, default=None) | |||||
return parser | |||||
def main(): | |||||
parser = create_parser() | |||||
args = parser.parse_args() | |||||
app = web.Application() | |||||
app.add_routes([ | |||||
web.get('/', get_index), | |||||
web.post('/fetch-blocks', post_fetch_blocks), | |||||
web.options('/fetch-blocks', options_fetch_blocks) | |||||
]) | |||||
if args.ssl_cert: | |||||
ssl_context = ssl.SSLContext(ssl.PROTOCOL_SSLv23) | |||||
ssl_context.load_cert_chain(args.ssl_cert) | |||||
else: | |||||
ssl_context = None | |||||
web.run_app(app, port=args.port, ssl_context=ssl_context) | |||||
if __name__ == '__main__': | |||||
main() |
@@ -0,0 +1,42 @@ | |||||
error_log /dev/null; | |||||
pid nginx.pid; | |||||
daemon off; | |||||
events { | |||||
} | |||||
http { | |||||
include /pstore/data/data_science/app/modules/nginx-1.17.8/conf/mime.types; | |||||
access_log /dev/null; | |||||
server { | |||||
listen 50080; | |||||
server_name rkalbhpc002.kau.roche.com; | |||||
client_body_temp_path tmp/client_body_temp; | |||||
fastcgi_temp_path tmp/fastcgi_temp; | |||||
proxy_temp_path tmp/proxy_temp; | |||||
scgi_temp_path tmp/scgi_temp; | |||||
uwsgi_temp_path tmp/uwsgi_temp; | |||||
if ( $request_uri ~ \.(js|css|html|woff|ttf|svg|woff2|eot|svg)$ ) { | |||||
break; | |||||
} | |||||
if ( $request_uri ~ ^/fetch-blocks$ ) { | |||||
break; | |||||
} | |||||
rewrite .* /index.html; | |||||
location / { | |||||
root /pstore/home/adaszews/workspace/arvados-workbench-advanced/frontend/dist; | |||||
index index.html; | |||||
} | |||||
location /fetch-blocks { | |||||
proxy_pass http://localhost:12358/fetch-blocks; | |||||
} | |||||
} | |||||
} |
@@ -0,0 +1,15 @@ | |||||
import BaseHTTPServer, SimpleHTTPServer | |||||
import ssl | |||||
class RequestHandler(SimpleHTTPServer.SimpleHTTPRequestHandler): | |||||
def do_GET(self): | |||||
print(self.path) | |||||
if '.' not in self.path: | |||||
self.path = '/' | |||||
SimpleHTTPServer.SimpleHTTPRequestHandler.do_GET(self) | |||||
# RequestHandler, self).do_GET() | |||||
httpd = BaseHTTPServer.HTTPServer(('0.0.0.0', 4445), RequestHandler) | |||||
httpd.socket = ssl.wrap_socket (httpd.socket, certfile='/pstore/home/adaszews/workspace/arvados-workbench-advanced/backend/server.pem', server_side=True) | |||||
httpd.serve_forever() | |||||
@@ -0,0 +1,4 @@ | |||||
[supervisord] | |||||
[program:wba-nginx] | |||||
command=/pstore/data/data_science/app/modules/nginx-1.17.8/sbin/nginx -p /pstore/home/adaszews/workspace/arvados-workbench-advanced/backend/nginx |
@@ -0,0 +1,10 @@ | |||||
FROM alpine:3.11.3 | |||||
RUN apk update && \ | |||||
apk add nginx gettext supervisor | |||||
COPY files/wba /wba | |||||
RUN chown -R nginx /wba/nginx/tmp /wba/nginx/run | |||||
ENTRYPOINT /bin/sh -c "cd /wba/supervisord/run && /usr/bin/supervisord -c /wba/supervisord/supervisord.conf" |
@@ -0,0 +1,18 @@ | |||||
# This is a default site configuration which will simply return 404, preventing | |||||
# chance access to any other virtualhost. | |||||
server { | |||||
listen ${PORT0} default_server; | |||||
listen [::]:${PORT0} default_server; | |||||
# Everything is a 404 | |||||
location / { | |||||
return 404; | |||||
} | |||||
# You may need this to prevent return 404 recursion. | |||||
location = /404.html { | |||||
internal; | |||||
} | |||||
} | |||||
@@ -0,0 +1,41 @@ | |||||
error_log /dev/null; | |||||
pid run/nginx.pid; | |||||
daemon off; | |||||
events { | |||||
} | |||||
http { | |||||
include /etc/nginx/mime.types; | |||||
access_log /dev/null; | |||||
server { | |||||
listen ${PORT0}; | |||||
server_name wba.ecaas.emea.roche.com; | |||||
client_body_temp_path tmp/client_body_temp; | |||||
fastcgi_temp_path tmp/fastcgi_temp; | |||||
proxy_temp_path tmp/proxy_temp; | |||||
scgi_temp_path tmp/scgi_temp; | |||||
uwsgi_temp_path tmp/uwsgi_temp; | |||||
if ( $request_uri ~ \.(js|css|html|woff|ttf|svg|woff2|eot|svg)$ ) { | |||||
break; | |||||
} | |||||
if ( $request_uri ~ ^/fetch-blocks$ ) { | |||||
break; | |||||
} | |||||
rewrite .* /index.html; | |||||
location / { | |||||
root /wba/dist; | |||||
index index.html; | |||||
} | |||||
location /fetch-blocks { | |||||
proxy_pass http://localhost:12358/fetch-blocks; | |||||
} | |||||
} | |||||
} |
@@ -0,0 +1,8 @@ | |||||
[supervisord] | |||||
logfile=/dev/null | |||||
nodaemon=true | |||||
user=root | |||||
[program:wba-nginx] | |||||
command=/usr/sbin/nginx -p /wba/nginx -c conf/nginx.conf | |||||
user=nginx |
@@ -0,0 +1,731 @@ | |||||
{ | |||||
"requires": true, | |||||
"lockfileVersion": 1, | |||||
"dependencies": { | |||||
"@babel/code-frame": { | |||||
"version": "7.8.3", | |||||
"resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.8.3.tgz", | |||||
"integrity": "sha512-a9gxpmdXtZEInkCSHUJDLHZVBgb1QS0jhss4cPP93EW7s+uC5bikET2twEF3KV+7rDblJcmNvTR7VJejqd2C2g==", | |||||
"requires": { | |||||
"@babel/highlight": "7.8.3" | |||||
} | |||||
}, | |||||
"@babel/highlight": { | |||||
"version": "7.8.3", | |||||
"resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.8.3.tgz", | |||||
"integrity": "sha512-PX4y5xQUvy0fnEVHrYOarRPXVWafSjTW9T0Hab8gVIawpl2Sj0ORyrygANq+KjcNlSSTw0YCLSNA8OyZ1I4yEg==", | |||||
"requires": { | |||||
"chalk": "2.4.2", | |||||
"esutils": "2.0.3", | |||||
"js-tokens": "4.0.0" | |||||
} | |||||
}, | |||||
"@babel/runtime": { | |||||
"version": "7.8.4", | |||||
"resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.8.4.tgz", | |||||
"integrity": "sha512-neAp3zt80trRVBI1x0azq6c57aNBqYZH8KhMm3TaB7wEI5Q4A2SHfBHE8w9gOhI/lrqxtEbXZgQIrHP+wvSGwQ==", | |||||
"requires": { | |||||
"regenerator-runtime": "0.13.3" | |||||
} | |||||
}, | |||||
"@fortawesome/fontawesome-free": { | |||||
"version": "5.12.0", | |||||
"resolved": "https://registry.npmjs.org/@fortawesome/fontawesome-free/-/fontawesome-free-5.12.0.tgz", | |||||
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}, | |||||
"@types/estree": { | |||||
"version": "0.0.39", | |||||
"resolved": "https://registry.npmjs.org/@types/estree/-/estree-0.0.39.tgz", | |||||
"integrity": "sha512-EYNwp3bU+98cpU4lAWYYL7Zz+2gryWH1qbdDTidVd6hkiR6weksdbMadyXKXNPEkQFhXM+hVO9ZygomHXp+AIw==" | |||||
}, | |||||
"@types/node": { | |||||
"version": "13.7.2", | |||||
"resolved": "https://registry.npmjs.org/@types/node/-/node-13.7.2.tgz", | |||||
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}, | |||||
"acorn": { | |||||
"version": "6.4.0", | |||||
"resolved": "https://registry.npmjs.org/acorn/-/acorn-6.4.0.tgz", | |||||
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}, | |||||
"acorn-dynamic-import": { | |||||
"version": "4.0.0", | |||||
"resolved": "https://registry.npmjs.org/acorn-dynamic-import/-/acorn-dynamic-import-4.0.0.tgz", | |||||
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}, | |||||
"acorn-jsx": { | |||||
"version": "5.1.0", | |||||
"resolved": "https://registry.npmjs.org/acorn-jsx/-/acorn-jsx-5.1.0.tgz", | |||||
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}, | |||||
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"integrity": "sha1-DNkKVhCT810KmSVsIrcGlDP60Rc=", | |||||
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"kind-of": "3.2.2", | |||||
"longest": "1.0.1", | |||||
"repeat-string": "1.6.1" | |||||
} | |||||
}, | |||||
"ansi-styles": { | |||||
"version": "3.2.1", | |||||
"resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-3.2.1.tgz", | |||||
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"color-convert": "1.9.3" | |||||
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}, | |||||
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"version": "1.0.10", | |||||
"resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz", | |||||
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"requires": { | |||||
"sprintf-js": "1.0.3" | |||||
} | |||||
}, | |||||
"bootstrap": { | |||||
"version": "4.4.1", | |||||
"resolved": "https://registry.npmjs.org/bootstrap/-/bootstrap-4.4.1.tgz", | |||||
"integrity": "sha512-tbx5cHubwE6e2ZG7nqM3g/FZ5PQEDMWmMGNrCUBVRPHXTJaH7CBDdsLeu3eCh3B1tzAxTnAbtmrzvWEvT2NNEA==" | |||||
}, | |||||
"buble": { | |||||
"version": "0.19.8", | |||||
"resolved": "https://registry.npmjs.org/buble/-/buble-0.19.8.tgz", | |||||
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"chalk": "2.4.2", | |||||
"magic-string": "0.25.6", | |||||
"minimist": "1.2.0", | |||||
"os-homedir": "2.0.0", | |||||
"regexpu-core": "4.6.0" | |||||
} | |||||
}, | |||||
"builtin-modules": { | |||||
"version": "2.0.0", | |||||
"resolved": "https://registry.npmjs.org/builtin-modules/-/builtin-modules-2.0.0.tgz", | |||||
"integrity": "sha512-3U5kUA5VPsRUA3nofm/BXX7GVHKfxz0hOBAPxXrIvHzlDRkQVqEn6yi8QJegxl4LzOHLdvb7XF5dVawa/VVYBg==" | |||||
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"lazy-cache": "1.0.4" | |||||
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}, | |||||
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"ansi-styles": "3.2.1", | |||||
"escape-string-regexp": "1.0.5", | |||||
"supports-color": "5.5.0" | |||||
} | |||||
}, | |||||
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"right-align": "0.1.3", | |||||
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"color-name": "1.1.3" | |||||
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"requires": { | |||||
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"jest-worker": "24.9.0", | |||||
"serialize-javascript": "2.1.2", | |||||
"uglify-js": "3.8.0" | |||||
}, | |||||
"dependencies": { | |||||
"source-map": { | |||||
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"resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz", | |||||
"integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==" | |||||
}, | |||||
"uglify-js": { | |||||
"version": "3.8.0", | |||||
"resolved": "https://registry.npmjs.org/uglify-js/-/uglify-js-3.8.0.tgz", | |||||
"integrity": "sha512-ugNSTT8ierCsDHso2jkBHXYrU8Y5/fY2ZUprfrJUiD7YpuFvV4jODLFmb3h4btQjqr5Nh4TX4XtgDfCU1WdioQ==", | |||||
"requires": { | |||||
"commander": "2.20.3", | |||||
"source-map": "0.6.1" | |||||
} | |||||
} | |||||
} | |||||
}, | |||||
"rollup-pluginutils": { | |||||
"version": "2.8.2", | |||||
"resolved": "https://registry.npmjs.org/rollup-pluginutils/-/rollup-pluginutils-2.8.2.tgz", | |||||
"integrity": "sha512-EEp9NhnUkwY8aif6bxgovPHMoMoNr2FulJziTndpt5H9RdwC47GSGuII9XxpSdzVGM0GWrNPHV6ie1LTNJPaLQ==", | |||||
"requires": { | |||||
"estree-walker": "0.6.1" | |||||
} | |||||
}, | |||||
"serialize-javascript": { | |||||
"version": "2.1.2", | |||||
"resolved": "https://registry.npmjs.org/serialize-javascript/-/serialize-javascript-2.1.2.tgz", | |||||
"integrity": "sha512-rs9OggEUF0V4jUSecXazOYsLfu7OGK2qIn3c7IPBiffz32XniEp/TX9Xmc9LQfK2nQ2QKHvZ2oygKUGU0lG4jQ==" | |||||
}, | |||||
"source-map": { | |||||
"version": "0.5.7", | |||||
"resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz", | |||||
"integrity": "sha1-igOdLRAh0i0eoUyA2OpGi6LvP8w=" | |||||
}, | |||||
"sourcemap-codec": { | |||||
"version": "1.4.8", | |||||
"resolved": "https://registry.npmjs.org/sourcemap-codec/-/sourcemap-codec-1.4.8.tgz", | |||||
"integrity": "sha512-9NykojV5Uih4lgo5So5dtw+f0JgJX30KCNI8gwhz2J9A15wD0Ml6tjHKwf6fTSa6fAdVBdZeNOs9eJ71qCk8vA==" | |||||
}, | |||||
"sprintf-js": { | |||||
"version": "1.0.3", | |||||
"resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz", | |||||
"integrity": "sha1-BOaSb2YolTVPPdAVIDYzuFcpfiw=" | |||||
}, | |||||
"streamsaver": { | |||||
"version": "2.0.3", | |||||
"resolved": "https://registry.npmjs.org/streamsaver/-/streamsaver-2.0.3.tgz", | |||||
"integrity": "sha512-IpXeZ67YxcsrfZHe3yg/IyZ5KPfRSn1teDy5mRX2e8M6K410NcJNcR+SFQ2Z92DO36VBUArQP4Vy3Qu33MwIOQ==" | |||||
}, | |||||
"supports-color": { | |||||
"version": "5.5.0", | |||||
"resolved": "https://registry.npmjs.org/supports-color/-/supports-color-5.5.0.tgz", | |||||
"integrity": "sha512-QjVjwdXIt408MIiAqCX4oUKsgU2EqAGzs2Ppkm4aQYbjm+ZEWEcW4SfFNTr4uMNZma0ey4f5lgLrkB0aX0QMow==", | |||||
"requires": { | |||||
"has-flag": "3.0.0" | |||||
} | |||||
}, | |||||
"tiny-invariant": { | |||||
"version": "1.1.0", | |||||
"resolved": "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.1.0.tgz", | |||||
"integrity": "sha512-ytxQvrb1cPc9WBEI/HSeYYoGD0kWnGEOR8RY6KomWLBVhqz0RgTwVO9dLrGz7dC+nN9llyI7OKAgRq8Vq4ZBSw==" | |||||
}, | |||||
"tiny-warning": { | |||||
"version": "1.0.3", | |||||
"resolved": "https://registry.npmjs.org/tiny-warning/-/tiny-warning-1.0.3.tgz", | |||||
"integrity": "sha512-lBN9zLN/oAf68o3zNXYrdCt1kP8WsiGW8Oo2ka41b2IM5JL/S1CTyX1rW0mb/zSuJun0ZUrDxx4sqvYS2FWzPA==" | |||||
}, | |||||
"uglify-js": { | |||||
"version": "2.8.29", | |||||
"resolved": "https://registry.npmjs.org/uglify-js/-/uglify-js-2.8.29.tgz", | |||||
"integrity": "sha1-KcVzMUgFe7Th913zW3qcty5qWd0=", | |||||
"requires": { | |||||
"source-map": "0.5.7", | |||||
"uglify-to-browserify": "1.0.2", | |||||
"yargs": "3.10.0" | |||||
} | |||||
}, | |||||
"uglify-to-browserify": { | |||||
"version": "1.0.2", | |||||
"resolved": "https://registry.npmjs.org/uglify-to-browserify/-/uglify-to-browserify-1.0.2.tgz", | |||||
"integrity": "sha1-bgkk1r2mta/jSeOabWMoUKD4grc=", | |||||
"optional": true | |||||
}, | |||||
"unicode-canonical-property-names-ecmascript": { | |||||
"version": "1.0.4", | |||||
"resolved": "https://registry.npmjs.org/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-1.0.4.tgz", | |||||
"integrity": "sha512-jDrNnXWHd4oHiTZnx/ZG7gtUTVp+gCcTTKr8L0HjlwphROEW3+Him+IpvC+xcJEFegapiMZyZe02CyuOnRmbnQ==" | |||||
}, | |||||
"unicode-match-property-ecmascript": { | |||||
"version": "1.0.4", | |||||
"resolved": "https://registry.npmjs.org/unicode-match-property-ecmascript/-/unicode-match-property-ecmascript-1.0.4.tgz", | |||||
"integrity": "sha512-L4Qoh15vTfntsn4P1zqnHulG0LdXgjSO035fEpdtp6YxXhMT51Q6vgM5lYdG/5X3MjS+k/Y9Xw4SFCY9IkR0rg==", | |||||
"requires": { | |||||
"unicode-canonical-property-names-ecmascript": "1.0.4", | |||||
"unicode-property-aliases-ecmascript": "1.0.5" | |||||
} | |||||
}, | |||||
"unicode-match-property-value-ecmascript": { | |||||
"version": "1.1.0", | |||||
"resolved": "https://registry.npmjs.org/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-1.1.0.tgz", | |||||
"integrity": "sha512-hDTHvaBk3RmFzvSl0UVrUmC3PuW9wKVnpoUDYH0JDkSIovzw+J5viQmeYHxVSBptubnr7PbH2e0fnpDRQnQl5g==" | |||||
}, | |||||
"unicode-property-aliases-ecmascript": { | |||||
"version": "1.0.5", | |||||
"resolved": "https://registry.npmjs.org/unicode-property-aliases-ecmascript/-/unicode-property-aliases-ecmascript-1.0.5.tgz", | |||||
"integrity": "sha512-L5RAqCfXqAwR3RriF8pM0lU0w4Ryf/GgzONwi6KnL1taJQa7x1TCxdJnILX59WIGOwR57IVxn7Nej0fz1Ny6fw==" | |||||
}, | |||||
"universalify": { | |||||
"version": "0.1.2", | |||||
"resolved": "https://registry.npmjs.org/universalify/-/universalify-0.1.2.tgz", | |||||
"integrity": "sha512-rBJeI5CXAlmy1pV+617WB9J63U6XcazHHF2f2dbJix4XzpUF0RS3Zbj0FGIOCAva5P/d/GBOYaACQ1w+0azUkg==" | |||||
}, | |||||
"value-equal": { | |||||
"version": "1.0.1", | |||||
"resolved": "https://registry.npmjs.org/value-equal/-/value-equal-1.0.1.tgz", | |||||
"integrity": "sha512-NOJ6JZCAWr0zlxZt+xqCHNTEKOsrks2HQd4MqhP1qy4z1SkbEP467eNx6TgDKXMvUOb+OENfJCZwM+16n7fRfw==" | |||||
}, | |||||
"watch": { | |||||
"version": "1.0.2", | |||||
"resolved": "https://registry.npmjs.org/watch/-/watch-1.0.2.tgz", | |||||
"integrity": "sha1-NApxe952Vyb6CqB9ch4BR6VR3ww=", | |||||
"requires": { | |||||
"exec-sh": "0.2.2", | |||||
"minimist": "1.2.0" | |||||
} | |||||
}, | |||||
"web-streams-polyfill": { | |||||
"version": "2.0.6", | |||||
"resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-2.0.6.tgz", | |||||
"integrity": "sha512-nXOi4fBykO4LzyQhZX3MAGib635KGZBoNTkNXrNIkz0zthEf2QokEWxRb0H632xNLDWtHFb1R6dFGzksjYMSDw==" | |||||
}, | |||||
"window-size": { | |||||
"version": "0.1.0", | |||||
"resolved": "https://registry.npmjs.org/window-size/-/window-size-0.1.0.tgz", | |||||
"integrity": "sha1-VDjNLqk7IC76Ohn+iIeu58lPnJ0=" | |||||
}, | |||||
"wordwrap": { | |||||
"version": "0.0.2", | |||||
"resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-0.0.2.tgz", | |||||
"integrity": "sha1-t5Zpu0LstAn4PVg8rVLKF+qhZD8=" | |||||
}, | |||||
"yargs": { | |||||
"version": "3.10.0", | |||||
"resolved": "https://registry.npmjs.org/yargs/-/yargs-3.10.0.tgz", | |||||
"integrity": "sha1-9+572FfdfB0tOMDnTvvWgdFDH9E=", | |||||
"requires": { | |||||
"camelcase": "1.2.1", | |||||
"cliui": "2.1.0", | |||||
"decamelize": "1.2.0", | |||||
"window-size": "0.1.0" | |||||
} | |||||
} | |||||
} | |||||
} |
@@ -0,0 +1,32 @@ | |||||
{ | |||||
"dependencies": { | |||||
"@fortawesome/fontawesome-free": "^5.12.0", | |||||
"bootstrap": "^4.4.1", | |||||
"crypto-js": "^3.1.9-1", | |||||
"filesize": "^6.0.1", | |||||
"history": "^4.10.1", | |||||
"jquery": "^3.4.1", | |||||
"js-uuid": "0.0.6", | |||||
"js-yaml": "^3.13.1", | |||||
"linkstate": "^1.1.1", | |||||
"papaya-viewer": "^1.0.1449", | |||||
"popper.js": "^1.16.1", | |||||
"preact": "^8.2.9", | |||||
"preact-router": "^2.6.1", | |||||
"rollup": "^0.66.6", | |||||
"rollup-plugin-buble": "^0.19.2", | |||||
"rollup-plugin-copy": "^0.2.3", | |||||
"rollup-plugin-includepaths": "^0.2.3", | |||||
"rollup-plugin-license": "^0.7.0", | |||||
"rollup-plugin-minify": "^1.0.3", | |||||
"rollup-plugin-node-resolve": "^3.3.0", | |||||
"rollup-plugin-uglify": "^6.0.4", | |||||
"streamsaver": "^2.0.3", | |||||
"watch": "^1.0.2", | |||||
"web-streams-polyfill": "^2.0.6" | |||||
}, | |||||
"scripts": { | |||||
"rollup": "rollup -c", | |||||
"watch": "watch \"rollup -c\" src" | |||||
} | |||||
} |
@@ -0,0 +1,67 @@ | |||||
import resolve from 'rollup-plugin-node-resolve' | |||||
import buble from 'rollup-plugin-buble'; | |||||
import copy from 'rollup-plugin-copy'; | |||||
import includePaths from 'rollup-plugin-includepaths'; | |||||
import license from 'rollup-plugin-license'; | |||||
import { uglify } from "rollup-plugin-uglify"; | |||||
export default { | |||||
// dest: 'dist/js/app.js', | |||||
input: 'src/js/index.js', | |||||
output: { | |||||
file: 'dist/js/app.min.js', | |||||
name: 'WBADV', | |||||
format: 'umd', | |||||
sourceMap: true | |||||
}, | |||||
plugins: [ | |||||
includePaths({ | |||||
paths: ['src/js', 'src/js/widget', 'src/js/misc', 'src/js/component', | |||||
'src/js/page', 'src/js/dialog', 'src/js/arvados/base', | |||||
'src/js/arvados/collection', 'src/js/arvados/process'] | |||||
}), | |||||
copy({ | |||||
'src/html/index.html': 'dist/index.html', | |||||
'src/css/index.css': 'dist/css/index.css', | |||||
'node_modules/bootstrap/dist/css/bootstrap.min.css': 'dist/css/bootstrap.min.css', | |||||
'node_modules/bootstrap/dist/js/bootstrap.min.js': 'dist/js/bootstrap.min.js', | |||||
'node_modules/jquery/dist/jquery.min.js': 'dist/js/jquery.min.js', | |||||
'node_modules/@fortawesome/fontawesome-free/js/fontawesome.min.js': 'dist/js/fontawesome.min.js', | |||||
'node_modules/@fortawesome/fontawesome-free/css/all.min.css': 'dist/css/all.min.css', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-regular-400.eot': 'dist/webfonts/fa-regular-400.eot', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-regular-400.svg': 'dist/webfonts/fa-regular-400.svg', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-regular-400.ttf': 'dist/webfonts/fa-regular-400.ttf', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-regular-400.woff': 'dist/webfonts/fa-regular-400.woff', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-regular-400.woff2': 'dist/webfonts/fa-regular-400.woff2', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.eot': 'dist/webfonts/fa-solid-900.eot', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.svg': 'dist/webfonts/fa-solid-900.svg', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.ttf': 'dist/webfonts/fa-solid-900.ttf', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.woff': 'dist/webfonts/fa-solid-900.woff', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-solid-900.woff2': 'dist/webfonts/fa-solid-900.woff2', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-brands-400.eot': 'dist/webfonts/fa-brands-400.eot', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-brands-400.svg': 'dist/webfonts/fa-brands-400.svg', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-brands-400.ttf': 'dist/webfonts/fa-brands-400.ttf', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-brands-400.woff': 'dist/webfonts/fa-brands-400.woff', | |||||
'node_modules/@fortawesome/fontawesome-free/webfonts/fa-brands-400.woff2': 'dist/webfonts/fa-brands-400.woff2', | |||||
'node_modules/js-uuid/js-uuid.js': 'dist/js/js-uuid.js', | |||||
'node_modules/filesize/lib/filesize.js': 'dist/js/filesize.js', | |||||
'node_modules/crypto-js/core.js': 'dist/js/crypto-js/core.js', | |||||
'node_modules/crypto-js/md5.js': 'dist/js/crypto-js/md5.js', | |||||
'src/js/worker/wb-manifest-worker.js': 'dist/js/wb-manifest-worker.js', | |||||
'node_modules/js-yaml/dist/js-yaml.min.js': 'dist/js/js-yaml.min.js', | |||||
'node_modules/streamsaver/mitm.html': 'dist/mitm.html', | |||||
'node_modules/streamsaver/sw.js': 'dist/sw.js', | |||||
'src/js/thirdparty/StreamSaver.js': 'dist/js/StreamSaver.js', | |||||
'node_modules/web-streams-polyfill/dist/ponyfill.js': 'dist/js/web-streams-polyfill/ponyfill.js', | |||||
'node_modules/papaya-viewer/release/current/standard/papaya.js': 'dist/js/papaya.js', | |||||
'node_modules/papaya-viewer/release/current/standard/papaya.css': 'dist/css/papaya.css', | |||||
verbose: true | |||||
}), | |||||
buble({jsx: 'h', objectAssign: 'Object.assign'}), | |||||
resolve({}), | |||||
license({ | |||||
banner: 'Copyright (C) Stanislaw Adaszewski, 2020.\nContact: s.adaszewski@gmail.com\nAll Rights Reserved.', | |||||
}), | |||||
// uglify() | |||||
] | |||||
} |
@@ -0,0 +1,27 @@ | |||||
pre.word-wrap { | |||||
white-space: pre-wrap; /* Since CSS 2.1 */ | |||||
white-space: -moz-pre-wrap; /* Mozilla, since 1999 */ | |||||
white-space: -pre-wrap; /* Opera 4-6 */ | |||||
white-space: -o-pre-wrap; /* Opera 7 */ | |||||
word-wrap: break-word; /* Internet Explorer 5.5+ */ | |||||
} | |||||
pre.terminal { | |||||
background: black; | |||||
color: #aaa; | |||||
height: 600px; | |||||
width: 100%; | |||||
} | |||||
.w-1 { | |||||
width: 1px !important; | |||||
} | |||||
div.wb-json-viewer { | |||||
font-family: "Courier New", fixed-width; | |||||
white-space: pre-wrap; | |||||
} | |||||
textarea.wb-json-editor { | |||||
font-family: "Courier New", fixed-width; | |||||
} |
@@ -0,0 +1,25 @@ | |||||
<html> | |||||
<head> | |||||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |||||
<link rel="stylesheet" type="text/css" href="/css/bootstrap.min.css" /> | |||||
<link rel="stylesheet" type="text/css" href="/css/all.min.css" /> | |||||
<link rel="stylesheet" type="text/css" href="/css/index.css" /> | |||||
<link rel="stylesheet" type="text/css" href="/css/papaya.css" /> | |||||
<script language="javascript" src="/js/web-streams-polyfill/ponyfill.js"></script> | |||||
<script language="javascript"> | |||||
window.process = { 'env': { 'NODE_ENV': 'production' } }; | |||||
</script> | |||||
<script language="javascript" src="/js/jquery.min.js"></script> | |||||
<script language="javascript" src="/js/bootstrap.min.js"></script> | |||||
<script language="javascript" src="/js/fontawesome.min.js"></script> | |||||
<script language="javascript" src="/js/js-uuid.js"></script> | |||||
<script language="javascript" src="/js/filesize.js"></script> | |||||
<script language="javascript" src="/js/crypto-js/core.js"></script> | |||||
<script language="javascript" src="/js/crypto-js/md5.js"></script> | |||||
<script language="javascript" src="/js/js-yaml.min.js"></script> | |||||
<script language="javascript" src="/js/StreamSaver.js"></script> | |||||
</head> | |||||
<body> | |||||
<script language="javascript" src="/js/app.min.js"></script> | |||||
</body> | |||||
</html> |
@@ -0,0 +1,20 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function arvadosObjectName(item) { | |||||
let typeName = arvadosTypeName(item['uuid']); | |||||
if (typeName === 'user') | |||||
return (item.first_name + ' ' + item.last_name); | |||||
else if (typeName === 'container') | |||||
return ('Container running image ' + item.container_image); | |||||
else | |||||
return item.name; | |||||
} | |||||
export default arvadosObjectName; |
@@ -0,0 +1,28 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
const typeIdToName = { | |||||
'tpzed': 'user', | |||||
'j7d0g': 'group', | |||||
'xvhdp': 'container_request', | |||||
'dz642': 'container', | |||||
'7fd4e': 'workflow', | |||||
'ozdt8': 'api_client', | |||||
'4zz18': 'collection' | |||||
}; | |||||
function arvadosTypeName(id) { | |||||
if (!id) | |||||
return; | |||||
if (id.length === 5) | |||||
return typeIdToName[id]; | |||||
else | |||||
return typeIdToName[id.split('-')[1]]; | |||||
} | |||||
export default arvadosTypeName; |
@@ -0,0 +1,34 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function detectHashes(obj) { | |||||
let Q = [ obj ]; | |||||
let matches = {}; | |||||
while (Q.length > 0) { | |||||
let item = Q.pop(); | |||||
if (!item) | |||||
continue; | |||||
if (typeof(item) === 'string') { | |||||
// use regexes | |||||
let rx = /[a-f0-9]{32}\+[0-9]+/g; | |||||
for (let m = rx.exec(item); m; m = rx.exec(item)) | |||||
matches[m[0]] = true; | |||||
} else if (typeof(item) === 'object') { | |||||
Object.keys(item).map(k => Q.push(item[k])); | |||||
} | |||||
} | |||||
matches = Object.keys(matches); | |||||
return matches; | |||||
} | |||||
export default detectHashes; |
@@ -0,0 +1,34 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function detectUuids(obj) { | |||||
let Q = [ obj ]; | |||||
let matches = {}; | |||||
while (Q.length > 0) { | |||||
let item = Q.pop(); | |||||
if (!item) | |||||
continue; | |||||
if (typeof(item) === 'string') { | |||||
// use regexes | |||||
let rx = /[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}/g; | |||||
for (let m = rx.exec(item); m; m = rx.exec(item)) | |||||
matches[m[0]] = true; | |||||
} else if (typeof(item) === 'object') { | |||||
Object.keys(item).map(k => Q.push(item[k])); | |||||
} | |||||
} | |||||
matches = Object.keys(matches); | |||||
return matches; | |||||
} | |||||
export default detectUuids; |
@@ -0,0 +1,51 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
function fetchObjectParents(arvHost, arvToken, uuid) { | |||||
let parents = []; | |||||
let cb = xhr => { | |||||
const item = xhr.response.items[0]; | |||||
if (!item) | |||||
return parents.reverse(); | |||||
item.name = arvadosObjectName(item); | |||||
parents.push(item); | |||||
if (!item.owner_uuid || | |||||
item.owner_uuid.endsWith('-tpzed-000000000000000')) { | |||||
return parents.reverse(); | |||||
} | |||||
const objectType = arvadosTypeName(item.owner_uuid); | |||||
const filters = [ | |||||
['uuid', '=', item.owner_uuid] | |||||
]; | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + objectType + 's' + | |||||
'?filters=' + encodeURIComponent(JSON.stringify(filters))).then(cb); | |||||
}; | |||||
const objectType = arvadosTypeName(uuid); | |||||
const filters = [ | |||||
['uuid', '=', uuid] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + objectType + 's' + | |||||
'?filters=' + encodeURIComponent(JSON.stringify(filters))); | |||||
prom = prom.then(cb); | |||||
return prom; | |||||
} | |||||
export default fetchObjectParents; |
@@ -0,0 +1,67 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import wbApplyPromiseOrdering from 'wb-apply-promise-ordering'; | |||||
const requestPromiseOrdering = {}; | |||||
function makeArvadosRequest(arvHost, arvToken, endpoint, params={}) { | |||||
const defaultParams = { | |||||
'method': 'GET', | |||||
'data': null, | |||||
'contentType': 'application/json;charset=utf-8', | |||||
'responseType': 'json', | |||||
'useSsl': true, | |||||
'requireToken': true, | |||||
'onProgress': () => {}, | |||||
'promiseOrdering': true, | |||||
'expectedStatus': 200 | |||||
}; | |||||
Object.keys(defaultParams).map(k => (params[k] = | |||||
(k in params ? params[k] : defaultParams[k]))); | |||||
let { method, data, contentType, responseType, | |||||
useSsl, requireToken, onProgress, promiseOrdering, | |||||
expectedStatus } = params; | |||||
if (!(arvHost && (arvToken || !requireToken))) | |||||
return new Promise((accept, reject) => reject()); | |||||
let xhr = new XMLHttpRequest(); | |||||
xhr.open(method, (useSsl ? 'https://' : 'http://') + arvHost + endpoint); | |||||
if (arvToken) | |||||
xhr.setRequestHeader('Authorization', 'OAuth2 ' + arvToken); | |||||
if (data !== null) | |||||
xhr.setRequestHeader('Content-Type', contentType); | |||||
xhr.responseType = responseType; | |||||
xhr.onprogress = onProgress; | |||||
let prom = new Promise((accept, reject) => { | |||||
xhr.onreadystatechange = () => { | |||||
if (xhr.readyState !== 4) | |||||
return; | |||||
if ((expectedStatus instanceof Array) && | |||||
expectedStatus.indexOf(xhr.status) !== -1) { | |||||
accept(xhr); | |||||
} else if (expectedStatus === xhr.status) { | |||||
accept(xhr); | |||||
} else { | |||||
reject(xhr); | |||||
} | |||||
}; | |||||
xhr.send(data); | |||||
}); | |||||
if (promiseOrdering) | |||||
prom = wbApplyPromiseOrdering(prom, requestPromiseOrdering); | |||||
return prom; | |||||
} | |||||
export default makeArvadosRequest; |
@@ -0,0 +1,35 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function urlForObject(item, mode='primary') { | |||||
let objectType = arvadosTypeName(item.uuid.split('-')[1]); | |||||
if (objectType === 'user') | |||||
return ('/browse/' + item.uuid); | |||||
else if (objectType === 'group' && item.group_class === 'project') { | |||||
if (mode === 'properties') | |||||
return ('/project/' + item.uuid); | |||||
else | |||||
return ('/browse/' + item.uuid); | |||||
} else if (objectType === 'container_request') | |||||
return ('/process/' + item.uuid); | |||||
else if (objectType === 'workflow') { | |||||
if (mode === 'launch') | |||||
return ('/workflow-launch/' + item.uuid) | |||||
else | |||||
return ('/workflow/' + item.uuid); | |||||
} else if (objectType === 'collection') { | |||||
if (mode === 'primary' || mode === 'browse') | |||||
return ('/collection-browse/' + item.uuid); | |||||
else | |||||
return ('/collection/' + item.uuid); | |||||
} else if (objectType === 'container') | |||||
return ('/container/' + item.uuid); | |||||
} | |||||
export default urlForObject; |
@@ -0,0 +1,18 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function wbDeleteObject(arvHost, arvToken, uuid) { | |||||
const typeName = arvadosTypeName(uuid); | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + | |||||
uuid, { 'method': 'DELETE' }); | |||||
} | |||||
export default wbDeleteObject; |
@@ -0,0 +1,45 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function wbFetchObjects(arvHost, arvToken, uuids) { | |||||
const unique = {}; | |||||
uuids.map(u => (unique[u] = true)); | |||||
uuids = {}; | |||||
Object.keys(unique).map(u => { | |||||
let typeName = arvadosTypeName(u); | |||||
if (!typeName) { | |||||
console.log('Unknown type name for UUID: ' + u); | |||||
return; | |||||
} | |||||
if (!(typeName in uuids)) | |||||
uuids[typeName] = []; | |||||
uuids[typeName].push(u); | |||||
}); | |||||
const lookup = {}; | |||||
let prom = new Promise(accept => accept()); | |||||
for (let typeName in uuids) { | |||||
let filters = [ | |||||
['uuid', 'in', uuids[typeName]] | |||||
]; | |||||
prom = prom.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)))); | |||||
prom = prom.then(xhr => xhr.response.items.map(it => ( | |||||
lookup[it.uuid] = it))); | |||||
prom = prom.catch(xhr => console.log(xhr.responseURL + ': ' + xhr.statusText)); | |||||
} | |||||
prom = prom.then(() => lookup); | |||||
return prom; | |||||
} | |||||
export default wbFetchObjects; |
@@ -0,0 +1,79 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
const UUID_PATTERN = '[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}'; | |||||
const PDH_PATTERN = '[a-f0-9]{32}\\+[0-9]+'; | |||||
const UUID_REGEX = new RegExp(UUID_PATTERN); | |||||
const PDH_REGEX = new RegExp(PDH_PATTERN); | |||||
const UUID_REGEX_G = new RegExp(UUID_PATTERN, 'g'); | |||||
const PDH_REGEX_G = new RegExp(PDH_PATTERN, 'g'); | |||||
class WBIdTools { | |||||
static isIdentifier(value) { | |||||
return ( this.isUuid(value) || this.isPDH(value) ); | |||||
} | |||||
static isUuid(value) { | |||||
const m = UUID_REGEX.exec(value); | |||||
return (m && m[0] === value); | |||||
} | |||||
static isPDH(value) { | |||||
const m = PDH_REGEX.exec(value); | |||||
return (m && m[0] === value); | |||||
} | |||||
static startsWithIdentifier(value) { | |||||
return ( this.startsWithUuid(value) || this.startsWithPDH(value) ); | |||||
} | |||||
static startsWithUuid(value) { | |||||
const m = UUID_REGEX.exec(value); | |||||
return ( m && m.index === 0 ); | |||||
} | |||||
static startsWithPDH(value) { | |||||
const m = PDH_REGEX.exec(value); | |||||
return ( m && m.index === 0 ); | |||||
} | |||||
static detectIdentifiers(value) { | |||||
return this.detectUuids(value).concat(this.detectPDHs(value)); | |||||
} | |||||
static detectUuids(value) { | |||||
let m; | |||||
const res = []; | |||||
while (m = UUID_REGEX_G.exec(value)) { | |||||
res.push(m); | |||||
} | |||||
return res; | |||||
} | |||||
static detectPDHs(value) { | |||||
let m; | |||||
const res = []; | |||||
while (m = PDH_REGEX_G.exec(value)) { | |||||
res.push(m); | |||||
} | |||||
return res; | |||||
} | |||||
static typeName(value) { | |||||
if (this.isPDH(value)) | |||||
return 'collection'; | |||||
if (this.isUuid(value)) | |||||
return arvadosTypeName(value); | |||||
throw Error('Given value is neither an UUID nor a PDH: ' + value); | |||||
} | |||||
} | |||||
export default WBIdTools; |
@@ -0,0 +1,20 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function wbMoveObject(arvHost, arvToken, uuid, newOwnerUuid) { | |||||
const typeName = arvadosTypeName(uuid); | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + | |||||
uuid, { 'method': 'PUT', 'data': JSON.stringify({ | |||||
'owner_uuid': newOwnerUuid | |||||
}) }); | |||||
} | |||||
export default wbMoveObject; |
@@ -0,0 +1,23 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function wbRenameObject(arvHost, arvToken, uuid, newName) { | |||||
const update = { | |||||
'name': newName | |||||
}; | |||||
const typeName = arvadosTypeName(uuid); | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + | |||||
uuid + '?' + typeName + '=' + | |||||
encodeURIComponent(JSON.stringify(update)), | |||||
{ 'method': 'PUT' }); | |||||
} | |||||
export default wbRenameObject; |
@@ -0,0 +1,23 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function wbUpdateField(arvHost, arvToken, uuid, fieldName, fieldValue) { | |||||
const typeName = arvadosTypeName(uuid); | |||||
const data = {}; | |||||
data[fieldName] = fieldValue; | |||||
const prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + uuid, { | |||||
method: 'PUT', | |||||
data: JSON.stringify(data) | |||||
}); | |||||
return prom; | |||||
} | |||||
export default wbUpdateField; |
@@ -0,0 +1,32 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
function wbCopyCollection(arvHost, arvToken, uuid, newOwnerUuid) { | |||||
const typeName = arvadosTypeName(uuid); | |||||
if (typeName !== 'collection') | |||||
throw Error('Specified UUID does not refer to a collection'); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections/' + uuid); | |||||
prom = prom.then(xhr => { | |||||
const { name, description, properties, portable_data_hash, | |||||
manifest_text } = xhr.response; | |||||
const dup = { name: name + ' (Copied at ' + new Date().toISOString() + ')', | |||||
description, properties, portable_data_hash, manifest_text, | |||||
owner_uuid: newOwnerUuid }; | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections', { | |||||
'method': 'POST', | |||||
'data': JSON.stringify(dup) | |||||
}); | |||||
}); | |||||
return prom; | |||||
} | |||||
export default wbCopyCollection; |
@@ -0,0 +1,64 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function wbDownloadFile(arvHost, arvToken, | |||||
manifestReader, path) { | |||||
const file = manifestReader.getFile(path); | |||||
const name = path.split('/').reverse()[0]; | |||||
const blockRefs = file[0]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/keep_services'); | |||||
prom = prom.then(xhr => { | |||||
const services = xhr.response['items']; | |||||
const proxies = services.filter(svc => (svc.service_type === 'proxy')); | |||||
const n = Math.floor(Math.random() * proxies.length); | |||||
const proxy = proxies[n]; | |||||
const blocks = []; | |||||
let prom_2 = new Promise(accept => accept()); | |||||
for (let i = 0; i < blockRefs.length; i++) { | |||||
const [ locator, position, size ] = blockRefs[i]; | |||||
const prom_1 = makeArvadosRequest( | |||||
proxy.service_host + ':' + proxy.service_port, | |||||
arvToken, | |||||
'/' + locator, | |||||
{ 'useSsl': proxy.service_ssl_flag, | |||||
'responseType': 'arraybuffer' } | |||||
); | |||||
prom_2 = prom_2.then(() => prom_1); | |||||
prom_2 = prom_2.then(xhr => (blocks.push(xhr.response.slice(position, | |||||
position + size)))); | |||||
} | |||||
prom_2 = prom_2.then(() => blocks); | |||||
return prom_2; | |||||
}); | |||||
/* prom = prom.then(() => { | |||||
const blob = new Blob(blocks); | |||||
const url = window.URL.createObjectURL(blob); | |||||
const a = document.createElement('a'); | |||||
a.href = url; | |||||
a.download = name; | |||||
a.click(); | |||||
}); */ | |||||
return prom; | |||||
} | |||||
export default wbDownloadFile; |
@@ -0,0 +1,35 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
class WBManifestWorkerWrapper { | |||||
constructor() { | |||||
this.worker = new Worker('/js/wb-manifest-worker.js'); | |||||
this.worker.onmessage = e => this.onMessage(e); | |||||
this.worker.onerror = e => console.log(e); | |||||
this.queue = []; | |||||
} | |||||
onMessage(e) { | |||||
if (this.queue.length === 0) | |||||
throw Error('Unexpected message from worker'); | |||||
const [msgType, accept, reject] = this.queue.splice(0, 1)[0]; | |||||
if (e.data[0] === msgType + 'Result') | |||||
accept(e); | |||||
else | |||||
reject(e); | |||||
} | |||||
postMessage(m) { | |||||
const prom = new Promise((accept, reject) => { | |||||
this.queue.push([ m[0], accept, reject ]); | |||||
this.worker.postMessage(m); | |||||
}); | |||||
return prom; | |||||
} | |||||
} | |||||
export default WBManifestWorkerWrapper; |
@@ -0,0 +1,21 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function wbInputSpecInfo(inputSpec) { | |||||
const isFile = (inputSpec.type === 'File' || inputSpec.type === 'File[]' || | |||||
(inputSpec.type.type === 'array' && [].concat(inputSpec.type.items).indexOf('File') !== -1)); | |||||
const isDirectory = (inputSpec.type === 'Directory' || inputSpec.type === 'Directory[]' || | |||||
(inputSpec.type.type === 'array' && [].concat(inputSpec.type.items).indexOf('Directory') !== -1)); | |||||
const isArray = (inputSpec.type === 'File[]' || inputSpec.type === 'Directory[]' || | |||||
inputSpec.type.type === 'array'); | |||||
return { isFile, isDirectory, isArray }; | |||||
} | |||||
export default wbInputSpecInfo; |
@@ -0,0 +1,18 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function wbParseWorkflowDef(text) { | |||||
let definition; | |||||
try { | |||||
definition = JSON.parse(text); | |||||
} catch (_) { | |||||
definition = jsyaml.load(text); | |||||
} | |||||
return definition; | |||||
} | |||||
export default wbParseWorkflowDef; |
@@ -0,0 +1,18 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function encodeURIComponentIncludingDots(s) { | |||||
return encodeURIComponent(s).replace('.', '%2E'); | |||||
} | |||||
function parseKeepRef(value) { | |||||
if (value && typeof(value) === 'object' && 'location' in value && value.location.startsWith('keep:')) | |||||
return value.location.substr(5); | |||||
return value; | |||||
} | |||||
export { encodeURIComponentIncludingDots, parseKeepRef } |
@@ -0,0 +1,27 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function wbProcessStateName(containerRequest, container) { | |||||
const cr = containerRequest; | |||||
const c = container; | |||||
if (!c) | |||||
return cr.state; | |||||
if (cr.state !== 'Uncommitted' && cr.priority === 0) | |||||
return 'Cancelled'; | |||||
if (cr.state === 'Uncommitted' || !cr.container_uuid || c.state === 'Queued' || c.state === 'Locked') | |||||
return 'Pending'; | |||||
if (c.state === 'Running') | |||||
return 'Running'; | |||||
if (c.state === 'Complete' && c.exit_code === 0) | |||||
return 'Complete'; | |||||
if (c.state === 'Complete' && c.exit_code !== 0) | |||||
return 'Failed'; | |||||
if (c.state === 'Cancelled') | |||||
return 'Cancelled'; | |||||
} | |||||
export default wbProcessStateName; |
@@ -0,0 +1,169 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import wbUuidsToCwl from 'wb-uuids-to-cwl'; | |||||
function wbParseWorkflowInputs(workflowDefinition, userInputs, errors) { | |||||
// first see if all inputs are parseable | |||||
const inputs = {}; | |||||
const main = workflowDefinition['$graph'].find(a => (a.id === '#main')); | |||||
for (let k in userInputs) { | |||||
try { | |||||
let val = jsyaml.safeLoad(userInputs[k]); | |||||
val = wbUuidsToCwl(val); | |||||
k = k.split('/').slice(1).join('/'); | |||||
inputs[k] = (val === undefined ? null : val); | |||||
} catch (exc) { | |||||
errors.push('Error parsing ' + k + ': ' + exc.message); | |||||
} | |||||
} | |||||
return inputs; | |||||
} | |||||
function ensureSubProject(arvHost, arvToken, projectUuid) { | |||||
const filters = [ | |||||
[ 'group_class', '=', 'project' ], | |||||
[ 'owner_uuid', '=', projectUuid ], | |||||
[ 'properties.type', '=', 'daily_process_subproject_container' ] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups?filters=' + encodeURIComponent(JSON.stringify(filters))); | |||||
prom = prom.then(xhr => { | |||||
if (xhr.response.items.length === 0) { | |||||
let prom_1 = new Promise(accept => accept()); | |||||
prom_1 = prom_1.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups', { method: 'POST', | |||||
data: JSON.stringify({ owner_uuid: projectUuid, | |||||
group_class: 'project', | |||||
name: 'Container for daily sub-projects for processes', | |||||
properties: { type: 'daily_process_subproject_container' } }) })); | |||||
prom_1 = prom_1.then(xhr_1 => xhr_1.response.uuid); | |||||
return prom_1; | |||||
} | |||||
return xhr.response.items[0].uuid; | |||||
}); | |||||
let date = new Date(); | |||||
date = (date.getYear() + 1900) + '-' + | |||||
('00' + (date.getMonth() + 1)).slice(-2) + '-' + | |||||
('00' + date.getDate()).slice(-2); | |||||
let containerUuid; | |||||
prom = prom.then(uuid => { | |||||
containerUuid = uuid; | |||||
const filters_1 = [ | |||||
[ 'group_class', '=', 'project'], | |||||
[ 'owner_uuid', '=', containerUuid ], | |||||
[ 'properties.type', '=', 'daily_process_subproject' ], | |||||
[ 'properties.date', '=', date ] | |||||
]; | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups?filters=' + encodeURIComponent(JSON.stringify(filters_1))); | |||||
}); | |||||
prom = prom.then(xhr => { | |||||
if (xhr.response.items.length === 0) { | |||||
let prom_1 = new Promise(accept => accept()); | |||||
prom_1 = prom_1.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups', { method: 'POST', | |||||
data: JSON.stringify({ owner_uuid: containerUuid, | |||||
group_class: 'project', | |||||
name: 'Daily processes sub-project for ' + date, | |||||
properties: { type: 'daily_process_subproject', date } }) })); | |||||
prom_1 = prom_1.then(xhr => xhr.response.uuid); | |||||
return prom_1; | |||||
} | |||||
return xhr.response.items[0].uuid; | |||||
}); | |||||
return prom; | |||||
} | |||||
// params: | |||||
// arvHost, arvToken, inputs, | |||||
// projectUuid, workflowDefinition, workflowUuid | |||||
// processName, processDescription, placeInSubProject | |||||
function wbSubmitContainerRequest(params) { | |||||
const { workflowDefinition, workflowUuid, | |||||
processName, processDescription, inputs, | |||||
arvHost, arvToken, | |||||
placeInSubProject } = params; | |||||
let { projectUuid } = params; | |||||
let prom = new Promise(accept => accept()); | |||||
if (placeInSubProject) { | |||||
prom = prom.then(() => ensureSubProject(arvHost, arvToken, projectUuid)); | |||||
prom = prom.then(subProjUuid => (projectUuid = subProjUuid)); | |||||
} | |||||
prom = prom.then(() => { | |||||
// prepare a request | |||||
const req = { | |||||
name: processName, | |||||
description: processDescription, | |||||
owner_uuid: projectUuid, | |||||
container_image: 'arvados/jobs', | |||||
properties: { | |||||
template_uuid: workflowUuid | |||||
}, | |||||
runtime_constraints: { | |||||
API: true, | |||||
vcpus: 1, | |||||
ram: 1073741824 | |||||
}, | |||||
cwd: '/var/spool/cwl', | |||||
command: [ | |||||
'arvados-cwl-runner', | |||||
'--local', | |||||
'--api=containers', | |||||
'--project-uuid=' + projectUuid, | |||||
'--collection-cache-size=256', | |||||
'/var/lib/cwl/workflow.json#main', | |||||
'/var/lib/cwl/cwl.input.json'], | |||||
output_path: '/var/spool/cwl', | |||||
priority: 1, | |||||
state: 'Committed', | |||||
mounts: { | |||||
'stdout': { | |||||
kind: 'file', | |||||
path: '/var/spool/cwl/cwl.output.json' | |||||
}, | |||||
'/var/spool/cwl': { | |||||
kind: 'collection', | |||||
writable: true | |||||
}, | |||||
'/var/lib/cwl/workflow.json': { | |||||
kind: 'json', | |||||
content: workflowDefinition | |||||
}, | |||||
'/var/lib/cwl/cwl.input.json': { | |||||
kind: 'json', | |||||
content: inputs | |||||
} | |||||
} | |||||
}; | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests', | |||||
{ method: 'POST', data: JSON.stringify(req) }); | |||||
}); | |||||
return prom; | |||||
} | |||||
export { wbParseWorkflowInputs, wbSubmitContainerRequest }; |
@@ -0,0 +1,32 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function wbUuidsToCwl(obj) { | |||||
if (obj instanceof Array) { | |||||
const res = []; | |||||
for (let k in obj) { | |||||
res[k] = wbUuidsToCwl(obj[k]); | |||||
} | |||||
return res; | |||||
} | |||||
if (typeof(obj) === 'string' && | |||||
(/^[0-9a-z]{5}-[0-9a-z]{5}-[0-9a-z]{15}/.exec(obj) || | |||||
/^[0-9a-f]{32}\+[0-9]+/.exec(obj))) { | |||||
const isDirectory = obj.endsWith('/'); | |||||
return { | |||||
'class': (isDirectory ? 'Directory' : 'File'), | |||||
'location': 'keep:' + (isDirectory ? obj.substr(0, obj.length - 1) : obj) | |||||
}; | |||||
} | |||||
throw Error('Expected Arvados path or array of paths'); | |||||
} | |||||
export default wbUuidsToCwl; |
@@ -0,0 +1,55 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBBreadcrumbs from 'wb-breadcrumbs'; | |||||
import fetchObjectParents from 'fetch-object-parents'; | |||||
class WBArvadosCrumbs extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.items = [ { 'name': 'All Projects' } ]; | |||||
} | |||||
fetchCrumbs() { | |||||
const { mode, uuid, app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
if (mode === 'shared-with-me') { | |||||
this.setState({ 'items': [ { 'name': 'Shared with Me' } ] }); | |||||
return; | |||||
} | |||||
if (!uuid) { | |||||
this.setState({ 'items': [ { 'name': 'All Projects' } ] }); | |||||
return; | |||||
} | |||||
let prom = fetchObjectParents(arvHost, arvToken, uuid); | |||||
prom = prom.then(parents => { | |||||
this.setState({ 'items': parents }); | |||||
}); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchCrumbs(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchCrumbs(); | |||||
} | |||||
render({ app }, { items }) { | |||||
return ( | |||||
<WBBreadcrumbs items={ items } | |||||
onItemClicked={ item => app.breadcrumbClicked(item) } /> | |||||
); | |||||
} | |||||
} | |||||
export default WBArvadosCrumbs; |
@@ -0,0 +1,251 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import WBBreadcrumbs from 'wb-breadcrumbs'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import wbDownloadFile from 'wb-download-file'; | |||||
import WBManifestWorkerWrapper from 'wb-manifest-worker-wrapper'; | |||||
function unescapeName(name) { | |||||
return name.replace(/(\\\\|\\[0-9]{3})/g, | |||||
(_, $1) => ($1 === '\\\\' ? '\\' : String.fromCharCode(parseInt($1.substr(1), 8)))); | |||||
} | |||||
function encodeURIComponentIncludingDots(s) { | |||||
return encodeURIComponent(s).replace('.', '%2E'); | |||||
} | |||||
function endsWith(what, endings) { | |||||
if (typeof(endings) === 'string') | |||||
return what.endsWith(endings); | |||||
if (endings instanceof Array) | |||||
return endings.map(a => what.endsWith(a)).reduce((a, b) => (a || b)); | |||||
throw Error('Expected second argument to be either a string or an array'); | |||||
} | |||||
function maskRows(rows) { | |||||
return rows.map(r => r.map(c => '-')); | |||||
} | |||||
class WBCollectionContent extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.manifestWorker = new WBManifestWorkerWrapper(); | |||||
this.state.loaded = 0; | |||||
this.state.total = 0; | |||||
this.state.mode = 'manifestDownload'; | |||||
this.state.parsedStreams = 0; | |||||
this.state.totalStreams = 1; | |||||
} | |||||
getUrl(params) { | |||||
let res = '/collection-browse/' + | |||||
('uuid' in params ? params.uuid : this.props.uuid) + '/' + | |||||
encodeURIComponentIncludingDots('collectionPath' in params ? params.collectionPath : this.props.collectionPath) + '/' + | |||||
('page' in params ? params.page : this.props.page); | |||||
return res; | |||||
} | |||||
componentDidMount() { | |||||
let { arvHost, arvToken } = this.props.app.state; | |||||
let { uuid, collectionPath } = this.props; | |||||
let { manifestWorker } = this.state; | |||||
let select = [ 'manifest_text' ]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections/' + uuid + | |||||
'?select=' + encodeURIComponent(JSON.stringify(select)), | |||||
{ 'onProgress': e => { | |||||
this.setState({ 'loaded': e.loaded, 'total': e.total }); | |||||
} }); | |||||
prom = prom.then(xhr => { | |||||
const streams = xhr.response.manifest_text.split('\n'); | |||||
const paths = streams.filter(s => s).map(s => { | |||||
const n = s.indexOf(' '); | |||||
return unescapeName(s.substr(0, n)); | |||||
}); | |||||
let prom_1 = new Promise(accept => accept()); | |||||
prom_1 = prom_1.then(() => { | |||||
this.setState({ | |||||
'totalStreams': streams.length, | |||||
'parsedStreams': 0, | |||||
'mode': 'manifestParse' | |||||
}); | |||||
return manifestWorker.postMessage([ 'precreatePaths', paths ]); | |||||
}); | |||||
let lastListingTimestamp = new Date(0); | |||||
for (let i = 0; i < streams.length; i++) { | |||||
prom_1 = prom_1.then(() => manifestWorker.postMessage([ 'parseStream', streams[i] ])); | |||||
prom_1 = prom_1.then(() => { | |||||
if (new Date() - lastListingTimestamp < 1000) | |||||
return; | |||||
lastListingTimestamp = new Date(); | |||||
let prom_2 = new Promise(accept => accept()); | |||||
prom_2 = prom_2.then(() => manifestWorker.postMessage([ | |||||
'listDirectory', '.' + this.props.collectionPath, true | |||||
])); | |||||
prom_2 = prom_2.then(e => { | |||||
this.prepareRows(e.data[1]); | |||||
this.setState({ 'parsedStreams': (i + 1) }); | |||||
}); | |||||
return prom_2; | |||||
}); | |||||
} | |||||
prom_1 = prom_1.then(() => manifestWorker.postMessage([ 'listDirectory', | |||||
'.' + this.props.collectionPath, true ])); | |||||
prom_1 = prom_1.then(e => { | |||||
this.state.mode = 'browsingReady'; | |||||
this.prepareRows(e.data[1]); | |||||
}); | |||||
return prom_1; | |||||
}); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.setState({ rows: maskRows(this.state.rows) }); | |||||
const { manifestWorker, mode } = this.state; | |||||
const { collectionPath } = this.props; | |||||
if (mode === 'browsingReady') { | |||||
let prom = manifestWorker.postMessage([ 'listDirectory', '.' + collectionPath, true ]); | |||||
prom = prom.then(e => this.prepareRows(e.data[1])); | |||||
} | |||||
} | |||||
prepareRows(listing) { | |||||
let { manifestWorker, mode } = this.state; | |||||
let { collectionPath, page, itemsPerPage, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
const numPages = Math.ceil(listing.length / itemsPerPage); | |||||
listing = listing.slice(page * itemsPerPage, | |||||
page * itemsPerPage + itemsPerPage); | |||||
this.setState({ | |||||
'numPages': numPages, | |||||
'rows': listing.map(item => ( | |||||
(item[0] === 'd') ? [ | |||||
(<a href={ this.getUrl({ 'collectionPath': collectionPath + '/' + item[1], 'page': 0 }) }>{ item[1] }/</a>), | |||||
'Directory', | |||||
null, | |||||
(<div></div>) | |||||
] : [ | |||||
item[1], | |||||
'File', | |||||
filesize(item[2]), | |||||
( (mode === 'browsingReady') ? ( | |||||
<div> | |||||
<button class="btn btn-outline-primary mx-1" title="Download" | |||||
onclick={ () => manifestWorker.postMessage([ 'getFile', | |||||
'.' + collectionPath + '/' + item[1] ]).then(e => { | |||||
const file = e.data[1]; | |||||
const blob = new Blob([ | |||||
JSON.stringify([ arvHost, arvToken, item[1], file ]) | |||||
]); | |||||
const blocksBlobUrl = URL.createObjectURL(blob); | |||||
window.open('/download/' + encodeURIComponent(blocksBlobUrl), '_blank'); | |||||
}) }><i class="fas fa-download"></i></button> | |||||
<button class="btn btn-outline-primary mx-1" title="View" | |||||
onclick={ () => { | |||||
alert('Not implemented.') | |||||
} }><i class="far fa-eye"></i></button> | |||||
{ endsWith(item[1].toLowerCase(), ['.nii', '.nii.gz']) ? ( | |||||
<button class="btn btn-outline-primary mx-1" title="View Image" | |||||
