@jbrowse/cli 5.0.0-beta.1 → 5.0.0-beta.2

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 (16) hide show
  1. package/README.md +98 -16
  2. package/bundle/index.js +82 -74
  3. package/dist/commands/add-track-utils/adapter-utils.js +49 -0
  4. package/dist/commands/add-track.js +26 -3
  5. package/dist/commands/make-density/density-generator.js +180 -0
  6. package/dist/commands/make-density/index.js +139 -0
  7. package/dist/commands/make-pif/index.js +54 -24
  8. package/dist/commands/make-pif/pif-generator.js +105 -133
  9. package/dist/commands/shared/density.js +12 -0
  10. package/dist/commands/validate/configManifest.generated.js +379 -8
  11. package/dist/commands/validate/index.js +5 -5
  12. package/dist/commands/validate/validateConfig.js +97 -32
  13. package/dist/index.js +5 -0
  14. package/dist/version.js +1 -1
  15. package/package.json +4 -4
  16. package/dist/commands/make-pif/cigar-utils.js +0 -67
package/dist/commands/validate/configManifest.generated.js CHANGED
@@ -26,6 +26,10 @@ export const configManifest = {
26
26
  "name": "fetchSizeLimit",
27
27
  "type": "(JexlString | number)"
28
28
  },
29
+ {
30
+ "name": "densityAdapter",
31
+ "type": "(JexlString | frozen)"
32
+ },
29
33
  {
30
34
  "name": "useSliceWorkerPool",
31
35
  "type": "(JexlString | boolean)"
@@ -71,6 +75,10 @@ export const configManifest = {
71
75
  {
72
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  "name": "fetchSizeLimit",
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  "type": "(JexlString | number)"
78
+ },
79
+ {
80
+ "name": "densityAdapter",
81
+ "type": "(JexlString | frozen)"
74
82
  }
75
83
  ],
76
84
  "shorthandKeys": [
@@ -112,6 +120,10 @@ export const configManifest = {
112
120
  {
113
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  "name": "htsgetTrackId",
114
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  "type": "(JexlString | string)"
123
+ },
124
+ {
125
+ "name": "densityAdapter",
126
+ "type": "(JexlString | frozen)"
115
127
  }
116
128
  ],
117
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  "shorthandKeys": []
@@ -137,6 +149,10 @@ export const configManifest = {
137
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  {
138
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  "name": "disableGeneHeuristic",
139
151
  "type": "(JexlString | boolean)"
152
+ },
153
+ {
154
+ "name": "densityAdapter",
155
+ "type": "(JexlString | frozen)"
140
156
  }
141
157
  ],
142
158
  "shorthandKeys": [
@@ -263,6 +279,10 @@ export const configManifest = {
263
279
  {
264
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  "name": "disableGeneHeuristic",
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  "type": "(JexlString | boolean)"
282
+ },
283
+ {
284
+ "name": "densityAdapter",
285
+ "type": "(JexlString | frozen)"
266
286
  }
267
287
  ],
268
288
  "shorthandKeys": [
@@ -472,6 +492,10 @@ export const configManifest = {
472
492
  {
473
493
  "name": "aggregateField",
474
494
  "type": "(JexlString | string)"
495
+ },
496
+ {
497
+ "name": "densityAdapter",
498
+ "type": "(JexlString | frozen)"
475
499
  }
476
500
  ],
477
501
  "shorthandKeys": [
@@ -507,6 +531,10 @@ export const configManifest = {
507
531
  {
508
532
  "name": "dontRedispatch",
509
533
  "type": "(JexlString | string[])"
534
+ },
535
+ {
536
+ "name": "densityAdapter",
537
+ "type": "(JexlString | frozen)"
510
538
  }
511
539
  ],
512
540
  "shorthandKeys": [
@@ -848,6 +876,10 @@ export const configManifest = {
848
876
  {
849
877
  "name": "fetchSizeLimit",
850
