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‎README.md

+3
Original file line numberDiff line numberDiff line change
@@ -53,16 +53,19 @@ npm run storybook
5353
#### Docker
5454

5555
##### Start all services
56+
5657
```bash
5758
make start
5859
```
5960

6061
##### Bootstrap the file_centric index
62+
6163
```bash
6264
make init-es
6365
```
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6567
##### Show other make targets
68+
6669
```bash
6770
make help
6871
```

‎docker-compose.yml

+7-7
Original file line numberDiff line numberDiff line change
@@ -10,8 +10,8 @@ services:
1010
discovery.type: single-node
1111
cluster.name: workflow.elasticsearch
1212
ES_JAVA_OPTS: -Xms512m -Xmx2048m
13-
ELASTIC_PASSWORD: "$ES_PASSWORD"
14-
xpack.security.enabled: "true"
13+
ELASTIC_PASSWORD: '$ES_PASSWORD'
14+
xpack.security.enabled: 'true'
1515
logging:
1616
driver: 'json-file'
1717
options:
@@ -35,9 +35,9 @@ services:
3535
depends_on:
3636
- elasticsearch
3737
environment:
38-
LOGGING_QUIET: "true"
39-
ELASTICSEARCH_USERNAME: "$ES_USERNAME"
40-
ELASTICSEARCH_PASSWORD: "$ES_PASSWORD"
38+
LOGGING_QUIET: 'true'
39+
ELASTICSEARCH_USERNAME: '$ES_USERNAME'
40+
ELASTICSEARCH_PASSWORD: '$ES_PASSWORD'
4141

4242
arranger-server:
4343
build:
@@ -50,8 +50,8 @@ services:
5050
- 5050:5050
5151
environment:
5252
ES_HOST: http://elasticsearch:9200
53-
ES_USER: "$ES_USERNAME"
54-
ES_PASS: "$ES_PASSWORD"
53+
ES_USER: '$ES_USERNAME'
54+
ES_PASS: '$ES_PASSWORD'
5555
arranger-ui:
5656
build:
5757
context: ./

‎docker/elasticsearch/index_config.json

+15-47
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,7 @@
1010
"properties": {
1111
"analysis_id": {
1212
"type": "keyword",
13-
"copy_to": [
14-
"file_autocomplete"
15-
]
13+
"copy_to": ["file_autocomplete"]
1614
},
1715
"analysis_state": {
1816
"type": "keyword"
@@ -30,18 +28,14 @@
3028
},
3129
"data_type": {
3230
"type": "keyword",
33-
"copy_to": [
34-
"file_autocomplete"
35-
]
31+
"copy_to": ["file_autocomplete"]
3632
},
3733
"donors": {
3834
"type": "nested",
3935
"properties": {
4036
"donor_id": {
4137
"type": "keyword",
42-
"copy_to": [
43-
"file_autocomplete"
44-
]
38+
"copy_to": ["file_autocomplete"]
4539
},
4640
"gender": {
4741
"type": "keyword"
@@ -54,32 +48,24 @@
5448
"properties": {
5549
"matched_normal_submitter_sample_id": {
5650
"type": "keyword",
57-
"copy_to": [
58-
"file_autocomplete"
59-
]
51+
"copy_to": ["file_autocomplete"]
6052
},
6153
"sample_id": {
6254
"type": "keyword",
63-
"copy_to": [
64-
"file_autocomplete"
65-
]
55+
"copy_to": ["file_autocomplete"]
6656
},
6757
"sample_type": {
6858
"type": "keyword"
6959
},
7060
"submitter_sample_id": {
7161
"type": "keyword",
72-
"copy_to": [
73-
"file_autocomplete"
74-
]
62+
"copy_to": ["file_autocomplete"]
7563
}
7664
}
7765
},
7866
"specimen_id": {
7967
"type": "keyword",
80-
"copy_to": [
81-
"file_autocomplete"
82-
]
68+
"copy_to": ["file_autocomplete"]
8369
},
8470
"specimen_tissue_source": {
8571
"type": "keyword"
@@ -89,9 +75,7 @@
8975
},
9076
"submitter_specimen_id": {
9177
"type": "keyword",
92-
"copy_to": [
93-
"file_autocomplete"
94-
]
78+
"copy_to": ["file_autocomplete"]
9579
},
9680
"tumour_normal_designation": {
9781
"type": "keyword"
@@ -100,9 +84,7 @@
10084
},
10185
"submitter_donor_id": {
10286
"type": "keyword",
103-
"copy_to": [
104-
"file_autocomplete"
105-
]
87+
"copy_to": ["file_autocomplete"]
10688
}
10789
}
10890
},
@@ -132,9 +114,7 @@
132114
},
133115
"name": {
134116
"type": "keyword",
135-
"copy_to": [
136-
"file_autocomplete"
137-
]
117+
"copy_to": ["file_autocomplete"]
138118
},
139119
"size": {
140120
"type": "long"
@@ -168,9 +148,7 @@
168148
},
169149
"object_id": {
170150
"type": "keyword",
171-
"copy_to": [
172-
"file_autocomplete"
173-
]
151+
"copy_to": ["file_autocomplete"]
174152
},
175153
"repositories": {
176154
"type": "nested",
@@ -194,9 +172,7 @@
194172
},
195173
"study_id": {
196174
"type": "keyword",
197-
"copy_to": [
198-
"file_autocomplete"
199-
]
175+
"copy_to": ["file_autocomplete"]
200176
}
201177
}
202178
},
@@ -215,23 +191,15 @@
215191
},
216192
"analyzer": {
217193
"autocomplete_analyzed": {
218-
"filter": [
219-
"lowercase",
220-
"edge_ngram"
221-
],
194+
"filter": ["lowercase", "edge_ngram"],
222195
"tokenizer": "standard"
223196
},
224197
"autocomplete_prefix": {
225-
"filter": [
226-
"lowercase",
227-
"edge_ngram"
228-
],
198+
"filter": ["lowercase", "edge_ngram"],
229199
"tokenizer": "keyword"
230200
},
231201
"lowercase_keyword": {
232-
"filter": [
233-
"lowercase"
234-
],
202+
"filter": ["lowercase"],
235203
"tokenizer": "keyword"
236204
}
237205
}