onclick={ () => manifestWorker.postMessage([ 'getFile', | |||||
'.' + collectionPath + '/' + item[1] ]).then(e => { | |||||
const file = e.data[1]; | |||||
const blob = new Blob([ | |||||
JSON.stringify({ 'name': item[1], 'file': file }) | |||||
]); | |||||
const blocksBlobUrl = URL.createObjectURL(blob); | |||||
window.open('/image-viewer/' + encodeURIComponent(blocksBlobUrl), '_blank'); | |||||
}) }><i class="fas fa-image"></i></button> | |||||
) : null } | |||||
</div> | |||||
) : null) | |||||
] | |||||
)) | |||||
}); | |||||
} | |||||
render({ collectionPath, page }, { manifestReader, rows, | |||||
numPages, loaded, total, mode, parsedStreams, totalStreams }) { | |||||
return ( | |||||
<div> | |||||
<WBBreadcrumbs items={ ('.' + collectionPath).split('/').map((name, index) => ({ name, index })) } | |||||
getItemUrl={ it => this.getUrl({ | |||||
collectionPath: ('.' + collectionPath).split('/').slice(0, it.index + 1).join('/').substr(1), | |||||
page: 0 | |||||
}) } /> | |||||
{ (mode === 'manifestDownload') ? | |||||
( | |||||
<div class="container-fluid"> | |||||
<div>Downloading manifest: { filesize(loaded) }</div> | |||||
<div class="progress"> | |||||
<div class="progress-bar progress-bar-striped progress-bar-animated" role="progressbar" | |||||
aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width: 100%"></div> | |||||
</div> | |||||
</div> | |||||
) : ( | |||||
<div> | |||||
{ mode === 'manifestParse' ? ( | |||||
<div class="container-fluid mb-2"> | |||||
<div>Parsing manifest: { parsedStreams }/{ totalStreams }</div> | |||||
<div class="progress"> | |||||
<div class="progress-bar progress-bar-striped progress-bar-animated bg-success" role="progressbar" | |||||
aria-valuenow={ totalStreams } aria-valuemin="0" aria-valuemax={ parsedStreams } style={ 'width: ' + Math.round(parsedStreams * 100 / totalStreams) + '%' }></div> | |||||
</div> | |||||
</div> | |||||
) : null } | |||||
<WBTable columns={ [ 'Name', 'Type', 'Size', 'Actions' ] } | |||||
rows={ rows } /> | |||||
<WBPagination activePage={ page } numPages={ numPages } | |||||
getPageUrl={ page => this.getUrl({ 'page': page }) } /> | |||||
</div> | |||||
) } | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBCollectionContent.defaultProps = { | |||||
'collectionPath': '', | |||||
'page': 0, | |||||
'itemsPerPage': 20 | |||||
}; | |||||
export default WBCollectionContent; |
@@ -0,0 +1,99 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import urlForObject from 'url-for-object'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import wbFormatSpecialValue from 'wb-format-special-value'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
import WBJsonEditor from 'wb-json-editor'; | |||||
import wbUpdateField from 'wb-update-field'; | |||||
class WBCollectionFields extends Component { | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
prepareRows(item) { | |||||
const { app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let rows = [ | |||||
[ 'Name', item.name ], | |||||
[ 'Description', wbFormatSpecialValue(item.description) ], | |||||
[ 'Properties', ( | |||||
<WBJsonEditor name="Properties" app={ app } value={ item.properties } | |||||
onChange={ value => wbUpdateField(arvHost, arvToken, item.uuid, 'properties', value) | |||||
.then(() => { item.properties = value; this.prepareRows(item); }) } /> | |||||
) ], | |||||
[ 'Portable Data Hash', item.portable_data_hash ], | |||||
[ 'Replication Desired', item.replication_desired ? item.replication_desired : ( | |||||
<i>{ String(item.replication_desired) }</i> | |||||
) ], | |||||
[ 'Replication Confirmed', item.replication_confirmed ? item.replication_confirmed : ( | |||||
<i>{ String(item.replication_confirmed) }</i> | |||||
) ], | |||||
[ 'Replication Confirmed At', wbFormatDate(item.replication_confirmed_at) ], | |||||
[ 'Trash At', wbFormatDate(item.trash_at) ], | |||||
[ 'Delete At', wbFormatDate(item.delete_at) ], | |||||
[ 'Is Trashed', String(item.is_trashed) ], | |||||
[ 'Current Version UUID', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.current_version_uuid } /> | |||||
) ], | |||||
[ 'Version', item.version ], | |||||
[ 'Preserve Version', String(item.preserve_version) ], | |||||
[ 'File Count', item.file_count ], | |||||
[ 'Total Size', filesize(item.file_size_total) ] | |||||
]; | |||||
this.setState({ 'rows': rows }); | |||||
} | |||||
fetchData() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
const filters = [ | |||||
['uuid', '=', uuid] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections?filters=' + encodeURIComponent(JSON.stringify(filters))); | |||||
prom = prom.then(xhr => { | |||||
const item = xhr.response.items[0]; | |||||
if (!item) | |||||
throw Error('Item not found'); | |||||
this.prepareRows(item); | |||||
}); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
rows={ rows } | |||||
verticalHeader={ true } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBCollectionFields; |
@@ -0,0 +1,191 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import urlForObject from 'url-for-object'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import WBCheckboxes from 'wb-checkboxes'; | |||||
class WBCollectionListing extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.numPages = 0; | |||||
this.state.orderStream = uuid.v4(); | |||||
this.state.collectionTypes = [ 'Intermediate', 'Output', 'Log', 'Other' ]; | |||||
this.state.collectionTypeMask = [ true, true, true, true ]; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchItems(); | |||||
} | |||||
prepareRows(items, ownerLookup) { | |||||
let { app, renderRenameLink, renderDeleteButton, | |||||
renderSelectionCell, renderSharingButton, | |||||
renderEditDescription } = this.props; | |||||
return items.map(item => [ | |||||
renderSelectionCell(item), | |||||
(<div> | |||||
<div> | |||||
<a href={ urlForObject(item) }> | |||||
{ item['name'] } | |||||
</a> { renderRenameLink(item, () => this.fetchItems()) } | |||||
</div> | |||||
<div>{ item['uuid'] }</div> | |||||
</div>), | |||||
(<div> | |||||
{ item['description'] } { renderEditDescription(item, () => this.fetchItems()) } | |||||
</div>), | |||||
(<div> | |||||
<div> | |||||
{ ownerLookup[item.owner_uuid] ? ( | |||||
<a href={ urlForObject(ownerLookup[item.owner_uuid]) }> | |||||
{ arvadosObjectName(ownerLookup[item.owner_uuid]) } | |||||
</a> | |||||
) : 'Not Found' } | |||||
</div> | |||||
<div>{ item.owner_uuid }</div> | |||||
</div>), | |||||
item['file_count'], | |||||
filesize(item['file_size_total']), | |||||
(<div> | |||||
<a class="btn btn-outline-primary m-1" title="Properties" | |||||
href={ urlForObject(item, 'properties') }> | |||||
<i class="fas fa-list-ul"></i> | |||||
</a> | |||||
{ renderDeleteButton(item, () => this.fetchItems()) } | |||||
{ renderSharingButton(item) } | |||||
</div>) | |||||
]); | |||||
} | |||||
fetchItems() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { activePage, itemsPerPage, ownerUuid, textSearch } = this.props; | |||||
const { collectionTypes, collectionTypeMask } = this.state; | |||||
let filters = []; | |||||
if (ownerUuid) | |||||
filters.push([ 'owner_uuid', '=', ownerUuid ]); | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]); | |||||
if (collectionTypeMask.filter(a => (!a)).length != 0) { | |||||
if (collectionTypeMask[3]) { | |||||
for (let i = 0; i < 3; i++) | |||||
if (!collectionTypeMask[i]) | |||||
filters.push([ 'properties.type', '!=', collectionTypes[i].toLowerCase() ]); | |||||
} else { | |||||
filters.push([ 'properties.type', 'in', | |||||
collectionTypes.filter((_, k) => collectionTypeMask[k]).map(a => a.toLowerCase()) ]); | |||||
} | |||||
} | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + encodeURIComponent(itemsPerPage) + | |||||
'&offset=' + encodeURIComponent(itemsPerPage * activePage)); | |||||
let collections; | |||||
let numPages | |||||
prom = prom.then(xhr => { | |||||
collections = xhr.response['items']; | |||||
numPages = Math.ceil(xhr.response['items_available'] / xhr.response['limit']); | |||||
let owners = {}; | |||||
collections.map(c => { | |||||
let typeName = arvadosTypeName(c.owner_uuid); | |||||
if (!(typeName in owners)) | |||||
owners[typeName] = []; | |||||
owners[typeName].push(c.owner_uuid); | |||||
}); | |||||
let lookup = {}; | |||||
let prom_1 = new Promise(accept => accept()); | |||||
for (let typeName in owners) { | |||||
let filters_1 = [ | |||||
['uuid', 'in', owners[typeName]] | |||||
]; | |||||
prom_1 = prom_1.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters_1)))); | |||||
prom_1 = prom_1.then(xhr => xhr.response.items.map(item => ( | |||||
lookup[item.uuid] = item))); | |||||
} | |||||
prom_1 = prom_1.then(() => lookup); | |||||
return prom_1; | |||||
}); | |||||
//let ownerLookup = {}; | |||||
//prom = prom.then(lookup => (ownerLookup = lookup)); | |||||
prom = prom.then(ownerLookup => | |||||
this.setState({ | |||||
'numPages': numPages, | |||||
'rows': this.prepareRows(collections, ownerLookup), | |||||
'error': null | |||||
})); | |||||
prom = prom.catch(() => this.setState({ | |||||
'error': 'An error occured querying the Arvados API', | |||||
'rows': [] | |||||
})); | |||||
} | |||||
componentWillReceiveProps(nextProps, nextState) { | |||||
this.props = nextProps; | |||||
this.fetchItems(); | |||||
} | |||||
render({ app, ownerUuid, activePage, getPageUrl }, { rows, numPages, error, | |||||
collectionTypes, collectionTypeMask }) { | |||||
return ( | |||||
<div> | |||||
{ error ? (<div class="alert alert-danger" role="alert"> | |||||
{ error } | |||||
</div>) : null } | |||||
<WBCheckboxes items={ collectionTypes } checked={ collectionTypeMask } | |||||
cssClass="float-left mx-2 my-2" title="Collection Type: " | |||||
onChange={ () => route(getPageUrl(0)) } /> | |||||
<WBTable columns={ [ '', 'Name', 'Description', 'Owner', 'File Count', 'Total Size', 'Actions' ] } | |||||
headerClasses={ [ 'w-1'] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } | |||||
activePage={ activePage } | |||||
getPageUrl={ getPageUrl } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBCollectionListing.defaultProps = { | |||||
'itemsPerPage': 100, | |||||
'ownerUuid': null, | |||||
'renderSharingButton': () => null, | |||||
'renderEditDescription': () => null | |||||
}; | |||||
export default WBCollectionListing; |
@@ -0,0 +1,79 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import urlForObject from 'url-for-object'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
class WBCommonFields extends Component { | |||||
componentDidMount() { | |||||
this.prepareRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
// this.setState({ 'rows': null }); | |||||
this.prepareRows(); | |||||
} | |||||
prepareRows() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
const typeName = arvadosTypeName(uuid); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + | |||||
encodeURIComponent(uuid)); | |||||
prom = prom.then(xhr => { | |||||
const item = xhr.response; | |||||
let rows = [ | |||||
[ 'UUID', item.uuid ], | |||||
[ 'Kind', item.kind ], | |||||
[ 'Owner', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.owner_uuid } /> | |||||
) ], | |||||
[ 'Created at', wbFormatDate(item.created_at) ], | |||||
[ 'Modified at', wbFormatDate(item.modified_at) ], | |||||
[ 'Modified by User', ( | |||||
item.modified_by_user_uuid ? (<WBNameAndUuid app={ app } uuid={ item.modified_by_user_uuid } />) : '-' | |||||
) ], | |||||
[ 'Modified by Client', ( | |||||
item.modified_by_client_uuid ? (<WBNameAndUuid app={ app } uuid={ item.modified_by_client_uuid } />) : '-' | |||||
) ], | |||||
[ 'API Url', ( | |||||
<a href={ 'https://' + app.state.arvHost + '/arvados/v1/' + typeName + 's/' + uuid }> | |||||
{ 'https://' + app.state.arvHost + '/arvados/v1/' + typeName + 's/' + uuid } | |||||
</a> | |||||
) ], | |||||
[ 'ETag', item.etag ] | |||||
]; | |||||
this.setState({ 'rows': rows }); | |||||
}); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
verticalHeader={ true } | |||||
rows={ rows } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBCommonFields; |
@@ -0,0 +1,114 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import urlForObject from 'url-for-object'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
class WBContainerFields extends Component { | |||||
componentDidMount() { | |||||
this.prepareRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.prepareRows(); | |||||
} | |||||
prepareRows() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let item; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/containers/' + uuid); | |||||
prom = prom.then(xhr => (item = xhr.response)); | |||||
prom = prom.then(() => { | |||||
let rows = [ | |||||
[ 'State', item.state ], | |||||
[ 'Started At', wbFormatDate(item.started_at) ], | |||||
[ 'Finished At', wbFormatDate(item.started_at) ], | |||||
[ 'Log', item.log ? ( | |||||
<WBNameAndUuid app={ app } uuid={ item.log } /> | |||||
) : ( <i>{ String(item.log) }</i> ) ], | |||||
[ 'Environment', ( | |||||
<WBAccordion names={ ['Environment'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.environment } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Working Directory', item.cwd ], | |||||
[ 'Command', ( | |||||
<WBJsonViewer app={ app } value={ item.command } pretty={ false } /> | |||||
) ], | |||||
[ 'Output Path', item.output_path ], | |||||
[ 'Mounts', ( | |||||
<WBAccordion names={ Object.keys(item.mounts) } | |||||
cardHeaderClass="card-header-sm"> | |||||
{ Object.keys(item.mounts).map(k => ( | |||||
<WBJsonViewer app={ app } value={ item.mounts[k] } /> | |||||
)) } | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Runtime Constraints', ( | |||||
<WBAccordion names={ ['Runtime Constraints'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.runtime_constraints } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Runtime Status', ( | |||||
<WBAccordion names={ ['Runtime Status'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.runtime_status } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Scheduling Parameters', ( | |||||
<WBAccordion names={ ['Scheduling Parameters'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.scheduling_parameters } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Output', item.output ? ( | |||||
<WBNameAndUuid app={ app } uuid={ item.output } /> | |||||
) : ( <i>{ String(item.output) }</i> )], | |||||
[ 'Container Image', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.container_image } /> | |||||
) ], | |||||
[ 'Progress', item.progress ], | |||||
[ 'Priority', item.priority ], | |||||
[ 'Exit Code', item.exit_code === null ? ( <i>null</i> ) : item.exit_code ], | |||||
[ 'Auth UUID', item.auth_uuid === null ? ( <i>null</i> ) : item.auth_uuid ], | |||||
[ 'Locked by UUID', item.locked_by_uuid === null ? ( <i>null</i> ) : item.locked_by_uuid ] | |||||
]; | |||||
rows = rows.map(r => [r[0], r[1] ? r[1] : (<i>{ String(r[1]) }</i>)]); | |||||
this.setState({ 'rows': rows }); | |||||
}); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
rows={ rows } | |||||
verticalHeader={ true } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBContainerFields; |
@@ -0,0 +1,139 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import urlForObject from 'url-for-object'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
import wbUpdateField from 'wb-update-field'; | |||||
import WBJsonEditor from 'wb-json-editor'; | |||||
class WBContainerRequestFields extends Component { | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
prepareRows(item) { | |||||
const { app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let rows = [ | |||||
[ 'Name', item.name ], | |||||
[ 'Description', item.description || (<i>{ String(item.description) }</i>) ], | |||||
[ 'Properties', ( | |||||
<WBJsonEditor name="Properties" app={ app } value={ item.properties } | |||||
onChange={ value => wbUpdateField(arvHost, arvToken, item.uuid, 'properties', value) | |||||
.then(() => { item.properties = value; this.prepareRows(item); }) } /> | |||||
) ], | |||||
[ 'State', item.state ], | |||||
[ 'Requesting Container', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.requesting_container_uuid } /> | |||||
) ], | |||||
[ 'Container', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.container_uuid } /> | |||||
) ], | |||||
[ 'Container Count Max', item.container_count_max ], | |||||
[ 'Mounts', ( | |||||
<WBAccordion names={ Object.keys(item.mounts) } | |||||
cardHeaderClass="card-header-sm"> | |||||
{ Object.keys(item.mounts).map(k => ( | |||||
<WBJsonViewer app={ app } value={ item.mounts[k] } /> | |||||
)) } | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Runtime Constraints', ( | |||||
<WBAccordion names={ ['Runtime Constraints'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.runtime_constraints } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Scheduling Parameters', ( | |||||
<WBAccordion names={ ['Scheduling Parameters'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.scheduling_parameters } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Container Image', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.container_image } /> | |||||
) ], | |||||
[ 'Environment', ( | |||||
<WBAccordion names={ ['Environment'] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ item.environment } /> | |||||
</WBAccordion> | |||||
) ], | |||||
[ 'Working Directory', item.cwd ], | |||||
[ 'Command', ( | |||||
<WBJsonViewer app={ app } value={ item.command } pretty={ false } /> | |||||
) ], | |||||
[ 'Output Path', item.output_path ], | |||||
[ 'Output Name', item.output_name ], | |||||
[ 'Output TTL', item.output_ttl ], | |||||
[ 'Priority', item.priority ], | |||||
[ 'Expires At', wbFormatDate(item.expires_at) ], | |||||
[ 'Use Existing', String(item.use_existing) ], | |||||
[ 'Log', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.log_uuid } /> | |||||
) ], | |||||
[ 'Output', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.output_uuid } /> | |||||
) ], | |||||
[ 'Filters', ( | |||||
item.filters ? (<WBJsonViewer app={ app } value={ item.filters } />) : (<i>{ String(item.filters) }</i>) | |||||
) ], | |||||
[ 'Runtime Token', item.runtime_token || (<i>{ String(item.runtime_token) }</i>) ], | |||||
[ 'Runtime User', ( | |||||
<WBNameAndUuid app={ app } uuid={ item.runtime_user } /> | |||||
) ], | |||||
[ 'Runtime Auth Scopes', ( | |||||
item.runtime_auth_scopes ? ( | |||||
<WBJsonViewer app={ app } value={ item.runtime_auth_scopes } /> | |||||
) : ( | |||||
<i>{ String(item.runtime_auth_scopes) }</i> | |||||
) | |||||
) ] | |||||
]; | |||||
rows = rows.map(r => [r[0], r[1] ? r[1] : (<i>{ String(r[1]) }</i>)]); | |||||
this.setState({ rows }); | |||||
} | |||||
fetchData() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let item; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests/' + uuid); | |||||
prom = prom.then(xhr => this.prepareRows(xhr.response)); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
rows={ rows } | |||||
verticalHeader={ true } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBContainerRequestFields; |
@@ -0,0 +1,22 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
class WBInlineSearch extends Component { | |||||
render({ textSearch, navigate }) { | |||||
return ( | |||||
<div class="form-inline my-2 my-lg-0"> | |||||
<input class="form-control mr-sm-2" type="search" placeholder="Search" aria-label="Search" | |||||
value={ textSearch } onchange={ navigate ? (e => navigate(e.target.value)) : null } /> | |||||
<button class="btn btn-outline-success my-2 my-sm-0" type="submit">Search</button> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBInlineSearch; |
@@ -0,0 +1,85 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import WBDialog from 'wb-dialog'; | |||||
class WbJsonEditorDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
} | |||||
render({ name, onChange }, { editValue, parseError }) { | |||||
return ( | |||||
<WBDialog title={ 'Edit ' + name } ref={ this.dialogRef } | |||||
accept={ () => { | |||||
onChange(JSON.parse(editValue)); | |||||
} } | |||||
canAccept={ () => { | |||||
try { JSON.parse(editValue) } | |||||
catch (exc) { this.setState({ parseError: exc.message }); return false; } | |||||
return true; | |||||
} }> | |||||
<div> | |||||
<textarea class="form-control wb-json-editor" value={ editValue } rows="10" | |||||
onChange={ e => this.setState({ editValue: e.target.value }) } /> | |||||
{ parseError ? ( | |||||
<div class="alert alert-danger mt-2" role="alert"> | |||||
{ parseError } | |||||
</div> | |||||
) : null } | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
show() { | |||||
this.dialogRef.current.show(); | |||||
} | |||||
} | |||||
class WBJsonEditor extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
} | |||||
render({ app, name, value, stringify, pretty, onChange }, { editValue, parseError }) { | |||||
return ( | |||||
<div> | |||||
<WbJsonEditorDialog name={ name } onChange={ onChange } ref={ this.dialogRef } /> | |||||
<WBAccordion names={ [ name ] } extraHeaderUi={ [ ( | |||||
<button class="btn btn-link px-0" title="Edit" | |||||
onclick={ () => { | |||||
const dlg = this.dialogRef.current; | |||||
dlg.setState({ parseError: null, | |||||
editValue: stringify ? | |||||
pretty ? JSON.stringify(value, null, 2) | |||||
: JSON.stringify(value) : value }); | |||||
dlg.show(); | |||||
} }> | |||||
<i class="fas fa-edit text-secondary" /> | |||||
</button> | |||||
) ] } cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ value } stringify={ stringify } | |||||
pretty={ pretty } /> | |||||
</WBAccordion> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBJsonEditor.defaultProps = { | |||||
stringify: true, | |||||
pretty: true, | |||||
onChange: () => {} | |||||
}; | |||||
export default WBJsonEditor; |
@@ -0,0 +1,50 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBIdTools from 'wb-id-tools'; | |||||
import urlForObject from 'url-for-object'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import WBLazyInlineName from 'wb-lazy-inline-name'; | |||||
function detectIds(value, app) { | |||||
const matches = WBIdTools.detectIdentifiers(value); | |||||
matches.sort((a, b) => (a.index - b.index)); | |||||
const res = []; | |||||
let ofs = 0; | |||||
for (let i = 0; i < matches.length; i++) { | |||||
const { index } = matches[i]; | |||||
const id = matches[i][0]; | |||||
const typeName = WBIdTools.typeName(id); | |||||
const url = (typeName === 'group' ? '/browse/' + id : | |||||
typeName === 'collection' ? '/collection-browse/' + id : | |||||
urlForObject({ uuid: id })); | |||||
res.push(value.substring(ofs, index)); | |||||
res.push(h(WBLazyInlineName, { identifier: id, app }, id)); | |||||
ofs = index + id.length; | |||||
} | |||||
res.push(value.substring(ofs)); | |||||
return res; | |||||
} | |||||
class WBJsonViewer extends Component { | |||||
render({ value, stringify, app, pretty }) { | |||||
if (stringify) | |||||
value = pretty ? JSON.stringify(value, null, 2) : JSON.stringify(value); | |||||
return ( | |||||
<div class="wb-json-viewer">{ detectIds(value, app) }</div> | |||||
); | |||||
} | |||||
} | |||||
WBJsonViewer.defaultProps = { | |||||
stringify: true, | |||||
pretty: true | |||||
}; | |||||
export default WBJsonViewer; |
@@ -0,0 +1,66 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBIdTools from 'wb-id-tools'; | |||||
import urlForObject from 'url-for-object'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
class WBLazyInlineName extends Component { | |||||
componentWillReceiveProps(nextProps) { | |||||
if (nextProps.identifier === this.props.identifier) | |||||
return; | |||||
this.setState({ item: null }); | |||||
} | |||||
fetchData() { | |||||
const { app, identifier } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
const typeName = WBIdTools.typeName(identifier); | |||||
if (WBIdTools.isPDH(identifier)) { | |||||
const filters = [ | |||||
[ 'portable_data_hash', '=', identifier ] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections?filters=' + encodeURIComponent(JSON.stringify(filters))); | |||||
prom = prom.then(xhr => this.setState({ item: { | |||||
uuid: xhr.response.items.length > 0 ? xhr.response.items[0].uuid : '', | |||||
name: xhr.response.items.length > 0 ? xhr.response.items[0].name : 'Not Found' + | |||||
( xhr.response.items_available > 1 ? ' (+' + (xhr.response.items_available - 1) + ' others)' : '' ) | |||||
}})); | |||||
return; | |||||
} | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + 's/' + identifier); | |||||
prom = prom.then(xhr => this.setState({ item: xhr.response })); | |||||
prom = prom.catch(() => this.setState({ item: { name: 'Not Found' }})); | |||||
} | |||||
render({ identifier }, { item }) { | |||||
if (item) { | |||||
return ( | |||||
<a href={ urlForObject(item) }>{ arvadosObjectName(item) }</a> | |||||
); | |||||
} | |||||
const typeName = WBIdTools.typeName(identifier); | |||||
const url = (typeName === 'group' ? '/browse/' + identifier : | |||||
typeName === 'collection' ? '/collection-browse/' + identifier : | |||||
urlForObject({ uuid: identifier })); | |||||
return ( | |||||
<span> | |||||
<a href={ url }>{ identifier }</a> <a href="#" title="Look up" | |||||
onclick={ e => { e.preventDefault(); this.fetchData(); } }> | |||||
<i class="fas fa-search"></i> | |||||
</a> | |||||
</span> | |||||
); | |||||
} | |||||
} | |||||
export default WBLazyInlineName; |
@@ -0,0 +1,82 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBPagination from 'wb-pagination'; | |||||
class WBLiveLogs extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.page = 0; | |||||
this.state.moreItemsPerPage = false; | |||||
this.terminalRef = createRef(); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
if (nextProps.uuid === this.props.uuid); | |||||
return; | |||||
this.props = nextProps; | |||||
this.state.page = 0; | |||||
this.fetchData(); | |||||
} | |||||
fetchData() { | |||||
const { uuid, app } = this.props; | |||||
let { itemsPerPage } = this.props; | |||||
const { page, moreItemsPerPage } = this.state; | |||||
if (moreItemsPerPage) | |||||
itemsPerPage *= 10; | |||||
const { arvHost, arvToken } = app.state; | |||||
const filters = [ | |||||
[ 'object_uuid', '=', uuid ] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/logs?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&offset=' + (itemsPerPage * page) + | |||||
'&limit=' + itemsPerPage); | |||||
prom = prom.then(xhr => { | |||||
const { items } = xhr.response; | |||||
this.setState({ | |||||
content: items | |||||
.filter(a => ('text' in a.properties)) | |||||
.map(a => a.properties.text.trim()).join('\n'), | |||||
numPages: Math.ceil(xhr.response.items_available / itemsPerPage) | |||||
}); | |||||
