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TASK-5120 - Port Patch 2.8.5 -> 2.12.0 (XB 1.6.5 - > 1.10.0) #2353

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merged 85 commits into from
Oct 27, 2023
Merged

TASK-5120 - Port Patch 2.8.5 -> 2.12.0 (XB 1.6.5 - > 1.10.0) #2353

merged 85 commits into from
Oct 27, 2023

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juanfeSanahuja
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TASK-5120 - Port Patch 1.6.5 - > 1.10.0

jtarraga and others added 30 commits July 18, 2023 09:47
@jtarraga
app: use the full qualified names for study IDs when calculating pedi…
36027f2 
…gree grap in migration step, #TASK-4770
@j-coll
storage: Fix aggregation on consecutive SNV and INS #TASK-4684
d3d0328
@j-coll
storage: Allow reloading an indexed variant file. #TASK-4684
e360776
@juanfeSanahuja
CLI: Fix CustomFilesCommandExecutor upload problems #4843
7b0a294
@juanfeSanahuja
Prepare next release 2.8.4-SNAPSHOT
a3de4e1
@j-coll
storage: Fix OOME on CatalogStorageMetadataSynchronizer for very larg…
eb632fa 
…e studies #TASK-4853
@j-coll
core: Fix cellbase validator to acknowledge tokens. #TASK-4913
4aeaa83
@j-coll
core: Do not validate empty string tokens. #TASK-4913
368084d
@j-coll
core: Improve exception message #TASK-4913
8abd155
@j-coll
core: Fix validation test #TASK-4913
483d556
@j-coll
Merge pull request #2329 from opencb/TASK-4913
abd4e68 
TASK-4913 - Unable to update cellbase-token
@juanfeSanahuja
Merge branch 'release-2.8.x' into TASK-4843
85644ed
@j-coll
Merge branch 'TASK-4688' into TASK-4688-2.8.4
a270dff
@j-coll
Merge pull request #2335 from opencb/TASK-4688-2.8.4
b596f37 
TASK-4688 - Avoid git.properties collision
@j-coll
storage: Do not modify the input query at VariantStorageEngine::count…
465289a 
… #TASK-4938
@j-coll
server: Fix meta/status cache update. #TASK-4945
759d74d
@j-coll
server: Populate status with async check. #TASK-4945
fedb939
@j-coll
storage: Fix NPE executing SampleIndexDuplicatedVariantsTest tests. #…
60b74ab 
…TASK-5027
@j-coll
Merge pull request #2340 from opencb/TASK-5027
4a38bbd 
TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor
@j-coll
Merge branch 'release-2.8.x' into TASK-4938
ecdcd82
@j-coll
Merge branch 'release-2.8.x' into TASK-4853
df43507
@j-coll
Merge branch 'release-2.8.x' into TASK-4945
04c6213
@j-coll
Merge pull request #2338 from opencb/TASK-4938
d282df8 
TASK-4938 - OpenCGA VariantExport tests sometimes throw a ConcurrentModificationException
@j-coll
Merge pull request #2339 from opencb/TASK-4945
d2cb09a 
TASK-4945 - OpenCGA Status not being updated
@j-coll
storage: Fix NPE at variant-secondary-sample-index with partial famil…
c2bc6c7 
…ies. #TASK-4872
@j-coll
Merge branch 'release-2.8.x' into TASK-4853
9ee46e9
@j-coll
Merge pull request #2324 from opencb/TASK-4853
29104d2 
TASK-4853 - OutOfMemoryError running CatalogStorageMetadataSynchronizer
@pfurio
catalog: improve delete error messages, #TASK-4210
db992c5
@juanfeSanahuja
Merge branch 'release-2.8.x' into TASK-4843
8c4e7a9
@j-coll
storage: Fix NPE when updating cellbase configuration on empty varian…
b11d9a8 
…t storages #TASK-4873
juanfeSanahuja and others added 23 commits October 4, 2023 16:01
@juanfeSanahuja
Merge branch 'release-2.8.x' of github.com:opencb/opencga into releas…
3c386f5 
…e-2.8.x
@juanfeSanahuja
client: Regenerate autogenerated code for release 2.8.4 Xetabase 1.6.5
aa049e3
@juanfeSanahuja
client: Regenerate autogenerated code for release 2.8.4 Xetabase 1.6.5
0049ae6
@juanfeSanahuja
client: Regenerate autogenerated code for release 2.8.4 Xetabase 1.6.5
d42cd6a
@juanfeSanahuja
cicd: undo step by step #TASK-5092
11a7c9d
@juanfeSanahuja
cicd: undo step by step #TASK-5092
7513399
@juanfeSanahuja
cicd: github.ref_name #TASK-5092
146499f
@juanfeSanahuja
cicd: simplify build #TASK-5092
4220c82
@juanfeSanahuja
cicd: simplify build #TASK-5092
cb7bff1
@juanfeSanahuja
cicd: simplify build #TASK-5092
5003c43
@juanfeSanahuja
cicd: added credentials to CLI #TASK-5092
e01b7ff
@juanfeSanahuja
cicd: added credentials to CLI #TASK-5092
b282cd8
@juanfeSanahuja
cicd: added credentials to CLI #TASK-5092
a39f410
@juanfeSanahuja
cicd: added credentials to CLI #TASK-5092
67d4e3d
@juanfeSanahuja
cicd: remove parameter credentials to CLI #TASK-5092
47a4c49
@juanfeSanahuja
cicd: add checkout and remove build #TASK-5092
16e7656
@imedina
cicd: remove inherit
9d056c9
@imedina
cicd: remove event
27253e6
@juanfeSanahuja
Merge branch 'release-2.8.x' into TASK-5092
0bc895f
@juanfeSanahuja
Merge pull request #2351 from opencb/TASK-5092
daabee4 
TASK-5092 - The CICD to delete docker on merge fails
@juanfeSanahuja
Prepare release 2.8.4
7aaab0c
@juanfeSanahuja
portpatch: Updated version to merge develop #TASK-5120
9450f6a
@juanfeSanahuja
Merge branch 'develop' into TASK-5120
5939cf0
@juanfeSanahuja
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Task linked: TASK-5120 Port Patch 1.6.5 -> 1.10.0

