Export metrics to OTel collector and define custom metrics

[p-j-smith]

Description

Fixes #642

• enable sending metrics to an otlp endpoint
• add a new function core.telemetry.configure_metrics to configure a metric provider
• define three custom metrics:
  • number of studies exported per project (used in the export API)
  • number of studies that failed to be de-identified, per project and failure reason (used in Orthanc anon)
  • number of instances that failed to be de-identified, per project, study_uid, and failure reason
• to get the queue depth, we can configure a scrate config in the OTel Collector, and RabbitMQ already exposes these metrics via prometheus. Add a config to the integration tests to scrape metrics RabbitMQ
• add unit tests for the custom metrics
• add note in the documentation about adding new metrics

Type of change

Please delete options accordingly to the description.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Suggested Checklist

• I have performed a self-review of my own code.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• I have commented my code, particularly in hard-to-understand areas.
• I have passed on my local host device. (see further details at the CONTRIBUTING document)
• Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
• I have requested review to this PR.
• I have addressed and marked as resolved all the review comments in my PR.
• Finally, I have selected squash and merge

Number of studies exported

Study de-identification failures

If we don't catch the SQLAlchemy DBAPIError exceptions and extract the first line, the error message contains the full SQL that caused the failure, which would make the message unsuitable for filtering / aggregating:

Instance de-identification failures

Queue depth

[codecov]

Codecov Report

❌ Patch coverage is 56.86275% with 22 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.10%. Comparing base (407861a) to head (a9f74a5).

Files with missing lines	Patch %	Lines
pixl_core/src/core/telemetry.py	31.57%	13 Missing ⚠️
pixl_core/src/core/metrics.py	71.42%	8 Missing ⚠️
pixl_export/src/pixl_export/main.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #649      +/-   ##
==========================================
- Coverage   88.52%   88.10%   -0.43%     
==========================================
  Files          80       81       +1     
  Lines        3834     3883      +49     
==========================================
+ Hits         3394     3421      +27     
- Misses        440      462      +22     

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