Merge 2.2.0 changes into master - #402

Merged

bcarlsenca merged 1048 commits into

Aug 22, 2025

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Commits on Jan 31, 2025

reindex not index
peter-va
committed
472f3c4
add tests
peter-va
committed
f84e688
fix test and switch to lowercase
peter-va
committed
58978f4
bug fix for audit counts
peter-va
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b15cdba
only major events cause new audit indexing
Peter Van Ausdeln
committed
a663236

Commits on Feb 4, 2025

TYPO: fix port to use for opensearch
bcarlsenca
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3618c2e
Merge branch 'master' into develop
bcarlsenca
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0fa875f
Merge branch 'develop' into develop-2.1
bcarlsenca
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35a15c7
Dss/evsrestapi 999 fhir r4 testing (#317)
shapirod2
authored
4e90551
EVSRESTAPI-550: fix logic for clearing old maps when loading new ones (#321)
bcarlsenca
authored
f8fd41a
RDFBROWSER-526: ensure max result window for evs_mappings is set high enough (#318)
bcarlsenca
authored
e5449c4
feedback, remove controller and change tests
peter-va
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155f9bb
edits to error catching
peter-va
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4913513
spotless formatting
peter-va
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c83561f
Merge pull request #322 from NCIEVS/PVA/EVSRESTAPI-542-index-terminology-runtimes
peter-va
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4902d4a
Merge branch 'develop-2.1' into PVA/EVSRESTAPI-539-add-pediatric-subsets
peter-va
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3ab83aa

Commits on Feb 5, 2025

move ncit.json for test
peter-va
committed
1164c7a
Merge pull request #319 from NCIEVS/PVA/EVSRESTAPI-539-add-pediatric-subsets
peter-va
authored
164c5ab

Commits on Feb 6, 2025

add log level to audit object
peter-va
committed
403c3d8
add details to audit object
peter-va
committed
3f8526a
add new constructor
peter-va
committed
e6e8cc4
add some audits to errors
peter-va
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7674cec
add more exception logging
peter-va
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dfef52f
add API error audit logging
peter-va
committed
4a51037

Commits on Feb 7, 2025

remove some audits and exceptions
peter-va
committed
5ff3e50
fix errors
peter-va
committed
52de595
create new audit function
peter-va
committed
08a4f09
new audit to baseController
peter-va
committed
c5c1c86
add more changes to audit
peter-va
committed
b325e23
block json-smart vulnerability
Peter Van Ausdeln
committed
e930f14
more audit changes
peter-va
committed
0eabaf5
rework the rest of the audits
peter-va
committed
61fb0dc

Commits on Feb 8, 2025

Jena changes for 2.1 release
akuppusamy-wci
authored
9924cfb
feedback, remove more audits and exception catching
peter-va
committed
61e4483
remove another try-catch
peter-va
committed
b6effa8
comment clarification
peter-va
committed
f47cbfd

Commits on Feb 10, 2025

Small edits and fix warnings
bcarlsenca
committed
6882917
spotless
Peter Van Ausdeln
committed
43ae96c
Merge pull request #325 from NCIEVS/PVA/EVSRESTAPI-542-add-error-tracking-audits
peter-va
authored
d1316f1

Commits on Feb 12, 2025

handle merge
bcarlsenca
committed
9d4a634
EVSRESTAPI-554: fixes to reindex.sh
bcarlsenca
committed
5448cb7

Commits on Feb 13, 2025

put back to perl
bcarlsenca
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888150a
dbs
bcarlsenca
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a05fb51
Fix up config
bcarlsenca
committed
785adde
fix typo
bcarlsenca
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b1c757c
Fixes to script for error handling
bcarlsenca
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2b3c62d
postman script runs in reindex.sh for each terminology with a collection
Peter Van Ausdeln
committed
07129e1
who's running this outside of src/main/bin
Peter Van Ausdeln
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e88ba14
try more robust way
Peter Van Ausdeln
committed
da745dc

Commits on Feb 14, 2025

Merge branch 'bac/fix-reindex' into pva/EVSRESTAPI-557-postman-content-qa
peter-va
committed
bb3b6bf
Adding Dockerfile to run Jena locally (#326)
akuppusamy-wci
authored
c6b261c
fix syntax crash
peter-va
committed
474c204
revert to old way
peter-va
committed
5db91d6
tweaks to psotman script + add for ncim terminologies
Peter Van Ausdeln
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2723a1d
standardize hidden urls
Peter Van Ausdeln
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e39beec