@j-coll
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j-coll commented Oct 23, 2023 •
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Merge pull request #2329 from opencb/TASK-4913 @j-coll
Merge pull request #2335 from opencb/TASK-4688-2.8.4 @j-coll
Merge pull request #2340 from opencb/TASK-5027 @j-coll
Merge pull request #2338 from opencb/TASK-4938 @j-coll
Merge pull request #2339 from opencb/TASK-4945 @j-coll
Merge pull request #2324 from opencb/TASK-4853 @j-coll
Merge pull request #2323 from opencb/TASK-4843 @juanfeSanahuja
Merge pull request #2343 from opencb/TASK-4210 @pfurio
Merge pull request #2346 from opencb/TASK-5038 @jtarraga
Merge pull request #2321 from opencb/TASK-4684 @j-coll
Merge pull request #2347 from opencb/TASK-5083 @pfurio
Merge pull request #2342 from opencb/TASK-4872 @j-coll
Merge pull request #2344 from opencb/TASK-4873 @j-coll
Merge pull request #2314 from opencb/TASK-4770 @jtarraga
Merge pull request #2348 from opencb/TASK-4889 @j-coll
Merge pull request #2349 from opencb/TASK-5092 @juanfeSanahuja
Merge pull request #2345 from opencb/TASK-4899 @j-coll
Merge pull request #2351 from opencb/TASK-5092 @juanfeSanahuja

@juanfeSanahuja juanfeSanahuja merged commit eca6390 into develop Oct 27, 2023
8 of 9 checks passed
@juanfeSanahuja juanfeSanahuja deleted the TASK-5120 branch October 27, 2023 16:30
@j-coll j-coll changed the title TASK-5120 - Port Patch 1.6.5 - > 1.10.0 TASK-5120 - Port Patch 2.8.5 -> 2.12.0 (XB 1.6.5 - > 1.10.0) Aug 28, 2024
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5 participants
@juanfeSanahuja @j-coll @jtarraga @pfurio @imedina