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Merged
skeating merged 181 commits into from
Aug 16, 2025
Merged

Throw when labs have no control id #91

skeating merged 181 commits into from
Aug 16, 2025

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@stefpiatek
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@stefpiatek stefpiatek commented May 16, 2025

plus a couple of editor suggested fixes

@jeremyestein
First pass at adding waveform data to Emap
be8944d
@jeremyestein
Write test which checks some of the data and passes
7911d23
@jeremyestein
checkstyle fixes and make test quicker
50d34f8
@jeremyestein
Merge branch 'develop' into jeremy/hf-data
36f7a84
@jeremyestein
Clarify validation run docs
4aff3a9
@jeremyestein
In new version of checkstyle, the encoding tag is no longer valid, and
5407881 
is not needed as long as project.build.sourceEncoding property is set.
@jeremyestein
Remove duplicated file set_mvn_proxy.sh
a6e11d9
@jeremyestein
Bare bones waveform-reader service. Docker image builds, but is
39a1fa7 
untested.
@jeremyestein
Initialise the fake UDS properly; add fake UDS and waveform reader to
cf27fe5 
emap setup; fix docs
@jeremyestein
Temporarily break the core proc RabbitMQ listener by only listening to
ff7db6f 
the waveform queue. Fixing this a proper way was too awkward.
@jeremyestein
Make data more realistic in terms of volume. Had to add some layers to
d1c1c9c 
get around Spring circular dependency problems.
@jeremyestein
Make message IDs more descriptive to enable better performance tracking
b7f10f2
@jeremyestein
Ten seconds of data per message
a3db3fc
@jeremyestein
call saveAll rather than save many times
a16adbf
@jeremyestein
Batch single-row INSERTs
a209f90
@jeremyestein
Couple of other tweaks, not sure what it'll do, but need a baseline
9615106 
before enabling multi-row INSERTs
@jeremyestein
Add reWriteBatchedInserts option to db connection string so that batched
e9bff1f 
inserts are merged into fewer multi-row inserts
@jeremyestein
Does this help?
3193369
@jeremyestein
Expicitly specify sequence Id generation so we don't have to query the
46ff9a4 
sequence for every single row.
@jeremyestein
Can't use existing sequence as it has a different increment value
5361af2
@jeremyestein
Use SQL arrays (of double precision DB type)
e2635c8
@jeremyestein
Fix copy constructor
7b9b01a
@jeremyestein
Copy constructor checker didn't know about Double[]
182d2c2
@jeremyestein
Put data from multiple patients to test it doesn't get mixed up. Shuffle
5558e48 
order of messages.
@jeremyestein
Make observation time in synthetic data evenly spread out, as real data
49d93d9 
would be
@jeremyestein
Make number of patients, start date, and warp factor configurable to
cd5567f 
allow more data to be put in during validation.
@jeremyestein
Add indexes to Waveform table
55e0c60
@jeremyestein
Cassandra is still running out of memory
73619d4
@jeremyestein
Make configurable the rabbitmq queues that core will listen on,
1c3cc09 
to allow for configurations where not all data sources are present.
@jeremyestein
Make the synthetic data values use a variable amount of digits to test
52dbc3a 
out the numeric SQL data type a bit better.
jeremyestein and others added 20 commits January 28, 2025 13:48
@jeremyestein
Add instructions for a uv venv
091de89
@jeremyestein
Add IntelliJ tips
d04e0ba
@jeremyestein
Merge pull request #75 from SAFEHR-data/jeremy/hf-data-fixes
10d5699 
Waveform various fixes
@jeremyestein @skeating
Update core/emap-portal/nginx.conf
0207325 
Co-authored-by: Sarah Keating <[email protected]>
@jeremyestein
Merge pull request #76 from SAFEHR-data/jeremy/hf-data-monitoring
74bf362 
Add streamlit data visualisation
@jeremyestein
Update to use new GH org (or shortened URLs where appropriate)
b8a862d
@jeremyestein
Suggest checking out docs repo
e5f8b5f
@jeremyestein
Fix links
34553cf
@jeremyestein
Merge branch 'develop' into jeremy/docs
2f96da3
@jeremyestein
Add extra SDE to form
ee4fc78
@jeremyestein
Match changes to hoover that have caused the expected messages to
e246b80 
change.
@jeremyestein
Match expected data now that SDE notes have been added.
d1edcd3
@jeremyestein
Test that valid_from/filed timestamps are being updated correctly whe…
85793f4 
…n SDEs change, and fix bug where sometimes they weren't.
@jeremyestein
Form instance ID namespacing, and check encounter string in test
08dbc18
@jeremyestein
Oops missed one
32619af
@jeremyestein
Merge pull request #89 from SAFEHR-data/jeremy/docs
f011a83 
Docs fixes (some from repo move)
@jeremyestein
Merge branch 'develop' into jeremy/sde-fixes
c6d1ef5
@jeremyestein
Merge pull request #85 from SAFEHR-data/jeremy/sde-fixes
c75cfb3 
SDE-related fixes
@stefpiatek
Throw exception if ORC order control Id is null
a41c732
@stefpiatek
Apply linting suggestions
f61f73e
skeating
skeating previously approved these changes Aug 16, 2025
View reviewed changes
@skeating skeating merged commit d5f8401 into main Aug 16, 2025
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@skeating skeating deleted the stefpiatek/fix_malformed_hl7 branch August 16, 2025 09:14
@skeating skeating mentioned this pull request Aug 16, 2025
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@skeating skeating skeating approved these changes

@jeremyestein jeremyestein Awaiting requested review from jeremyestein

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@stefpiatek @skeating @jeremyestein