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TASK-6357 - Port Patch 1.10.5 -> 2.2.0 #2463

Merged
merged 145 commits into from
Jun 18, 2024
Merged

TASK-6357 - Port Patch 1.10.5 -> 2.2.0 #2463

merged 145 commits into from
Jun 18, 2024

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juanfeSanahuja
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TASK-6357 - Port Patch 1.10.5 -> 2.2.0

pfurio and others added 30 commits February 22, 2024 11:45
@pfurio
catalog: increment sample version when new file is added, #TASK-5668
b01934d
@j-coll
storage: Do not fail on missing trios. Do not execute family-index on…
6757c74 
… each variant-index. #TASK-2306
@pfurio
catalog: calls to updates are always sent to the DBAdaptors, #TASK-5668
41fb753
@pfurio
Merge branch 'release-2.12.x' into TASK-5668
3cfd850
@pfurio
catalog: implement file move in MongoDBAdaptor, #TASK-5716
d095e97
@juanfeSanahuja
Prepare next release 2.12.4-SNAPSHOT
85ff3e4
@jtarraga
analysis: improve alignment and coverage index by taking into account…
060c26f 
… the blob storage behaviour #TASK-5858
@j-coll
storage: Do not use cellbase-client mixin converter. #TASK-5563
ed003a5
@j-coll
storage: Accept non-normalized variants when filtering by ID or XREF.…
a37f1b4 
… #TASK-5877
@j-coll
storage: Do return invalid cohort stats #TASK-5876
16d0a62
@pfurio
Merge branch 'release-2.12.x' into TASK-5668
c51cf26
@pfurio
Merge branch 'release-2.12.x' into TASK-5716
85767cf
@j-coll
Merge branch 'release-2.12.x' into TASK-2306
e3d180e
@j-coll
Merge pull request #2406 from opencb/TASK-2306
1794d54 
TASK-2306 - Family index error is raised when variant-secondary-sample-index is run for non-family samples
@jtarraga
tests: add Junit tests, #TASK-5858
57fbbe1
@jtarraga
client: generate clients, #TASK-5858
c550fd3
@pfurio
Merge branch 'release-2.12.x' into TASK-5716
d0f46fe
@jtarraga
core: fix Integer conversion, #TASK-5858
f26c9e8
@jtarraga
analysis: remove jobID check from OpenCgaTool, #TASK-5858
1e5f15b
@pfurio
catalog: replace status.name indexes, #TASK-5796
7756021
@pfurio
Merge branch 'release-2.12.x' into TASK-5668
8d7d4e7
@pfurio
Merge pull request #2409 from opencb/TASK-5668
0b14a2e 
Linked file not shown under sample when retrieving an Individual
@jtarraga
analysis: take into account the clinical analysis type before running…
29e75fe 
… the Exomiser analysis; and add JUnit test, #TASK-5603
@jtarraga
tests: improve JUnit tests, #TASK-5603
ac07643
@jtarraga
app: fix Exomiser parameters, #TASK-5603
dbd516f
@jtarraga
clients: generate clients, #TASK-5603
339c0cf
@j-coll
pom: Add log4j2-test.xml #TASK-5603
f9f4051
@pfurio
Merge branch 'release-2.12.x' into TASK-5796
28f4852
@pfurio
Merge branch 'release-2.12.x' into TASK-5716
fe319af
@pfurio
Merge pull request #2410 from opencb/TASK-5716
1b6cd53 
TASK-5716 - Renaming a file is not reflected on the list of files contained by samples
juanfeSanahuja and others added 23 commits May 14, 2024 19:33
@juanfeSanahuja
Merge pull request #2448 from opencb/TASK-6231
422cfb8 
TASK-6231 - Port Patch 1.10.4.1 -> 1.10.5
@juanfeSanahuja
Merge branch 'release-2.12.x' into TASK-464
42d04b9
@juanfeSanahuja
Merge pull request #2439 from opencb/TASK-464
ff2b0c8 
TASK-464 - Login - Forgot Password option
@j-coll
storage: Fix last split parse at SampleIndexTableRecordReader #TASK-6005
c668143
@j-coll
storage: Fix return annotation from sample data. Fix test. #TASK-6005
f6b73fe
@j-coll
storage: Mark symbolic inversion as supported. #TASK-6240
9c31131
@j-coll
app: Fix migration illegal_concurrent_file_loadings. #TASK-6078
8eb0843
@j-coll
Merge pull request #2450 from opencb/TASK-6240
37b1618 
TASK-6240 - Symbolic inversions <INV> not indexed during data load
@j-coll
Merge pull request #2449 from opencb/TASK-6005
0e5a9e6 
TASK-6005 - Error loading variants : "Row length 45522 is > 32767"
@j-coll
Merge pull request #2443 from opencb/TASK-5888
9233577 
TASK-5888 - REST Error : 414 URI too large and 431 Header too large
@j-coll
Merge branch 'release-2.12.x' into TASK-6078
c0e914b
@j-coll
core: Register new index status INVALID in catalog #TASK-6078
214f963
@j-coll
app: Synchronize storage-catalog status after running migration. #TAS…
17129ab 
…K-6078
@j-coll
analysis: Allow force variant file remove. #TASK-6078
53b67f0
@j-coll
Merge branch 'TASK-6078' of github.com:opencb/opencga into TASK-6078
e1500e7
@j-coll
Merge pull request #2442 from opencb/TASK-6078
c74ea8a 
TASK-6078 - Concurrent variant-index from same sample without --load-multi-file-data
@j-coll
app: Remove "manual=true" from migration illegal_concurrent_file_load…
bdfa4d6 
…ings #TASK-6305
@j-coll
Merge pull request #2456 from opencb/TASK-6305
98cbe6f 
TASK-6305 - Error executing migrations. "requires additional parameters and need to be run manually."
@juanfeSanahuja
cicd: Update action version to test for compatibility with test and r…
373fe21 
…elease process #TASK-6264
@juanfeSanahuja
Prepare release 2.12.5
e5dd72f
@juanfeSanahuja
Prepare merge #TASK-6357
4210acd
@juanfeSanahuja
Merge branch 'develop' into TASK-6357
01c2201
@pfurio
catalog: fix catalog tests failing, #TASK-6357
60279a1
@juanfeSanahuja juanfeSanahuja requested a review from pfurio June 10, 2024 08:16
@juanfeSanahuja juanfeSanahuja requested a review from pfurio June 18, 2024 16:03
@juanfeSanahuja juanfeSanahuja merged commit 9383c2f into develop Jun 18, 2024
5 of 6 checks passed
@juanfeSanahuja juanfeSanahuja deleted the TASK-6357 branch June 18, 2024 17:03
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@juanfeSanahuja @pfurio @j-coll @jtarraga @imedina