Complete manuscript data pipeline successfully generated 9869 deduplicated trials with tables and figures
Source type:
obs· Harvested: 2026-05-04 · Original date: 2026-05-04T01:48:40.327Z Metadata:{"project":"oncology-fih-research/oncology-fih-research","type":"feature","obs_id":65254}
obs/65254 · feature · 2026-05-04T01:48:40.327Z
Complete manuscript data pipeline successfully generated 9869 deduplicated trials with tables and figures
Successfully completed end-to-end manuscript data generation pipeline for Journal of Hematology and Oncology submission after resolving five critical technical challenges. The pipeline collected clinical trial data from ClinicalTrials.gov across 14 search terms covering first-in-human and early-phase oncology studies, processed 9869 unique trial records after deduplication, and generated publication-ready outputs including structured CSV data, formatted tables, and analytical figures. The successful completion required sequential resolution of: (1) Rscript path detection using commandArgs instead of sys.frame, (2) broken R httr library bypassed with system curl, (3) shell argument quoting with shQuote, (4) API timeout prevention through 250-record pagination with field filtering and file-based caching, and (5) defensive type checking to handle inconsistent API data structures. The final data freeze documentation provides reproducibility tracking for the 2026-05-04 collection date, enabling transparent reporting of the data acquisition methodology in the manuscript methods section.
Concepts: [“how-it-works”,“problem-solution”,“pattern”]
Facts: [“Pipeline completed successfully collecting and processing 9869 unique clinical trial records from 14 search queries”,“Generated CSV file at manuscript/analysis/ctgov_jho_trials_latest.csv with complete trial metadata”,“Created publication tables in manuscript/tables/ directory”,“Generated manuscript figures in manuscript/figures/ directory”,“Documented data collection in data-freeze-jho-2026-05-04.md freeze file”,“Total execution completed with exit code 0 indicating no errors”,“Deduplication reduced raw query results to 9869 unique studies”]
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