@jbrowse/img 2.4.2 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (9) hide show
  1. package/dist/renderRegion.d.ts +1 -1
  2. package/dist/renderRegion.js +1 -1
  3. package/dist/renderRegion.js.map +1 -1
  4. package/esm/renderRegion.d.ts +1 -1
  5. package/esm/renderRegion.js +1 -1
  6. package/esm/renderRegion.js.map +1 -1
  7. package/package.json +5 -5
  8. package/src/index.test.ts +20 -36
  9. package/src/renderRegion.tsx +2 -2
package/dist/renderRegion.d.ts CHANGED
@@ -10,7 +10,7 @@ export interface Opts {
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  aliases?: string;
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  cytobands?: string;
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  defaultSession?: string;
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- trackList: Entry[];
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+ trackList?: Entry[];
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  tracks?: string;
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  }
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  interface Assembly {
package/dist/renderRegion.js CHANGED
@@ -300,7 +300,7 @@ function process(trackEntry, view, extra = c => c) {
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  else if (opt.startsWith('force:')) {
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  const [, force] = opt.split(':');
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  if (force) {
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- display.updateStatsLimit({ bytes: Number.MAX_VALUE });
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+ display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE });
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  }
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  }
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  // apply wiggle autoscale
package/dist/renderRegion.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/renderRegion.d.ts CHANGED
@@ -10,7 +10,7 @@ export interface Opts {
10
10
  aliases?: string;
11
11
  cytobands?: string;
12
12
  defaultSession?: string;
13
- trackList: Entry[];
13
+ trackList?: Entry[];
14
14
  tracks?: string;
15
15
  }
16
16
  interface Assembly {
package/esm/renderRegion.js CHANGED
@@ -293,7 +293,7 @@ function process(trackEntry, view, extra = c => c) {
293
293
  else if (opt.startsWith('force:')) {
294
294
  const [, force] = opt.split(':');
295
295
  if (force) {
296
- display.updateStatsLimit({ bytes: Number.MAX_VALUE });
296
+ display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE });
297
297
  }
298
298
  }
299
299
  // apply wiggle autoscale
package/esm/renderRegion.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/img",
3
- "version": "2.4.2",
3
+ "version": "2.5.0",
4
4
  "main": "dist/index.js",
5
5
  "module": "esm/index.js",
6
6
  "author": "JBrowse Team",
@@ -29,11 +29,11 @@
29
29
  "@babel/runtime": "^7.17.9",
30
30
  "@emotion/cache": "^11.7.1",
31
31
  "@emotion/react": "^11.9.0",
32
- "@jbrowse/plugin-linear-genome-view": "^2.4.2",
33
- "@jbrowse/react-linear-genome-view": "^2.4.2",
32
+ "@jbrowse/plugin-linear-genome-view": "^2.5.0",
33
+ "@jbrowse/react-linear-genome-view": "^2.5.0",
34
34
  "abortcontroller-polyfill": "^1.7.3",
35
35
  "canvas": "^2.9.1",
36
- "jsdom": "^20.0.3",
36
+ "jsdom": "^21.1.1",
37
37
  "mobx": "^6.6.0",
38
38
  "node-fetch": "^2.6.7",
39
39
  "react": "^17.0.0",
@@ -44,5 +44,5 @@
44
44
  "publishConfig": {
45
45
  "access": "public"
46
46
  },
47
- "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
47
+ "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
48
48
  }
package/src/index.test.ts CHANGED
@@ -3,13 +3,13 @@
3
3
  * @jest-environment node
4
4
  */
5
5
 
6
- // the above jest-environment node is important to check true usage as a CLI tool
6
+ // the above jest-environment node is important to check true usage
7
+ // as a CLI tool
7
8
 
8
9
  import { renderRegion } from './renderRegion'
9
10
  import path from 'path'
10
11
  import fs from 'fs'
11
12
  import { JSDOM } from 'jsdom'
12
- import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
13
13
  import { Image, createCanvas } from 'canvas'
14
14
  import fetch, { Headers, Response, Request } from 'node-fetch'
15
15
 
@@ -30,29 +30,31 @@ global.nodeImage = Image
30
30
  // @ts-expect-error
31
31
  global.nodeCreateCanvas = createCanvas
32
32
 
33
+ function pa(s: string) {
34
+ return path.join(__dirname, s)
35
+ }
36
+
33
37
  xtest('renders a region with --session and --config args', async () => {
34
- // @ts-expect-error
35
38
  const result = await renderRegion({
36
- session: path.join(__dirname, '../test/clingen_session.json'),
37
- config: path.join(__dirname, '../data/config.json'),
39
+ session: pa('../test/clingen_session.json'),
40
+ config: pa('../data/config.json'),
38
41
  })
39
42
  fs.writeFileSync('svg_from_config_and_session_param.svg', result)
40
43
  expect(result).toMatchSnapshot()
41
44
  }, 40000)
42
45
 
