JP-3914: Catch incomplete extraction gracefully

[melanieclarke]

Resolves JP-3914

Add some safety catches for data that is not expected to successfully complete extraction.

Triggering observation is PID 1209 obs 1, a NIRISS SOSS observation in FULL frame. Extraction is appropriately aborted, but the spec3 pipeline currently crashes trying to run combine_1d on a non-spectral input. The fix is to modify combine_1d to ignore inappropriate input, but also skip trying to run photom or combine_1d in this case in spec3, so that confusing "x1d" and "c1d" products that contain no spectra are not saved.

A related issue in spec2 for this observation was fixed in #8575, but now that spec2 gracefully completes, we see the crash in spec3 instead.

Tasks

• request a review from someone specific, to avoid making the maintainers review every PR
• add a build milestone, i.e. Build 11.3 (use the latest build if not sure)
• Does this PR change user-facing code / API? (if not, label with no-changelog-entry-needed)
  • write news fragment(s) in changes/: echo "changed something" > changes/<PR#>.<changetype>.rst (see below for change types)
  • update or add relevant tests
  • update relevant docstrings and / or docs/ page
  • start a regression test and include a link to the running job (click here for instructions)
    • Do truth files need to be updated ("okified")?
      • after the reviewer has approved these changes, run okify_regtests to update the truth files
• if a JIRA ticket exists, make sure it is resolved properly

news fragment change types...

• changes/<PR#>.general.rst: infrastructure or miscellaneous change
• changes/<PR#>.docs.rst
• changes/<PR#>.stpipe.rst
• changes/<PR#>.datamodels.rst
• changes/<PR#>.scripts.rst
• changes/<PR#>.set_telescope_pointing.rst
• changes/<PR#>.pipeline.rst

stage 1

• changes/<PR#>.group_scale.rst
• changes/<PR#>.dq_init.rst
• changes/<PR#>.emicorr.rst
• changes/<PR#>.saturation.rst
• changes/<PR#>.ipc.rst
• changes/<PR#>.firstframe.rst
• changes/<PR#>.lastframe.rst
• changes/<PR#>.reset.rst
• changes/<PR#>.superbias.rst
• changes/<PR#>.refpix.rst
• changes/<PR#>.linearity.rst
• changes/<PR#>.rscd.rst
• changes/<PR#>.persistence.rst
• changes/<PR#>.dark_current.rst
• changes/<PR#>.charge_migration.rst
• changes/<PR#>.jump.rst
• changes/<PR#>.clean_flicker_noise.rst
• changes/<PR#>.ramp_fitting.rst
• changes/<PR#>.gain_scale.rst

stage 2

• changes/<PR#>.assign_wcs.rst
• changes/<PR#>.badpix_selfcal.rst
• changes/<PR#>.msaflagopen.rst
• changes/<PR#>.nsclean.rst
• changes/<PR#>.imprint.rst
• changes/<PR#>.background.rst
• changes/<PR#>.extract_2d.rst
• changes/<PR#>.master_background.rst
• changes/<PR#>.wavecorr.rst
• changes/<PR#>.srctype.rst
• changes/<PR#>.straylight.rst
• changes/<PR#>.wfss_contam.rst
• changes/<PR#>.flatfield.rst
• changes/<PR#>.fringe.rst
• changes/<PR#>.pathloss.rst
• changes/<PR#>.barshadow.rst
• changes/<PR#>.photom.rst
• changes/<PR#>.pixel_replace.rst
• changes/<PR#>.resample_spec.rst
• changes/<PR#>.residual_fringe.rst
• changes/<PR#>.cube_build.rst
• changes/<PR#>.extract_1d.rst
• changes/<PR#>.resample.rst

stage 3

• changes/<PR#>.assign_mtwcs.rst
• changes/<PR#>.mrs_imatch.rst
• changes/<PR#>.tweakreg.rst
• changes/<PR#>.skymatch.rst
• changes/<PR#>.exp_to_source.rst
• changes/<PR#>.outlier_detection.rst
• changes/<PR#>.tso_photometry.rst
• changes/<PR#>.stack_refs.rst
• changes/<PR#>.align_refs.rst
• changes/<PR#>.klip.rst
• changes/<PR#>.spectral_leak.rst
• changes/<PR#>.source_catalog.rst
• changes/<PR#>.combine_1d.rst
• changes/<PR#>.ami.rst

other

• changes/<PR#>.wfs_combine.rst
• changes/<PR#>.white_light.rst
• changes/<PR#>.cube_skymatch.rst
• changes/<PR#>.engdb_tools.rst
• changes/<PR#>.guider_cds.rst

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 72.56%. Comparing base (97db183) to head (ab44cb5).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/pipeline/calwebb_spec3.py	0.00%	5 Missing ⚠️
jwst/combine_1d/combine1d.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #9266      +/-   ##
==========================================
- Coverage   72.56%   72.56%   -0.01%     
==========================================
  Files         371      371              
  Lines       37167    37179      +12     
==========================================
+ Hits        26970    26978       +8     
- Misses      10197    10201       +4     

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[melanieclarke]

Regression tests here: https://github.com/spacetelescope/RegressionTests/actions/runs/13795141218

No failures.

[emolter]

LGTM