Feature/sanitize jsons - #1535
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allanbolipata wants to merge 6 commits into
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buehlere
approved these changes
Aug 5, 2026
sivkovic
approved these changes
Aug 19, 2026
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Let's have everyone sign off on this before merging.
This contains small PR from #1534, so let's merge that first.
Summary
100XX_D→99990_D)What was sanitized
C-123456→C-PPPPP3100XX_D→99990_D*@mskcc.org→*@example.orgJohn Smith→Lab Head BWhat was preserved
MSKCCsequencing center, gene panel names (IMPACT468,HemePACT_v4), public GitHub URLsPRIMARY_ID_REGEX(e.g., single-letter project suffixes must be[B-Z], notA)DONOR00-TPkeeps the hyphen that operators split on)Key fixes during sanitization
patient.cmofields in DMP metadata use bare patient IDs without theC-prefix — these required separate replacement from theC-XXXXXformloaddataresolves fixtures by filename)BEAGLE_FASTQ_DEFAULT_LOCATION_PREFIXandBEAGLE_FASTQ_IRIS_LOCATION_PREFIXto.env.localto fix pre-existing test failures unrelated to sanitization