Save track data method on base track model

[cmdcolin]

This adds a basic concept of performing a "save track data" function on the base track model

xref #3094

It attempts to export all feature types as GFF3 for the currently visible region right now

It downloads the features to the main thread and makes a best effort to translate them into GFF3 format

• Allow plugins to register extra data format exports: this could be a pluggable element that the "SaveTrackData" dialog could ask for perhaps
• Allow different track types to say what types of data formats they support exporting to. This would make it so that e.g. VariantTrack would primarily export as VCF, or AlignmentTracks as SAM
• Allow adapter to provide the exported data. This could potentially provide "exact" exports matching the source data, giving original data lines instead of round-tripping through SimpleFeature
• Incorporate current filters (e.g. filterBy from alignments track)
• Unify the rubberband "get sequence" function with the "get features" function...e.g. we could highlight to get features to

As noted in the title, the "Save track data" feature is on the "Base track model". this is a bit awkward and currently accesses the "dynamic blocks of the view". this could suggest that this feature should be placed on the display model instead, or have some other way of obtaining regions

[cmdcolin]

tried making a minimal genbank export here

https://github.com/GMOD/jbrowse-components/tree/save_track_data_genbank

i'm not really fully in-the-know about how genbank works but the steps for this export are

1. get features visible in view
2. get min and max coordinate of these features
3. fetch the underlying reference sequence between min..max
4. export the genbank using a very base-level format similar to https://community.alliancegenome.org/t/genbank-format-downloading-from-jbrowse1-2/6772/4

this means the sequence exported is only that which spans the features in question. this is inspired by looking at this sample genbank record https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html which refers to a sequence of about 5kb from 1..5028, but is actually in the middle of chrIX on yeast https://yeastgenome.org/locus/S000001402/sequence

that led me to subtract everything relative to this currently viewed region. the alternative would be exporting the entire chromosome sequence (which can be large) and then using true start/end coords.

cc @scottcain xref https://community.alliancegenome.org/t/genbank-format-downloading-from-jbrowse1-2/6772/4

[cmdcolin]

added some genbank export to this branch

also downloaded snapgene free trial. the exports from this branch look approximately similar to a gbrowse genbank exports made from maizemine

Example

https://jbrowse.org/code/jb2/save_track_data/?config=test_data%2Fconfig_demo.json&session=share-FK-AH5RGz7&password=roZPQ

[codecov]

Codecov Report

Attention: Patch coverage is 6.27451% with 239 lines in your changes missing coverage. Please review.

Project coverage is 62.14%. Comparing base (a097560) to head (83cbc05).
Report is 127 commits behind head on main.

❗ Current head 83cbc05 differs from pull request most recent head f51bb83

Please upload reports for the commit f51bb83 to get more accurate results.

Files	Patch %	Lines
...eElementTypes/models/saveTrackFileTypes/genbank.ts	4.10%	70 Missing ⚠️
...leElementTypes/models/components/SaveTrackData.tsx	0.00%	51 Missing ⚠️
...ableElementTypes/models/saveTrackFileTypes/gff3.ts	6.25%	30 Missing ⚠️
packages/core/assemblyManager/util.ts	0.00%	19 Missing ⚠️
packages/core/rpc/methods/CoreSaveFeatureData.ts	0.00%	19 Missing ⚠️
packages/core/assemblyManager/loadRefNameMap.ts	0.00%	14 Missing ⚠️
.../variants/src/VariantTrack/saveTrackFormats/vcf.ts	0.00%	9 Missing ⚠️
packages/core/rpc/methods/CoreGetRegions.ts	11.11%	8 Missing ⚠️
...rc/LinearPileupDisplay/components/SetMaxHeight.tsx	0.00%	5 Missing ⚠️
...src/LinearBasicDisplay/components/SetMaxHeight.tsx	0.00%	5 Missing ⚠️
... and 4 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3439      +/-   ##
==========================================
- Coverage   62.61%   62.14%   -0.47%     
==========================================
  Files        1088     1096       +8     
  Lines       31495    31696     +201     
  Branches     7531     7565      +34     
==========================================
- Hits        19721    19699      -22     
- Misses      11602    11824     +222     
- Partials      172      173       +1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[scottcain]

Added a bug report for GFF3 generation in that it doesn't produce a ##sequence-region directive: #3679

[scottcain]

Added a bug report for GFF3 production that it gets strand wrong (1 or -1 instead of the standard + or -): #3678

[scottcain]

Added a feature request to have the location info embedded in saved track data filenames: #3680

[cmdcolin]

updated to latest main at v2.6.2 @scottcain

[cmdcolin]

new work trying to push this forward a little bit that makes the set of file formats part of the track model. could also look at display model and/or adapter model potentially, but this is a step towards a little less hardcoded format

[cmdcolin]

address comment here #4029 (comment)