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Prepare for SweFreq v26 #598

Merged
merged 147 commits into from
Aug 26, 2019
Merged

Prepare for SweFreq v26 #598

merged 147 commits into from
Aug 26, 2019

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talavis
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@talavis talavis commented Aug 22, 2019

Describe the pull request:

  • Bug fix
  • Functional change
  • New feature
  • Code cleanup
  • Build system change
  • Documentation change
  • Language translation

Pull request long description:

Updates to requirements (versions), new tests (mainly import), style changes (pylint), and bug fixes.

talavis and others added 30 commits June 27, 2019 09:28
@talavis
Update requirements for importer
519e93d
@viklund
Merge pull request #577 from NBISweden/feature/import-requirements
57b1e72 
Update requirements for importer
@MalinAhlberg
Rename data.mate to mates
88d6455
@talavis
Merge pull request #578 from NBISweden/feature/rename_mate
5dd4ecf 
Rename table mate to mates
@talavis
Replace old error management with new the new errors for coverage.
6154963
@talavis
Remove unnecessary whitespace.
7613776
@viklund
Merge pull request #581 from NBISweden/bugfix/transcript-not-found
36515a7 
Bugfix/transcript not found
@talavis
More logging for Elixir login errors to allow debugging.
dc1a4b7
@viklund
Merge pull request #582 from NBISweden/feature/log-more-elixir-error
ddafa9d 
More logging for Elixir login errors to allow debugging.
@talavis
Prepare travis script
f444aab
@talavis
Dataset etc sql file
2fc6553
@talavis
Vcf file from Beacon testing as dataset 2_1.
a8ae8c6
@talavis
Coverage data for dataset 1_1 and 1_2.
50376b6
@talavis
Dataset1_1 and Dataset1_2 vcf files.
c50fc84
@talavis
Relevant genes/transcripts from Gencode 19 extracted.
f99e1e4
@talavis
Relevant genes extracted from dbNSFP2.9_gene.
3f7148f
@talavis
Reference database contents added.
08aaaef
@talavis
Add import testing to travis.
e3c8c25
@talavis
Make sure cause is chained when exception is raised after catching an…
24419b0 
… exception.
@viklund
Merge pull request #583 from NBISweden/feature/raise-from
f059660 
Make sure exception cause is chained
@talavis
Simplify diff reporting in Travis.
fa3654c
@talavis
Update reference data.
8826fa7
@talavis
Ignore id column as it may wary due to dictionaries.
e8e6fd3
@talavis
Fix incorrect coverage file names.
3510c8e
@MalinAhlberg @talavis
Test beacon counts
61fe7f1
@MalinAhlberg @talavis
Add test for parsing mates (breakends)
536c771
@talavis
Test the code used for batches as well.
e9a6452
@talavis
Use small batch for references as well.
39213d8
@viklund
Merge pull request #584 from NBISweden/feature/test-importer
8403714 
Add basic testing for import
@talavis
Sort approved users by their application date.
8af6f08
talavis and others added 28 commits August 21, 2019 08:34
@talavis
Use functions for parsing, simplify code.
c2693e5
@talavis
Merge pull request #594 from NBISweden/variant-importer-refactor
d621acc 
Split parse rows from insert_variants
@talavis
Add tests for schema and country list.
415a436
@talavis
No longer necessecary to handle exceptions as they are managed within…
4c16acb 
… get_dataset_version().
@MalinAhlberg
Make methods private, make function static methods
890a625
@talavis
Don't crash GetVariant.get() if there is a dataset with only non-rele…
08fc825 
…ased versions.
@talavis
Test GetDataset.
c7bfa94
@talavis
Add test dataset and versions to test unreleased versions.
96042ad
@MalinAhlberg
order helpers alphabetically
a81166b
@MalinAhlberg
Remove newlines
bf7d48a
@MalinAhlberg
Fix docstring
a4e2b45
@MalinAhlberg
fix word order
053e611
@talavis @MalinAhlberg
Use filter instead of a list comprehension.
ca424d2 
Co-Authored-By: MalinAhlberg <ahlberg.malin@gmail.com>
@talavis
Fix docstring style.
1058bd3
@talavis
Check no longer needed as its handled by the earlier exception.
0d14839
@talavis
Don't handle exceptions that are not raised by the function.
b07993f
@talavis
Add negative tests for coverage pos and variant.
2c8e251
@talavis
More bad request tests for coverage pos.
811c070
@MalinAhlberg
docstyling
82691ac
@MalinAhlberg
Merge pull request #596 from NBISweden/feature/code_cleanup
688ebf6 
Some more bnd code cleanup
@talavis
Merge pull request #597 from NBISweden/feature/code_cleanup
61cc6c6 
BND docstrings
@talavis
Merge pull request #595 from NBISweden/testing/extended
8172f2e 
Increase test coverage
@talavis
eslint fixes.
a012d6e
@talavis
Fix bad f-string.
7d22eaa
@talavis
Fix spelling error (attachement).
ac8e1d8
@talavis
Add filename check to download tests.
ea3bb87
@talavis
Merge pull request #600 from NBISweden/fix-fstring
f0ada55 
Fix bad f-string when downloading file
@talavis
Merge pull request #599 from NBISweden/eslint-fixes
5b836d9 
eslint fixes
@talavis talavis merged commit 575f066 into master Aug 26, 2019
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@MalinAhlberg MalinAhlberg MalinAhlberg approved these changes

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3 participants
@talavis @MalinAhlberg @viklund