Commits on Feb 19, 2025

go content qa
peter-va
committed
39b4edd
Merge branch 'pva/EVSRESTAPI-557-postman-content-qa' of https://github.com/NCIEVS/evsrestapi into pva/EVSRESTAPI-557-postman-content-qa
peter-va
committed
4e40d4a
hgnc postman
peter-va
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0879b5f
EVSRESTAPI-554: more work to get jena changes deployed and running on dev (#327)
bcarlsenca
authored
e6d86f0
more sampling
peter-va
committed
b998117
more content qa
peter-va
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2522f8f
default to production API
peter-va
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1fbfa2a
add postman output folder to gitignore
peter-va
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82fe3c0
comment out postman qa from ncim.sh until ncim content qa ready
peter-va
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98a469b
Merge branch 'develop' into pva/EVSRESTAPI-557-postman-content-qa
peter-va
committed
ab02e8e

Commits on Feb 20, 2025

add trailing slash fail tests
peter-va
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de2b171
spotless
peter-va
committed
639660e
Merge pull request #330 from NCIEVS/PVA/EVSRESTAPI-trailing-slashes-tests
peter-va
authored
af98794
tweaks to script and content qa
peter-va
committed
b54ff8a
move orig directory line
peter-va
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be8b127
Merge pull request #328 from NCIEVS/pva/EVSRESTAPI-557-postman-content-qa
peter-va
authored
55ef98c

Commits on Feb 24, 2025

shouldn't end devreset if we dont find a collection
peter-va
committed
876f09e
Merge pull request #331 from NCIEVS/PVA/devreset-fix
peter-va
authored
81a4d88

Commits on Feb 28, 2025

EVSRESTAPI-562: remove stardog and get devreset working with jena (#332)
bcarlsenca
authored
48bde10

Commits on Mar 5, 2025

EVSRESTAPI-557: temporarily remove the postman handling from reindex becuase it enforces requirements that may not be true in local or dev deployments
bcarlsenca
committed
c45f739

Commits on Mar 18, 2025

Commits on Mar 28, 2025

Update swagger-ui in README.md
bcarlsenca
committed
a0fe7f1

Commits on Mar 31, 2025

Merge branch 'master' into develop
bcarlsenca
committed
0c84fd0
Merge branch 'master' into develop
bcarlsenca
committed
8111f18
Merge develop 2.2 (#341)

bcarlsenca
and
shapirod2
authored
771ac6b
Dss/evsrestapi 521 (#338)

shapirod2
and
bcarlsenca
authored
272734a

Commits on Apr 3, 2025

EVSRESTAPI-597: update docker image to 5.3.0
bcarlsenca
committed
bcae11e

Commits on Apr 4, 2025

EVSRESTAPI-597: update docker image to 5.3.0
bcarlsenca
committed
80f647f
HOTFIX: extend timeout on axioms loading to 15 min
bcarlsenca
committed
6087f8a

Commits on Apr 8, 2025

make swagger links to github open in new tab automatically
peter-va
committed
f27ce58
spotless
peter-va
committed
e92a583
Merge pull request #344 from NCIEVS/PVA/RDFBROWSER-552-link-to-sdk-in-new-tab
peter-va
authored
518f885

Commits on Apr 9, 2025

add what i've got so far
peter-va
committed
88aefff

Commits on Apr 14, 2025

Commits on Apr 17, 2025

add new endpoint for overview in evs-explore
peter-va
committed
2663867
undo getMappings
peter-va
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2674703
Merge branch 'PVA/RDFBROWSER-331-gray-out-empty-doc-tabs' of https://github.com/NCIEVS/evsrestapi into pva/RDFBROWSER-331-gray-out-empty-doc-tabs
peter-va
committed
c8dd489
Merge pull request #346 from NCIEVS/PVA/RDFBROWSER-331-gray-out-empty-doc-tabs
peter-va
authored
2651cab