this.terminalRef.current.scrollTo(0, 0); | |||||
}); | |||||
} | |||||
render({}, { content, page, numPages, moreItemsPerPage }) { | |||||
return ( | |||||
<div> | |||||
<div class="custom-control custom-switch"> | |||||
<input type="checkbox" class="custom-control-input" id="morePerPageSwitch" | |||||
checked = { moreItemsPerPage ? 'checked' : null } | |||||
onchange={ e => { this.state.moreItemsPerPage = e.target.checked; | |||||
this.state.page = 0; this.fetchData(); } } /> | |||||
<label class="custom-control-label" for="morePerPageSwitch">More log entries per page</label> | |||||
</div> | |||||
<WBPagination activePage={ page } numPages={ numPages } | |||||
onPageChanged={ page => { this.state.page = page; this.fetchData(); } } /> | |||||
<pre class="word-wrap terminal" ref={ this.terminalRef }> | |||||
{ content } | |||||
</pre> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBLiveLogs.defaultProps = { | |||||
itemsPerPage: 100 | |||||
}; | |||||
export default WBLiveLogs; |
@@ -0,0 +1,130 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import urlForObject from 'url-for-object'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
class WBNameAndUuid extends Component { | |||||
fetchData() { | |||||
const { uuid, app, lookup } = this.props; | |||||
if (!uuid) | |||||
return; | |||||
if (lookup && (uuid in lookup)) { | |||||
this.setState({ 'item': lookup[uuid]}); | |||||
return; | |||||
} | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = new Promise(accept => accept()); | |||||
if (/[0-9a-f]{32}\+[0-9]+/g.exec(uuid)) { | |||||
let filters = [ | |||||
['portable_data_hash', '=', uuid] | |||||
]; | |||||
prom = prom.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)))); | |||||
prom = prom.then(xhr => { | |||||
if (xhr.response.items.length === 0) { | |||||
this.setState({ | |||||
'item': { | |||||
'uuid': uuid, | |||||
'name': 'Collection with portable data hash ' + uuid | |||||
} | |||||
}); | |||||
return; | |||||
} | |||||
let item = xhr.response.items[0]; | |||||
if (xhr.response.items.length > 1) | |||||
item.name += ' +' + (xhr.response.items.length - 1) + ' others'; | |||||
this.setState({ item }); | |||||
}); | |||||
} else if (/[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}/.exec(uuid)) { | |||||
let typeName = arvadosTypeName(uuid); | |||||
const filters = [ | |||||
['uuid', '=', uuid] | |||||
]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + typeName + | |||||
's?filters=' + encodeURIComponent(JSON.stringify(filters))); | |||||
prom = prom.then(xhr => { | |||||
const item = xhr.response.items[0]; | |||||
if (!item) | |||||
this.setState({ 'error': 'Item not found' }); | |||||
else | |||||
this.setState({ | |||||
'item': item | |||||
}); | |||||
}); | |||||
prom = prom.catch(xhr => { | |||||
this.setState({ | |||||
'error': 'Unable to retrieve: ' + xhr.status + ' (' + xhr.statusText + ')' | |||||
}); | |||||
}); | |||||
} else { | |||||
this.setState({ | |||||
'item': { | |||||
'uuid': uuid | |||||
} | |||||
}); | |||||
} | |||||
} | |||||
componentDidMount() { | |||||
if (this.props.lazy) | |||||
;//this.setState({ item: { uuid: this.props.uuid }}); | |||||
else | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
if (this.props.uuid === nextProps.uuid) | |||||
return; | |||||
if (nextProps.lazy) { | |||||
this.setState({ item: null }); | |||||
} else { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
} | |||||
render({ uuid, onLinkClicked, lazy }, { error, item }) { | |||||
if (!uuid) | |||||
return ( | |||||
<div><i>{ String(uuid) }</i></div> | |||||
); | |||||
return ( | |||||
<div> | |||||
<div> | |||||
{ error ? error : (item ? ( | |||||
<a href={ urlForObject(item) } onclick={ onLinkClicked }>{ arvadosObjectName(item) }</a> | |||||
) : (lazy ? null : 'Loading...')) } | |||||
</div> | |||||
<div> | |||||
{ uuid } { (lazy && !item) ? ( | |||||
<a href="#" title="Look up" onclick={ e => { e.preventDefault(); this.fetchData(); } }> | |||||
<i class="fas fa-search"></i> | |||||
</a> | |||||
) : null } | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBNameAndUuid; |
@@ -0,0 +1,38 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbar from 'wb-navbar'; | |||||
import WBInlineSearch from 'wb-inline-search'; | |||||
class WBNavbarCommon extends Component { | |||||
render({ app, items, activeItem, textSearch, textSearchNavigate }) { | |||||
return ( | |||||
<WBNavbar | |||||
items={ [ | |||||
{ 'name': 'Home', 'id': 'home' }, | |||||
{ 'name': 'All Projects', 'id': 'all-projects' }, | |||||
{ 'name': 'All Users', 'id': 'all-users' }, | |||||
{ 'name': 'Shared with Me', 'id': 'shared-with-me' }, | |||||
{ 'name': 'Current User', 'dropdown': [ { 'id': 'sign-out', 'name': 'Sign Out' } ]}, | |||||
{ name: (<span>What's New <sup><span class="badge badge-info">Info</span></sup></span>), id: 'whatsnew' } | |||||
].concat(items) } | |||||
rhs={ textSearchNavigate ? ( | |||||
<WBInlineSearch textSearch={ textSearch } navigate={ textSearchNavigate } /> | |||||
) : null } | |||||
titleUrl = { '/browse/' + app.state.currentUser.uuid } | |||||
getItemUrl={ item => app.navbarItemUrl(item) } | |||||
activeItem={ activeItem } /> | |||||
); | |||||
} | |||||
} | |||||
WBNavbarCommon.defaultProps = { | |||||
'items': [] | |||||
}; | |||||
export default WBNavbarCommon; |
@@ -0,0 +1,60 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import { encodeURIComponentIncludingDots } from 'wb-process-misc'; | |||||
class WBPathDisplay extends Component { | |||||
fetchData() { | |||||
const { app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let { path } = this.props; | |||||
if (path.endsWith('/')) | |||||
path = path.substr(0, path.length - 1); | |||||
let m; | |||||
if (m = /^[0-9a-f]{32}\+[0-9]+/.exec(path)); | |||||
else if (m = /^[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}/.exec(path)); | |||||
else return; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections/' + m[0]); | |||||
prom = prom.then(xhr => this.setState({ | |||||
item: xhr.response, | |||||
tail: path.substr(m[0].length) | |||||
})); | |||||
prom = prom.catch(() => this.setState({ 'error': 'Cannot load' })); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
render({}, { item, tail, error }) { | |||||
if (error) | |||||
return error; | |||||
if (!item) | |||||
return 'Loading...'; | |||||
return ( | |||||
<span> | |||||
<a href={ '/collection-browse/' + item.uuid }> | |||||
{ item.name || item.uuid } | |||||
</a><a href={ '/collection-browse/' + item.uuid + '/' + encodeURIComponentIncludingDots(tail) }> | |||||
{ tail } | |||||
</a> | |||||
</span> | |||||
); | |||||
} | |||||
} | |||||
export default WBPathDisplay; |
@@ -0,0 +1,141 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import wbProcessStateName from 'wb-process-state-name'; | |||||
function getAll(makeRequest) { | |||||
let prom = makeRequest(0); | |||||
prom = prom.then(xhr => { | |||||
const { items, limit, items_available } = xhr.response; | |||||
let res = [].concat(items); | |||||
let prom_1 = new Promise(accept => accept()); | |||||
for (let ofs = limit; ofs < items_available; ofs += limit) { | |||||
prom_1 = prom_1.then(() => makeRequest(ofs)); | |||||
prom_1 = prom_1.then(xhr_1 => { | |||||
res = res.concat(xhr_1.response.items); | |||||
}); | |||||
} | |||||
prom_1 = prom_1.then(() => res); | |||||
return prom_1; | |||||
}); | |||||
return prom; | |||||
} | |||||
class WBProcessDashboard extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = Array(5).fill(Array(6).fill('-')); | |||||
} | |||||
fetchData() { | |||||
const { app, parentProcessUuid } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = new Promise(accept => accept()); | |||||
if (parentProcessUuid) { | |||||
prom = prom.then(() => { | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests/' + encodeURIComponent(parentProcessUuid)); | |||||
}); | |||||
prom = prom.then(xhr => { | |||||
const cr = xhr.response; | |||||
if (!cr.container_uuid) | |||||
return []; | |||||
const filters = [ [ 'requesting_container_uuid', '=', cr.container_uuid ] ]; | |||||
return getAll(ofs => | |||||
makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)) + | |||||
'&order=' + encodeURIComponent(JSON.stringify(['uuid asc'])) + | |||||
'&offset=' + ofs)); | |||||
}); | |||||
} else { | |||||
prom = prom.then(() => { | |||||
return getAll(ofs => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests?order=' + | |||||
encodeURIComponent(JSON.stringify(['uuid asc'])) + '&offset=' + ofs)); | |||||
}); | |||||
} | |||||
let crlist; | |||||
prom = prom.then(crl => { | |||||
crlist = crl; | |||||
const uuids = crlist.map(a => a.container_uuid); | |||||
// uuids = uuids.slice(0, 2); | |||||
// crlist.map(a => ( crdict[a.uuid] = a)); | |||||
const filters = [ [ 'uuid', 'in', uuids ] ]; | |||||
return getAll(ofs => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/containers?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&order=' + encodeURIComponent(JSON.stringify([ 'uuid asc' ])) + | |||||
'&offset=' + ofs)); | |||||
}); | |||||
prom = prom.then(cl => { | |||||
cl.map(a => (crlist.find(b => (b.container_uuid === a.uuid)).container = a)); | |||||
crlist.map(a => (a.wb_state = wbProcessStateName(a, a.container))); | |||||
const stats = {}; | |||||
for (let state in { 'Pending': 1, 'Running': 1, 'Complete': 1, 'Failed': 1, 'Cancelled': 1 }) { | |||||
const f = crlist.filter(a => (a.wb_state === state)); | |||||
stats[state] = { 'Count': f.length }; | |||||
if (state === 'Pending') | |||||
f.map(a => (a.wb_wait_time = (new Date() - new Date(a.created_at)) / 3.6e6)); | |||||
else | |||||
f.map(a => (a.wb_wait_time = Math.max(0, (a.container ? new Date(a.container.started_at) : new Date(0)) - new Date(a.created_at)) / 3.6e6)); | |||||
f.sort((a, b) => (a.wb_wait_time - b.wb_wait_time)); | |||||
stats[state]['Shortest Wait Time'] = f.length ? (f[0].wb_wait_time.toFixed(2) + ' hours') : '-'; | |||||
stats[state]['Longest Wait Time'] = f.length ? (f[f.length - 1].wb_wait_time.toFixed(2) + ' hours') : '-'; | |||||
if (state === 'Pending') | |||||
f.map(a => (a.wb_run_time = 0)); | |||||
else if (state === 'Running') | |||||
f.map(a => (a.wb_run_time = (new Date() - new Date(a.container.started_at)) / 3.6e6)); | |||||
else | |||||
f.map(a => (a.wb_run_time = Math.max(0, a.container ? new Date(a.container.finished_at) - new Date(a.container.started_at) : 0) / 3.6e6)); | |||||
f.sort((a, b) => (a.wb_run_time - b.wb_run_time)); | |||||
stats[state]['Shortest Run Time'] = f.length ? (f[0].wb_run_time.toFixed(2) + ' hours') : '-'; | |||||
stats[state]['Longest Run Time'] = f.length ? (f[f.length - 1].wb_run_time.toFixed(2) + ' hours') : '-'; | |||||
} | |||||
const rows = []; | |||||
for (let st in { 'Count': 1, 'Shortest Wait Time': 1, 'Longest Wait Time': 1, | |||||
'Shortest Run Time': 1, 'Longest Run Time': 1}) { | |||||
rows.push([st].concat(['Pending', 'Running', 'Complete', 'Failed', 'Cancelled'].map(a => stats[a][st]))); | |||||
} | |||||
this.setState({ rows }); | |||||
}); | |||||
} | |||||
componentDidMount() { | |||||
if (!this.props.lazy) | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
if (nextProps.parentProcessUuid === this.props.parentProcessUuid) | |||||
return; | |||||
if (this.props.lazy) { | |||||
this.setState({ rows: Array(5).fill(Array(6).fill('-')) }); | |||||
return; | |||||
} | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
render({ lazy }, { rows }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ [ 'State', 'Pending', 'Running', 'Complete', 'Failed', 'Cancelled' ] } | |||||
rows={ rows } verticalHeader={ true } /> | |||||
{ lazy ? ( | |||||
<a href="#" onclick={ e => { e.preventDefault(); this.fetchData(); } }>Refresh</a> | |||||
) : null } | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBProcessDashboard; |
@@ -0,0 +1,155 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import WBCheckboxes from 'wb-checkboxes'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import wbFetchObjects from 'wb-fetch-objects'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import WBProcessState from 'wb-process-state'; | |||||
function maskRows(rows) { | |||||
return rows.map(r => r.map(c => '-')); | |||||
} | |||||
class WBProcessListing extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.numPages = 0; | |||||
this.state.requestStates = [ 'Uncommitted', 'Committed', 'Final' ]; | |||||
this.state.reqStateMask = [ true, true, true ]; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchItems(); | |||||
} | |||||
cancelProcess(uuid) { | |||||
const { app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests/' + encodeURIComponent(uuid), | |||||
{ method: 'PUT', data: JSON.stringify({ priority: 0 }) }); | |||||
prom = prom.then(() => { | |||||
this.setState({ rows: maskRows(this.state.rows) }); | |||||
this.fetchItems(); | |||||
}); | |||||
} | |||||
prepareRows(requests, containerLookup, ownerLookup, outputLookup) { | |||||
const { app, renderRenameLink, renderDeleteButton, | |||||
renderSelectionCell, renderSharingButton, | |||||
renderEditDescription } = this.props; | |||||
return requests.map(item => { | |||||
return ( [ | |||||
renderSelectionCell(item), | |||||
(<div> | |||||
<div> | |||||
<a href={ '/process/' + item['uuid'] }> | |||||
{ item['name'] } | |||||
</a> { renderRenameLink(item, () => this.fetchItems()) } | |||||
</div> | |||||
<div>{ item['uuid'] }</div> | |||||
<div class="mt-2"> | |||||
{ item.description } { renderEditDescription(item, () => this.fetchItems()) } | |||||
</div> | |||||
</div>), | |||||
( <WBProcessState app={ app } process={ item } lazy={ true } /> ), | |||||
( <WBNameAndUuid app={ app } uuid={ item['owner_uuid'] } lazy={ true } /> ), | |||||
wbFormatDate(item['created_at']), | |||||
( <WBNameAndUuid app={ app } uuid={ item['output_uuid'] } lazy={ true } /> ), | |||||
(<div> | |||||
<button class="btn btn-outline-warning m-1" onclick={ () => this.cancelProcess(item.uuid) }> | |||||
<i class="fas fa-stop-circle"></i> | |||||
</button> | |||||
{ renderDeleteButton(item, () => this.fetchItems()) } | |||||
{ renderSharingButton(item) } | |||||
</div>) | |||||
] ); | |||||
}); | |||||
} | |||||
fetchItems() { | |||||
const { arvHost, arvToken } = this.props.appState; | |||||
const { requestStates, reqStateMask } = this.state; | |||||
const { activePage, itemsPerPage, ownerUuid, | |||||
requestingContainerUuid, waitForNextProps, | |||||
textSearch } = this.props; | |||||
if (waitForNextProps) | |||||
return; | |||||
const filters = [ | |||||
[ 'requesting_container_uuid', '=', requestingContainerUuid ] | |||||
]; | |||||
if (!reqStateMask.reduce((a, b) => a & b)) | |||||
filters.push([ 'state', 'in', requestStates.filter((_, idx) => reqStateMask[idx]) ]); | |||||
if (ownerUuid) | |||||
filters.push([ 'owner_uuid', '=', ownerUuid ]); | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]) | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (itemsPerPage * activePage)); | |||||
prom = prom.then(xhr => | |||||
this.setState({ | |||||
'numPages': Math.ceil(xhr.response['items_available'] / xhr.response['limit']), | |||||
'rows': this.prepareRows(xhr.response.items) | |||||
})); | |||||
} | |||||
componentWillReceiveProps(nextProps, nextState) { | |||||
this.props = nextProps; | |||||
this.setState({ 'rows': maskRows(this.state.rows) }); | |||||
this.fetchItems(); | |||||
} | |||||
render({ appState, ownerUuid, activePage, onPageChanged, getPageUrl }, | |||||
{ rows, numPages, requestStates, containerStates, | |||||
reqStateMask, contStateMask }) { | |||||
return ( | |||||
<div> | |||||
<WBCheckboxes items={ requestStates } checked={ reqStateMask } | |||||
cssClass="float-left mx-2 my-2" title="Request State: " | |||||
onChange={ () => this.fetchItems() } /> | |||||
<WBTable columns={ [ '', 'Name', 'Status', 'Owner', 'Created At', 'Output', 'Actions' ] } | |||||
headerClasses={ [ 'w-1' ] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } | |||||
activePage={ activePage } | |||||
getPageUrl={ getPageUrl } | |||||
onPageChanged={ onPageChanged } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBProcessListing.defaultProps = { | |||||
itemsPerPage: 100, | |||||
ownerUuid: null, | |||||
requestingContainerUuid: null, | |||||
renderRenameLink: () => null, | |||||
renderDeleteButton: () => null, | |||||
renderSelectionCell: () => null, | |||||
renderSharingButton: () => null, | |||||
renderEditDescription: () => null | |||||
}; | |||||
export default WBProcessListing; |
@@ -0,0 +1,64 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import wbProcessStateName from 'wb-process-state-name'; | |||||
class WBProcessState extends Component { | |||||
componentDidMount() { | |||||
if (!this.props.lazy) | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
if (this.props.lazy) { | |||||
this.setState({ container: null, apiError: null }); | |||||
} else { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
} | |||||
fetchData() { | |||||
const { app, process } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
if (!process.container_uuid) | |||||
return; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/containers/' + process.container_uuid); | |||||
prom = prom.then(xhr => this.setState({ 'container': xhr.response })); | |||||
prom = prom.catch(() => this.setState({ 'apiError': 'Failed to fetch container' })); | |||||
} | |||||
render({ process, lazy }, { container, apiError }) { | |||||
const runtimeStatus = container ? container.runtime_status : null; | |||||
const error = runtimeStatus ? runtimeStatus.error : null; | |||||
const warning = runtimeStatus ? runtimeStatus.warning : null; | |||||
return ( | |||||
<div> | |||||
{ wbProcessStateName(process, container) } | |||||
{ apiError ? <i>{ [ ' / ', apiError ] }</i> : null } | |||||
{ error ? [" / ", <a href={ '/container/' + container.uuid } | |||||
title={ error }>E</a> ] : null } | |||||
{ warning ? [ " / ", <a href={ '/container/' + container.uuid } | |||||
title={ warning }>W</a> ] : null } {} | |||||
{ lazy && !container && !apiError ? ( | |||||
<a href="#" title="Look up" onclick={ e => { e.preventDefault(); this.fetchData(); } }> | |||||
<i class="fas fa-search"></i> | |||||
</a> | |||||
) : null } | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBProcessState; |
@@ -0,0 +1,77 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
import wbFormatSpecialValue from 'wb-format-special-value'; | |||||
import WBLazyInlineName from 'wb-lazy-inline-name'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import wbUpdateField from 'wb-update-field'; | |||||
import WBJsonEditor from 'wb-json-editor'; | |||||
class WBProjectFields extends Component { | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchData(); | |||||
} | |||||
prepareRows(item) { | |||||
const { app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
const rows = [ | |||||
[ 'Name', wbFormatSpecialValue(item.name) ], | |||||
[ 'Description', wbFormatSpecialValue(item.description) ], | |||||
[ 'Properties', ( | |||||
<WBJsonEditor name="Properties" app={ app } value={ item.properties } | |||||
onChange={ value => wbUpdateField(arvHost, arvToken, item.uuid, 'properties', value) | |||||
.then(() => { item.properties = value; this.prepareRows(item); }) } /> | |||||
) ], | |||||
[ 'Writable by', item.writable_by | |||||
.map(a => (<WBLazyInlineName app={ app } identifier={ a } />)) | |||||
.reduce((a, b) => [].concat(a).concat(', ').concat(b)) | |||||
], | |||||
[ 'Trash At', wbFormatDate(item.trash_at) ], | |||||
[ 'Delete At', wbFormatDate(item.delete_at) ], | |||||
[ 'Is Trashed', wbFormatSpecialValue(item.is_trashed) ] | |||||
]; | |||||
this.setState({ rows }); | |||||
} | |||||
fetchData() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups/' + uuid); | |||||
prom = prom.then(xhr => this.prepareRows(xhr.response)); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
rows={ rows } | |||||
verticalHeader={ true } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBProjectFields; |
@@ -0,0 +1,110 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import urlForObject from 'url-for-object'; | |||||
class WBProjectListing extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.numPages = 0; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchItems(); | |||||
} | |||||
prepareRows(items) { | |||||
const { app, renderRenameLink, renderDeleteButton, | |||||
renderSelectionCell, renderSharingButton, | |||||
renderEditDescription } = this.props; | |||||
return items.map(item => [ | |||||
renderSelectionCell(item), | |||||
(<div> | |||||
<div> | |||||
<a href={ '/browse/' + item.uuid }> | |||||
{ item['name'] } | |||||
</a> { renderRenameLink(item, () => this.fetchItems()) } | |||||
</div> | |||||
<div>{ item['uuid'] }</div> | |||||
</div>), | |||||
(<div> | |||||
{ item['description'] } { renderEditDescription(item, () => this.fetchItems()) } | |||||
</div>), | |||||
( <WBNameAndUuid app={ app } uuid={ item['owner_uuid'] } lazy={ true } /> ), | |||||
(<div> | |||||
<a class="btn btn-outline-primary m-1" title="Properties" | |||||
href={ urlForObject(item, 'properties') }> | |||||
<i class="fas fa-list-ul"></i> | |||||
</a> | |||||
{ renderDeleteButton(item, () => this.fetchItems()) } | |||||
{ renderSharingButton(item) } | |||||
</div>) | |||||
]); | |||||
} | |||||
fetchItems() { | |||||
let { activePage, mode, itemsPerPage, ownerUuid, app, textSearch } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let filters = [ | |||||
[ 'group_class', '=', 'project' ] | |||||
]; | |||||
if (ownerUuid) | |||||
filters.push([ 'owner_uuid', '=', ownerUuid ]); | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups' + (mode === 'shared-with-me' ? '/shared' : '') + | |||||
'?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (itemsPerPage * activePage)); | |||||
prom = prom.then(xhr => | |||||
this.setState({ | |||||
'numPages': Math.ceil(xhr.response['items_available'] / xhr.response['limit']), | |||||
'rows': this.prepareRows(xhr.response['items']) | |||||
})); | |||||
} | |||||
componentWillReceiveProps(nextProps, nextState) { | |||||
// this.setState({ 'rows': [] }); // .rows = []; | |||||
this.props = nextProps; | |||||
this.fetchItems(); | |||||
} | |||||
render({ arvHost, arvToken, ownerUuid, activePage, getPageUrl }, { rows, numPages }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ [ '', 'Name', 'Description', 'Owner', 'Actions' ] } | |||||
headerClasses={ [ 'w-1' ] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } | |||||
activePage={ activePage } | |||||
getPageUrl={ getPageUrl } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBProjectListing.defaultProps = { | |||||
'itemsPerPage': 100, | |||||
'ownerUuid': null, | |||||
'renderRenameLink': () => null, | |||||
'renderDeleteButton': () => null, | |||||
'renderSelectionCell': () => null, | |||||
'renderEditDescription': () => null | |||||
}; | |||||
export default WBProjectListing; |
@@ -0,0 +1,75 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import urlForObject from 'url-for-object'; | |||||
class WBUserListing extends Component { | |||||
componentDidMount() { | |||||
this.preparePage(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.preparePage(); | |||||
} | |||||
preparePage() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { itemsPerPage, page, textSearch } = this.props; | |||||
const order = ['last_name asc']; | |||||
const filters = []; | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/users?order=' + encodeURIComponent(JSON.stringify(order)) + | |||||
'&filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + '&offset=' + (itemsPerPage * page)); | |||||
prom = prom.then(xhr => { | |||||
this.setState({ | |||||
'items': xhr.response['items'], | |||||
'numPages': Math.ceil(xhr.response['items_available'] / itemsPerPage) | |||||
}); | |||||
}); | |||||
} | |||||
render({ app, page, getPageUrl }, { items, numPages }) { | |||||
return ( | |||||
<div class="container-fluid"> | |||||
<h1>Users</h1> | |||||
<div class="d-flex flex-wrap"> | |||||
{ items ? items.map(it => ( | |||||
<div class="card mx-2 my-2"> | |||||
<h5 class="card-header"> | |||||
<a href={ urlForObject(it) }>{ it.last_name + ', ' + it.first_name }</a> | |||||
</h5> | |||||
<div class="card-body"> | |||||
<div><a href={ 'mailto:' + it.email }>{ it.email }</a></div> | |||||
<div>{ it.uuid }</div> | |||||
</div> | |||||
</div> | |||||
)) : 'Loading...' } | |||||
</div> | |||||
<WBPagination activePage={ page } numPages={ numPages } | |||||
getPageUrl={ getPageUrl } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBUserListing.defaultProps = { | |||||
'itemsPerPage': 20, | |||||
'page': 0 | |||||
}; | |||||
export default WBUserListing; |
@@ -0,0 +1,112 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBAccordion from 'wb-accordion'; | |||||
import WBJsonViewer from 'wb-json-viewer'; | |||||
class WBWorkflowFields extends Component { | |||||
componentDidMount() { | |||||
this.prepareRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.prepareRows(); | |||||
} | |||||
prepareRows() { | |||||
let { uuid, app } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/workflows/' + uuid); | |||||
prom = prom.then(xhr => { | |||||
const item = xhr.response; | |||||
let definition; | |||||
try { | |||||
definition = JSON.parse(item.definition); | |||||
} catch (_) { | |||||
definition = jsyaml.load(item.definition); | |||||
} | |||||
const graph = definition['$graph']; | |||||
let rows = [ | |||||
[ 'Name', item.name ], | |||||
[ 'Description', item.description || (<i>{ String(item.description) }</i>) ], | |||||
[ 'CWL Version', definition.cwlVersion ], | |||||
]; | |||||
let keys = graph.map(it => it.id); | |||||
keys.sort(); | |||||
keys = keys.splice(keys.indexOf('#main'), 1).concat(keys); | |||||
keys.map(k => { | |||||
const it = graph.find(it => (it.id === k)); | |||||
rows.push([ | |||||
it.id, ( | |||||
<div> | |||||
<div>Class: { it['class'] }</div> | |||||
{ it.label ? <div>Label: { it.label }</div> : null } | |||||
{ it.doc ? <div>Doc: { it.doc }</div> : null } | |||||
<WBAccordion names={ [ 'Inputs', 'Outputs', 'Rest' ] } | |||||
cardHeaderClass="card-header-sm"> | |||||
<WBJsonViewer app={ app } value={ it.inputs } /> | |||||
<WBJsonViewer app={ app } value={ it.outputs } /> | |||||
{ (() => { | |||||
delete it['inputs']; | |||||
delete it['outputs']; | |||||
delete it['class']; | |||||
delete it['label']; | |||||
delete it['doc']; | |||||
delete it['id']; | |||||
return ( | |||||
<WBJsonViewer app={ app } value={ it } /> | |||||
); | |||||
})() } | |||||
</WBAccordion> | |||||
</div> | |||||
)]); | |||||
}); | |||||
/* [ 'Graph', ( | |||||
<WBAccordion names={ graph.map(it => it.id) } | |||||
cardHeaderClass="card-header-sm"> | |||||
{ graph.map(it => ( | |||||