‎integration-tests/admin/test/index.test.js

+1-1
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ describe('@arranger/admin', () => {
4848
const adminApp = await adminGraphql({ esHost });
4949
adminApp.applyMiddleware({ app, path: adminPath });
5050
app.use(router);
51-
await new Promise(resolve => {
51+
await new Promise((resolve) => {
5252
http.listen(port, () => {
5353
resolve();
5454
});

‎integration-tests/server/test/index.test.js

+2-2
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ describe('@arranger/server', () => {
4343
const adminPath = '/admin/graphql';
4444
const graphqlField = 'model';
4545
const projectId = 'arranger_server_test';
46-
before(async function() {
46+
before(async function () {
4747
console.log('===== Initializing Elasticsearch data =====');
4848
this.timeout(10000);
4949
try {
@@ -82,7 +82,7 @@ describe('@arranger/server', () => {
8282
const adminApp = await adminGraphql({ esHost });
8383
adminApp.applyMiddleware({ app, path: adminPath });
8484
app.use(router);
85-
await new Promise(resolve => {
85+
await new Promise((resolve) => {
8686
http.listen(port, () => {
8787
resolve();
8888
});

‎integration-tests/server/test/manageSets.js

+1-1
Original file line numberDiff line numberDiff line change
@@ -41,6 +41,6 @@ export default ({ api, graphqlField, gqlPath }) => {
4141
},
4242
});
4343
expect(response.errors).to.be.undefined;
44-
expect(response.data.sets.hits.edges.map(edge => edge.node.id)).to.include(setId);
44+
expect(response.data.sets.hits.edges.map((edge) => edge.node.id)).to.include(setId);
4545
});
4646
};

‎integration-tests/server/test/readSearchData.js

+1-1
Original file line numberDiff line numberDiff line change
@@ -228,7 +228,7 @@ export default ({ api, graphqlField, gqlPath }) => {
228228
`),
229229
},
230230
});
231-
expect(response.data.model.hits.edges.every(e => !e.node.access_denied)).to.eql(true);
231+
expect(response.data.model.hits.edges.every((e) => !e.node.access_denied)).to.eql(true);
232232
});
233233
it('cannot request for access_denied item', async () => {
234234
let response = await api.post({

‎integration-tests/server/test/spinupActive.js

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
import { expect } from 'chai';
22

33
export default ({ server, projectId, port, api }) =>
4-
it(`should register active projects' ping/graphql endpoints`, done => {
4+
it(`should register active projects' ping/graphql endpoints`, (done) => {
55
server.listen(port, async () => {
66
let response = await api.get({
77
endpoint: `${projectId}/ping`,
8-
then: r => r.text(),
8+
then: (r) => r.text(),
99
});
1010
expect(response).to.equal('ok');
1111
server.close();

‎modules/admin-ui/README.md

+2-2
Original file line numberDiff line numberDiff line change
@@ -455,7 +455,7 @@ class App extends Component {
455455
.then(({ moduleA }) => {
456456
// Use moduleA
457457
})
458-
.catch(err => {
458+
.catch((err) => {
459459
// Handle failure
460460
});
461461
};
@@ -1986,7 +1986,7 @@ const app = express();
19861986