Commits on Apr 21, 2025

controller fixes
peter-va
committed
4e7adee
spotless
peter-va
committed
e8154b1
Merge pull request #347 from NCIEVS/PVA/EVSRESTAPI-fix-metadata-controller
peter-va
authored
e25117a

Commits on Apr 22, 2025

Dss/evsrestapi 599 fhir defs syns (#345)
shapirod2
authored
841accb
EVSRESTAPI-516: url/system modifications and related tests esp for Co… (#339)

shapirod2
and
bcarlsenca
authored
a13166a
Update ValueSetProviderR5.java (#348)
shapirod2
authored
e3ef20a

Commits on Apr 24, 2025

bunch of changes, probably not finished yet
peter-va
committed
5f9b539

Commits on Apr 28, 2025

Dss/evsrestapi 569 fhir gen ops (#353)
shapirod2
authored
111c566
Dss/evsrestapi 527 fhir coding params (#352)
shapirod2
authored
78a7f18
Merge branch 'develop' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
2bf7296
Merge branch 'master' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
fb44840

Commits on Apr 29, 2025

Merge branch 'master' into develop
bcarlsenca
committed
ecee493
final config changes
peter-va
committed
8c62ccc
Merge branch 'develop' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
f7f7f0b

Commits on Apr 30, 2025

Merge branch 'master' into develop
bcarlsenca
committed
2f2de0e
EVSRESTAPI-550: throw an exception if delete by query fails
bcarlsenca
committed
f7d5cd0
Merge branch 'master' into develop
bcarlsenca
committed
6b0caba
versioning
peter-va
committed
5ea8bae
Merge branch 'master' into develop
bcarlsenca
committed
5b3497e

Commits on May 1, 2025

Merge branch 'master' into develop
bcarlsenca
committed
74a0b11
EVSRESTAPI-550: improve logging for mapping loader (#354)
bcarlsenca
authored
18841c5
Merge branch 'develop' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
e4dbb5e
update spring boot version
peter-va
committed
9c32bcb
Merge branch 'PVA/EVSRESTAPI-605-update-spring-boot' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
de4993c

Commits on May 2, 2025

Merge pull request #356 from NCIEVS/PVA/EVSRESTAPI-605-update-spring-boot
peter-va
authored
737f06d
Merge branch 'develop' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
1bf3fdd
RDFBROWSER-476: npo definitions cleanup (#357)

bcarlsenca
and
peter-va
authored
9fafe0d

Commits on May 6, 2025

Merge branch 'develop' into PVA/EVSRESTAPI-childhood-neoplasm-contain-itself
peter-va
committed
0d6b87e

Commits on May 7, 2025

change ftp url and use previous version as backup for history
peter-va
committed
628cb07
only try downloading again if prev_version is found
peter-va
committed
e5df494

Commits on May 9, 2025

Merge pull request #359 from NCIEVS/PVA/EVSRESTAPI-607-move-ftp-url-and-use-prev-version-backup
peter-va
authored
bd6687a
add tweak and test
peter-va
committed
1535cc0
Merge pull request #358 from NCIEVS/PVA/EVSRESTAPI-childhood-neoplasm-contain-itself
peter-va
authored
5fa7ab8
Merge branch 'develop' into PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
committed
4c50ddf

Commits on May 13, 2025

add index runtime to terminology metadata
peter-va
committed
8a6fb52
check concept count
peter-va
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6b2a922
EVSRESTAPI-570: handle properly, handle no previous monthly version (e.g. the first time running) and call local server (#361)
bcarlsenca
authored
ea2222f

Commits on May 19, 2025

Dss/evsrestapi 550 dup maps (#360)
shapirod2
authored
99e2f05
Merge pull request #355 from NCIEVS/PVA/EVSRESTAPI-532-rename-classes-to-opensearch
peter-va
authored
7e77fb9
Merge pull request #362 from NCIEVS/PVA/EVSRESTAPI-502-store-reindex-time-in-metadata
peter-va
authored
5c2d2d8
beginning
peter-va
committed
87f6cde
Merge branch 'develop' into pva/EVSRESTAPI-570-handle-cumulative-history-in-reindex
peter-va
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ece52ed
formatting
peter-va
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7e62a72
move loadhistory
peter-va
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4b73273
reload terminology on reconcile indexes, when new history is available
peter-va
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c5e0c0a
pull reload logic out into LoaderService
peter-va
committed
2fe33d2
rework logic to use filenames
peter-va
committed
31c9f89

