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TADs are missing from variant data in 20210728 and 20210728b #625

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holtgrewe opened this issue Aug 26, 2022 · 2 comments · Fixed by #623
Closed

TADs are missing from variant data in 20210728 and 20210728b #625

holtgrewe opened this issue Aug 26, 2022 · 2 comments · Fixed by #623
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@holtgrewe
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holtgrewe commented Aug 26, 2022

Describe the bug
The TAD annotation data is missing in the prebuilt databases for anthenea.

To Reproduce
In dbshell

select * from genomicfeatures_tadset;
 id | sodar_uuid | release | name | version | title | comment 
----+------------+---------+------+---------+-------+---------
(0 rows)

Expected behavior
The TAD data should be imported in the database.

Screenshots
N/A

Additional context

@holtgrewe holtgrewe added the bug Something isn't working label Aug 26, 2022
@holtgrewe
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holtgrewe commented Aug 26, 2022

Root Cause Analysis
The import_tables.py command interprets the always None output of _create_import_info_record as a boolean and thus never imports TADs. The same is true for gene intervals.

@holtgrewe holtgrewe added this to the bollonaster-2.0.0 (dev) milestone Aug 26, 2022
@holtgrewe holtgrewe changed the title TADs are missing from variant data TADs are missing from variant data in 20210728 and 20210728b Aug 26, 2022
@holtgrewe
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holtgrewe commented Aug 26, 2022

Resolution Proposal
Simply remove the if constructs from import_tables.py.

Affected Components
VarFish server

Affected Modules/Files
importer/management/commands/import_tables.py

Required Architectural Changes
None

Required Database Changes
None

Backport Possible?
Not necessary, SVs experimental in anthenea.

Resolution Sketch
See above.

@holtgrewe holtgrewe linked a pull request Aug 26, 2022 that will close this issue
holtgrewe added a commit that referenced this issue Aug 26, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 26, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 29, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Aug 29, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Sep 6, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Sep 6, 2022
Related-Issue: #625
Closes: #625
Projected-Results-Impact: none
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