<WBJsonViewer app={ app } value={ it } /> | |||||
)) } | |||||
</WBAccordion> | |||||
) ] | |||||
];*/ | |||||
this.setState({ 'rows': rows }); | |||||
}); | |||||
} | |||||
render({}, { rows }) { | |||||
return ( | |||||
rows ? ( | |||||
<WBTable columns={ [ "Name", "Value" ] } | |||||
headerClasses={ [ "col-sm-2", "col-sm-4" ] } | |||||
rows={ rows } | |||||
verticalHeader={ true } /> | |||||
) : ( | |||||
<div>Loading...</div> | |||||
) | |||||
); | |||||
} | |||||
} | |||||
export default WBWorkflowFields; |
@@ -0,0 +1,78 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import wbInputSpecInfo from 'wb-input-spec-info'; | |||||
import WBPathDisplay from 'wb-path-display'; | |||||
import { parseKeepRef } from 'wb-process-misc'; | |||||
class WBWorkflowInput extends Component { | |||||
render({ app, inputSpec, inputsDict, browseDialogRef }) { | |||||
const { isFile, isDirectory, isArray } = wbInputSpecInfo(inputSpec); | |||||
if (!isFile && !isDirectory) | |||||
return ( | |||||
<div> | |||||
<input class="form-control w-100" type="text" placeholder={ inputSpec.label } | |||||
value={ inputsDict[inputSpec.id] } | |||||
onchange={ e => (inputsDict[inputSpec.id] = e.target.value) }></input> | |||||
<div class="mt-2 text-muted">{ inputSpec.doc }</div> | |||||
</div> | |||||
); | |||||
const button = ( | |||||
<button class="btn btn-outline-primary" | |||||
onclick={ e => { | |||||
e.preventDefault(); | |||||
browseDialogRef.current.show( | |||||
[].concat(isFile ? 'file' : []).concat(isDirectory ? 'directory' : []), | |||||
isArray, | |||||
v => { | |||||
inputsDict[inputSpec.id] = JSON.stringify(v); | |||||
this.setState({}); | |||||
}); | |||||
} }> | |||||
Browse... | |||||
</button> | |||||
); | |||||
let value = inputsDict[inputSpec.id]; | |||||
if (value) { | |||||
try { | |||||
value = jsyaml.load(value); | |||||
} catch (_) {} | |||||
} | |||||
return ( | |||||
<div> | |||||
<div class="input-group"> | |||||
<input class="form-control w-100" type="text" placeholder={ inputSpec.label } | |||||
value={ inputsDict[inputSpec.id] } | |||||
onchange={ e => (inputsDict[inputSpec.id] = e.target.value) }></input> | |||||
<div class="input-group-append"> | |||||
{ button } | |||||
</div> | |||||
</div> | |||||
<div class="mt-2 text-muted">{ inputSpec.doc }</div> | |||||
{ value ? | |||||
isArray ? ( | |||||
<ul class="mb-0"> | |||||
{ value.map(path => ( | |||||
<li> | |||||
<WBPathDisplay app={ app } path={ parseKeepRef(path) } /> | |||||
</li> | |||||
)) } | |||||
</ul> | |||||
) : ( | |||||
<WBPathDisplay app={ app } path={ parseKeepRef(value) } /> | |||||
) : null } | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBWorkflowInput; |
@@ -0,0 +1,116 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import wbFetchObjects from 'wb-fetch-objects'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
import urlForObject from 'url-for-object'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
class WBWorkflowListing extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.numPages = 0; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchItems(); | |||||
} | |||||
prepareRows(items, ownerLookup) { | |||||
const { renderRenameLink, renderDeleteButton, | |||||
renderSelectionCell, renderSharingButton, | |||||
renderEditDescription } = this.props; | |||||
return items.map(item => [ | |||||
renderSelectionCell(item), | |||||
( | |||||
<div> | |||||
<div> | |||||
<a href={ urlForObject(item) }> | |||||
{ arvadosObjectName(item) } | |||||
</a> { renderRenameLink(item, () => this.fetchItems()) } | |||||
</div> | |||||
<div>{ item.uuid }</div> | |||||
</div> | |||||
), | |||||
(<div> | |||||
{ item.description } { renderEditDescription(item, () => this.fetchItems()) } | |||||
</div>), | |||||
( <WBNameAndUuid uuid={ item.owner_uuid } lookup={ ownerLookup } /> ), | |||||
wbFormatDate(item.created_at), | |||||
(<div> | |||||
<a class="btn btn-outline-success mx-1 my-1" title="Launch" | |||||
href={ urlForObject(item, 'launch') }><i class="fas fa-running"></i></a> | |||||
<button class="btn btn-outline-primary mx-1 my-1" title="View"><i class="far fa-eye"></i></button> | |||||
{ renderDeleteButton(item, () => this.fetchItems()) } | |||||
{ renderSharingButton(item) } | |||||
</div>) | |||||
]); | |||||
} | |||||
fetchItems() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { page, itemsPerPage, ownerUuid, textSearch } = this.props; | |||||
const filters = []; | |||||
if (ownerUuid) | |||||
filters.push([ 'owner_uuid', '=', ownerUuid ]); | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]); | |||||
const select = ['uuid', 'name', 'description', 'owner_uuid', 'created_at']; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/workflows?filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&select=' + encodeURIComponent(JSON.stringify(select)) + | |||||
'&limit=' + encodeURIComponent(itemsPerPage) + | |||||
'&offset=' + encodeURIComponent(itemsPerPage * page)); | |||||
let workflowResp; | |||||
prom = prom.then(xhr => (workflowResp = xhr.response)); | |||||
prom = prom.then(() => wbFetchObjects(arvHost, arvToken, | |||||
workflowResp.items.map(it => it.owner_uuid))); | |||||
let ownerLookup; | |||||
prom = prom.then(lookup => (ownerLookup = lookup)); | |||||
prom = prom.then(() => | |||||
this.setState({ | |||||
'numPages': Math.ceil(workflowResp['items_available'] / workflowResp['limit']), | |||||
'rows': this.prepareRows(workflowResp.items, ownerLookup) | |||||
})); | |||||
} | |||||
componentWillReceiveProps(nextProps, nextState) { | |||||
this.props = nextProps; | |||||
this.fetchItems(); | |||||
} | |||||
render({ app, ownerUuid, page, getPageUrl }, { rows, numPages }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ [ '', 'Name', 'Description', 'Owner', 'Created At', 'Actions' ] } | |||||
headerClasses={ [ 'w-1' ] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } | |||||
activePage={ page } | |||||
getPageUrl={ getPageUrl } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBWorkflowListing.defaultProps = { | |||||
'itemsPerPage': 100, | |||||
'ownerUuid': null, | |||||
'renderSharingButton': () => null, | |||||
'renderEditDescription': () => null | |||||
}; | |||||
export default WBWorkflowListing; |
@@ -0,0 +1,50 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function fetchProjectParents(arvHost, arvToken, uuid) { | |||||
let parents = []; | |||||
let cb = xhr => { | |||||
let objectType = xhr.response['uuid'].split('-')[1]; | |||||
if (objectType === 'tpzed') { | |||||
let name = xhr.response['first_name'] + ' ' + xhr.response['last_name']; | |||||
parents.push({ 'name': name, 'uuid': xhr.response['uuid'] }); | |||||
} else { | |||||
parents.push({ 'name': xhr.response['name'], | |||||
'uuid': xhr.response['uuid'] }); | |||||
} | |||||
if (!xhr.response['owner_uuid'] || | |||||
xhr.response['owner_uuid'].endsWith('-tpzed-000000000000000')) { | |||||
return parents.reverse(); | |||||
} | |||||
objectType = xhr.response['owner_uuid'].split('-')[1]; | |||||
if (objectType === 'tpzed') { | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/users/' + xhr.response['owner_uuid']).then(cb); | |||||
} else { | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups/' + xhr.response['owner_uuid']).then(cb); | |||||
} | |||||
}; | |||||
let objectType = uuid.split('-')[1]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + (objectType === 'tpzed' ? 'users' : 'groups') + '/' + uuid); | |||||
prom = prom.then(cb); | |||||
return prom; | |||||
} | |||||
export default fetchProjectParents; |
@@ -0,0 +1,57 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBArvadosCollection { | |||||
constructor(arvHost, arvToken, uuid) { | |||||
this.arvHost = arvHost; | |||||
this.arvToken = arvToken; | |||||
this.uuid = uuid; | |||||
this.meta = null; | |||||
} | |||||
fetchMeta() { | |||||
let prom = makeArvadosRequest(this.arvHost, this.arvToken, | |||||
'/arvados/v1/collections/' + this.uuid); | |||||
prom = prom.then(xhr => { | |||||
this.meta = xhr.response; | |||||
}); | |||||
return prom; | |||||
} | |||||
parseManifest() { | |||||
if (this.meta === null) | |||||
throw Error('You must call fetchMeta() first and wait for the returned Promise.'); | |||||
let manifest = this.meta.manifest_text; | |||||
let streams = manifest.split('\n'); | |||||
this.content = streams.map(s => { | |||||
let tokens = s.split(' '); | |||||
let streamName = tokens[0]; | |||||
let rx = /^[a-f0-9]{32}\+[0-9]+/; | |||||
let n = tokens.map(t => rx.exec(t)); | |||||
n = n.indexOf(null); | |||||
let locators = tokens.slice(1, n) | |||||
let fileTokens = tokens.slice(n); | |||||
let fileNames = fileTokens.map(t => t.split(':')[2]); | |||||
let fileSizes = {}; | |||||
fileTokens.map(t => { | |||||
let [ start, end, name ] = t.split(':'); | |||||
if (!(name in fileSizes)) | |||||
fileSizes[name] = 0; | |||||
fileSizes[name] += Number(end) - Number(start); | |||||
}); | |||||
fileSizes = fileNames.map(n => fileSizes[n]); | |||||
return [ streamName, fileNames, fileSizes ]; | |||||
}); | |||||
return this.content; | |||||
} | |||||
} | |||||
export WBArvadosCollection; |
@@ -0,0 +1,42 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
class WBBrowseDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
} | |||||
render({ id }) { | |||||
return ( | |||||
<div class="modal" id={ id } tabindex="-1" role="dialog"> | |||||
<div class="modal-dialog modal-lg" role="document"> | |||||
<div class="modal-content"> | |||||
<div class="modal-header"> | |||||
<h5 class="modal-title">Browse</h5> | |||||
<button type="button" class="close" data-dismiss="modal" aria-label="Close"> | |||||
<span aria-hidden="true">×</span> | |||||
</button> | |||||
</div> | |||||
<div class="modal-body m-0 p-0"> | |||||
<iframe style="width: 100%;" src="/browse" /> | |||||
</div> | |||||
<div class="modal-footer"> | |||||
<button type="button" class="btn btn-primary">Accept</button> | |||||
<button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBBrowseDialog; |
@@ -0,0 +1,187 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
// | |||||
// Directory: Hash[string, [Directory, File]] | |||||
// File = [blockRefs, size] | |||||
// blockRefs: Array[blockRef] | |||||
// blockRef: [locator, position, size] | |||||
// locator: String | |||||
// position: Number | |||||
// size: Number | |||||
// | |||||
class WBManifestReader { | |||||
constructor(manifest_text) { | |||||
this.rootDir = {}; | |||||
if (!manifest_text) | |||||
return; | |||||
this.parse(manifest_text); | |||||
} | |||||
makeDir(parent, name) { | |||||
if (!(name in parent)) | |||||
parent[name] = {}; | |||||
if (parent[name] instanceof Array) | |||||
throw Error('Conflict trying to create a directory - a file with the same name already exists: ' + name); | |||||
return parent[name]; | |||||
} | |||||
makePath(path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
let dir = this.rootDir; | |||||
for (let i = 1; i < path.length; i++) | |||||
dir = this.makeDir(dir, path[i]); | |||||
return dir; | |||||
} | |||||
appendFile(streamName, locators, position, size, fileName) { | |||||
let path = streamName + '/' + fileName; | |||||
path = path.split('/'); | |||||
let dir = this.makePath(path.slice(0, path.length - 1)); | |||||
if (!(fileName in dir)) | |||||
dir[fileName] = [[], 0]; | |||||
if (!(dir[fileName] instanceof Array)) | |||||
throw Error('Conflict trying to create a file - a directory with the same name already exists: ' + fileName); | |||||
//this.appendReferences(dir[fileName], locators, position, size); | |||||
} | |||||
appendReferences(file, locators, position, size) { | |||||
if (size === 0) | |||||
return; | |||||
let cum = 0; | |||||
let locHashes = locators.map(loc => loc[0]); | |||||
let locSizes = locators.map(loc => loc[1]); | |||||
let locPositions = locators.map(loc => { | |||||
let res = cum; | |||||
cum += loc[1]; | |||||
return res; | |||||
}); | |||||
let used = locators.map((_, i) => (locPositions[i] + locSizes[i] > position && | |||||
locPositions[i] < position + size)); | |||||
let startBlock = used.indexOf(true); | |||||
let endBlock = used.lastIndexOf(true) + 1; | |||||
// console.log('startBlock: ' + startBlock + ', endBlock: ' + endBlock); | |||||
if (startBlock === -1) | |||||
return; | |||||
let blockRefs = []; | |||||
let runPos = position; | |||||
let runSize = size; | |||||
for (let i = startBlock; i < endBlock; i++) { | |||||
let blockPos = runPos - locPositions[i]; | |||||
let blockSize = Math.min(runSize, locSizes[i] - blockPos); | |||||
blockRefs.push([ locHashes[i], blockPos, blockSize ]); | |||||
runPos += blockSize; | |||||
runSize -= blockSize; | |||||
} | |||||
file[0] = file[0].concat(blockRefs); | |||||
file[1] += size; | |||||
} | |||||
parse(manifest_text) { | |||||
let rx = /^[a-f0-9]{32}\+[0-9]+/; | |||||
let streams = manifest_text.split('\n'); | |||||
if (!streams[streams.length - 1]) | |||||
streams = streams.slice(0, streams.length - 1); | |||||
streams.map(s => { | |||||
let tokens = s.split(' '); | |||||
let streamName = this.unescapeName(tokens[0]); | |||||
let n = tokens.map(t => rx.exec(t)); | |||||
n = n.indexOf(null, 1); | |||||
let locators = tokens.slice(1, n); | |||||
locators = locators.map(loc => [ loc, Number(loc.split('+')[1]) ]); | |||||
let fileTokens = tokens.slice(n); | |||||
fileTokens.map(t => { | |||||
let [ position, size, ...fileName ] = t.split(':'); | |||||
fileName = fileName.join(':'); | |||||
fileName = this.unescapeName(fileName); | |||||
this.appendFile(streamName, locators, | |||||
Number(position), Number(size), fileName); | |||||
}); | |||||
}); | |||||
} | |||||
findDir(path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
if (path[0] !== '.') | |||||
throw Error('Path must begin with a dot component'); | |||||
let dir = this.rootDir; | |||||
for (let i = 1; i < path.length; i++) { | |||||
if (!(path[i] in dir)) | |||||
throw Error('Directory not found'); | |||||
if (dir[path[i]] instanceof Array) | |||||
throw Error('Path is a file not directory'); | |||||
dir = dir[path[i]]; | |||||
} | |||||
return dir; | |||||
} | |||||
listDirectory(path) { | |||||
let dir = this.findDir(path); | |||||
let keys = Object.keys(dir); | |||||
keys.sort(); | |||||
let subdirs = keys.filter(k => !(dir[k] instanceof Array)); | |||||
let files = keys.filter(k => (dir[k] instanceof Array)); | |||||
let res = subdirs.map(k => [ 'd', k, null ]); | |||||
res = res.concat(files.map(k => [ 'f', k, dir[k][1] ])); | |||||
return res; | |||||
} | |||||
unescapeName(name) { | |||||
return name.replace(/(\\\\|\\[0-9]{3})/g, (_, $1) => ($1 === '\\\\' ? '\\' : String.fromCharCode(parseInt($1.substr(1), 8)))); | |||||
} | |||||
escapeName(name) { | |||||
return name.replace(/ /g, '\\040'); | |||||
} | |||||
/* let ids = { '\\': 1, '0': 2, '4': 3 }; | |||||
let transitions = [ | |||||
[ [0, 0], [1, ''], [0, 0], [0, 0] ], | |||||
[ [0, 0], [0, '\\'], [2, ''], [0, 0] ], | |||||
]; | |||||
let mode = 0; | |||||
for (let i = 0; i < name.length; i++) { | |||||
let b = name[i]; | |||||
let tokenId = Number(ids[b]); | |||||
[ mode, out ] = transitions[mode][tokenId]; | |||||
if (out === 0) | |||||
out = b; | |||||
} | |||||
}*/ | |||||
getFile(path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
if (path.length < 2) | |||||
throw Error('Invalid file path'); | |||||
let name = path[path.length - 1]; | |||||
let dir = this.findDir(path.slice(0, path.length - 1)); | |||||
if (!(name in dir)) | |||||
throw Error('File not found'); | |||||
if (!(dir[name] instanceof Array)) | |||||
throw Error('Path points to a directory not a file'); | |||||
return dir[name]; | |||||
} | |||||
} | |||||
export { WBManifestReader }; |
@@ -0,0 +1,72 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function rdvHash(serviceId, locator) { | |||||
let blockHash = /^[0-9a-f]{32}/.exec(locator); | |||||
if (!blockHash) | |||||
throw Error('Invalid locator'); | |||||
if (typeof(serviceId) !== 'string') | |||||
throw Error('Invalid service ID'); | |||||
let res = CryptoJS.MD5(serviceId + blockHash).toString(); | |||||
return res; | |||||
} | |||||
function wbDownloadFile(arvHost, arvToken, | |||||
manifestReader, path) { | |||||
const file = manifestReader.getFile(path); | |||||
const name = path.split('/').reverse()[0]; | |||||
const blockRefs = file[0]; | |||||
let services; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/keep_services/accessible'); | |||||
prom = prom.then(xhr => (services = xhr.response['items'])); | |||||
const blocks = []; | |||||
for (let i = 0; i < blockRefs.length; i++) { | |||||
prom = prom.then(() => { | |||||
const [ locator, position, size ] = blockRefs[i]; | |||||
const weights = services.map(s => rdvHash(s['uuid'], locator)); | |||||
const order = Object.keys(services).sort((a, b) => weights[b].localeCompare(weights[a])); | |||||
const orderedServices = order.map(i => services[i]); | |||||
let k = 0; | |||||
const cb = () => { | |||||
if (k >= orderedServices.length) | |||||
throw Error('Block not found'); | |||||
const svc = orderedServices[k]; | |||||
k++; | |||||
let prom_1 = makeArvadosRequest(svc.service_host + | |||||
':' + svc.service_port, arvToken, | |||||
'/' + locator, { 'useSsl': svc.service_ssl_flag, | |||||
'responseType': 'arraybuffer' }); | |||||
//prom_1 = prom_1.then(xhr => xhr.response); | |||||
prom_1 = prom_1.catch(cb); | |||||
return prom_1; | |||||
}; | |||||
return cb().then(xhr => (blocks.append(xhr.response.slice(position, size)))); | |||||
}); | |||||
} | |||||
prom = prom.then(() => { | |||||
const blob = new Blob(blocks); | |||||
const url = window.URL.createObjectURL(blob); | |||||
const a = document.createElement('a'); | |||||
a.href = url; | |||||
a.download = name; | |||||
}); | |||||
} | |||||
export default wbDownloadFile; |
@@ -0,0 +1,188 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function mkdir(parent, name) { | |||||
if (name in parent && (parent[name] instanceof Array)) | |||||
throw Error('File with the same name already exists'); | |||||
if (name in parent) | |||||
return parent[name]; | |||||
const dir = {}; | |||||
parent[name] = dir; | |||||
return dir; | |||||
} | |||||
function mkpath(parent, path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
let dir = parent; | |||||
for (let i = 1; i < path.length; i++) { | |||||
dir = mkdir(dir, path[i]); | |||||
} | |||||
return dir; | |||||
} | |||||
function makeFile(dir, name) { | |||||
if (name in dir) { | |||||
if (!(dir[name] instanceof Array)) | |||||
throw Error('Directory with the same name already exists'); | |||||
return dir[name]; | |||||
} | |||||
const f = [[], 0]; | |||||
dir[name] = f; | |||||
return f; | |||||
} | |||||
function appendFile(f, sidx, seg) { | |||||
f[0].push([ sidx, seg[0], seg[1] ]); | |||||
//f[1] += seg[1]; | |||||
return f; | |||||
} | |||||
function unescapeName(name) { | |||||
return name.replace(/(\\\\|\\[0-9]{3})/g, | |||||
(_, $1) => ($1 === '\\\\' ? '\\' : String.fromCharCode(parseInt($1.substr(1), 8)))); | |||||
} | |||||
function process(streams) { | |||||
const rootDir = {}; | |||||
streams.map((s, sidx) => { | |||||
const [ streamName, locators, segments ] = s; | |||||
const streamDir = mkpath(rootDir, streamName); | |||||
segments.map((seg, segidx) => { | |||||
let name = seg[2].split('/'); | |||||
const dir = (name.length === 1 ? streamDir : | |||||
mkpath(streamDir, ['.'].concat(name.slice(0, name.length - 1)))); | |||||
name = name[name.length - 1]; | |||||
appendFile(dir, name, sidx, seg); | |||||
}); | |||||
}); | |||||
return rootDir; | |||||
} | |||||
function parse(manifestText) { | |||||
const M_STREAM_NAME = 0; | |||||
const M_LOCATORS = 1; | |||||
const M_FILE_SEGMENTS = 2; | |||||
let mode = M_STREAM_NAME; | |||||
const streams = []; | |||||
let locators = []; | |||||
let streamName; | |||||
let accum = ''; | |||||
let tokenStart = 0; | |||||
let lastFile = null; | |||||
let lastPath = null; | |||||
const rootDir = {}; | |||||
for (let i = 0; i < manifestText.length; i++) { | |||||
const c = manifestText[i]; | |||||
if (mode === M_STREAM_NAME) { | |||||
if (c === ' ') { | |||||
mode = M_LOCATORS; | |||||
streamName = unescapeName(accum); | |||||
accum = ''; | |||||
tokenStart = i + 1; | |||||
} else { | |||||
accum += c; | |||||
} | |||||
} else if (mode === M_LOCATORS) { | |||||
if (c === ':') { | |||||
mode = M_FILE_SEGMENTS; | |||||
accum = ''; | |||||
i = tokenStart - 1; | |||||
let pos = 0; | |||||
locators = locators.map(loc => { | |||||
const r = loc.concat([ pos, pos + loc[1] ]); | |||||
pos += loc[1]; | |||||
return r; | |||||
}); | |||||
} else if (c === ' ') { | |||||
const sz = Number(accum.split('+')[1]); | |||||
locators.push([accum, sz]); | |||||
accum = ''; | |||||
tokenStart = i + 1; | |||||
} else { | |||||
accum += c; | |||||
} | |||||
} else if (mode === M_FILE_SEGMENTS) { | |||||
if (c === ' ' || c === '\n') { | |||||
let seg = accum.split(':'); | |||||
seg = [Number(seg[0]), Number(seg[1]), seg.slice(2).join(':')]; | |||||
const path = streamName + '/' + unescapeName(seg[2]); | |||||
let f; | |||||
if (path !== lastPath) { | |||||
let dirName = path.split('/'); | |||||
const fileName = dirName[dirName.length - 1]; | |||||
dirName = dirName.slice(0, dirName.length - 1); | |||||
const dir = mkpath(rootDir, dirName); | |||||
f = makeFile(dir, fileName); | |||||
lastPath = path; | |||||
lastFile = f; | |||||
} else { | |||||
f = lastFile; | |||||
} | |||||
appendFile(f, streams.length, seg); | |||||
accum = ''; | |||||
tokenStart = i + 1; | |||||
if (c === '\n') { | |||||
streams.push([ streamName, locators ]); | |||||
locators = []; | |||||
mode = M_STREAM_NAME; | |||||
} | |||||
} else { | |||||
accum += c; | |||||
} | |||||
} | |||||
} | |||||
return { rootDir, streams }; | |||||
} | |||||
function findDir(parent, path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
if (path[0] !== '.') | |||||
throw Error('Path must start with a dot (.)'); | |||||
let dir = parent; | |||||
for (let i = 1; i < path.length; i++) { | |||||
if (!(path[i] in dir)) | |||||
throw Error('Directory not found'); | |||||
dir = dir[path[i]]; | |||||
} | |||||
return dir; | |||||
} | |||||
class WBManifestReader { | |||||
constructor(manifestText) { | |||||
const {rootDir, streams} = parse(manifestText); | |||||
this.rootDir = rootDir; | |||||
this.streams = streams; | |||||
//this.rootDir = process(this.streams); | |||||
} | |||||
listDirectory(path) { | |||||
let dir = findDir(this.rootDir, path); | |||||
let keys = Object.keys(dir); | |||||
keys.sort(); | |||||
let subdirs = keys.filter(k => !(dir[k] instanceof Array)); | |||||
let files = keys.filter(k => (dir[k] instanceof Array)); | |||||
let res = subdirs.map(k => [ 'd', k, null ]); | |||||
res = res.concat(files.map(k => [ 'f', k, dir[k][1] ])); | |||||
return res; | |||||
} | |||||
} | |||||
export default WBManifestReader; |
@@ -0,0 +1,46 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBBreadcrumbs from 'wb-breadcrumbs'; | |||||
import fetchProjectParents from 'fetch-project-parents'; | |||||
class WBProjectCrumbs extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.items = [ { 'name': 'All Projects' } ]; | |||||
} | |||||
fetchCrumbs() { | |||||
if (!this.props.uuid) { | |||||
this.setState({ 'items': [ { 'name': 'All Projects' } ] }); | |||||
return; | |||||
} | |||||
let { arvHost, arvToken } = this.props.appState; | |||||
let prom = fetchProjectParents(arvHost, arvToken, this.props.uuid); | |||||
prom = prom.then(parents => this.setState({ 'items': parents })); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchCrumbs(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchCrumbs(); | |||||
} | |||||
render({ onItemClicked }, { items }) { | |||||
return ( | |||||
<WBBreadcrumbs items={ items } | |||||
onItemClicked={ onItemClicked } /> | |||||
); | |||||
} | |||||
} | |||||
export default WBProjectCrumbs; |
@@ -0,0 +1,89 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
class WBRootDirWrapper { | |||||
constructor(rootDir, streams) { | |||||
this.rootDir = rootDir; | |||||
this.streams = streams; | |||||
} | |||||
findDir(path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
if (path[0] !== '.') | |||||
throw Error('Path must begin with a dot component'); | |||||
let dir = this.rootDir; | |||||
for (let i = 1; i < path.length; i++) { | |||||
if (!(path[i] in dir)) | |||||
throw Error('Directory not found'); | |||||
if (dir[path[i]] instanceof Array) | |||||
throw Error('Path is a file not directory'); | |||||
dir = dir[path[i]]; | |||||
} | |||||
return dir; | |||||
} | |||||
listDirectory(path) { | |||||
let dir = this.findDir(path); | |||||
let keys = Object.keys(dir); | |||||
keys.sort(); | |||||
let subdirs = keys.filter(k => !(dir[k] instanceof Array)); | |||||
let files = keys.filter(k => (dir[k] instanceof Array)); | |||||
let res = subdirs.map(k => [ 'd', k, null ]); | |||||
res = res.concat(files.map(k => [ 'f', k, dir[k][1] ])); | |||||
return res; | |||||
} | |||||
unescapeName(name) { | |||||
return name.replace(/(\\\\|\\[0-9]{3})/g, (_, $1) => ($1 === '\\\\' ? '\\' : String.fromCharCode(parseInt($1.substr(1), 8)))); | |||||
} | |||||
escapeName(name) { | |||||
return name.replace(/ /g, '\\040'); | |||||
} | |||||
getFile(path) { | |||||
if (typeof(path) === 'string') | |||||
path = path.split('/'); | |||||
if (path.length < 2) | |||||
throw Error('Invalid file path'); | |||||
const name = path[path.length - 1]; | |||||
const dir = this.findDir(path.slice(0, path.length - 1)); | |||||
if (!(name in dir)) | |||||
throw Error('File not found'); | |||||
if (!(dir[name] instanceof Array)) | |||||
throw Error('Path points to a directory not a file'); | |||||
const streams = this.streams; | |||||
let file = dir[name]; | |||||
file = [ file[0].map(seg => { | |||||
const stm = streams[seg[0]]; | |||||
const used = stm.map(loc => !( loc[2] <= seg[1] || loc[1] >= seg[1] + seg[2] ) ); | |||||
const start = used.indexOf(true); | |||||
const end = used.lastIndexOf(true) + 1; | |||||
if (start === -1) | |||||
return []; | |||||
const res = []; | |||||
for (let i = start; i < end; i++) { | |||||
const loc = stm[i]; | |||||
res.push([ loc[0], Math.max(0, seg[1] - loc[1]), | |||||
Math.min(loc[2] - loc[1], seg[1] + seg[2] - loc[1]) ]); | |||||
} | |||||
return res; | |||||
}), file[1] ]; | |||||
file[0] = file[0].reduce((a, b) => a.concat(b)); | |||||
return file; | |||||
} | |||||
} | |||||
export default WBRootDirWrapper; |
@@ -0,0 +1,125 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBManifestWorkerWrapper from 'wb-manifest-worker-wrapper'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
function unescapeName(name) { | |||||
return name.replace(/(\\\\|\\[0-9]{3})/g, | |||||
(_, $1) => ($1 === '\\\\' ? '\\' : String.fromCharCode(parseInt($1.substr(1), 8)))); | |||||
