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NMDC Updates#204

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mattldawson wants to merge 8 commits intomainfrom
develop-fix-nmdc
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NMDC Updates#204
mattldawson wants to merge 8 commits intomainfrom
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 22:34
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github-actions bot commented Mar 30, 2026

PR Preview Action v1.8.1

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🚀 View preview at
https://kbase.github.io/dts/pr-preview/pr-204/

Built to branch gh-pages at 2026-03-31 15:50 UTC.
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codecov bot commented Mar 31, 2026

Codecov Report

❌ Patch coverage is 75.00000% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 62.16%. Comparing base (597f7e9) to head (bf4d88a).

Files with missing lines Patch % Lines
databases/nmdc/database.go 73.52% 5 Missing and 4 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #204      +/-   ##
==========================================
- Coverage   64.69%   62.16%   -2.54%     
==========================================
  Files          34       34              
  Lines        4501     4525      +24     
==========================================
- Hits         2912     2813      -99     
- Misses       1265     1399     +134     
+ Partials      324      313      -11     

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2 participants