878
  "type": "(JexlString | number)"
879
+ },
880
+ {
881
+ "name": "densityAdapter",
882
+ "type": "(JexlString | frozen)"
851
883
  }
852
884
  ],
853
885
  "shorthandKeys": [
@@ -881,6 +913,10 @@ export const configManifest = {
881
913
  {
882
914
  "name": "fetchSizeLimit",
883
915
  "type": "(JexlString | number)"
916
+ },
917
+ {
918
+ "name": "densityAdapter",
919
+ "type": "(JexlString | frozen)"
884
920
  }
885
921
  ],
886
922
  "shorthandKeys": []
@@ -1562,6 +1598,10 @@ export const configManifest = {
1562
1598
  "name": "disableGeneHeuristic",
1563
1599
  "type": "(JexlString | boolean)"
1564
1600
  },
1601
+ {
1602
+ "name": "densityAdapter",
1603
+ "type": "(JexlString | frozen)"
1604
+ },
1565
1605
  {
1566
1606
  "name": "scoreTransform",
1567
1607
  "type": "(JexlString | string)"
@@ -2778,6 +2818,14 @@ export const configManifest = {
2778
2818
  "name": "forceLoad",
2779
2819
  "type": "(JexlString | boolean)"
2780
2820
  },
2821
+ {
2822
+ "name": "densityTier",
2823
+ "type": "(JexlString | Density tier)"
2824
+ },
2825
+ {
2826
+ "name": "densityTierBpPerPx",
2827
+ "type": "(JexlString | number)"
2828
+ },
2781
2829
  {
2782
2830
  "name": "height",
2783
2831
  "type": "(JexlString | number)"
@@ -2790,10 +2838,6 @@ export const configManifest = {
2790
2838
  "name": "jexlFilters",
2791
2839
  "type": "(JexlString | string[])"
2792
2840
  },
2793
- {
2794
- "name": "maxHeight",
2795
- "type": "(JexlString | number)"
2796
- },
2797
2841
  {
2798
2842
  "name": "heightMode",
2799
2843
  "type": "(JexlString | (heightMode | undefined))"
@@ -2952,6 +2996,14 @@ export const configManifest = {
2952
2996
  "name": "forceLoad",
2953
2997
  "type": "(JexlString | boolean)"
2954
2998
  },
2999
+ {
3000
+ "name": "densityTier",
3001
+ "type": "(JexlString | Density tier)"
3002
+ },
3003
+ {
3004
+ "name": "densityTierBpPerPx",
3005
+ "type": "(JexlString | number)"
3006
+ },
2955
3007
  {
2956
3008
  "name": "height",
2957
3009
  "type": "(JexlString | number)"
@@ -3062,6 +3114,14 @@ export const configManifest = {
3062
3114
  "name": "forceLoad",
3063
3115
  "type": "(JexlString | boolean)"
3064
3116
  },
3117
+ {
3118
+ "name": "densityTier",
3119
+ "type": "(JexlString | Density tier)"
3120
+ },
3121
+ {
3122
+ "name": "densityTierBpPerPx",
3123
+ "type": "(JexlString | number)"
3124
+ },
3065
3125
  {
3066
3126
  "name": "height",
3067
3127
  "type": "(JexlString | number)"
@@ -3338,6 +3398,14 @@ export const configManifest = {
3338
3398
  {
3339
3399
  "name": "displayId",
3340
3400
  "type": "identifier"
3401
+ },
3402
+ {
3403
+ "name": "drawCurves",
3404
+ "type": "(JexlString | (boolean | undefined))"
3405
+ },
3406
+ {
3407
+ "name": "drawLocationMarkers",
3408
+ "type": "(JexlString | (boolean | undefined))"
3341
3409
  }
3342
3410
  ],
3343
3411
  "stateModelProps": [
@@ -3368,6 +3436,14 @@ export const configManifest = {
3368
3436
  "name": "forceLoad",
3369
3437
  "type": "(JexlString | boolean)"
3370
3438
  },
3439
+ {
3440
+ "name": "densityTier",
3441
+ "type": "(JexlString | Density tier)"
3442
+ },
3443
+ {
3444
+ "name": "densityTierBpPerPx",
3445
+ "type": "(JexlString | number)"
3446
+ },
3371
3447
  {
3372
3448
  "name": "height",
3373
3449
  "type": "(JexlString | number)"
@@ -3602,6 +3678,14 @@ export const configManifest = {
3602
3678
  "name": "forceLoad",
3603
3679
  "type": "(JexlString | boolean)"
3604
3680
  },
3681
+ {
3682
+ "name": "densityTier",
3683
+ "type": "(JexlString | Density tier)"
3684
+ },
3685
+ {
3686
+ "name": "densityTierBpPerPx",
3687