Commits on May 20, 2025

change base loadhistory message
peter-va
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df05477
redundant flag
peter-va
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04bf4a7
FIX: somewhere the loading of subsetMember in extra subsets handling got lost, put back in
bcarlsenca
committed
11d05bb
rework skipConcepts skipMetadata to update histories
peter-va
committed
9e7244b
Merge branch 'develop' into pva/EVSRESTAPI-570-handle-cumulative-history-in-reindex
peter-va
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687b89e
extract repeated code
peter-va
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5aed145
Remove the 'software' directory (#363)
bcarlsenca
authored
e1f1791
update from discussion with Brian
peter-va
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4adb3c9
change to deciding when to update history
peter-va
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b51fef9
fix logic
peter-va
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293bcdd
Merge branch 'develop' into pva/EVSRESTAPI-570-handle-cumulative-history-in-reindex
peter-va
committed
99d018a

Commits on May 21, 2025

fix some crashes
peter-va
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518ae76
spotless
peter-va
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12c545a
port switch 8080 -> 8082
peter-va
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b5ad7b3

Commits on May 23, 2025

EVSRESTAPI-532: fix to use http://localhost:9201 still instead of Windows_NT
bcarlsenca
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821b476
switch back env variables
peter-va
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e97c173
Merge branch 'develop' into PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex
peter-va
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766dbdf
spotless
peter-va
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76fdb38
wrong switch
peter-va
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cfc7ea2
temp change url in reindex
Peter Van Ausdeln
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e7b4d99
skip instead of exit when failing to find ncit version
Peter Van Ausdeln
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e51ad66

Commits on May 27, 2025

CLEANUP: spotless fix
bcarlsenca
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7f5a459
add logging to java command
Peter Van Ausdeln
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611643c
add pwd
Peter Van Ausdeln
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7d5f0a1
cd back out before continue
Peter Van Ausdeln
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25dd4a4
refactor ncit history processing
Peter Van Ausdeln
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e36351e

Commits on May 28, 2025

return empty history map if there's no history file
peter-va
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791ee76
Update application-test.yml (#367)
shapirod2
authored
f5c12c6
rework exceptions and audits in history file opening
peter-va
committed
69b2a37
fortify empty check
peter-va
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4edfde0

Commits on Jun 2, 2025

get server port for local vs deployed environment
Peter Van Ausdeln
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6c8dbee
Merge branch 'PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex' of https://github.com/NCIEVS/evsrestapi into PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex
Peter Van Ausdeln
committed
f729c91
remove evs server export
Peter Van Ausdeln
committed
6386371
Revert "remove evs server export"
Peter Van Ausdeln
committed
ffd7969
try direct port numbers
Peter Van Ausdeln
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f950427
re-writing the error check
Peter Van Ausdeln
committed
747f1e6

Commits on Jun 3, 2025

expand the error messages
Peter Van Ausdeln
committed
a44f070
EVSRESTAPI-611: Updates to unit test data and devreset.sh to manage mapping data locally (#365)
bcarlsenca
authored
1e930b6
fix version get
Peter Van Ausdeln
committed
8819b8a
try another rework
Peter Van Ausdeln
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024d718
Merge branch 'develop' into PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex
Peter Van Ausdeln
committed
7058540

Commits on Jun 4, 2025

remove the skip reconcile
Peter Van Ausdeln
committed
a4d79c9
Dss/evsrestapi 604 fhir tx ig tooling (#366)
shapirod2
authored
a44dc4f
add logging
Peter Van Ausdeln
committed
bc6bb45
add more logging
Peter Van Ausdeln
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46737f5
more logging
Peter Van Ausdeln
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3142c25
some more tweaks
Peter Van Ausdeln
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e34c412
remove a pwd log
Peter Van Ausdeln
committed
8c090aa
fix option
Peter Van Ausdeln
committed
9823051
spotless apply
Peter Van Ausdeln
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eff5eeb
remove another logging statement
Peter Van Ausdeln
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9b838de
remove output redirect
Peter Van Ausdeln
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6c81d7d
more logging
Peter Van Ausdeln
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2f61905
switching around version calculation
Peter Van Ausdeln
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3f71684
add history clause
Peter Van Ausdeln
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b022079
null check
Peter Van Ausdeln
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9eb9794
full term info logged
peter-va
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9cd471f
don't need this
peter-va
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4b76c33
get terminology differently
peter-va
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1cad406
changes to logging
peter-va
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cb86772
more logging in updateHistory
peter-va
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427caf2
fix a variable bug
peter-va
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939cd10
rework some logging
Peter Van Ausdeln
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155d880