19871987
app.use(express.static(path.join(__dirname, 'build')));
19881988

1989-
app.get('/', function(req, res) {
1989+
app.get('/', function (req, res) {
19901990
res.sendFile(path.join(__dirname, 'build', 'index.html'));
19911991
});
19921992

‎modules/admin-ui/public/index.html

+1-3
Original file line numberDiff line numberDiff line change
@@ -23,9 +23,7 @@
2323
</head>
2424

2525
<body>
26-
<noscript>
27-
You need to enable JavaScript to run this app.
28-
</noscript>
26+
<noscript> You need to enable JavaScript to run this app. </noscript>
2927
<div id="root"></div>
3028
<!--
3129
This HTML file is a template.

‎modules/admin-ui/src/pages/ConfigEditorDashboard/AggsStateEditor/ReduxContainer.ts

+1-1
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ export const mapStateToProps = (
2828
return { aggsState: [] };
2929
} else {
3030
const currentProjectIndexData = state.configEditor.currentProjectData.project.indices.find(
31-
index => index.graphqlField === graphqlField,
31+
(index) => index.graphqlField === graphqlField,
3232
);
3333
if (currentProjectIndexData) {
3434
return {

‎modules/admin-ui/src/pages/ConfigEditorDashboard/AggsStateEditor/SortableAggsStateList.tsx

+1-1
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ const SortableItem = compose<
4242
connect(mapStateToProps, mapDispatchToProps),
4343
curry(React.memo)(__, (lastProps, nextProps) => equals(lastProps.item, nextProps.item)),
4444
)(({ item, aggsState, onFieldSortChange, onFieldPropertyChange }) => {
45-
const positionOptions = range(0, aggsState.length).map(val => ({
45+
const positionOptions = range(0, aggsState.length).map((val) => ({
4646
text: String(val),
4747
value: String(val),
4848
}));

‎modules/admin-ui/src/pages/ConfigEditorDashboard/AggsStateEditor/index.tsx

+2-2
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ interface IExternalProps {
2727

2828
export const booleanFilterOptions = [
2929
{ text: 'none', value: null },
30-
...Object.values(BOOLEAN_FILTER_VALUES).map(val => ({
30+
...Object.values(BOOLEAN_FILTER_VALUES).map((val) => ({
3131
text: val,
3232
value: val,
3333
})),
@@ -73,7 +73,7 @@ export default connect(
7373
}));
7474
const getFilteredFields = (s: IStateContainer) =>
7575
aggsStateWithIndex.filter(
76-
i =>
76+
(i) =>
7777
i.field.includes(s.state.fieldFilter) &&
7878
(s.state.active !== null ? String(i.active) === s.state.active : true) &&
7979
(s.state.show !== null ? String(i.show) === s.state.show : true),

‎modules/admin-ui/src/pages/ConfigEditorDashboard/ColumnsStateEditor/ReduxContainer.ts

+2-2
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ export const mapDispatchToProps = (
3030
dispatch: Dispatch<TReduxAction>,
3131
{ graphqlField }: IReduxExternalProps,
3232
): IReduxDisplatProps => ({
33-
onFieldSortChange: sortEvent => {
33+
onFieldSortChange: (sortEvent) => {
3434
dispatch({
3535
type: ActionType.COLUMNS_STATE_FIELD_ORDER_CHANGE,
3636
payload: {
@@ -40,7 +40,7 @@ export const mapDispatchToProps = (
4040
},
4141
});
4242
},
43-
onColumnPropertyChange: newColumn => {
43+
onColumnPropertyChange: (newColumn) => {
4444
dispatch({
4545
type: ActionType.COLUMNS_STATE_COLUMN_PROPERTY_CHANGE,
4646
payload: {

‎modules/admin-ui/src/pages/ConfigEditorDashboard/ColumnsStateEditor/SortableColumnsList.tsx

+1-1
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ const SortableItem = compose<
4141
return <div>LOADING...</div>;
4242
}
4343
const { columns } = columnsState;
44-
const positionOptions = range(0, columns.length).map(val => ({
44+
const positionOptions = range(0, columns.length).map((val) => ({
4545
text: String(val),
4646
value: String(val),
4747
}));

‎modules/admin-ui/src/pages/ConfigEditorDashboard/ColumnsStateEditor/index.tsx

+1-1
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ export default connect(
113113
};
114114
const getFilteredColumns = (s: IFilterStateContainer) =>
115115
columnsWithIndex.filter(
116-
c =>
116+
(c) =>
117117
c.field.includes(s.state.filter.fieldFilter) &&
118118
(s.state.filter.show !== null ? String(c.show) === s.state.filter.show : true) &&
119119
(s.state.filter.sortable !== null

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