+ "type": "(JexlString | number)"
3688
+ },
3605
3689
  {
3606
3690
  "name": "height",
3607
3691
  "type": "(JexlString | number)"
@@ -3714,6 +3798,14 @@ export const configManifest = {
3714
3798
  "name": "forceLoad",
3715
3799
  "type": "(JexlString | boolean)"
3716
3800
  },
3801
+ {
3802
+ "name": "densityTier",
3803
+ "type": "(JexlString | Density tier)"
3804
+ },
3805
+ {
3806
+ "name": "densityTierBpPerPx",
3807
+ "type": "(JexlString | number)"
3808
+ },
3717
3809
  {
3718
3810
  "name": "height",
3719
3811
  "type": "(JexlString | number)"
@@ -3726,10 +3818,6 @@ export const configManifest = {
3726
3818
  "name": "jexlFilters",
3727
3819
  "type": "(JexlString | string[])"
3728
3820
  },
3729
- {
3730
- "name": "maxHeight",
3731
- "type": "(JexlString | number)"
3732
- },
3733
3821
  {
3734
3822
  "name": "heightMode",
3735
3823
  "type": "(JexlString | (heightMode | undefined))"
@@ -3877,6 +3965,14 @@ export const configManifest = {
3877
3965
  "name": "forceLoad",
3878
3966
  "type": "(JexlString | boolean)"
3879
3967
  },
3968
+ {
3969
+ "name": "densityTier",
3970
+ "type": "(JexlString | Density tier)"
3971
+ },
3972
+ {
3973
+ "name": "densityTierBpPerPx",
3974
+ "type": "(JexlString | number)"
3975
+ },
3880
3976
  {
3881
3977
  "name": "height",
3882
3978
  "type": "(JexlString | number)"
@@ -4010,6 +4106,14 @@ export const configManifest = {
4010
4106
  "name": "forceLoad",
4011
4107
  "type": "(JexlString | boolean)"
4012
4108
  },
4109
+ {
4110
+ "name": "densityTier",
4111
+ "type": "(JexlString | Density tier)"
4112
+ },
4113
+ {
4114
+ "name": "densityTierBpPerPx",
4115
+ "type": "(JexlString | number)"
4116
+ },
4013
4117
  {
4014
4118
  "name": "height",
4015
4119
  "type": "(JexlString | number)"
@@ -4127,6 +4231,14 @@ export const configManifest = {
4127
4231
  "name": "forceLoad",
4128
4232
  "type": "(JexlString | boolean)"
4129
4233
  },
4234
+ {
4235
+ "name": "densityTier",
4236
+ "type": "(JexlString | Density tier)"
4237
+ },
4238
+ {
4239
+ "name": "densityTierBpPerPx",
4240
+ "type": "(JexlString | number)"
4241
+ },
4130
4242
  {
4131
4243
  "name": "height",
4132
4244
  "type": "(JexlString | number)"
@@ -4233,6 +4345,14 @@ export const configManifest = {
4233
4345
  "name": "forceLoad",
4234
4346
  "type": "(JexlString | boolean)"
4235
4347
  },
4348
+ {
4349
+ "name": "densityTier",
4350
+ "type": "(JexlString | Density tier)"
4351
+ },
4352
+ {
4353
+ "name": "densityTierBpPerPx",
4354
+ "type": "(JexlString | number)"
4355
+ },
4236
4356
  {
4237
4357
  "name": "height",
4238
4358
  "type": "(JexlString | number)"
@@ -4835,6 +4955,14 @@ export const configManifest = {
4835
4955
  "name": "forceLoad",
4836
4956
  "type": "(JexlString | boolean)"
4837
4957
  },
4958
+ {
4959
+ "name": "densityTier",
4960
+ "type": "(JexlString | Density tier)"
4961
+ },
4962
+ {
4963
+ "name": "densityTierBpPerPx",
4964
+ "type": "(JexlString | number)"
4965
+ },
4838
4966
  {
4839
4967
  "name": "height",
4840
4968
  "type": "(JexlString | (number | undefined))"
@@ -4879,6 +5007,10 @@ export const configManifest = {
4879
5007
  "name": "showRowLabels",
4880
5008
  "type": "(JexlString | boolean)"
4881
5009
  },
5010
+ {
5011
+ "name": "showLegend",
5012
+ "type": "(JexlString | (boolean | undefined))"
5013
+ },
4882
5014
  {
4883
5015
  "name": "showCoverage",
4884
5016
  "type": "(JexlString | boolean)"
@@ -4964,6 +5096,14 @@ export const configManifest = {
4964
5096
  "name": "forceLoad",
4965
5097
  "type": "(JexlString | boolean)"
4966
5098
  },
5099
+ {
5100
