8000 Restore local database and fix bugs by GopiGugan · Pull Request #520 · PoonLab/covizu · GitHub
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Restore local database and fix bugs #520

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Merged
merged 43 commits into from
Apr 10, 2024
Merged

Restore local database and fix bugs #520

merged 43 commits into from
Apr 10, 2024

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GopiGugan
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@GopiGugan GopiGugan commented Mar 21, 2024 •
edited
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SandeepThokala and others added 30 commits July 3, 2023 23:08
@SandeepThokala
Creating a temporary database for #485
73b0953
@SandeepThokala
Adding features table.
bbd1b00
@SandeepThokala
Creating index on fvecs column
26147cd
@SandeepThokala
Required changes for apply_features function #488
7d91fac
@SandeepThokala
Removing comma separated concatenation logic #485
3a4536e
@SandeepThokala
sqlite to postgresql, try except block for full db
c0cb581
@SandeepThokala
Replicating changes from 20644fc and 0254ac4
a1c5f3b
@SandeepThokala
adding index on qname column
867dbe4
@SandeepThokala
Fixing diffs and missing retreived as lists
d90b272
@SandeepThokala
Added psycopg2 to dependencies
bc7c35b
@SandeepThokala
Adding steps for postgresql installation
2f372b5
@GopiGugan
Merge branch 'master' into dev
0b79398
@GopiGugan
Merge branch 'master' into dev
c18c24e
@GopiGugan
Create postgres database if it doesn't exist
bef0040
@GopiGugan
Merge branch 'dev' into iss485
bbdbff7
@GopiGugan
Update PostgreSQL Installation instructions
882db83
@ArtPoon
Merge pull request #501 from PoonLab/iss485
661ce10 
Iss485 - backend database
@GopiGugan
Make database to extract features optional #508
3807bb0
@GopiGugan
Merge branch 'master' into dev
0302592
@GopiGugan
Update Dockerfile for backend environment
f04d492
@GopiGugan
Add tables to store clustering results #493
657120c
@ArtPoon
Merge pull request #510 from PoonLab/iss493
2c3e755 
Store cluster results in a database
@GopiGugan
Update frontend Dockerfile to copy subdirectories #511
8b78709
@GopiGugan
Update docker instructions
024cf45
@GopiGugan
Update batch.py to upload xbbtree.nwk
1ea93f2 
Upload xbbtree.nwk to epicov folder on the web server
@GopiGugan
Fix issue with drawing time-scaled tree #512
561a6f3
@GopiGugan
Update tooltip #512
3a8d4dd
@ArtPoon
removed default clock setting to 8e-4; use XBB sequence as outgroup f…
acf51c3 
…or rooting XBB tree, see Art for FASTA; modified build_timetree() to take outgroup as optional arg; modified retrieve_genomes to load outgroup
@ArtPoon
updating gitignore
6085b07
@GopiGugan
Update earliest date for each display
e1451f5
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GopiGugan commented Mar 25, 2024 •
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Full dry run completed successfully. ~15.8 million sequence records take up ~19 GB of space.

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GopiGugan commented Mar 25, 2024 •
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Checking the following:

  • Search
    • Search by accession number
    • Search by lineage
    • Search by country
    • Search by country (with date filter)
  • Tree filtering
  • Download Time-scaled tree (nwk)
  • Download Time-scaled tree (csv)
  • Download Beadplot (svg)
  • Download Beadplot (nwk)
  • Download mutation list (csv)
  • Beadplot cutoff slider
  • Expanding Beadplot
  • Translated pages
  • Changing the colour of the tree based on divergence, collection date, etc.
  • Left/Right arrow key to move between beads
  • Tooltips
  • Countries/Samples/Mutations tabs are populating the correct information
  • Build front-end database without issues
  • Port front-end change to epicov branch

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There seems to be samples missing when using the database.

150,000 samples without database:
image
150,000 samples using database solution:
image

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Testing was successful

@GopiGugan GopiGugan merged commit 12a9d08 into master Apr 10, 2024
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3 participants
@GopiGugan @SandeepThokala @ArtPoon
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