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Add Geo tab to explorer pages #244

Merged
merged 3 commits into from
Apr 5, 2023
Merged

Add Geo tab to explorer pages #244

merged 3 commits into from
Apr 5, 2023

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lukepereira
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@lukepereira lukepereira commented Apr 3, 2023

Summary of changes

  • Add new lib react-tabs
  • Add higher-order component for rendering tabs on Sequence and Family pages in explorer and fetching all RunIDs
  • Handle conditional behaviour for large number of run_ids in query params
  • Add info about available geo data vs total runs
  • Misc request: change text from Analyse -> Palmprint

Related issues

Checklist

  • Add tests or provide evidence of manual testing (if applicable)
  • PR checks pass (see CONTRIBUTING.md for how to fix failing checks)

@ababaian
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ababaian commented Apr 4, 2023

test link: https://add-geo-to-explorer.serratus.io/

Notes:

  • Remove text The Planetary RNA Virome from geo tab
  • Add Loading icon while SQL runs
  • Change text from Analyse --> palmID *

load_units
load_glow

@lukepereira lukepereira force-pushed the add-geo-to-explorer branch from f49b854 to fb5ec20 Compare April 4, 2023 14:39
@lukepereira lukepereira marked this pull request as ready for review April 4, 2023 16:17
@ababaian
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ababaian commented Apr 4, 2023

Not sure if this is off-topic, but beside palmID linkout button, we should add a BLAST linkout as well using this template

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&USER_FORMAT_DEFAULTS=on&SET_SAVED_SEARCH=true&PAGE=Proteins&PROGRAM=blastp&QUERY=VEVDFTEFDRNQTLATRDLEVEVTSHLLGFDCLDDYKALRAGSYCQLRDLAQTETGCERTSGEPATLLHNTIVGMAMAMRMVPPGLPWAGIFQGDDMVL&JOB_TITLE=%3EpalmID_u131679&GAPCOSTS=11%201&DATABASE=nr&BLAST_PROGRAMS=blastp&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=0.05&WORD_SIZE=6&MATRIX_NAME=BLOSUM62&COMPOSITION_BASED_STATISTICS=2&PROG_DEFAULTS=on&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NEW_VIEW=on&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML

or just swap out <palmID_uXXXXX> and

https://blast.ncbi.nlm.nih.gov/Blast.cgi?

PAGE_TYPE=BlastSearch&USER_FORMAT_DEFAULTS=on&

SET_SAVED_SEARCH=true&PAGE=Proteins&PROGRAM=blastp&

QUERY=<SEQUENCE>&

JOB_TITLE=<palmID_uXXXXX>&

GAPCOSTS=11%201&DATABASE=nr&BLAST_PROGRAMS=blastp&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=0.05&WORD_SIZE=6&MATRIX_NAME=BLOSUM62&COMPOSITION_BASED_STATISTICS=2&PROG_DEFAULTS=on&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NEW_VIEW=on&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML

@lukepereira
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I'll add the BLAST linkout in a separate PR

@lukepereira lukepereira merged commit 69e4dcd into main Apr 5, 2023
@lukepereira lukepereira deleted the add-geo-to-explorer branch April 5, 2023 16:59
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2 participants