43
46
  xtest('renders a region with --session, --tracks, and --assembly args', async () => {
44
- // @ts-expect-error
45
47
  const result = await renderRegion({
46
- session: path.join(__dirname, '../test/clingen_session.json'),
47
- tracks: path.join(__dirname, '../data/tracks.json'),
48
- assembly: path.join(__dirname, '../data/assembly.json'),
48
+ session: pa('../test/clingen_session.json'),
49
+ tracks: pa('../data/tracks.json'),
50
+ assembly: pa('../data/assembly.json'),
49
51
  })
50
52
  fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result)
51
53
  expect(result).toMatchSnapshot()
52
54
  }, 40000)
53
55
 
54
56
  test('renders volvox with variety of args', async () => {
55
- const fp = (f: string) => path.join(__dirname, '../data/volvox/' + f)
57
+ const fp = (f: string) => pa('../data/volvox/' + f)
56
58
  const result = await renderRegion({
57
59
  fasta: fp('volvox.fa'),
58
60
  trackList: [
@@ -66,10 +68,7 @@ test('renders volvox with variety of args', async () => {
66
68
  ],
67
69
  loc: 'ctgA:1000-2000',
68
70
  })
69
- fs.writeFileSync(
70
- path.join(__dirname, '../test/svg_from_volvox_fasta_and_bam.svg'),
71
- result,
72
- )
71
+ fs.writeFileSync(pa('../test/svg_from_volvox_fasta_and_bam.svg'), result)
73
72
  expect(result).toBeTruthy()
74
73
  }, 40000)
75
74
 
@@ -87,10 +86,7 @@ xtest('renders human large region with remote urls', async () => {
87
86
  ],
88
87
  loc: '1:10,000,000-10,030,000',
89
88
  })
90
- fs.writeFileSync(
91
- path.join(__dirname, '../test/human_remote_urls_large_region.svg'),
92
- result,
93
- )
89
+ fs.writeFileSync(pa('../test/human_remote_urls_large_region.svg'), result)
94
90
  expect(result).toBeTruthy()
95
91
  }, 120000)
96
92
 
@@ -107,15 +103,12 @@ xtest('renders volvox with remote urls', async () => {
107
103
  ],
108
104
  loc: 'ctgA:1-1000',
109
105
  })
110
- fs.writeFileSync(
111
- path.join(__dirname, '../test/volvox_remote_region.svg'),
112
- result,
113
- )
106
+ fs.writeFileSync(pa('../test/volvox_remote_region.svg'), result)
114
107
  expect(result).toBeTruthy()
115
108
  }, 20000)
116
109
 
117
110
  test('renders volvox with variety of args (noRasterize)', async () => {
118
- const fp = (f: string) => path.join(__dirname, '../data/volvox/' + f)
111
+ const fp = (f: string) => pa('../data/volvox/' + f)
119
112
  const result = await renderRegion({
120
113
  fasta: fp('volvox.fa'),
121
114
  trackList: [
@@ -131,10 +124,7 @@ test('renders volvox with variety of args (noRasterize)', async () => {
131
124
  noRasterize: true,
132
125
  })
133
126
  fs.writeFileSync(
134
- path.join(
135
- __dirname,
136
- '../test/svg_from_volvox_fasta_and_bam_norasterize.svg',
137
- ),
127
+ pa('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
138
128
  result,
139
129
  )
140
130
  expect(result).toBeTruthy()
@@ -154,15 +144,12 @@ xtest('configtracks arg with urls', async () => {
154
144
 
155
145
  test('configtracks arg with local files', async () => {
156
146
  const result = await renderRegion({
157
- config: path.join(__dirname, '../data/volvox/config.json'),
147
+ config: pa('../data/volvox/config.json'),
158
148
  trackList: [['configtracks', ['volvox_sv']]],
159
149
  assembly: 'volvox',
160
150
  loc: 'ctgA:1-50,000',
161
151
  })
162
- fs.writeFileSync(
163
- path.join(__dirname, '../test/svg_configtracks_local.svg'),
164
- result,
165
- )
152
+ fs.writeFileSync(pa('../test/svg_configtracks_local.svg'), result)
166
153
  expect(result).toBeTruthy()
167
154
  }, 40000)
168
155
 
@@ -179,9 +166,6 @@ xtest('renders --hic', async () => {
179
166
  ],
180
167
  loc: '1:2,000,000-10,000,000',
181
168
  })
182
- fs.writeFileSync(
183
- path.join(__dirname, '../test/svg_from_human_hic.svg'),
184
- result,
185
- )
169
+ fs.writeFileSync(pa('../test/svg_from_human_hic.svg'), result)
186
170
  expect(result).toBeTruthy()
187
171
  }, 20000)
package/src/renderRegion.tsx CHANGED
@@ -24,7 +24,7 @@ export interface Opts {
24
24
  aliases?: string
25
25
  cytobands?: string
26
26
  defaultSession?: string
27
- trackList: Entry[]
27
+ trackList?: Entry[]
28
28
  tracks?: string
29
29
  }
30
30
 
@@ -367,7 +367,7 @@ function process(
367
367
  else if (opt.startsWith('force:')) {
368
368
  const [, force] = opt.split(':')
369
369
  if (force) {
370
- display.updateStatsLimit({ bytes: Number.MAX_VALUE })
370
+ display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE })
371
371
  }
372
372
  }
373
373