Fix 2024 add track

[nathandunn]

fixes #2024

Allow upload of certain track types. This may be difficult (will need status or something) for VERY large files.

• test on large files, honeybee and human
• fix canvas evidence for GFF3 (and others)
• refactor to remove redundant methods
• allow instructors to upload

---

• fix GFF3 upload:
  • is it the tabix, the gzip, the gff3?
• allow deletion of "added" tracks
• remove / implement edit / hide buttons
• add category to fields and template
• update suffix based on selection
• make sure that all types work, especially GFF3, and files that have weird file name locations
  • VCF
  • VCF Canvas
  • GFF3
  • GFF3 Canvas
  • GFF3Tabix
  • GFF3Tabix Canvas
  • check for BAM
  • check for BAM Canvas
  • bigwig
  • bigwig XY
  • after the initial file save, rename the files from:
    • /opt/temporary/apollo/6496-V2/raw/testabcd/volvox-paired.bam
    • to: /opt/temporary/apollo/6496-V2/raw/testabcd.bam OR /opt/temporary/apollo/6496-V2/raw/testabcd/testabcd.bam . . e tc.
• handle names with appropriate suffix locations (e.g., if name has name.othername.suffix -> newname.suffix) - add unit test
• fix loadTracks after update

---

• check for errors WRT filename vs type for index as well
• add additional validation checks?

---

• admin only
• specifying the file sets the index type (similar to JBrowse)
• automatically specify the index files on selection
• add error page without a reset
• allow a proper "completed" message that auto-closes or errors
• trigger refresh locally on completion (or ask to refresh the page)

---

• indicate "added" tracks:
  • add apollo section to the track by default and source:upload

---

• allow a default for BAM, BigWig, etc. as a radio box
  • trigger for type, storeClass, urlTemplate for raw/autogenerated.type, and label (is autogenerated)
  • update button name
  • add extra hidden field if an indexable type ?
  • key field for name
• fix permission on OrganismController
• add a placeholder for trackList.json (with link to JBrowse doc)
• implement upload client on the UI https://stackoverflow.com/a/7182344/1739366
• link to server method

[nathandunn]

Almost work, but but bad file name.

Writes file to: /opt/temporary/apollo/6503-nf_test3/raw/asdf/volvox-sorted.bam -> but needs to be moved to /opt/temporary/apollo/6503-nf_test3/raw/asdf.bam

NEW NAME transferring track file to /opt/temporary/apollo/6503-nf_test3/raw/asdf/volvox-sorted.bam
/opt/temporary/apollo/6503-nf_test3/raw/asdf/volvox-sorted.bam (No such file or directory)
NEW NAME transferring track file to /opt/temporary/apollo/6503-nf_test3/raw/asdf/volvox-sorted.bam.bai
/opt/temporary/apollo/6503-nf_test3/raw/asdf/volvox-sorted.bam.bai (No such file or directory)
array [{"storeClass":"JBrowse/Store/SeqFeature/BAM","urlTemplate":"raw/asdf.bam","label":"asdf","apollo":{"source":"upload"},"type":"JBrowse/View/Track/Alignments","key":"asdf"}]
object {"tracks":[{"storeClass":"JBrowse/Store/SeqFeature/BAM","urlTemplate":"raw/asdf.bam","label":"asdf","apollo":{"source":"upload"},"type":"JBrowse/View/Track/Alignments","key":"asdf"}]}
trackJsonWriter: -> /opt/temporary/apollo/6503-nf_test3/extendedTrackList.json, {"tracks": [{
    "storeClass": "JBrowse/Store/SeqFeature/BAM",
    "urlTemplate": "raw/asdf.bam",
    "label": "asdf",
    "apollo": {"source": "upload"},
    "type": "JBrowse/View/Track/Alignments",
    "key": "asdf"
}]}

[nathandunn]

@deepakunni3 If you wouldn't mind looking this over. It would be very helpful. I may merge it or not, but just getting 5 minutes of your feedback would be helpful.

[nathandunn]

You can delete them right now, but I want to make them editable in a restricted way (though they are editable in the filesystem).