Commits on Jun 5, 2025

more debug logging
peter-va
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8ddaa8e
spotless again
peter-va
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0152b84
show comparison of dates
Peter Van Ausdeln
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7e8806c
more logging
Peter Van Ausdeln
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001981a
change how the dates parse, reset concept history in handleHistory
Peter Van Ausdeln
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68acfd5
add concept existence check in history update
Peter Van Ausdeln
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83d13c3
condense logging
Peter Van Ausdeln
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cdaff38
reword messages
Peter Van Ausdeln
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b8e6abe
log new history version
Peter Van Ausdeln
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ec4abd1
fix tests
peter-va
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76ca9e2
change indexing method for terminology metadata
peter-va
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9b36f4e
don't use "this"
peter-va
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236c28a
change comparator to not go backwards
peter-va
committed
bd30971

Commits on Jun 6, 2025

expand history update bailout messages
Peter Van Ausdeln
committed
a3722fd
Merge branch 'PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex' of https://github.com/NCIEVS/evsrestapi into PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex
Peter Van Ausdeln
committed
d9c9911
Merge branch 'develop' into PVA/EVSRESTAPI-570-handle-cumulative-history-in-reindex
bcarlsenca
committed
1abed8f
EVSRESTAPI-563: get unit tests passing and update CHANGELOG.md. (#369)
bcarlsenca
authored
c877431
reindex changes
Peter Van Ausdeln
committed
4e46021

Commits on Jun 9, 2025

Commits on Jun 10, 2025

EVSRESTAPI-563: update changelog date
bcarlsenca
committed
20a3282
Cleanup warnings and verify tests (#371)
bcarlsenca
authored
5a28c5d

Commits on Jun 11, 2025

Update OPENSEARCH.md info on refresh interval
bcarlsenca
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3d84ac5

Commits on Jun 12, 2025

reindex hotfix for non-ncit
peter-va
committed
4ae5988
Merge pull request #372 from NCIEVS/reindex-hotfix
peter-va
authored
0078d74
add filepath match check to null check
peter-va
committed
e4bb367
spotless
peter-va
committed
d4ce244
Merge pull request #374 from NCIEVS/reindex-hotfix-2
peter-va
authored
549b23e

Commits on Jun 13, 2025

EVSRESTAPI-patch: resolve exception on fhir System Operations tab (#375)
shapirod2
authored
a4a63dd

Commits on Jun 19, 2025

EVSRESTAPI-625: fix issue with swagger baseUrl (#379)
bcarlsenca
authored
dd919a1

Commits on Jun 21, 2025

FIX swagger for FHIR to allow the public URL to be the server-side "base url" (#380)
bcarlsenca
authored
2d0b5f2

Commits on Jun 26, 2025

Add comments for cacheMills = 0
bcarlsenca
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a615b6b

Commits on Jun 27, 2025

CLEANUP: ensure urls are available with resource providers
bcarlsenca
committed
c1acc47

Commits on Jul 9, 2025

EVSRESTAPI-636: swagger link fix (#390)
shapirod2
authored
a29d6cb

Commits on Jul 16, 2025

add test cases for childhood neoplasm and change index to update
peter-va
committed
dc37cd6
Add childhood neoplasm test
bcarlsenca
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0125ad4

Commits on Jul 18, 2025

fix WriteOnlyProperties being removed on reindexing concepts
peter-va
committed
c0788d3
tweak test
peter-va
committed
3c3b133

Commits on Jul 21, 2025

Commits on Jul 22, 2025

EVSRESTAPI-642: small test fixes
bcarlsenca
committed
49d3fe8

Commits on Aug 5, 2025

Fix to support running reindexing in a shell on the mac
bcarlsenca
committed
3876c98