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NMDC updates#203

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mattldawson wants to merge 4 commits intokbase:mainfrom
mattldawson:develop-fix-nmdc
Closed

NMDC updates#203
mattldawson wants to merge 4 commits intokbase:mainfrom
mattldawson:develop-fix-nmdc

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@mattldawson
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This PR modifies the NMDC database to request file information in batches. It also loosens the restriction on transferring raw data files and files with unknown workflow ID prefixes.

A few tests were also modified to avoid hard failures when you run locally with expired credentials, and to timeout for transfer requests that hang.

I'll leave this in draft until we have a chance to test actual NMDC transfers with these updates

@mattldawson mattldawson requested a review from jeff-cohere March 30, 2026 21:17
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codecov bot commented Mar 30, 2026

Codecov Report

❌ Patch coverage is 77.41935% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.65%. Comparing base (597f7e9) to head (1616afc).

Files with missing lines Patch % Lines
databases/nmdc/database.go 77.41% 4 Missing and 3 partials ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #203       +/-   ##
===========================================
- Coverage   64.69%   54.65%   -10.05%     
===========================================
  Files          34       34               
  Lines        4501     4521       +20     
===========================================
- Hits         2912     2471      -441     
- Misses       1265     1787      +522     
+ Partials      324      263       -61     

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@mattldawson
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will re-open on local branch so all actions run

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