IF YOU WOULD LIKE TO GET AN ACCOUNT, please write an email to s dot adaszewski at gmail dot com. User accounts are meant only to report issues and/or generate pull requests. This is a purpose-specific Git hosting for ADARED projects. Thank you for your understanding!
Selaa lähdekoodia

Breaking out some pieces from wb-launch-workflow-page.

pull/1/head
Stanislaw Adaszewski 4 vuotta sitten
vanhempi
commit
89fe88a41b
6 muutettua tiedostoa jossa 122 lisäystä ja 108 poistoa
  1. +14
    -0
      frontend/src/js/arvados/process/wb-input-spec-info.js
  2. +11
    -0
      frontend/src/js/arvados/process/wb-parse-workflow-def.js
  3. +11
    -0
      frontend/src/js/arvados/process/wb-process-misc.js
  4. +25
    -0
      frontend/src/js/arvados/process/wb-uuids-to-cwl.js
  5. +53
    -0
      frontend/src/js/component/wb-path-display.js
  6. +8
    -108
      frontend/src/js/page/wb-launch-workflow-page.js

+ 14
- 0
frontend/src/js/arvados/process/wb-input-spec-info.js Näytä tiedosto

@@ -0,0 +1,14 @@
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;

+ 11
- 0
frontend/src/js/arvados/process/wb-parse-workflow-def.js Näytä tiedosto

@@ -0,0 +1,11 @@
function wbParseWorkflowDef(text) {
let definition;
try {
definition = JSON.parse(text);
} catch (_) {
definition = jsyaml.load(text);
}
return definition;
}
export default wbParseWorkflowDef;

+ 11
- 0
frontend/src/js/arvados/process/wb-process-misc.js Näytä tiedosto

@@ -0,0 +1,11 @@
function encodeURIComponentIncludingDots(s) {
return encodeURIComponent(s).replace('.', '%2E');
}
function parseKeepRef(value) {
if (typeof(value) === 'object' && 'location' in value && value.location.startsWith('keep:'))
return value.location.substr(5);
return value;
}
export { encodeURIComponentIncludingDots, parseKeepRef }

+ 25
- 0
frontend/src/js/arvados/process/wb-uuids-to-cwl.js Näytä tiedosto

@@ -0,0 +1,25 @@
function wbUuidsToCwl(obj) {
if (obj instanceof Array) {
const res = [];
for (let k in obj) {
res[k] = uuidsToCwl(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;

+ 53
- 0
frontend/src/js/component/wb-path-display.js Näytä tiedosto

@@ -0,0 +1,53 @@
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;

+ 8
- 108
frontend/src/js/page/wb-launch-workflow-page.js Näytä tiedosto

@@ -8,111 +8,11 @@ import WBNameAndUuid from 'wb-name-and-uuid';
import makeArvadosRequest from 'make-arvados-request';
import { wbDisableControls, wbEnableControls } from 'wb-disable-controls';
import linkState from 'linkstate';
function parseDefinition(text) {
let definition;
try {
definition = JSON.parse(text);
} catch (_) {
definition = jsyaml.load(text);
}
return definition;
}
function encodeURIComponentIncludingDots(s) {
return encodeURIComponent(s).replace('.', '%2E');
}
function inputSpecInfo(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 };
}
function uuidsToCwl(obj) {
if (obj instanceof Array) {
const res = [];
for (let k in obj) {
res[k] = uuidsToCwl(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');
}
function parseKeepRef(value) {
if (typeof(value) === 'object' && 'location' in value && value.location.startsWith('keep:'))
return value.location.substr(5);
return value;
}
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>
);
}
}
import wbParseWorkflowDef from 'wb-parse-workflow-def';
import wbInputSpecInfo from 'wb-input-spec-info';
import wbUuidsToCwl from 'wb-uuids-to-cwl';
import { encodeURIComponentIncludingDots, parseKeepRef } from 'wb-process-misc';
import WBPathDisplay from 'wb-path-display';
class WBLaunchWorkflowPage extends Component {
constructor(...args) {
@@ -129,7 +29,7 @@ class WBLaunchWorkflowPage extends Component {
let prom = makeArvadosRequest(arvHost, arvToken,
'/arvados/v1/workflows/' + workflowUuid);
prom = prom.then(xhr => {
const def = parseDefinition(xhr.response.definition);
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(a.default)));
@@ -146,7 +46,7 @@ class WBLaunchWorkflowPage extends Component {
renderInput(inputSpec) {
const { app } = this.props;
const { isFile, isDirectory, isArray } = inputSpecInfo(inputSpec);
const { isFile, isDirectory, isArray } = wbInputSpecInfo(inputSpec);
if (!isFile && !isDirectory)
return (
@@ -219,7 +119,7 @@ class WBLaunchWorkflowPage extends Component {
for (let k in this.state.inputs) {
try {
let val = jsyaml.safeLoad(this.state.inputs[k]);
val = uuidsToCwl(val);
val = wbUuidsToCwl(val);
k = k.split('/').slice(1).join('/');
inputs[k] = (val === undefined ? null : val);
} catch (exc) {


Loading…
Peruuta
Tallenna