TASK-5387 - Add Polygenic Scores (PGS) - #697

Open

jtarraga wants to merge 187 commits into

Commits on Dec 18, 2023

lib: download polygenic scores (PGS), #TASK-5406, #TASK-5387
jtarraga
committed
278fdbd

Commits on Dec 19, 2023

lib: update the build command to support PGS data, #TASK-5407, #TASK-5387
jtarraga
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d327c47
lib: copy PGS version file from download to generated json directory, #TASK-5407, #TASK-5387
jtarraga
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fd6ac92
lib: update the load command to support PGS data, #TASK-5410, #TASK-5387
jtarraga
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53aa886

Commits on Dec 22, 2023

Commits on Jan 2, 2024

lib: add support for annotating using PGS, #TASK-5411, #TASK-5387
jtarraga
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314786d

Commits on Jan 3, 2024

Commits on Jan 21, 2024

download: gwas catalog fixes
imedina
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6346c97

Commits on Jan 29, 2024

lib: take into account the NumberFormatException, #TASK-5407, #TASK-5387
jtarraga
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d343315

Commits on Feb 2, 2024

lib: improve PGS builder, #TASK-5407, #TASK-5387
jtarraga
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268f591
lib: remove System.out in PGS builder, #TASK-5407, #TASK-5387
jtarraga
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5972c15

Commits on Feb 7, 2024

Commits on Mar 1, 2024

Merge branch 'TASK-5392' into TASK-5564
imedina
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19368e6
Update configuration.yml
imedina
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89264c2

Commits on Mar 7, 2024

Commits on Mar 8, 2024

Commits on Mar 22, 2024

lib: improve conservation downloader by updating versions from config file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564
jtarraga
committed
f308f25

Commits on Mar 28, 2024

lib: update regulation download manager, and the configuration file, to take into account the version for miRBase and miRTarBase, #TASK-5775, #TASK-5564
jtarraga
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2e6e895

Commits on Apr 3, 2024

Commits on Apr 4, 2024

lib: fix Gwas Catalog builder for clinical variants, #TASK-5776, #TASK-5564
jtarraga
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df0f1e0

Commits on Apr 5, 2024

lib: refactor code by changing the DownloadProperties.URLProperties, #TASK-5775, #TASK-5564
jtarraga
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d4cba15

Commits on Apr 12, 2024

lib: update CellBase downloaders, #TASK-5775, #TASK-5564
jtarraga
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e18506b

Commits on Apr 15, 2024

core: update CellBase configuration file, #TASK-5775, #TASK-5564
jtarraga
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69a58bf

Commits on Apr 18, 2024

Commits on Apr 19, 2024

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Commits on May 10, 2024

Commits on May 11, 2024

Commits on May 15, 2024

Commits on May 16, 2024

lib: improve gene downloader by taking into account the manually downloaded files and creating the data source version files, #TASK-5575, #TASK-5564
jtarraga
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a8a047c

Commits on May 17, 2024

Commits on May 18, 2024

lib: refactor PGS builder to solve the RocksDB issue, #TASK-5407, #TASK-5387
jtarraga
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910ffd3

Commits on May 20, 2024

lib: improve PGS builder by speeding-up RocksDB, #TASK-5407, #TASK-5387
jtarraga
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3939ac3

Commits on May 27, 2024

Commits on Jun 22, 2024

Merge branch 'develop' into TASK-5564
imedina
committed
4d965d7

Commits on Jun 23, 2024

lib: add hpo filter to GeneQuery
imedina
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fc65d14

Commits on Jul 2, 2024

Commits on Jul 3, 2024

test: update JUnit tests, #TASK-5564
jtarraga
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c8e719a
cicd: update task.yml to deploy cellbase-builder docker, #TASK-5564
jtarraga
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19efdf4

Commits on Jul 4, 2024

Commits on Jul 5, 2024

Add VariationDownloader
imedina
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0a6a84f
Add VariationDownloader
imedina
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3dcad47

Commits on Jul 8, 2024

Commits on Jul 9, 2024

lib: add variation to the EtlCommons dataVersionFilenamesMap, #TASK-5575, #TASK-5564
jtarraga
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2b226fe

Commits on Jul 22, 2024

Merge branch 'develop' into TASK-5564
jtarraga
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510819c

Commits on Jul 23, 2024

Commits on Jul 24, 2024

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Commits on Jul 26, 2024

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Commits on Aug 5, 2024

Commits on Aug 6, 2024

Commits on Aug 8, 2024

Commits on Aug 9, 2024

lib: fix the function to save status and message of the downloaded files; improve summary log and update downloader managers according to these changes, #TASK-5575, #TASK-5564
jtarraga
committed
1f3572c

Commits on Aug 10, 2024

Merge branch 'develop' into TASK-5564
jtarraga
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6056655
core: add dbSNP in config file (removed after merging), #TASK-5564
jtarraga
committed
a8d6368

Commits on Aug 13, 2024

Merge branch 'TASK-5564' into TASK-5387
jtarraga
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2950c0e

Commits on Sep 12, 2024

lib: limit WriteBatch for number of items, #TASK-5407, #TASK-5387
jtarraga
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2889192

Commits on Oct 1, 2024

lib: improve PGS builder, #TASK-5407, #TASK-5387
jtarraga
committed
8c8a4ea
lib: fix sonnar issues, #TASK-5407, #TASK-5387
jtarraga
committed
28a57ba