+ "name": "densityTier",
5101
+ "type": "(JexlString | Density tier)"
5102
+ },
5103
+ {
5104
+ "name": "densityTierBpPerPx",
5105
+ "type": "(JexlString | number)"
5106
+ },
4967
5107
  {
4968
5108
  "name": "height",
4969
5109
  "type": "(JexlString | number)"
@@ -5037,6 +5177,14 @@ export const configManifest = {
5037
5177
  "name": "forceLoad",
5038
5178
  "type": "(JexlString | boolean)"
5039
5179
  },
5180
+ {
5181
+ "name": "densityTier",
5182
+ "type": "(JexlString | Density tier)"
5183
+ },
5184
+ {
5185
+ "name": "densityTierBpPerPx",
5186
+ "type": "(JexlString | number)"
5187
+ },
5040
5188
  {
5041
5189
  "name": "height",
5042
5190
  "type": "(JexlString | number)"
@@ -5109,6 +5257,14 @@ export const configManifest = {
5109
5257
  "name": "forceLoad",
5110
5258
  "type": "(JexlString | boolean)"
5111
5259
  },
5260
+ {
5261
+ "name": "densityTier",
5262
+ "type": "(JexlString | Density tier)"
5263
+ },
5264
+ {
5265
+ "name": "densityTierBpPerPx",
5266
+ "type": "(JexlString | number)"
5267
+ },
5112
5268
  {
5113
5269
  "name": "height",
5114
5270
  "type": "(JexlString | number)"
@@ -5162,6 +5318,14 @@ export const configManifest = {
5162
5318
  "name": "forceLoad",
5163
5319
  "type": "(JexlString | boolean)"
5164
5320
  },
5321
+ {
5322
+ "name": "densityTier",
5323
+ "type": "(JexlString | Density tier)"
5324
+ },
5325
+ {
5326
+ "name": "densityTierBpPerPx",
5327
+ "type": "(JexlString | number)"
5328
+ },
5165
5329
  {
5166
5330
  "name": "height",
5167
5331
  "type": "(JexlString | number)"
@@ -5369,6 +5533,213 @@ export const configManifest = {
5369
5533
  ]
5370
5534
  }
5371
5535
  },
5536
+ "views": {
5537
+ "LinearGenomeView": {
5538
+ "stateModelProps": [
5539
+ "id",
5540
+ "displayName",
5541
+ "minimized",
5542
+ "highlight",
5543
+ "showHighlightChips",
5544
+ "type",
5545
+ "windowStartBp",
5546
+ "windowWidthBp",
5547
+ "legacyBpPerPx",
5548
+ "displayedRegions",
5549
+ "tracks",
5550
+ "hideHeader",
5551
+ "hideHeaderOverview",
5552
+ "hideNoTracksActive",
5553
+ "trackSelectorType",
5554
+ "showCenterLine",
5555
+ "showCytobands",
5556
+ "trackLabels",
5557
+ "showGridlines",
5558
+ "labelsVisible",
5559
+ "colorByCDS",
5560
+ "showAminoAcids",
5561
+ "showTrackOutlines",
5562
+ "scalebarOnly",
5563
+ "launch"
5564
+ ],
5565
+ "launchKeys": [
5566
+ "assembly",
5567
+ "displayedRegionNames",
5568
+ "grow",
5569
+ "highlight",
5570
+ "loc",
5571
+ "nav",
5572
+ "tracklist",
5573
+ "tracks"
5574
+ ],
5575
+ "passThrough": [
5576
+ "bpPerPx",
5577
+ "offsetPx"
5578
+ ]
5579
+ },
5580
+ "CircularView": {
5581
+ "stateModelProps": [
5582
+ "id",
5583
+ "displayName",
5584
+ "minimized",
5585
+ "type",
5586
+ "offsetRadians",
5587
+ "bpPerPx",
5588
+ "autoFit",
5589
+ "tracks",
5590
+ "hideVerticalResizeHandle",
5591
+ "hideTrackSelectorButton",
5592
+ "disableImportForm",
5593
+ "height",
5594
+ "displayedRegions",
5595
+ "minimumRadiusPx",
5596
+ "spacingPx",
5597
+ "paddingPx",
5598
+ "minVisibleWidth",
5599
+ "trackSelectorType",
5600
+ "launch"
5601
+ ],
5602
+ "launchKeys": [
5603
+ "assembly",
5604
+ "displayedRegionNames",
5605
+ "tracks"
5606
+ ]
5607
+ },
5608
+ "DotplotView": {
5609
+ "stateModelProps": [
5610
+ "id",
5611
+ "displayName",
5612
+ "minimized",
5613
+ "highlight",
5614
+ "showHighlightChips",
5615
+ "colorBy",
5616
+ "trackColorBy",
5617
+ "trackColors",
5618
+ "showColorLegend",
5619
+ "type",
5620
+ "height",
5621
+ "trackSelectorType",
5622
+ "assemblyNames",
5623
+ "drawCigar",
5624
+ "showGridlines",
5625
+ "lodMode",
5626
