# The DDE pipeline for NCT01797120: python -m pipeline --study ../data/protocols/NCT01797120/pipeline.yaml
# (run from src/). Paths are relative to this file. The review files sit beside it: they hold the
# answers a person gives, and each stage applies its file when it exists and writes it back. The
# define patch is applied by stage A and rewritten by stage F, once the defaults are filled.
study: NCT01797120
usdm_file: NCT01797120-latest.json
crf_spec_file: ../../crf_specializations/cdisc_crf_specializations_draft.csv
# Stage A's output, the Define DDS (DDS1)
dds_define: ../../../src/define-xml/output/NCT_DDS.json
# everything generated after Stage A: define-patch-stageA.yaml, dds-crf.json, crf-2.0.xml, acrf.pdf,
# acrf.pagerefs.json, dds-origin.json, dds-defaults.json, defaults-report.yaml, define.xml,
# pipeline-run.json
output_dir: ../../../output/NCT01797120
sdtmig: "3.4"
# 2026-03-27 does not have every codelist the SDTMIG variables link to (C102580), and the
# Define loader stops on a missing codelist; 2025-09-26 is what the 2026-08 and 2026-09 runs used
sdtmct: "2025-09-26"
cdashig: "2.3"
cdashct: "2026-03-27"
page_size: letter
review:
  define_patch: define-patch.yaml
  crf_refinement: crf-refinement.yaml
  origin_review: origin-review.yaml
# Stage F's well-known defaults; later files win, so a study file listed after the shared one
# (e.g. study-defaults.json beside this file) overrides it
defaults:
  - ../../defaults/well_known_defaults.json
# crfutils is a separate install; these are looked up on PATH unless given as paths
commands:
  crfvalidate: crfvalidate
  crfpdf: crfpdf