} | |||||
class WBBrowseDialogCollectionContent extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.manifestWorker = new WBManifestWorkerWrapper(); | |||||
this.state.mode = 'manifestDownload'; | |||||
this.state.rows = []; | |||||
} | |||||
componentDidMount() { | |||||
const { app, collectionUuid } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
const { manifestWorker } = this.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections/' + collectionUuid); | |||||
let streams; | |||||
prom = prom.then(xhr => { | |||||
streams = xhr.response.manifest_text.split('\n'); | |||||
const paths = streams.filter(s => s).map(s => { | |||||
const n = s.indexOf(' '); | |||||
return unescapeName(s.substr(0, n)); | |||||
}); | |||||
return manifestWorker.postMessage([ 'precreatePaths', paths ]); | |||||
}); | |||||
prom = prom.then(() => { | |||||
this.setState({ 'mode': 'manifestParse' }); | |||||
let prom_1 = new Promise(accept => accept()); | |||||
for (let i = 0; i < streams.length; i++) { | |||||
prom_1 = prom_1.then(() => manifestWorker.postMessage([ 'parseStream', streams[i] ])); | |||||
prom_1 = prom_1.then(() => manifestWorker.postMessage([ 'listDirectory', '.' + this.props.collectionPath, true ])); | |||||
prom_1 = prom_1.then(e => this.prepareRows(e.data[1])); | |||||
} | |||||
return prom_1; | |||||
}); | |||||
prom = prom.then(() => manifestWorker.postMessage([ 'listDirectory', '.' + this.props.collectionPath, true ])); | |||||
prom = prom.then(e => { | |||||
this.state.mode = 'browsingReady'; | |||||
this.prepareRows(e.data[1]) | |||||
}); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
if (this.state.mode !== 'browsingReady') | |||||
return; | |||||
let prom = this.state.manifestWorker.postMessage([ | |||||
'listDirectory', '.' + this.props.collectionPath, true | |||||
]); | |||||
prom = prom.then(e => this.prepareRows(e.data[1])); | |||||
} | |||||
prepareRows(listing) { | |||||
const { makeSelectionCell, collectionPath, navigate, | |||||
page, itemsPerPage, collectionUuid, textSearch, selectWhat } = this.props; | |||||
const textLower = textSearch.toLowerCase(); | |||||
listing = listing.filter(it => (it[1].toLowerCase().indexOf(textLower) !== -1)); | |||||
const numPages = Math.ceil(listing.length / itemsPerPage); | |||||
const rows = listing.slice(page * itemsPerPage, | |||||
(page + 1) * itemsPerPage).map(it => [ | |||||
((it[0] === 'd' && [].concat(selectWhat).indexOf('directory') !== -1) || | |||||
(it[0] === 'f' && [].concat(selectWhat).indexOf('file') !== -1)) ? | |||||
makeSelectionCell(collectionUuid + collectionPath + '/' + it[1] + (it[0] === 'd' ? '/' : '')) : | |||||
null, | |||||
it[0] === 'd' ? ( | |||||
<a href="#" onclick={ e => { | |||||
e.preventDefault(); | |||||
navigate({ 'collectionPath': collectionPath + '/' + it[1], | |||||
'bottomPage': 0 }); | |||||
} }>{ it[1] }</a> | |||||
) : it[1], | |||||
it[0] === 'f' ? filesize(it[2]) : '' | |||||
]); | |||||
this.setState({ rows, numPages }); | |||||
} | |||||
render({ page, navigate }, { rows, mode, numPages }) { | |||||
return ( | |||||
<div> | |||||
{ mode === 'browsingReady' ? ( | |||||
null | |||||
) : [ | |||||
<div>{ mode === 'manifestParse' ? 'Parsing manifest...' : 'Downloading manifest...' }</div>, | |||||
<div class="progress my-2"> | |||||
<div class={ 'progress-bar progress-bar-striped progress-bar-animated' + | |||||
(mode === 'manifestParse' ? ' bg-success': '') } role="progressbar" | |||||
aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width: 100%"></div> | |||||
</div> | |||||
] } | |||||
<WBTable headerClasses={ [ 'w-1' ] } | |||||
columns={ [ '', 'Name', 'Size' ] } rows={ rows } /> | |||||
<WBPagination numPages={ numPages } activePage={ page } | |||||
onPageChanged={ i => navigate({ 'bottomPage': i }) } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBBrowseDialogCollectionContent.defaultProps = { | |||||
'itemsPerPage': 20 | |||||
}; | |||||
export default WBBrowseDialogCollectionContent; |
@@ -0,0 +1,78 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBBrowseDialogCollectionList extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchRows(); | |||||
} | |||||
prepareRows(items) { | |||||
const { navigate, selectWhat, makeSelectionCell } = this.props; | |||||
return items.map(it => [ | |||||
([].concat(selectWhat).indexOf('directory') !== -1 ? makeSelectionCell(it.uuid + '/') : null), | |||||
( | |||||
<a href="#" onclick={ e => { e.preventDefault(); | |||||
navigate('/browse-dialog/content/' + it.uuid + '////'); } }>{ it.name }</a> | |||||
), | |||||
it.uuid | |||||
]); | |||||
} | |||||
fetchRows() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { ownerUuid, textSearch, page, itemsPerPage } = this.props; | |||||
const filters = []; | |||||
if (ownerUuid) | |||||
filters.push(['owner_uuid', '=', ownerUuid]); | |||||
if (textSearch) | |||||
filters.push(['name', 'ilike', '%' + textSearch + '%']); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/collections?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (itemsPerPage * page)); | |||||
prom = prom.then(xhr => this.setState({ | |||||
'rows': this.prepareRows(xhr.response.items), | |||||
'numPages': Math.ceil(xhr.response.items_available / itemsPerPage) | |||||
})); | |||||
return prom; | |||||
} | |||||
render({ selectWhat, page, navigate }, { rows, numPages }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ ['', 'Name', 'UUID'] } | |||||
headerClasses={ ['w-1'] } | |||||
rows={ rows } /> | |||||
<WBPagination activePage={ page } numPages={ numPages } | |||||
onPageChanged={ i => navigate({ 'bottomPage': i }) } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBBrowseDialogCollectionList.defaultProps = { | |||||
'itemsPerPage': 20 | |||||
}; | |||||
export default WBBrowseDialogCollectionList; |
@@ -0,0 +1,113 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import WBTable from 'wb-table'; | |||||
class WBBrowseDialogProjectList extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.history = []; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchRows(); | |||||
} | |||||
prepareRows(items) { | |||||
const { navigate, selectWhat, makeSelectionCell } = this.props; | |||||
return items.map(it => ([].concat(selectWhat).indexOf('owner') !== -1 ? [ makeSelectionCell(it.uuid, 'project') ] : []).concat([ | |||||
( | |||||
<a href="#" onclick={ e => { | |||||
e.preventDefault(); | |||||
navigate('/browse-dialog/browse/' + it.uuid); | |||||
} }>{ it.name }</a> | |||||
), | |||||
it.uuid | |||||
])); | |||||
} | |||||
fetchSharedWithMe() { | |||||
const { arvHost, arvToken, currentUser } = this.props.app.state; | |||||
const { textSearch, itemsPerPage, page } = this.props; | |||||
const filters = [ | |||||
['group_class', '=', 'project'] | |||||
]; | |||||
if (textSearch) | |||||
filters.push([ 'name', 'ilike', '%' + textSearch + '%']); | |||||
const prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups/shared?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (itemsPerPage * page)); | |||||
return prom; | |||||
} | |||||
fetchOwned() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { ownerUuid, page, textSearch, itemsPerPage } = this.props; | |||||
const filters = [ | |||||
['group_class', '=', 'project'] | |||||
]; | |||||
if (ownerUuid) | |||||
filters.push(['owner_uuid', '=', ownerUuid]); | |||||
if (textSearch) | |||||
filters.push(['name', 'ilike', '%' + textSearch + '%']); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (page * itemsPerPage)); | |||||
return prom; | |||||
} | |||||
fetchRows() { | |||||
const { mode, itemsPerPage } = this.props; | |||||
let prom = (mode === 'shared-with-me') ? | |||||
this.fetchSharedWithMe() : | |||||
this.fetchOwned(); | |||||
prom = prom.then(xhr => { | |||||
this.setState({ | |||||
'rows': this.prepareRows(xhr.response.items), | |||||
'numPages': Math.ceil(xhr.response.items_available / itemsPerPage) | |||||
}); | |||||
}); | |||||
return prom; | |||||
} | |||||
render({ app, navigate, page, selectWhat }, { numPages, rows }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ ([].concat(selectWhat).indexOf('owner') !== -1 ? [''] : []).concat(['Name', 'UUID']) } | |||||
headerClasses={ [].concat(selectWhat).indexOf('owner') !== -1 ? ['col-sm-1', 'col-sm-4', 'col-sm-4'] : [] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } activePage={ page } | |||||
onPageChanged={ i => navigate({ 'topPage': i }) } | |||||
chunkSize="3" /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBBrowseDialogProjectList.defaultProps = { | |||||
'itemsPerPage': 5, | |||||
'resetSearch': () => {} | |||||
}; | |||||
export default WBBrowseDialogProjectList; |
@@ -0,0 +1,78 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBBrowseDialogUserList extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchRows(); | |||||
} | |||||
prepareRows(items) { | |||||
const { navigate } = this.props; | |||||
return items.map(it => [ | |||||
( | |||||
<a href="#" onclick={ e => { e.preventDefault(); | |||||
navigate('/browse-dialog/browse/' + it.uuid); } }> | |||||
{ it.last_name + ', ' + it.first_name } | |||||
</a> | |||||
), | |||||
it.uuid | |||||
]); | |||||
} | |||||
fetchRows() { | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { itemsPerPage, page, textSearch } = this.props; | |||||
const order = ['last_name asc', 'first_name asc']; | |||||
const filters = []; | |||||
if (textSearch) | |||||
filters.push([ 'any', 'ilike', '%' + textSearch + '%' ]); | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/users?order=' + | |||||
encodeURIComponent(JSON.stringify(order)) + | |||||
'&filters=' + | |||||
encodeURIComponent(JSON.stringify(filters)) + | |||||
'&limit=' + itemsPerPage + | |||||
'&offset=' + (itemsPerPage * page)); | |||||
prom = prom.then(xhr => this.setState({ | |||||
'rows': this.prepareRows(xhr.response.items), | |||||
'numPages': Math.ceil(xhr.response.items_available / itemsPerPage) | |||||
})); | |||||
} | |||||
render({ page, navigate }, { rows, numPages }) { | |||||
return ( | |||||
<div> | |||||
<WBTable columns={ [ 'Name', 'UUID' ] } | |||||
rows={ rows } /> | |||||
<WBPagination numPages={ numPages } activePage={ page } | |||||
onPageChanged={ i => navigate({ 'topPage': i }) } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBBrowseDialogUserList.defaultProps = { | |||||
'itemsPerPage': 20 | |||||
}; | |||||
export default WBBrowseDialogUserList; |
@@ -0,0 +1,269 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBBrowseDialogProjectList from 'wb-browse-dialog-project-list'; | |||||
import WBBrowseDialogCollectionList from 'wb-browse-dialog-collection-list'; | |||||
import WBBrowseDialogCollectionContent from 'wb-browse-dialog-collection-content'; | |||||
import WBBrowseDialogUserList from 'wb-browse-dialog-user-list'; | |||||
import linkState from 'linkstate'; | |||||
import { Router } from 'preact-router'; | |||||
import { createHashHistory } from 'history'; | |||||
// | |||||
// internal URLs look like this | |||||
// | |||||
// /browse-dialog/browse/( owner-uuid )/( project-page )/( text-search ) | |||||
// /browse-dialog/users//( users-page )/( text-search ) | |||||
// /browse-dialog/shared-with-me//( project-page )/( collection-page )/( text-search ) | |||||
// /browse-dialog/content/( collection-uuid )//( content-page )/( text-search )/( collection-path ) | |||||
// | |||||
// general pattern therefore: | |||||
// /browse-dialog/( mode )/( uuid )/( top-page )/( bottom-page )/( text-search ) | |||||
// | |||||
// props: | |||||
// selectMany: Boolean | |||||
// selectWhat: [ 'file', 'directory', 'owner' ] | |||||
// | |||||
// state: | |||||
// selected: Array of UUID | |||||
// textSearch: string | |||||
// textSearchInput: string | |||||
// | |||||
class WBBrowseDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.history = []; | |||||
this.state.selected = {}; | |||||
this.state.selectedOrder = []; | |||||
const { currentUser } = this.props.app.state; | |||||
this.state.currentUrl = '/browse-dialog/browse/' + currentUser.uuid; | |||||
this.state.uuid = currentUser.uuid; | |||||
this.state.mode = 'browse'; | |||||
this.state.topPage = 0; | |||||
this.state.bottomPage = 0; | |||||
this.state.collectionPath = ''; | |||||
this.state.textSearch = ''; | |||||
this.state.id = ('id' in this.props) ? this.props.id : uuid.v4(); | |||||
this.state.accept = () => {}; | |||||
this.modalRef = createRef(); | |||||
} | |||||
navigateBack() { | |||||
if (this.state.history.length === 0) | |||||
return; | |||||
const url = this.state.history.pop(); | |||||
this.navigate(url, false); | |||||
} | |||||
navigate(url, useHistory=true, stateUpdate={}) { | |||||
if (typeof(url) === 'object') { | |||||
url = ['', 'browse-dialog', | |||||
'mode' in url ? url.mode : this.state.mode, | |||||
'uuid' in url ? url.uuid : this.state.uuid, | |||||
'topPage' in url ? url.topPage : this.state.topPage, | |||||
'bottomPage' in url ? url.bottomPage : this.state.bottomPage, | |||||
'textSearch' in url ? url.textSearch : this.state.textSearch, | |||||
encodeURIComponent('collectionPath' in url ? url.collectionPath : this.state.collectionPath) | |||||
].join('/'); | |||||
} | |||||
url = url.substr(url.indexOf('/browse-dialog/')); | |||||
if (useHistory) | |||||
this.state.history.push(this.state.currentUrl); | |||||
let [ _1, _2, mode, uuid, topPage, bottomPage, textSearch, collectionPath ] = url.split('/'); | |||||
topPage = parseInt(topPage, 10) || 0; | |||||
bottomPage = parseInt(bottomPage, 10) || 0; | |||||
collectionPath = decodeURIComponent(collectionPath || ''); | |||||
this.setState(Object.assign({ | |||||
'currentUrl': url, | |||||
mode, uuid, topPage, bottomPage, textSearch, collectionPath | |||||
}, stateUpdate)); | |||||
} | |||||
select(uuid) { | |||||
let { selected, selectedOrder } = this.state; | |||||
if (uuid in selected) { | |||||
const n = selectedOrder.indexOf(uuid); | |||||
selectedOrder = selected.splice(n, n + 1); | |||||
} | |||||
selected[uuid] = true; | |||||
selectedOrder.push(uuid); | |||||
/* this.setState({ | |||||
selected, selectedOrder | |||||
}); */ | |||||
} | |||||
deselect(uuid) { | |||||
let { selected, selectedOrder } = this.state; | |||||
if (!(uuid in selected)) | |||||
return; | |||||
const n = selectedOrder.indexOf(uuid); | |||||
selectedOrder = selected.splice(n, n + 1); | |||||
delete selected[uuid]; | |||||
/* this.setState({ | |||||
selected, selectedOrder | |||||
}); */ | |||||
} | |||||
resetSelection() { | |||||
this.setState({ | |||||
'selected': {}, | |||||
'selectedOrder': [] | |||||
}); | |||||
} | |||||
makeSelectionCell(uuid) { | |||||
const { selected, accept, selectMany, id } = this.state; | |||||
return selectMany ? ( | |||||
<div> | |||||
<input type="checkbox" checked={ (uuid in selected) } | |||||
onChange={ e => { | |||||
if (e.target.checked) | |||||
this.select(uuid); | |||||
else | |||||
this.deselect(uuid); | |||||
} } /> { '\u00A0' } | |||||
</div> | |||||
) : ( | |||||
<button class="btn btn-outline-primary" title="Use" | |||||
onclick={ () => { | |||||
$('#' + id).modal('hide'); | |||||
accept(uuid); | |||||
} }> | |||||
<i class="fas fa-hand-pointer"></i> | |||||
</button> | |||||
); | |||||
} | |||||
show(selectWhat, selectMany, accept=(() => {})) { | |||||
const { app } = this.props; | |||||
const { currentUser } = app.state; | |||||
this.navigate('/browse-dialog/browse/' + currentUser.uuid, false, | |||||
{ selectWhat, selectMany, accept, history: [], | |||||
selected: {}, selectedOrder: [] }); | |||||
$('#' + this.state.id).modal(); | |||||
} | |||||
componentWillUnmount() { | |||||
$(this.modalRef.current).modal('hide'); | |||||
} | |||||
render({ app }, | |||||
{ history, currentUrl, mode, uuid, | |||||
topPage, bottomPage, textSearch, | |||||
collectionPath, id, accept, selectedOrder, | |||||
selectMany, selectWhat }) { | |||||
return ( | |||||
<div class="modal" id={ id } tabindex="-1" role="dialog" ref={ this.modalRef }> | |||||
<div class="modal-dialog modal-lg" role="document"> | |||||
<div class="modal-content"> | |||||
<div class="modal-header"> | |||||
{ false ? <h5 class="modal-title">Browse</h5> : null } | |||||
<div>{ currentUrl }</div> | |||||
<button type="button" class="close" data-dismiss="modal" aria-label="Close"> | |||||
<span aria-hidden="true">×</span> | |||||
</button> | |||||
</div> | |||||
<div class="modal-body"> | |||||
<div class="mb-3"> | |||||
<a href="#" class={ 'btn btn-outline-secondary mr-2' + | |||||
(history.length === 0 ? ' disabled': '') } | |||||
onclick={ e => { e.preventDefault(); | |||||
this.navigateBack(); } }>Back</a> | |||||
<a href="#" class="btn btn-outline-primary mr-2" | |||||
onclick={ e => { e.preventDefault(); | |||||
this.navigate('/browse-dialog/browse/' + app.state.currentUser.uuid); } }>Home</a> | |||||
<a href="#" class="btn btn-outline-primary mr-2" | |||||
onclick={ e => { e.preventDefault(); | |||||
this.navigate('/browse-dialog/browse'); } }>All Projects</a> | |||||
<a href="#" class="btn btn-outline-primary mr-2" | |||||
onclick={ e => { e.preventDefault(); | |||||
this.navigate('/browse-dialog/users'); } }>All Users</a> | |||||
<a href="#" class="btn btn-outline-primary mr-2" | |||||
onclick={ e => { e.preventDefault(); | |||||
this.navigate('/browse-dialog/shared-with-me'); } }>Shared with Me</a> | |||||
</div> | |||||
<div class="input-group mb-3"> | |||||
<input type="text" class="form-control" placeholder="Search" | |||||
aria-label="Search" value={ textSearch } | |||||
onChange={ e => this.navigate({ | |||||
'textSearch': e.target.value, | |||||
'topPage': 0, | |||||
'bottomPage': 0}) } /> | |||||
<div class="input-group-append"> | |||||
<button class="btn btn-outline-primary" type="button">Search</button> | |||||
</div> | |||||
</div> | |||||
{ (mode === 'browse' || mode === 'shared-with-me') ? ( | |||||
<div> | |||||
<h5>Projects</h5> | |||||
<WBBrowseDialogProjectList app={ app } | |||||
navigate={ url => this.navigate(url) } | |||||
mode={ mode } ownerUuid={ uuid } | |||||
page={ topPage } textSearch={ textSearch } | |||||
selectWhat={ selectWhat } | |||||
makeSelectionCell={ uuid => this.makeSelectionCell(uuid) } /> | |||||
</div> | |||||
) : null } | |||||
{ (mode === 'users') ? ( | |||||
<WBBrowseDialogUserList app={ app } | |||||
navigate={ url => this.navigate(url) } | |||||
page={ topPage } textSearch={ textSearch }/> | |||||
) : null } | |||||
{ (mode === 'content') ? ( | |||||
<div> | |||||
<h5>Content</h5> | |||||
<WBBrowseDialogCollectionContent app={ app } | |||||
collectionUuid={ uuid } collectionPath={ collectionPath } | |||||
page={ bottomPage } selectWhat={ selectWhat } | |||||
makeSelectionCell={ uuid => this.makeSelectionCell(uuid) } | |||||
navigate={ url => this.navigate(url) } | |||||
textSearch={ textSearch } /> | |||||
</div> | |||||
) : (selectWhat !== 'owner' && mode === 'browse') ? ( | |||||
<div> | |||||
<h5>Collections</h5> | |||||
<WBBrowseDialogCollectionList app={ app } | |||||
page={ bottomPage } textSearch={ textSearch } | |||||
navigate={ url => this.navigate(url) } | |||||
ownerUuid={ uuid } selectWhat={ selectWhat } | |||||
makeSelectionCell={ uuid => this.makeSelectionCell(uuid) } /> | |||||
</div> | |||||
) : null } | |||||
</div> | |||||
<div class="modal-footer"> | |||||
{ selectMany ? ( | |||||
<button type="button" class="btn btn-primary" | |||||
onclick={ e => { e.preventDefault(); accept(selectedOrder); $('#' + id).modal('hide'); } }>Accept</button> | |||||
) : null } | |||||
<button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBBrowseDialog.defaultProps = { | |||||
'accept': () => {} | |||||
}; | |||||
export default WBBrowseDialog; |
@@ -0,0 +1,60 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBDialog from 'wb-dialog'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import linkState from 'linkstate'; | |||||
import wbDeleteObject from 'wb-delete-object'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
class WBDeleteDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
} | |||||
show(item, callback) { | |||||
this.setState({ | |||||
'item': item, | |||||
'callback': callback || (() => {}) | |||||
}); | |||||
this.dialogRef.current.show(); | |||||
} | |||||
hide() { | |||||
this.dialogRef.current.hide(); | |||||
} | |||||
render({ app }, { item, callback }) { | |||||
const { arvHost, arvToken } = app.state; | |||||
return ( | |||||
<WBDialog title="Delete" ref={ this.dialogRef }> | |||||
<div> | |||||
<div class="mb-3"> | |||||
Are you sure you want to delete the following { item ? arvadosTypeName(item.uuid) : null }: | |||||
</div> | |||||
{ item ? <WBArvadosCrumbs app={ app } uuid={ item.uuid } /> : null } | |||||
<div>???</div> | |||||
</div> | |||||
<div> | |||||
<input type="submit" class="btn btn-danger mr-2" value="Delete" | |||||
onclick={ e => { e.preventDefault(); this.hide(); | |||||
wbDeleteObject(arvHost, arvToken, item.uuid).then(callback); } } /> | |||||
<button class="btn btn-secondary mr-2" onclick={ e => { e.preventDefault(); | |||||
this.hide(); } }> | |||||
Cancel | |||||
</button> | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
} | |||||
export default WBDeleteDialog; |
@@ -0,0 +1,59 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBDialog from 'wb-dialog'; | |||||
import linkState from 'linkstate'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
class WBEditDescriptionDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
this.state.inputId = uuid.v4(); | |||||
} | |||||
show(item, callback) { | |||||
const { inputId } = this.state; | |||||
this.setState({ | |||||
'item': item, | |||||
'newDescription': null, | |||||
'callback': callback || (() => {}) | |||||
}); | |||||
this.dialogRef.current.show(); | |||||
$('#' + inputId).focus(); | |||||
} | |||||
hide() { | |||||
this.dialogRef.current.hide(); | |||||
} | |||||
render({ app }, { item, newDescription, callback, inputId }) { | |||||
const { arvHost, arvToken } = app.state; | |||||
return ( | |||||
<WBDialog title="Edit Description" ref={ this.dialogRef } accept={ () => | |||||
makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + arvadosTypeName(item.uuid) + | |||||
's/' + item.uuid, { | |||||
method: 'PUT', | |||||
data: JSON.stringify({ | |||||
description: newDescription || null | |||||
}) | |||||
}).then(callback) | |||||
}> | |||||
<div> | |||||
<input type="text" class="form-control" id={ inputId } | |||||
placeholder={ (item && item.description) ? item.description : 'Type new description here' } | |||||
value={ newDescription } onChange={ linkState(this, 'newDescription') } /> | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
} | |||||
export default WBEditDescriptionDialog; |
@@ -0,0 +1,73 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBDialog from 'wb-dialog'; | |||||
import linkState from 'linkstate'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBNewProjectDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
this.state.inputId = uuid.v4(); | |||||
} | |||||
show(ownerUuid, callback) { | |||||
const { inputId } = this.state; | |||||
this.setState({ | |||||
'ownerUuid': ownerUuid, | |||||
'newName': null, | |||||
'placeholderName': 'New Project (' + (new Date()).toISOString() + ')', | |||||
'callback': callback || (() => {}) | |||||
}); | |||||
this.dialogRef.current.show(); | |||||
$('#' + inputId).focus(); | |||||
} | |||||
hide() { | |||||
this.dialogRef.current.hide(); | |||||
} | |||||
render({ app }, { ownerUuid, newName, placeholderName, callback, inputId, | |||||
projectDescription }) { | |||||
const { arvHost, arvToken } = app.state; | |||||
return ( | |||||
<WBDialog title="New Project" ref={ this.dialogRef } accept={ () => { | |||||
const group = { | |||||
'group_class': 'project', | |||||
'name': newName || placeholderName, | |||||
'description': projectDescription || null, | |||||
'owner_uuid': ownerUuid | |||||
}; | |||||
makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/groups', { 'method': 'POST', | |||||
'data': JSON.stringify(group), | |||||
'expectedStatus': [200, 202] } | |||||
).then(callback); | |||||
} }> | |||||
<div> | |||||
<div class="form-group"> | |||||
<label for={ inputId }>Project Name</label> | |||||
<input type="text" class="form-control" id={ inputId } | |||||
placeholder={ placeholderName } | |||||
value={ newName } onChange={ linkState(this, 'newName') } /> | |||||
</div> | |||||
<div class="form-group"> | |||||
<label for="projectDescription">Project Description (optional)</label> | |||||
<input type="text" class="form-control" id="projectDescription" | |||||
placeholder="Project Description (optional)" | |||||
value={ projectDescription } onChange={ linkState(this, 'projectDescription') } /> | |||||
</div> | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
} | |||||
export default WBNewProjectDialog; |
@@ -0,0 +1,118 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBDialog from 'wb-dialog'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPagination from 'wb-pagination'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import arvadosObjectName from 'arvados-object-name'; | |||||
class WBPickObjectDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.title = 'WBPickObjectDialog'; | |||||
this.state.rows = []; | |||||
this.state.textSearch = null; | |||||
this.dialogRef = createRef(); | |||||
} | |||||
show(title, objectType, accept, filters=[]) { | |||||
this.setState({ title, objectType, page: 0, rows: [], accept, filters, textSearch: null }); | |||||
this.dialogRef.current.show(); | |||||
this.fetchData(); | |||||
} | |||||
hide() { | |||||
this.dialogRef.current.hide(); | |||||
} | |||||
fetchData() { | |||||
const { app, itemsPerPage } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
const { objectType, page, textSearch } = this.state; | |||||
let { filters } = this.state; | |||||
if (textSearch) | |||||
filters = filters.concat([['any', 'ilike', '%' + textSearch + '%']]); | |||||
const order = (objectType === 'user') ? | |||||
['last_name asc', 'first_name asc'] : | |||||
['name asc']; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/' + objectType + | |||||
's?offset=' + (page * itemsPerPage) + | |||||
'&limit=' + itemsPerPage + | |||||
'&filters=' + encodeURIComponent(JSON.stringify(filters)) + | |||||
'&order=' + encodeURIComponent(JSON.stringify(order)) | |||||
); | |||||
prom = prom.then(xhr => this.setState({ | |||||
numPages: Math.ceil(xhr.response.items_available / itemsPerPage), | |||||
rows: this.prepareRows(xhr.response.items) | |||||
})); | |||||
return prom; | |||||
} | |||||
prepareRows(items) { | |||||
const { accept } = this.state; | |||||
const { dialogRef } = this; | |||||
return items.map(it => [ | |||||
(<div> | |||||
<div> | |||||