+ "lockAspectRatio",
5627
+ "lineWidth",
5628
+ "alpha",
5629
+ "minAlignmentLength",
5630
+ "minIdentity",
5631
+ "hview",
5632
+ "vview",
5633
+ "tracks",
5634
+ "launch"
5635
+ ],
5636
+ "launchKeys": [
5637
+ "autoDiagonalize",
5638
+ "highlight",
5639
+ "tracks",
5640
+ "views"
5641
+ ]
5642
+ },
5643
+ "LinearSyntenyView": {
5644
+ "stateModelProps": [
5645
+ "id",
5646
+ "displayName",
5647
+ "minimized",
5648
+ "type",
5649
+ "trackSelectorType",
5650
+ "linkViews",
5651
+ "followSynteny",
5652
+ "sameScale",
5653
+ "followAnchorIndex",
5654
+ "followMatchOrientation",
5655
+ "levels",
5656
+ "views",
5657
+ "colorBy",
5658
+ "trackColorBy",
5659
+ "trackColors",
5660
+ "showColorLegend",
5661
+ "cigarMode",
5662
+ "showOffscreenMates",
5663
+ "bidirectionalFetch",
5664
+ "overdrawPx",
5665
+ "alpha",
5666
+ "minAlignmentLength",
5667
+ "lodMode",
5668
+ "opacityByIdentity",
5669
+ "fadeThinAlignmentsMode",
5670
+ "launch"
5671
+ ],
5672
+ "launchKeys": [
5673
+ "autoDiagonalize",
5674
+ "collapseEmptyRows",
5675
+ "drawCurves",
5676
+ "drawLocationMarkers",
5677
+ "levelHeights",
5678
+ "sameScale",
5679
+ "tracks",
5680
+ "views"
5681
+ ]
5682
+ },
5683
+ "SpreadsheetView": {
5684
+ "stateModelProps": [
5685
+ "id",
5686
+ "displayName",
5687
+ "minimized",
5688
+ "type",
5689
+ "height",
5690
+ "hideVerticalResizeHandle",
5691
+ "importWizard",
5692
+ "spreadsheet",
5693
+ "launch"
5694
+ ],
5695
+ "launchKeys": [
5696
+ "assembly",
5697
+ "baseUri",
5698
+ "fileType",
5699
+ "filterText",
5700
+ "uri"
5701
+ ]
5702
+ },
5703
+ "SvInspectorView": {
5704
+ "stateModelProps": [
5705
+ "id",
5706
+ "displayName",
5707
+ "minimized",
5708
+ "type",
5709
+ "height",
5710
+ "onlyDisplayRelevantRegionsInCircularView",
5711
+ "spreadsheetWidthFraction",
5712
+ "spreadsheetView",
5713
+ "circularView",
5714
+ "launch"
5715
+ ],
5716
+ "launchKeys": [
5717
+ "assembly",
5718
+ "baseUri",
5719
+ "fileType",
5720
+ "filterText",
5721
+ "uri"
5722
+ ]
5723
+ },
5724
+ "BreakpointSplitView": {
5725
+ "stateModelProps": [
5726
+ "id",
5727
+ "displayName",
5728
+ "minimized",
5729
+ "type",
5730
+ "height",
5731
+ "showIntraviewLinks",
5732
+ "linkViews",
5733
+ "interactiveOverlay",
5734
+ "showHeader",
5735
+ "views",
5736
+ "launch"
5737
+ ],
5738
+ "launchKeys": [
5739
+ "views"
5740
+ ]
5741
+ }
5742
+ },
5372
5743
  "migratedDisplayKeys": {
5373
5744
  "*": [
5374
5745
  "heightPreConfig"
package/dist/commands/validate/index.js CHANGED
@@ -9,14 +9,14 @@ nothing. That is what this command is mainly for.
9
9
  Two levels are reported:
10
10
 
11
11
  error JBrowse accepts it and silently does the wrong thing — an unknown
12
- slot, a track naming an assembly the config never defines, a
13
- defaultSession naming a trackId that does not exist, a duplicate
14
- trackId. Exits 1.
12
+ slot, a key a defaultSession view or display does not declare, a
13
+ track naming an assembly the config never defines, a defaultSession
14
+ naming a trackId that does not exist, a duplicate trackId. Exits 1.
15
15
 
16
16
  warning JBrowse will complain by itself on load, or handles it — a type name
17
17
  the core plugins do not register (expected if one of your plugins
18
- registers it), or a legacy key a migration rewrites. Never fails
19
- the run.
18
+ registers it), or a legacy key a migration rewrites, such as a view
19
+ nesting its settings under "init". Never fails the run.
20
20
 
21
21
  Types registered by plugins are not known to this command, so they come through
22
22
  as warnings rather than errors.`;