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Updating Phenotype DB with updated SQL tables #484

Merged
merged 53 commits into from
May 31, 2024
Merged

Updating Phenotype DB with updated SQL tables #484

merged 53 commits into from
May 31, 2024

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orzut
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@orzut orzut commented May 14, 2024

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vlagrassa added 30 commits April 24, 2024 13:33
@vlagrassa
Add launch config for POPULATE_PHENOTYPES_DATABASE
6f3df24
@vlagrassa
Add trait display names to Google Sheet > GCP db op
46e2e32
@vlagrassa
Add trait display names to datastore entity class
f066a1b
@vlagrassa
Better fallback behavior for display name
5a00d1f
@vlagrassa
Display tags column as flex-row
1663022 
Fixes rendering error if tags list is shorter than other columns (height-wise)
@vlagrassa
Render empty table cell if no short description
68e4ee6
@vlagrassa
Remove unused "label" field from trait report & link with "View Repor…
2f30540 
…t" col
@vlagrassa
Move trait multiline HTML to new utils file
0e93036
@vlagrassa
Render trait display name in reports page w new macro
27af180
@vlagrassa
Move trait JSON query to util function
e6977d7
@vlagrassa
When selecting trait, query info from database directly
ff0756e 
Replaces ad-hoc object construction with a structured query.  This is the same query we run to fill out the offcanvas sidebar.

Removes `data-description` and `data-species` fields from table rows, since we're now looking this information up in the database directly.
@vlagrassa
Render trait display name in trait selectors
948f914
@vlagrassa
Remove repeat listings for display name fields
ed37d45
@vlagrassa
Reorganize TraitFile props a bit
9278b1c
@vlagrassa
Render trait display names in graph axes
2c44450
@vlagrassa
Move report list individual tool cols to Jinja
f72fbf2 
Store as Jinja dict linked to tool bp name. Rendered with macros.
@vlagrassa
Cache trait display names in report objects
f1615ce 
Adds new class method for `PhenotypeReport` to recompute all cached names.
@vlagrassa
Render trait display names in reports list w custom renderer
6b49f96
@vlagrassa
Fix initial trait none check (again)
9538026
@vlagrassa
Sort out PhenotypeReport trait name fields (see desc)
e46371d 
- Replace `trait_{n}_name` with `trait_{n}_name_caendr`
- Compute display name(s) when creating new report & in the recompute function
- Now use `trait_{n}_name_display` directly to render report page
@vlagrassa
Render report axis labels with styling (bold, italics, etc)
40a8dcf
@vlagrassa
Add DbOp for recomputing cached phenotype report display names
3c7d1e3
@vlagrassa
Set full CaeNDR trait name as display name for Zhang traits
6577a83
@vlagrassa
Use trait display names in offcanvas header
bb48389
@vlagrassa
Fix: render axis labels as HTML in single-trait report
315f0db
@vlagrassa
Fix: move display name computation to Trait & use to initialize Zhang…
18e1538 
… trait in selector properly
@vlagrassa
Set expiration policy for subscription to never
6e1f4e1
@vlagrassa
Move strain labels to first element of result tuples
c7f0734 
This matches the intended CSV/TSV format, where the strain name is the first column, and the phenotype trait measurements are subsequent columns
@vlagrassa
Add TSV download route for phenotype report
0223e86
@vlagrassa
Add code to download SVGs
02b438d
vlagrassa and others added 19 commits April 24, 2024 13:36
@vlagrassa
Show download buttons
7cb18d7
@vlagrassa
Connect SVG download buttons to download function
a9fbb09
@vlagrassa
Fix indentation
595a4ab
@vlagrassa
Add download as PDF button
cbe9c19
@natalieroman
Changed PDF icon and changed copy
39cd76f
@natalieroman
Removed custom no-print css classes and replaced with Bootstrap no pr…
7eee7cc 
…int classes
@natalieroman
Fixed height of chart container to show ranked barplot "download svg"…
ce9a2bf 
… button
@vlagrassa
Check Google Sheet columns before parsing rows
15e1553
@vlagrassa
Fix: trait lookup request data
6ba326d
@vlagrassa
Flash error message if trait metadata request fails
9080429
Merge remote-tracking branch 'refs/remotes/origin/development' into d…
35d94be 
…evelopment
Merge remote-tracking branch 'origin/development' into development
25e2382
Fixing the POST request for trait details, adding off-canvas header ID
daf5913
Changing trait_name -> trait_id when fetching trait details
a01dde6
Updating Phenotype metadata parsing function - setting dataset correctly
874d050
Passing trait_id for zhang traits in analyze link()
c592c25
Updating display name for zhang files
5b40e07
Update module version of db_operations
758d91d
Adding bleach module to db_operations
21c6441
@orzut orzut requested a review from r-vieira May 14, 2024 20:02
r-vieira
r-vieira approved these changes May 31, 2024
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approved

@r-vieira r-vieira merged commit e39ec56 into development May 31, 2024
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@r-vieira r-vieira deleted the fix/phenotype-db branch May 31, 2024 15:26
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@r-vieira r-vieira r-vieira approved these changes

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4 participants
@orzut @r-vieira @vlagrassa @natalieroman