<a href="#" onclick={ () => { dialogRef.current.hide(); accept(it); } }> | |||||
{ arvadosObjectName(it) } | |||||
</a> | |||||
</div> | |||||
<div>{ it.uuid }</div> | |||||
</div>) | |||||
]); | |||||
} | |||||
search(textSearch) { | |||||
this.setState({ textSearch, page: 0}); | |||||
this.fetchData(); | |||||
} | |||||
render({}, { title, rows, page, numPages, textSearch }) { | |||||
return ( | |||||
<WBDialog title={ title } ref={ this.dialogRef }> | |||||
<div> | |||||
<div class="input-group mb-3"> | |||||
<input type="text" class="form-control" placeholder="Search" | |||||
aria-label="Search" value={ textSearch } | |||||
onkeydown={ e => { if (e.keyCode === 13) { | |||||
e.preventDefault(); | |||||
this.search(e.target.value); | |||||
} } } | |||||
onchange={ e => this.search(e.target.value) } /> | |||||
<div class="input-group-append"> | |||||
<button class="btn btn-outline-primary" type="button" onclick={ e => e.preventDefault() }>Search</button> | |||||
</div> | |||||
</div> | |||||
<WBTable columns={ [ 'Name' ] } rows={ rows } /> | |||||
<WBPagination activePage={ page } numPages={ numPages } chunkSize={ 3 } | |||||
onPageChanged={ i => { this.setState({ page: i }); this.fetchData(); } } /> | |||||
</div> | |||||
<div> | |||||
<button class="btn btn-secondary" | |||||
onclick={ e => { e.preventDefault(); this.hide(); } }> | |||||
Cancel | |||||
</button> | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
} | |||||
WBPickObjectDialog.defaultProps = { | |||||
itemsPerPage: 20 | |||||
}; | |||||
export default WBPickObjectDialog; |
@@ -0,0 +1,52 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBDialog from 'wb-dialog'; | |||||
import linkState from 'linkstate'; | |||||
import wbRenameObject from 'wb-rename-object'; | |||||
class WBRenameDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.dialogRef = createRef(); | |||||
this.state.inputId = uuid.v4(); | |||||
} | |||||
show(item, callback) { | |||||
const { inputId } = this.state; | |||||
this.setState({ | |||||
'item': item, | |||||
'newName': null, | |||||
'callback': callback || (() => {}) | |||||
}); | |||||
this.dialogRef.current.show(); | |||||
$('#' + inputId).focus(); | |||||
} | |||||
hide() { | |||||
this.dialogRef.current.hide(); | |||||
} | |||||
render({ app }, { item, newName, callback, inputId }) { | |||||
const { arvHost, arvToken } = app.state; | |||||
return ( | |||||
<WBDialog title="Rename" ref={ this.dialogRef } accept={ () => { | |||||
if (newName) | |||||
wbRenameObject(arvHost, arvToken, item.uuid, newName).then(callback); | |||||
} }> | |||||
<div> | |||||
<input type="text" class="form-control" id={ inputId } | |||||
placeholder={ item ? item.name : 'Type new name here' } | |||||
value={ newName } onChange={ linkState(this, 'newName') } /> | |||||
</div> | |||||
</WBDialog> | |||||
); | |||||
} | |||||
} | |||||
export default WBRenameDialog; |
@@ -0,0 +1,154 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBTable from 'wb-table'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import wbFetchObjects from 'wb-fetch-objects'; | |||||
import wbFormatDate from 'wb-format-date'; | |||||
class WBToolboxDialog extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.state.selectedValues = {}; | |||||
} | |||||
componentDidMount() { | |||||
this.fetchRows(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.fetchRows(); | |||||
} | |||||
fetchRows() { | |||||
const { items, id, selectMany, onAccepted } = this.props; | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
const { selectedValues } = this.state; | |||||
let prom = wbFetchObjects(arvHost, arvToken, | |||||
items); | |||||
let lookup; | |||||
prom = prom.then(lkup => (lookup = lkup)); | |||||
prom = prom.then(() => wbFetchObjects(arvHost, arvToken, | |||||
items.map(uuid => lookup[uuid].owner_uuid))); | |||||
let ownerLookup; | |||||
prom = prom.then(lkup => (ownerLookup = lkup)); | |||||
prom = prom.then(() => { | |||||
const rows = items.map((uuid, idx) => { | |||||
const it = lookup[uuid]; | |||||
const ow = ownerLookup[it.owner_uuid]; | |||||
let r = []; | |||||
if (selectMany) | |||||
r.push(); | |||||
r = r.concat([ | |||||
selectMany ? ( | |||||
<div> | |||||
<input type="checkbox" checked={ (uuid in selectedValues) } | |||||
onChange={ e => { | |||||
if (e.target.value === 'on') | |||||
selectedValues[uuid] = true; | |||||
else | |||||
delete selectedValues[uuid]; | |||||
} } /> { '\u00A0' } | |||||
</div> | |||||
) : ( | |||||
<button class="btn btn-outline-primary" title="Use" | |||||
onclick={ () => { | |||||
$('#' + id).modal('hide'); | |||||
onAccepted(uuid); | |||||
} }> | |||||
<i class="fas fa-hand-pointer"></i> | |||||
</button> | |||||
), | |||||
( <WBNameAndUuid uuid={ uuid } lookup={ lookup } | |||||
onLinkClicked={ () => $('#' + id).modal('hide') } /> ), | |||||
it.kind, | |||||
wbFormatDate(it.created_at), | |||||
( <WBNameAndUuid uuid={ it.owner_uuid } lookup={ ownerLookup } | |||||
onLinkClicked={ () => $('#' + id).modal('hide') } /> ) | |||||
]); | |||||
return r; | |||||
}); | |||||
this.setState({ rows }); | |||||
}); | |||||
} | |||||
render({ id, selectMany, onAccepted, items, app }, { rows, selectedValues }) { | |||||
return ( | |||||
<div class="modal" id={ id } tabindex="-1" role="dialog"> | |||||
<div class="modal-dialog modal-lg" role="document"> | |||||
<div class="modal-content"> | |||||
<div class="modal-header"> | |||||
<h5 class="modal-title">Browse Toolbox</h5> | |||||
<button type="button" class="close" data-dismiss="modal" aria-label="Close"> | |||||
<span aria-hidden="true">×</span> | |||||
</button> | |||||
</div> | |||||
<div class="modal-body"> | |||||
<div class="mb-2"> | |||||
{ selectMany ? ( | |||||
<button class="btn btn-outline-primary mr-2" onclick={ () => { | |||||
items.map(uuid => (selectedValues[uuid] = true)); | |||||
this.fetchRows(); | |||||
} }> | |||||
Select All | |||||
</button> | |||||
) : null } | |||||
{ selectMany ? ( | |||||
<button class="btn btn-outline-primary mr-2" onclick={ () => { | |||||
this.setState({ 'selectedValues' : {} }); | |||||
this.fetchRows(); | |||||
} }> | |||||
Select None | |||||
</button> | |||||
) : null } | |||||
<button class="btn btn-outline-primary mr-2" onclick={ () => { | |||||
app.clearToolbox(); | |||||
this.props.items = []; | |||||
this.fetchRows(); | |||||
} } > | |||||
Clear Toolbox | |||||
</button> | |||||
<button class="btn btn-outline-primary mr-2" onclick={ () => { | |||||
app.loadToolbox(); | |||||
this.props.items = app.state.toolboxItems; | |||||
this.fetchRows(); | |||||
} } > | |||||
Refresh Toolbox | |||||
</button> | |||||
</div> | |||||
<WBTable columns={ [ '', 'Name', 'Kind', 'Created At', 'Owner' ] } | |||||
rows={ rows } /> | |||||
</div> | |||||
<div class="modal-footer"> | |||||
{ selectMany ? ( | |||||
<button type="button" class="btn btn-primary" onclick={ | |||||
() => { | |||||
$('#' + id).modal('hide'); | |||||
onAccepted(items.filter(uuid => (uuid in selectedValues))); | |||||
} | |||||
}>Accept</button> | |||||
) : null } | |||||
<button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
WBToolboxDialog.defaultProps = { | |||||
'onAccepted': () => {} | |||||
}; | |||||
export default WBToolboxDialog; |
@@ -0,0 +1,13 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, render } from 'preact'; | |||||
import WBApp from 'wb-app'; | |||||
render(( | |||||
<WBApp /> | |||||
), document.body); |
@@ -0,0 +1,120 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
const defaultOrderRegistry = {}; | |||||
/* function notify(orderRegistry) { | |||||
if (!('listeners' in orderRegistry)) | |||||
return; | |||||
for (let k in orderRegistry.listeners) { | |||||
orderRegistry.listeners[k](orderRegistry); | |||||
} | |||||
} */ | |||||
function cursorDecor() { | |||||
let d = $('#cursor-decor'); | |||||
if (d.length === 1) | |||||
return $(d[0]); | |||||
d = $('<div id="cursor-decor" style="z-index: 10000; position: absolute; left: 10px; top: 10px;"> \ | |||||
<div class="progress" style="height: 8px;"> \ | |||||
<div class="progress-bar progress-bar-striped progress-bar-animated" \ | |||||
role="progressbar" aria-valuenow="100" aria-valuemin="0" \ | |||||
aria-valuemax="100" style="width: 32px;"></div> \ | |||||
</div> \ | |||||
</div>'); | |||||
$(document.body).append(d); | |||||
let pageX = 0, pageY = 0, scrollX = 0, scrollY = 0; | |||||
document.addEventListener('mousemove', e => { | |||||
pageX = e.pageX; | |||||
pageY = e.pageY; | |||||
d.css({ left: (e.pageX + 16) + 'px', top: (e.pageY + 16) + 'px' }) | |||||
scrollX = window.scrollX; | |||||
scrollY = window.scrollY; | |||||
}); | |||||
document.addEventListener('scroll', e => { | |||||
d.css({ left: (pageX + window.scrollX - scrollX + 16) + 'px', | |||||
top: (pageY + window.scrollY - scrollY + 16) + 'px' }); | |||||
}); | |||||
return d; | |||||
} | |||||
function updateCursorDecor(orderRegistry) { | |||||
const d = cursorDecor(); | |||||
if (Object.keys(orderRegistry.pendingCompletion).length === 0) | |||||
d.hide(); | |||||
else | |||||
d.show(); | |||||
} | |||||
function wbApplyPromiseOrdering(prom, orderRegistry) { | |||||
let orderId; | |||||
if (!orderRegistry) | |||||
orderRegistry = defaultOrderRegistry; | |||||
//if (Object.keys(orderRegistry).length === 0) { | |||||
if (!('started' in orderRegistry)) { | |||||
orderRegistry.started = 0; | |||||
orderRegistry.pendingCompletion = {}; | |||||
orderRegistry.completed = { 0: true }; | |||||
} | |||||
orderRegistry.started += 1; | |||||
orderId = orderRegistry.started; | |||||
// console.log('New orderId: ' + orderId); | |||||
// notify(orderRegistry); | |||||
cursorDecor().show(); | |||||
const orderCallback = ((isCatch, payload) => { | |||||
// console.log('orderId: ' + orderId + | |||||
// ', pendingCompletion: ' + Object.keys(orderRegistry.pendingCompletion) + | |||||
// ', completed: ' + Object.keys(orderRegistry.completed)); | |||||
if ((orderId - 1) in orderRegistry.completed) { | |||||
// console.log('Running: ' + orderId); | |||||
orderRegistry.completed[orderId] = true; | |||||
delete orderRegistry.pendingCompletion[orderId]; | |||||
const keys = Object.keys(orderRegistry.pendingCompletion); | |||||
keys.sort((a, b) => (a - b)); | |||||
keys.map(k => { | |||||
if ((k - 1) in orderRegistry.completed) { | |||||
// console.log('Running: ' + k); | |||||
orderRegistry.pendingCompletion[k](); | |||||
orderRegistry.completed[k] = true; | |||||
delete orderRegistry.pendingCompletion[k]; | |||||
} | |||||
}); | |||||
if (orderRegistry.started in orderRegistry.completed) { | |||||
// console.log('Garbage collect'); | |||||
orderRegistry.started = 0; | |||||
orderRegistry.completed = { 0: true }; | |||||
cursorDecor().hide(); | |||||
} | |||||
if (isCatch) | |||||
throw payload; | |||||
else | |||||
return payload; | |||||
} | |||||
const prom_1 = new Promise((accept, reject) => { | |||||
orderRegistry.pendingCompletion[orderId] = (() => | |||||
(isCatch ? reject(payload) : accept(payload))); | |||||
}); | |||||
return prom_1; | |||||
}); | |||||
prom = prom.then(xhr => orderCallback(false, xhr)); | |||||
prom = prom.catch(e => orderCallback(true, e)); | |||||
return prom; | |||||
} | |||||
export default wbApplyPromiseOrdering; |
@@ -0,0 +1,19 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
function wbDisableControls() { | |||||
$('input, select, button').attr('disabled', 'disabled'); | |||||
$('a').each(function() { $(this).data('old_href', $(this).attr('href')); }); | |||||
$('a').attr('href', null); | |||||
} | |||||
function wbEnableControls() { | |||||
$('input, select, button').attr('disabled', null); | |||||
$('a').each(function() { $(this).attr('href', $(this).data('old_href')); }); | |||||
} | |||||
export { wbEnableControls, wbDisableControls }; |
@@ -0,0 +1,19 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h } from 'preact'; | |||||
function wbFormatDate(dateStr) { | |||||
if (!dateStr) | |||||
return ( | |||||
<i>{ String(dateStr) }</i> | |||||
); | |||||
let date = new Date(dateStr); | |||||
return date.toLocaleString(); | |||||
} | |||||
export default wbFormatDate; |
@@ -0,0 +1,18 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h } from 'preact'; | |||||
function wbFormatSpecialValue(value) { | |||||
if (value === null) return (<i>null</i>); | |||||
if (value === undefined) return (<i>undefined</i>); | |||||
if (typeof(value) === 'boolean') return (<i>{ String(value) }</i>); | |||||
if (value === '') return '-'; | |||||
return String(value); | |||||
} | |||||
export default wbFormatSpecialValue; |
@@ -0,0 +1,120 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import { Router, route } from 'preact-router'; | |||||
import WBBrowse from 'wb-browse'; | |||||
import WBSignIn from 'wb-sign-in'; | |||||
import WBSignOut from 'wb-sign-out'; | |||||
import WBLandingPage from 'wb-landing-page'; | |||||
import WBProcessView from 'wb-process-view'; | |||||
import WBContainerView from 'wb-container-view'; | |||||
import WBCollectionView from 'wb-collection-view'; | |||||
import WBCollectionBrowse from 'wb-collection-browse'; | |||||
import WBUsersPage from 'wb-users-page'; | |||||
import WBWorkflowView from 'wb-workflow-view'; | |||||
import WBLaunchWorkflowPage from 'wb-launch-workflow-page'; | |||||
import WBDownloadPage from 'wb-download-page'; | |||||
import WBImageViewerPage from 'wb-image-viewer-page'; | |||||
import WBSharingPage from 'wb-sharing-page'; | |||||
import WBProjectView from 'wb-project-view'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
class WBApp extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.arvHost = window.localStorage['arvHost']; | |||||
this.state.arvToken = window.localStorage['arvToken']; | |||||
if ('currentUser' in window.localStorage) | |||||
this.state.currentUser = JSON.parse(window.localStorage['currentUser']); | |||||
this.loadToolbox(); | |||||
} | |||||
navbarItemUrl(item) { | |||||
if (item['id'] === 'sign-out') { | |||||
return ('/sign-out'); | |||||
} else if (item['id'] === 'home') { | |||||
return ('/browse/' + this.state.currentUser.uuid); | |||||
} else if (item['id'] === 'all-projects') { | |||||
return ('/browse'); | |||||
} else if (item['id'] === 'all-users') { | |||||
return ('/users'); | |||||
} else if (item['id'] === 'shared-with-me') { | |||||
return ('/shared-with-me'); | |||||
} else if (item['id'] === 'whatsnew') { | |||||
return ('https://adared.ch/wba'); | |||||
} | |||||
} | |||||
breadcrumbClicked(item) { | |||||
let objectType = arvadosTypeName(item.uuid.split('-')[1]); | |||||
if (objectType === 'user') | |||||
route('/browse/' + item.uuid) | |||||
else if (objectType === 'group' && item.group_class === 'project') | |||||
route('/browse/' + item.uuid); | |||||
else if (objectType === 'container_request') | |||||
route('/process/' + item.uuid) | |||||
} | |||||
addToToolbox(uuid) { | |||||
this.state.toolboxItems.push(uuid); | |||||
window.localStorage['toolboxItems'] = | |||||
JSON.stringify(this.state.toolboxItems); | |||||
} | |||||
clearToolbox() { | |||||
this.state.toolboxItems = []; | |||||
delete window.localStorage['toolboxItems']; | |||||
} | |||||
loadToolbox() { | |||||
this.state.toolboxItems = ('toolboxItems' in window.localStorage) ? | |||||
JSON.parse(window.localStorage['toolboxItems']) : []; | |||||
} | |||||
render() { | |||||
return ( | |||||
<Router> | |||||
<WBLandingPage path="/" /> | |||||
<WBSignIn path="/sign-in/:mode?" appState={ this.state } /> | |||||
<WBSignOut path='/sign-out' app={ this } /> | |||||
<WBBrowse path="/browse/:ownerUuid?/:activePage?/:objTypeTab?/:collectionPage?/:processPage?/:workflowPage?/:textSearch?" | |||||
app={ this } mode="browse" /> | |||||
<WBBrowse path="/shared-with-me/:activePage?/:textSearch?" | |||||
app={ this } mode="shared-with-me" /> | |||||
<WBProcessView path="/process/:uuid/:page?" app={ this } /> | |||||
<WBContainerView path="/container/:uuid" app={ this } /> | |||||
<WBCollectionView path="/collection/:uuid" app={ this } /> | |||||
<WBCollectionBrowse path='/collection-browse/:uuid/:collectionPath?/:page?' app={ this } /> | |||||
<WBUsersPage path='/users/:page?/:textSearch?' app={ this } /> | |||||
<WBWorkflowView path="/workflow/:uuid" app={ this } /> | |||||
<WBLaunchWorkflowPage path="/workflow-launch/:workflowUuid" app={ this } /> | |||||
<WBDownloadPage path="/download/:blocksBlobUrl/:inline?" app={ this } /> | |||||
<WBImageViewerPage path="/image-viewer/:blobUrl" app={ this } /> | |||||
<WBSharingPage path="/sharing/:uuid" app={ this } /> | |||||
<WBProjectView path="/project/:uuid" app={ this } /> | |||||
</Router> | |||||
); | |||||
} | |||||
} | |||||
export default WBApp; |
@@ -0,0 +1,255 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBProjectListing from 'wb-project-listing'; | |||||
import WBInlineSearch from 'wb-inline-search'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBTabs from 'wb-tabs'; | |||||
import WBProcessListing from 'wb-process-listing'; | |||||
import WBCollectionListing from 'wb-collection-listing'; | |||||
import WBWorkflowListing from 'wb-workflow-listing'; | |||||
import WBRenameDialog from 'wb-rename-dialog'; | |||||
import WBDeleteDialog from 'wb-delete-dialog'; | |||||
import WBNewProjectDialog from 'wb-new-project-dialog'; | |||||
import WBEditDescriptionDialog from 'wb-edit-description-dialog'; | |||||
import wbMoveObject from 'wb-move-object'; | |||||
import wbCopyCollection from 'wb-copy-collection'; | |||||
import arvadosTypeName from 'arvados-type-name'; | |||||
class WBBrowseProjectTabs extends Component { | |||||
render({ ownerUuid, selected, newProjectDialogRef, projectListingRef, | |||||
moveHere, copyHere }) { | |||||
return ( | |||||
<WBTabs tabs={ [ | |||||
{ 'name': 'Projects', 'isActive': true }, | |||||
ownerUuid ? { 'name': ( <span><i class="fas fa-plus-square text-success"></i> New Project</span> ), | |||||
'onClick': () => newProjectDialogRef.current.show(ownerUuid, | |||||
() => projectListingRef.current.fetchItems() ) } : null, | |||||
( ownerUuid && Object.keys(selected).length > 0 ) ? | |||||
{ 'name': ( <span><i class="fas fa-compress-arrows-alt text-warning"></i> Move Here</span> ), | |||||
'onClick': moveHere } : null, | |||||
( ownerUuid && (uuids => uuids.length > 0 && uuids.length === | |||||
uuids.map(arvadosTypeName).filter(a => (a === 'collection')).length )(Object.keys(selected)) ) ? | |||||
{ 'name': ( <span><i class="fas fa-file-import text-warning"></i> Copy Here</span> ), | |||||
'onClick': copyHere } : null | |||||
] } /> | |||||
); | |||||
} | |||||
} | |||||
class WBBrowse extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.renameDialogRef = createRef(); | |||||
this.deleteDialogRef = createRef(); | |||||
this.newProjectDialogRef = createRef(); | |||||
this.projectListingRef = createRef(); | |||||
this.projectTabsRef = createRef(); | |||||
this.editDescriptionDialogRef = createRef(); | |||||
this.state.selected = {}; | |||||
} | |||||
getUrl(params) { | |||||
const mode = ('mode' in params ? params.mode : this.props.mode); | |||||
if (mode === 'shared-with-me') | |||||
return '/shared-with-me/' + | |||||
('activePage' in params ? params.activePage : (this.props.activePage || '')) + '/' + | |||||
('textSearch' in params ? params.textSearch : (this.props.textSearch || '')); | |||||
let res = '/browse/' + | |||||
('ownerUuid' in params ? params.ownerUuid : (this.props.ownerUuid || '')) + '/' + | |||||
('activePage' in params ? params.activePage : (this.props.activePage || '')) + '/' + | |||||
('objTypeTab' in params ? params.objTypeTab : (this.props.objTypeTab || '')) + '/' + | |||||
('collectionPage' in params ? params.collectionPage : (this.props.collectionPage || '')) + '/' + | |||||
('processPage' in params ? params.processPage : (this.props.processPage || '')) + '/' + | |||||
('workflowPage' in params ? params.workflowPage : (this.props.workflowPage || '')) + '/' + | |||||
encodeURIComponent('textSearch' in params ? params.textSearch : (this.props.textSearch || '')); | |||||
return res; | |||||
} | |||||
route(params) { | |||||
route(this.getUrl(params)); | |||||
} | |||||
renameDialog(item, callback) { | |||||
// throw Error('Not implemented'); | |||||
this.renameDialogRef.current.show(item, callback); | |||||
} | |||||
renderRenameLink(item, callback) { | |||||
return ( | |||||
<a href="#" title="Rename" onclick={ e => { e.preventDefault(); this.renameDialog(item, callback); } }> | |||||
<i class="fas fa-edit text-secondary"></i> | |||||
</a> | |||||
); | |||||
} | |||||
renderEditDescription(item, callback) { | |||||
return ( | |||||
<a href="#" title="Edit description" onclick={ e => { e.preventDefault(); | |||||
this.editDescriptionDialogRef.current.show(item, callback); } }> | |||||
<i class="fas fa-edit text-secondary"></i> | |||||
</a> | |||||
); | |||||
} | |||||
renderDeleteButton(item, callback) { | |||||
return ( | |||||
<button class="btn btn-outline-danger m-1" title="Delete" | |||||
onclick={ () => this.deleteDialogRef.current.show(item, callback) }> | |||||
<i class="fas fa-trash"></i> | |||||
</button> | |||||
); | |||||
} | |||||
renderSelectionCell(item) { | |||||
const { selected } = this.state; | |||||
const { uuid } = item; | |||||
return ( | |||||
<div> | |||||
<input type="checkbox" checked={ (uuid in selected) } | |||||
onChange={ e => { | |||||
if (e.target.checked) | |||||
selected[uuid] = true; | |||||
else | |||||
delete selected[uuid]; | |||||
this.projectTabsRef.current.setState({}); | |||||
} } /> { '\u00A0' } | |||||
</div> | |||||
); | |||||
} | |||||
renderSharingButton(item) { | |||||
return ( | |||||
<a class="btn btn-outline-success m-1" title="Share" | |||||
href={ '/sharing/' + item.uuid }> | |||||
<i class="fas fa-share-alt"></i> | |||||
</a> | |||||
); | |||||
} | |||||
moveOrCopyOp(op) { | |||||
const { ownerUuid, app } = this.props; | |||||
const { selected } = this.state; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = new Promise(accept => accept()); | |||||
const uuids = Object.keys(selected); | |||||
for (let i = 0; i < uuids.length; i++) { | |||||
prom = prom.then(() => op(arvHost, arvToken, uuids[i], ownerUuid)); | |||||
prom = prom.then(() => ( delete selected[uuids[i]] )); | |||||
prom = prom.catch(() => {}); | |||||
} | |||||
prom = prom.then(() => this.setState({})); | |||||
} | |||||
moveHere() { | |||||
this.moveOrCopyOp(wbMoveObject); | |||||
} | |||||
copyHere() { | |||||
this.moveOrCopyOp(wbCopyCollection); | |||||
} | |||||
render({ mode, ownerUuid, activePage, app, | |||||
objTypeTab, collectionPage, processPage, workflowPage, | |||||
textSearch }, { selected }) { | |||||
const commonProps = { | |||||
renderRenameLink: (it, cb) => this.renderRenameLink(it, cb), | |||||
renderEditDescription: (it, cb) => this.renderEditDescription(it, cb), | |||||
renderDeleteButton: (it, cb) => this.renderDeleteButton(it, cb), | |||||
renderSelectionCell: it => this.renderSelectionCell(it), | |||||
renderSharingButton: it => this.renderSharingButton(it), | |||||
textSearch, | |||||
app, | |||||
appState: app.state, | |||||
arvHost: app.state.arvHost, | |||||
arvToken: app.state.arvToken, | |||||
ownerUuid | |||||
}; | |||||
const { currentUser } = app.state; | |||||
const noDefaultTab = (!ownerUuid || ownerUuid === currentUser.uuid); | |||||
return ( | |||||
<div> | |||||
<WBRenameDialog app={ app } ref={ this.renameDialogRef } /> | |||||
<WBDeleteDialog app={ app } ref={ this.deleteDialogRef } /> | |||||
<WBNewProjectDialog app={ app } ref={ this.newProjectDialogRef } /> | |||||
<WBEditDescriptionDialog app={ app } ref={ this.editDescriptionDialogRef } /> | |||||
<WBNavbarCommon app={ app } | |||||
activeItem={ mode === 'shared-with-me' ? 'shared-with-me' : | |||||
(!ownerUuid) ? 'all-projects' : | |||||
(ownerUuid === app.state.currentUser.uuid) ? 'home' : null } | |||||
textSearch={ textSearch } | |||||
textSearchNavigate={ textSearch => route(this.getUrl({ textSearch, | |||||
activePage: 0, collectionPage: 0, processPage: 0, workflowPage: 0 })) } /> | |||||
<WBArvadosCrumbs mode={ mode } uuid={ ownerUuid } app={ app } /> | |||||
<WBBrowseProjectTabs ref={ this.projectTabsRef } ownerUuid={ ownerUuid } | |||||
selected={ selected } newProjectDialogRef={ this.newProjectDialogRef } | |||||
projectListingRef={ this.projectListingRef } moveHere={ () => this.moveHere() } | |||||
copyHere={ () => this.copyHere() } /> | |||||
<WBProjectListing ref={ this.projectListingRef } | |||||
mode={ mode } | |||||
itemsPerPage="5" | |||||
activePage={ Number(activePage || 0) } | |||||
getPageUrl={ i => this.getUrl({ 'activePage': i }) } | |||||
{ ...commonProps } /> | |||||
{ (mode !== 'browse') ? null : ( | |||||
<WBTabs tabs={ [ | |||||
{ 'id': 'collection', 'name': 'Collections', 'isActive': ((!objTypeTab && !noDefaultTab) || objTypeTab === 'collection') }, | |||||
{ 'id': 'process', 'name': 'Processes', 'isActive': (objTypeTab === 'process') }, | |||||
{ 'id': 'workflow', 'name': 'Workflows', 'isActive': (objTypeTab === 'workflow') } ] } | |||||
onTabChanged={ tab => this.route({ 'objTypeTab': tab['id'] }) } /> | |||||
) } | |||||
{ | |||||
(mode !== 'browse') ? null : | |||||
((!objTypeTab && !noDefaultTab) || objTypeTab === 'collection') ? ( | |||||
<WBCollectionListing | |||||
itemsPerPage="20" | |||||
activePage={ Number(collectionPage || 0) } | |||||
getPageUrl={ i => this.getUrl({ 'collectionPage': i }) } | |||||
{ ...commonProps } /> | |||||
) : (objTypeTab === 'process') ? ( | |||||
<WBProcessListing | |||||
itemsPerPage="20" | |||||
activePage={ Number(processPage || 0) } | |||||
onPageChanged={ i => this.route({ 'processPage': i }) } | |||||
{ ...commonProps } /> | |||||
) : (objTypeTab === 'workflow') ? ( | |||||
<WBWorkflowListing | |||||
itemsPerPage="20" | |||||
page={ Number(workflowPage || 0) } | |||||
getPageUrl={ i => this.getUrl({ 'workflowPage': i }) } | |||||
{ ...commonProps } /> | |||||
) : null | |||||
} | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBBrowse; |
@@ -0,0 +1,32 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBCollectionContent from 'wb-collection-content'; | |||||
class WBCollectionBrowse extends Component { | |||||
render({ app, uuid, collectionPath, page }, {}) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="my-2"> | |||||
This is the collection browser for { uuid } | |||||
</div> | |||||
<WBCollectionContent app={ app } uuid={ uuid } | |||||
collectionPath={ collectionPath } page={ Number(page || 0) } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBCollectionBrowse; |
@@ -0,0 +1,36 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBCommonFields from 'wb-common-fields'; | |||||
import WBCollectionFields from 'wb-collection-fields'; | |||||
class WBCollectionView extends Component { | |||||
