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Release v2.0.0 #90

Merged
merged 127 commits into from
Jan 16, 2023
Merged

Release v2.0.0 #90

merged 127 commits into from
Jan 16, 2023

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priesgo
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@priesgo priesgo commented Jan 14, 2023

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priesgo and others added 30 commits October 5, 2022 12:17
@priesgo
update system design diagram
8f2a562
@priesgo
parse host from CVODI-19 Data Portal as it should
c38d07a
@priesgo
avoid writing the configuration in logs multiple times
a9c72fa
@priesgo
log error
eb09e14
@priesgo
change acc by id in the COVID19 data portal API
50e3b98
@priesgo
change acc by id in the COVID19 data portal API
7013ab3
@priesgo
makes sure that run_accession is properly read and add binary search …
beb38bb 
…on sample ids
@priesgo
add search based on python set
900bf9a
@priesgo
set accessor to have infinite retries
0255a46
@priesgo
add logs
c3ecd14
@priesgo
rollbacks the change to use exclusion by coverage based on external c…
114c985 
…overage
@priesgo
fix issue building URL
4da5194
@priesgo
correct logs
8bf01f4
@priesgo
skip pangolin in the pipeline for COVID-19 data portal
8dce0c1
@priesgo
avoid interlock between nodes when waiting for completion
53c3808
@priesgo
avoid interlock between nodes when queueing jobs
a320e67
@priesgo
fix mistake with list...
d3435c8
@priesgo
avoid processing missing pangolin results in C19 processor
342857f
@priesgo
avoid accessor issue with repeated samples in the API
f2955cb
@priesgo
introduce retry on Json parsing from the API
50a23d4
@priesgo
add some logs to COVID-19 Data Portal
e55dd44
@priesgo
query API by months
f5c809b
@priesgo
update COVID19 data portal accessor to query by months
14b448c
@priesgo
fix covid19 data portal accessor
7f80f67
@priesgo
make sure that repeated samples do not stop the whole accessor
8716508
@priesgo
add an alternative pipeline to rephase and reannotate mutations
f5441c1
@priesgo
bump pipeline version
2224e63
@priesgo
add support for complex variants in the data loading
c5cbf3c
@priesgo
include COMPLEX variant type in a drop down
c8d3348
@priesgo
include rephasing option in the COVID19 data portal
1763d01
priesgo and others added 28 commits January 9, 2023 23:36
@priesgo
update figure 03
9e08ff7
@priesgo
update size letters in figure 03
76edd61
@priesgo
update figure 04
7674cb7
@priesgo
rollbacks session in the dashboard after DB error, this avoids a dash…
b6428f8 
…board restart
@priesgo
Merge pull request #84 from TRON-Bioinformatics/rollback-session-afte…
5185585 
…r-error

Rollback session after error
@priesgo
include teaser information for every tab
ec0f3d1
@priesgo
#80 change values of VAF filter
3e6a333
@priesgo
fix issue with intrahost query and samples without collection_date
3a1072b
@priesgo
include supplementary screenshots
cb872f3
@johausmann
Updated raw SQL queries in queries.py to use SQLAlchemy text clause o…
f1d9b46 
…bjects and parameter substitution with placeholders

Added additional colors from ColorBrewer palette to improve plots in mutation stats tab
@johausmann
Removed quotation mark from query that caused unit test to fail
d8ec9f5
@priesgo
avoid trying to fetch co-occurrence matrix in C19DP
781765c
@priesgo
edit the download tab to adapt to new classification of mutations
22c64cd
@priesgo
try to fix style issue reported by codacy
66db948
@priesgo
try to fix style issue reported by codacy... again
ac46a7d
@priesgo
add word cloud + summary to overview page
1fa3f50
@priesgo
bump version
18a9986
@priesgo
Merge pull request #87 from TRON-Bioinformatics/update_sql_queries
cc4460c 
Update sql queries and extend mutation color palette
@priesgo
remove commented code
2b5212b
@priesgo
Merge pull request #83 from TRON-Bioinformatics/update-screenshots
c191255 
Update screenshots
@priesgo
some updates to the documentation
a09fd13
@priesgo
add word cloud to readme
a7871f0
@priesgo
Merge pull request #88 from TRON-Bioinformatics/update-docs
391ce83 
Update docs
@priesgo
fix bash escaped variables
157d8d5
@priesgo
fix "could be a function" issues from codacy
e7beee9
@priesgo
avoid too complex method
d45deb0
@priesgo
fix vcf loader + add missing storage of low quality clonal variants...
b3c106e
@priesgo
Merge pull request #91 from TRON-Bioinformatics/fix-codacy-issues
9a55f64 
Fix codacy issues
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codecov bot commented Jan 16, 2023

Codecov Report

❗ No coverage uploaded for pull request base (main@417a467). Click here to learn what that means.
Patch has no changes to coverable lines.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main      #90   +/-   ##
=======================================
  Coverage        ?   83.17%           
=======================================
  Files           ?       46           
  Lines           ?     4238           
  Branches        ?        0           
=======================================
  Hits            ?     3525           
  Misses          ?      713           
  Partials        ?        0

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@priesgo priesgo merged commit 83a4469 into main Jan 16, 2023
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@priesgo @johausmann