render({ app, uuid }, {}) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="my-2"> | |||||
This is the collection view for { uuid } | |||||
</div> | |||||
<h2>Common Fields</h2> | |||||
<WBCommonFields app={ app } uuid={ uuid } /> | |||||
<h2>Collection Fields</h2> | |||||
<WBCollectionFields app={ app } uuid={ uuid } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBCollectionView; |
@@ -0,0 +1,40 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBCommonFields from 'wb-common-fields'; | |||||
import WBContainerFields from 'wb-container-fields'; | |||||
import WBLiveLogs from 'wb-live-logs'; | |||||
class WBContainerView extends Component { | |||||
render({ app, uuid }) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="my-2"> | |||||
This is the container view for { uuid } | |||||
</div> | |||||
<h2>Common Fields</h2> | |||||
<WBCommonFields app={ app } uuid={ uuid } /> | |||||
<h2>Container Fields</h2> | |||||
<WBContainerFields app={ app } uuid={ uuid } /> | |||||
<h2>Live Logs</h2> | |||||
<WBLiveLogs app={ app } uuid={ uuid } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBContainerView; |
@@ -0,0 +1,133 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function contentTypeFromFilename(name) { | |||||
let ext = name.split('.'); | |||||
ext = ext[ext.length - 1].toUpperCase(); | |||||
if (ext === 'TXT') | |||||
return 'text/plain; charset=utf-8'; | |||||
if (ext === 'JPG' || ext === 'JPEG') | |||||
return 'image/jpeg'; | |||||
if (ext === 'PNG') | |||||
return 'image/png'; | |||||
return 'application/octet-stream; charset=utf-8'; | |||||
} | |||||
class WBDownloadPage extends Component { | |||||
componentDidMount() { | |||||
const { app, blocksBlobUrl, inline } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = new Promise((accept, reject) => { | |||||
const xhr = new XMLHttpRequest(); | |||||
xhr.open('GET', blocksBlobUrl); | |||||
xhr.onreadystatechange = () => { | |||||
if (xhr.readyState !== 4) | |||||
return; | |||||
if (xhr.status !== 200) | |||||
reject(xhr); | |||||
else | |||||
accept(xhr); | |||||
}; | |||||
xhr.responseType = 'blob'; | |||||
xhr.send(); | |||||
}); | |||||
prom = prom.then(xhr => xhr.response.text()); | |||||
let name, file; | |||||
const { streamSaver, location } = window; | |||||
streamSaver.mitm = location.protocol + '//' + | |||||
location.hostname + (location.port ? | |||||
':' + location.port : '') + '/mitm.html'; | |||||
let fileStream; | |||||
let writer; | |||||
let done = false; | |||||
prom = prom.then(text => { | |||||
let _; | |||||
[ _, _, name, file ] = JSON.parse(text); | |||||
fileStream = streamSaver.createWriteStream(name, { | |||||
size: file[1], | |||||
inline: inline, | |||||
contentType: contentTypeFromFilename(name) | |||||
}); | |||||
writer = fileStream.getWriter(); | |||||
window.onunload = () => { | |||||
writer.abort() | |||||
}; | |||||
window.onbeforeunload = evt => { | |||||
if (!done) { | |||||
evt.returnValue = `Are you sure you want to leave?`; | |||||
} | |||||
}; | |||||
const filters = [ | |||||
['service_type', '=', 'proxy'] | |||||
]; | |||||
return makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/keep_services?filters=' + | |||||
encodeURIComponent(JSON.stringify(filters))); | |||||
}); | |||||
prom = prom.then(xhr => { | |||||
const services = xhr.response.items; | |||||
const i = Math.floor(Math.random() * services.length); | |||||
const proxy = services[i]; | |||||
let prom_1 = new Promise(accept => accept()); | |||||
for (let k = 0; k < file[0].length; k++) { | |||||
const loc = file[0][k]; | |||||
prom_1 = prom_1.then(() => makeArvadosRequest( | |||||
proxy.service_host + ':' + proxy.service_port, | |||||
arvToken, | |||||
'/' + loc[0], | |||||
{ 'useSsl': proxy.service_ssl_flag, | |||||
'responseType': 'arraybuffer' } | |||||
)); | |||||
prom_1 = prom_1.then(xhr_1 => { | |||||
const blk = xhr_1.response.slice(loc[1], loc[2]); | |||||
// const r = new Response(blk); | |||||
// r.body.pipeTo(fileStream); | |||||
return writer.write(new Uint8Array(blk)); | |||||
}); | |||||
} | |||||
return prom_1; | |||||
}); | |||||
prom = prom.then(() => { | |||||
writer.close(); | |||||
done = true; | |||||
}); | |||||
} | |||||
render() { | |||||
return ( | |||||
<div class="container-fluid"> | |||||
<div class="card my-3"> | |||||
<div class="card-body"> | |||||
Downloading, please wait... | |||||
</div> | |||||
</div> | |||||
<div class="alert alert-danger" role="alert"> | |||||
Do not close this window until the download is finished. | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBDownloadPage; |
@@ -0,0 +1,110 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
function downloadFile(arvHost, arvToken, file) { | |||||
const blockRefs = file[0]; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/keep_services'); | |||||
let proxy; | |||||
prom = prom.then(xhr => { | |||||
const services = xhr.response['items']; | |||||
const proxies = services.filter(svc => (svc.service_type === 'proxy')); | |||||
const n = Math.floor(Math.random() * proxies.length); | |||||
proxy = proxies[n]; | |||||
}); | |||||
const blocks = []; | |||||
for (let i = 0; i < blockRefs.length; i++) { | |||||
let locator, start, end; | |||||
prom = prom.then(() => { | |||||
[ locator, start, end ] = blockRefs[i]; | |||||
return makeArvadosRequest( | |||||
proxy.service_host + ':' + proxy.service_port, | |||||
arvToken, '/' + locator, | |||||
{ 'useSsl': proxy.service_ssl_flag, | |||||
'responseType': 'arraybuffer' } | |||||
); | |||||
}); | |||||
prom = prom.then(xhr => blocks.push(xhr.response.slice(start, end))); | |||||
} | |||||
prom = prom.then(() => { | |||||
const url = URL.createObjectURL(new Blob(blocks)); | |||||
const totalSize = blocks.reduce((a, b) => a.length + b.length); | |||||
const big = new Uint8Array(totalSize); | |||||
for (let i = 0, pos = 0; i < blocks.length; i++) { | |||||
big.set(blocks[i], pos); | |||||
pos += blocks[i].length; | |||||
} | |||||
// papayaContainers[0].startPapaya(); | |||||
const poll = () => { | |||||
setTimeout(() => { | |||||
console.log('Polling Papaya startup...') | |||||
if (window.papaya && window.papaya.Container) { // window.papayaContainers && window.papayaContainers[0]) { | |||||
console.log('Great, Papaya started!'); | |||||
papaya.Container.startPapaya(); | |||||
//papaya.Container.addImage(0, big.buffer); | |||||
document.body.id = "bod"; | |||||
document.body.style.background = "#555"; | |||||
papaya.Container.addViewer("bod", { | |||||
'binaryImages': [ big.buffer ], | |||||
'noNewFiles': true, | |||||
}); | |||||
} else | |||||
poll(); | |||||
}, 1000); | |||||
}; | |||||
//setTimeout(poll, 10000); | |||||
poll(); | |||||
}); | |||||
} | |||||
class WBImageViewerPage extends Component { | |||||
componentDidMount() { | |||||
const { blobUrl, app } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = new Promise((accept, reject) => { | |||||
const xhr = new XMLHttpRequest(); | |||||
xhr.open('GET', blobUrl); | |||||
xhr.onreadystatechange = () => { | |||||
if (xhr.readyState !== 4) return; | |||||
if (xhr.status !== 200) reject(xhr); | |||||
else accept(xhr); | |||||
}; | |||||
xhr.responseType = 'blob'; | |||||
xhr.send(); | |||||
}); | |||||
prom = prom.then(xhr => xhr.response.text()); | |||||
prom = prom.then(data => { | |||||
data = JSON.parse(data); | |||||
downloadFile(arvHost, arvToken, data.file); | |||||
}); | |||||
} | |||||
render() { | |||||
return ( | |||||
<div> | |||||
<script language="javascript" src="/js/papaya.js"></script> | |||||
<div id="papaya" style="width: auto; height: 100%; margin: 0;"></div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBImageViewerPage; |
@@ -0,0 +1,27 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import { route } from 'preact-router'; | |||||
class WBLandingPage extends Component { | |||||
componentDidMount() { | |||||
let { arvHost, arvToken } = window.localStorage; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, '/arvados/v1/users/current'); | |||||
prom = prom.then(xhr => route('/browse/' + xhr.response['uuid'])); | |||||
prom = prom.catch(() => route('/sign-in')); | |||||
} | |||||
render() { | |||||
return ( | |||||
<div>Please wait...</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBLandingPage; |
@@ -0,0 +1,185 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBBrowseDialog from 'wb-browse-dialog'; | |||||
import WBTable from 'wb-table'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import { wbDisableControls, wbEnableControls } from 'wb-disable-controls'; | |||||
import linkState from 'linkstate'; | |||||
import wbParseWorkflowDef from 'wb-parse-workflow-def'; | |||||
import { wbParseWorkflowInputs, wbSubmitContainerRequest } from 'wb-submit-container-request'; | |||||
import WBWorkflowInput from 'wb-workflow-input'; | |||||
import { parseKeepRef } from 'wb-process-misc'; | |||||
class WBLaunchWorkflowPage extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.browseDialogRef = createRef(); | |||||
this.state.inputs = {}; | |||||
this.state.errors = []; | |||||
this.state.placeInSubProject = true; | |||||
} | |||||
componentDidMount() { | |||||
let { app, workflowUuid } = this.props; | |||||
let { arvHost, arvToken } = app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/workflows/' + workflowUuid); | |||||
prom = prom.then(xhr => { | |||||
const def = wbParseWorkflowDef(xhr.response.definition); | |||||
const inputs = {}; | |||||
const main = def['$graph'].find(a => (a.id === '#main')); | |||||
main.inputs.map(a => (inputs[a.id] = JSON.stringify(parseKeepRef(a.default)))); | |||||
this.setState({ | |||||
'workflow': xhr.response, | |||||
'workflowDefinition': def, | |||||
'defaultProcessName': xhr.response.name + ' ' + (new Date().toISOString()), | |||||
'defaultProcessDescription': xhr.response.description, | |||||
inputs | |||||
}); | |||||
}); | |||||
} | |||||
submit() { | |||||
// first see if all inputs are parseable | |||||
const { app, workflowUuid } = this.props; | |||||
const { arvHost, arvToken, currentUser } = app.state; | |||||
const { workflowDefinition, projectUuid, | |||||
processName, processDescription, | |||||
defaultProcessName, defaultProcessDescription, | |||||
placeInSubProject } = this.state; | |||||
const errors = []; | |||||
const inputs = wbParseWorkflowInputs(workflowDefinition, | |||||
this.state.inputs, errors); | |||||
if (errors.length > 0) { | |||||
this.setState({ errors }); | |||||
return; | |||||
} | |||||
const params = { | |||||
arvHost, arvToken, inputs, | |||||
processName: processName || defaultProcessName, | |||||
processDescription: processDescription || defaultProcessDescription, | |||||
projectUuid: projectUuid || currentUser.uuid, | |||||
workflowUuid, workflowDefinition, placeInSubProject | |||||
} | |||||
wbDisableControls(); | |||||
let prom = wbSubmitContainerRequest(params); | |||||
prom = prom.then(xhr => { | |||||
wbEnableControls(); | |||||
route('/process/' + xhr.response.uuid); | |||||
}); | |||||
prom = prom.catch(exc => { | |||||
wbEnableControls(); | |||||
this.setState({ errors: [ exc.message ] }); | |||||
}); | |||||
} | |||||
render({ app, workflowUuid }, | |||||
{ workflow, workflowDefinition, projectUuid, processName, processDescription, | |||||
defaultProcessName, defaultProcessDescription, errors, placeInSubProject }) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBBrowseDialog app={ app } ref={ this.browseDialogRef } /> | |||||
{ workflow ? | |||||
(<form class="container-fluid"> | |||||
<h1>Launch Workflow</h1> | |||||
<div class="form-group"> | |||||
<label>Workflow</label> | |||||
<WBArvadosCrumbs app={ app } uuid={ workflowUuid } /> | |||||
</div> | |||||
<div class="form-group"> | |||||
<label for="projectUuid">Project UUID</label> | |||||
<div class="input-group mb-3"> | |||||
<input type="text" class="form-control" id="projectUuid" | |||||
placeholder="Enter Project UUID" aria-label="Project UUID" | |||||
aria-describedby="button-addon2" value={ projectUuid } | |||||
onChange={ linkState(this, 'projectUuid') } /> | |||||
<div class="input-group-append"> | |||||
<button class="btn btn-primary" type="button" | |||||
id="button-addon2" onclick={ e => { e.preventDefault(); | |||||
this.browseDialogRef.current.show('owner', false, | |||||
projectUuid => this.setState({ projectUuid })); } }>Browse</button> | |||||
</div> | |||||
</div> | |||||
{ projectUuid ? ( | |||||
<WBArvadosCrumbs app={ app } uuid={ projectUuid } /> | |||||
) : null } | |||||
</div> | |||||
<div class="form-check mb-3"> | |||||
<input class="form-check-input" type="checkbox" | |||||
checked={ placeInSubProject ? 'checked' : null } | |||||
onchange={ e => (this.state.placeInSubProject = e.target.checked) } | |||||
id="placeInSubProject" /> | |||||
<label class="form-check-label" for="placeInSubProject"> | |||||
Place in a daily sub-project | |||||
</label> | |||||
</div> | |||||
<div class="form-group"> | |||||
<label for="processName">Process Name</label> | |||||
<input type="text" class="form-control" id="processName" | |||||
placeholder={ defaultProcessName } value={ processName } | |||||
onChange={ linkState(this, 'processName') }/> | |||||
</div> | |||||
<div class="form-group"> | |||||
<label for="processDescription">Process Description</label> | |||||
<input type="text" class="form-control" id="processDescription" | |||||
placeholder={ defaultProcessDescription } value={ processDescription } | |||||
onChange={ linkState(this, 'processDescription') } /> | |||||
</div> | |||||
<div class="form-group"> | |||||
<label for="inputs">Inputs</label> | |||||
<WBTable columns={ [ 'Name', 'Value'] } | |||||
rows={ workflowDefinition.$graph.find(a => (a.id === '#main')).inputs.map(it => [ | |||||
it.label || it.id, | |||||
( <WBWorkflowInput app={ app } inputSpec={ it } | |||||
inputsDict={ this.state.inputs } | |||||
browseDialogRef={ this.browseDialogRef } /> ) | |||||
]) } /> | |||||
</div> | |||||
{ errors.length > 0 ? ( | |||||
<div class="form-group"> | |||||
{ errors.map(err => ( | |||||
<div class="alert alert-danger" role="alert"> | |||||
{ err } | |||||
</div> | |||||
))} | |||||
</div> | |||||
) : null } | |||||
<div class="form-group"> | |||||
<button class="btn btn-success" onclick={ e => { e.preventDefault(); this.submit(); } }> | |||||
Submit | |||||
</button> | |||||
</div> | |||||
</form>) : <div>Loading...</div> } | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBLaunchWorkflowPage; |
@@ -0,0 +1,95 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
import WBCommonFields from 'wb-common-fields'; | |||||
import WBContainerRequestFields from 'wb-container-request-fields'; | |||||
import WBProcessListing from 'wb-process-listing'; | |||||
import WBProcessDashboard from 'wb-process-dashboard'; | |||||
class WBProcessView extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.objectUrls = []; | |||||
} | |||||
getUrl(props) { | |||||
const page = ('page' in props ? props.page : this.props.page); | |||||
return ('/process/' + this.props.uuid + | |||||
(page ? '/' + page : '')); | |||||
} | |||||
fetchData() { | |||||
let { arvHost, arvToken } = this.props.app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/container_requests/' + this.props.uuid); | |||||
let req; | |||||
let cont; | |||||
prom = prom.then(xhr => { | |||||
req = xhr.response; | |||||
if (req.container_uuid) { | |||||
let prom_1 = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/containers/' + req.container_uuid); | |||||
prom_1 = prom_1.then(xhr => (cont = xhr.response)); | |||||
return prom_1; | |||||
} | |||||
}); | |||||
prom = prom.then(() => { | |||||
this.setState({ | |||||
'request': req, | |||||
'container': cont | |||||
}); | |||||
}); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
componentWillReceiveProps(nextProps) { | |||||
this.props = nextProps; | |||||
this.setState({ 'objectUrls': [], 'request': null, 'container': null }); | |||||
this.fetchData(); | |||||
} | |||||
render({ app, uuid, page }, { container }) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="my-2"> | |||||
This is the process view for { uuid } | |||||
</div> | |||||
<h2>Children Dashboard</h2> | |||||
<WBProcessDashboard app={ app } parentProcessUuid={ uuid } lazy={ true } /> | |||||
<h2>Common Fields</h2> | |||||
<WBCommonFields app={ app } uuid={ uuid } /> | |||||
<h2>Container Request Fields</h2> | |||||
<WBContainerRequestFields app={ app } uuid={ uuid } /> | |||||
<h2>Children</h2> | |||||
<WBProcessListing app={ app } | |||||
appState={ app.state } | |||||
requestingContainerUuid={ container ? container.uuid : null } | |||||
waitForNextProps={ !container } | |||||
itemsPerPage="20" | |||||
activePage={ Number(page || 0) } | |||||
getPageUrl={ page => this.getUrl({ page }) } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBProcessView; |
@@ -0,0 +1,36 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBCommonFields from 'wb-common-fields'; | |||||
import WBProjectFields from 'wb-project-fields'; | |||||
class WBProjectView extends Component { | |||||
render({ app, uuid }, {}) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="my-2"> | |||||
This is the project view for { uuid } | |||||
</div> | |||||
<h2>Common Fields</h2> | |||||
<WBCommonFields app={ app } uuid={ uuid } /> | |||||
<h2>Project Fields</h2> | |||||
<WBProjectFields app={ app } uuid={ uuid } /> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBProjectView; |
@@ -0,0 +1,177 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component, createRef } from 'preact'; | |||||
import WBNavbarCommon from 'wb-navbar-common'; | |||||
import WBArvadosCrumbs from 'wb-arvados-crumbs'; | |||||
import WBNameAndUuid from 'wb-name-and-uuid'; | |||||
import WBSelect from 'wb-select'; | |||||
import WBTable from 'wb-table'; | |||||
import WBPickObjectDialog from 'wb-pick-object-dialog'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBSharingPage extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
this.state.rows = []; | |||||
this.dialogRef = createRef(); | |||||
} | |||||
componentDidMount() { | |||||
this.fetchData(); | |||||
} | |||||
fetchData() { | |||||
const { app, uuid } = this.props; | |||||
const { arvHost, arvToken } = app.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/permissions/' + encodeURIComponent(uuid) + | |||||
'?limit=100000'); | |||||
prom = prom.then(xhr => this.setState({ | |||||
'entries': xhr.response.items, | |||||
'rows': this.prepareRows(xhr.response.items) | |||||
})); | |||||
} | |||||
deleteEntry(it) { | |||||
it._delete = true; | |||||
this.setState({ rows: this.prepareRows(this.state.entries) }); | |||||
} | |||||
prepareRows(items) { | |||||
const { app } = this.props; | |||||
return items.filter(it => (!it._delete)).map(it => [ | |||||
( <WBNameAndUuid app={ app } uuid={ it.tail_uuid } /> ), | |||||
( <WBSelect value={ it.name } | |||||
options={ ['can_read', 'can_write', 'can_manage'] } | |||||
onChange={ e => this.modifyEntry(it, e.target.value) } /> ), | |||||
( <button class="btn btn-outline-danger m-1" title="Delete" | |||||
onclick={ () => this.deleteEntry(it) }> | |||||
<i class="fas fa-trash"></i> | |||||
</button> ) | |||||
]); | |||||
} | |||||
modifyEntry(it, newPermissionName) { | |||||
it.name = newPermissionName; | |||||
it._dirty = true; | |||||
// this.setState({ rows: this.prepareRows(this.state.entries) }); | |||||
} | |||||
addEntry(it, permissionName='can_read') { | |||||
// throw Error('Not implemented'); | |||||
const { uuid } = this.props; | |||||
let { entries } = this.state; | |||||
if (entries.filter(e => (e.tail_uuid === it.uuid)).length > 0) | |||||
return; // already in the list | |||||
const e = { | |||||
//_dirty: true, | |||||
link_class: 'permission', | |||||
head_uuid: uuid, | |||||
tail_uuid: it.uuid, | |||||
name: permissionName | |||||
}; | |||||
entries = entries.concat([e]); | |||||
this.setState({ | |||||
entries, | |||||
rows: this.prepareRows(entries) | |||||
}); | |||||
} | |||||
disableControls() { | |||||
$('input, select, button').attr('disabled', 'disabled'); | |||||
$('a').each(function() { $(this).data('old_href', $(this).attr('href')); }); | |||||
$('a').attr('href', null); | |||||
} | |||||
enableControls() { | |||||
$('input, select, button').attr('disabled', null); | |||||
$('a').each(function() { $(this).attr('href', $(this).data('old_href')); }); | |||||
} | |||||
save() { | |||||
const { entries } = this.state; | |||||
const { arvHost, arvToken } = this.props.app.state; | |||||
let prom = new Promise(accept => accept()); | |||||
this.disableControls(); | |||||
this.setState({ working: true }); | |||||
for (let i = 0; i < entries.length; i++) { | |||||
const e = entries[i]; | |||||
//if (!e._dirty && !e._delete) | |||||
//continue; | |||||
if (!e.uuid) { | |||||
prom = prom.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/links', | |||||
{ 'method': 'POST', | |||||
'data': JSON.stringify({ | |||||
'link_class': 'permission', | |||||
'head_uuid': e.head_uuid, | |||||
'tail_uuid': e.tail_uuid, | |||||
'name': e.name | |||||
}) })); | |||||
} else if (e._delete) { | |||||
prom = prom.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/links/' + e.uuid, | |||||
{ 'method': 'DELETE' })); | |||||
} else if (e._dirty) { | |||||
prom = prom.then(() => makeArvadosRequest(arvHost, arvToken, | |||||
'/arvados/v1/links/' + e.uuid, | |||||
{ 'method': 'PUT', | |||||
'data': JSON.stringify({ | |||||
'name': e.name | |||||
}) })); | |||||
} | |||||
prom = prom.catch(() => {}); | |||||
} | |||||
prom = prom.then(() => { | |||||
this.enableControls(); | |||||
this.fetchData(); | |||||
this.setState({ working: false }); | |||||
}); | |||||
} | |||||
render({ app, uuid }, { rows, working }) { | |||||
return ( | |||||
<div> | |||||
<WBNavbarCommon app={ app } /> | |||||
<WBArvadosCrumbs app={ app } uuid={ uuid } /> | |||||
<div class="container-fluid"> | |||||
<div class="my-2"> | |||||
This is the sharing management page for { uuid } | |||||
</div> | |||||
<WBTable columns={ [ 'Name', 'Permission', '' ] } | |||||
headerClasses={ [ null, null, 'w-1' ] } | |||||
rows={ rows } /> | |||||
<WBPickObjectDialog app={ app } ref={ this.dialogRef } /> | |||||
{ working ? (<div class="progress my-2"> | |||||
<div class={ 'progress-bar progress-bar-striped progress-bar-animated' } | |||||
role="progressbar" aria-valuenow="100" aria-valuemin="0" | |||||
aria-valuemax="100" style="width: 100%"></div> | |||||
</div>) : null } | |||||
<button class="btn btn-outline-secondary mr-2" | |||||
onclick={ () => this.dialogRef.current.show('Select User', 'user', it => this.addEntry(it)) }>Add User...</button> | |||||
<button class="btn btn-outline-secondary mr-2" | |||||
onclick={ () => this.dialogRef.current.show('Select Group', 'group', it => this.addEntry(it), [['group_class', '=', 'role']]) }>Add Group...</button> | |||||
<button class="btn btn-primary mr-2" | |||||
onclick={ () => this.save() }>Save</button> | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBSharingPage; |
@@ -0,0 +1,109 @@ | |||||
// | |||||
// Copyright (C) Stanislaw Adaszewski, 2020 | |||||
// Contact: s.adaszewski@gmail.com | |||||
// Website: https://adared.ch/wba | |||||
// License: GPLv3 | |||||
// | |||||
import { h, Component } from 'preact'; | |||||
import { route } from 'preact-router'; | |||||
import WBNavbar from 'wb-navbar'; | |||||
import WBTabs from 'wb-tabs'; | |||||
import linkState from 'linkstate'; | |||||
import makeArvadosRequest from 'make-arvados-request'; | |||||
class WBSignIn extends Component { | |||||
constructor(...args) { | |||||
super(...args); | |||||
const search = new URLSearchParams(window.location.search); | |||||
this.state.arvHost = window.localStorage.arvHost; | |||||
this.state.arvToken = search.get('api_token'); | |||||
} | |||||
componentDidMount() { | |||||
// const arvHost = window.localStorage.arvHost; | |||||
// const arvToken = search.get('api_token'); | |||||
const { arvHost, arvToken } = this.state; | |||||
if (arvHost && arvToken) { | |||||
this.state.arvHost = arvHost; | |||||
this.state.arvToken = arvToken; | |||||
this.submitToken(); | |||||
} | |||||
} | |||||
submit() { | |||||
const { mode } = this.props; | |||||
if (mode === 'token') | |||||
this.submitToken(); | |||||
else if (!mode || mode === 'sso') | |||||
this.submitSingleSignOn(); | |||||
else | |||||
throw Error('Unsupported mode'); | |||||
} | |||||
submitSingleSignOn() { | |||||
const { arvHost } = this.state; | |||||
window.localStorage.arvHost = arvHost; | |||||
window.location = 'https://' + arvHost + '/login?return_to=' | |||||
+ encodeURIComponent(window.location.protocol + '//' + window.location.host + '/sign-in/token'); | |||||
} | |||||
submitToken() { | |||||
let { appState } = this.props; | |||||
let { arvHost, arvToken } = this.state; | |||||
let prom = makeArvadosRequest(arvHost, arvToken, '/arvados/v1/users/current'); | |||||
prom = prom.then(xhr => { | |||||
window.localStorage['arvHost'] = arvHost; | |||||
window.localStorage['arvToken'] = arvToken; | |||||
window.localStorage['currentUser'] = JSON.stringify(xhr.response); | |||||
appState.arvHost = arvHost; | |||||
appState.arvToken = arvToken; | |||||
appState.currentUser = xhr.response; | |||||
route('/browse/' + xhr.response['uuid']); | |||||
}); | |||||
prom = prom.catch(() => { | |||||
alert('Sign in unsuccessful. Verify your input and try again.') | |||||
}); | |||||
} | |||||
render({ mode }, { arvHost, arvToken }) { | |||||
return ( | |||||
<div> | |||||
<WBNavbar /> | |||||
<div class="container my-3"> | |||||
<div class="row justify-content-center"> | |||||
<div class="col-6"> | |||||
<h1>Sign In</h1> | |||||
<WBTabs class="my-3" tabs={ [ { name: 'SSO', isActive: (!mode || mode === 'sso') }, | |||||
{ name: 'Token', isActive: (mode === 'token') } ] } | |||||
onTabChanged={ t => route(t.name === 'Token' ? '/sign-in/token' : '/sign-in/sso') } /> | |||||
<form> | |||||
<div class="form-group"> | |||||
<label for="arvHost">Arvados API Host</label> | |||||
<input type="text" class="form-control" id="arvHost" | |||||
placeholder="Enter Arvados API Host" | |||||
value={ arvHost } | |||||
onInput={ linkState(this, 'arvHost') } /> | |||||
</div> | |||||
{ mode === 'token' ? ( | |||||
<div class="form-group"> | |||||
<label for="arvToken">Token</label> | |||||
<input type="text" class="form-control" id="arvToken" | |||||
placeholder="Enter Arvados API Token" | |||||
value={ arvToken } | |||||
onInput={ linkState(this, 'arvToken') } /> | |||||
</div> | |||||
) : null } | |||||
<button type="submit" class="btn btn-primary" | |||||
onclick={ e => { e.preventDefault(); this.submit(); } }>Submit</button> | |||||
</form> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
</div> | |||||
); | |||||
} | |||||
} | |||||
export default WBSignIn; |