From a37f0d82125a8effb4681df1b20cb5c23b146780 Mon Sep 17 00:00:00 2001 From: zmyers23 <31746721+zmyers23@users.noreply.github.com> Date: Fri, 15 Dec 2017 15:01:19 -0800 Subject: [PATCH] Adds query to pull unreleased files. --- ENCODE_is_complete.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/ENCODE_is_complete.py b/ENCODE_is_complete.py index 7d4b10f4..b91b09a0 100644 --- a/ENCODE_is_complete.py +++ b/ENCODE_is_complete.py @@ -113,15 +113,18 @@ def main(): results['status issues'] = status_issues # Inspect files + query = "/search/?type=File&dataset=/experiments/"+obj['accession']+'/' + r = get_ENCODE(query, connection, frame='embedded') + all_files = r['@graph'] - good_files = [f for f in obj['files'] + good_files = [f for f in all_files if f['status'] in ['released', 'in progress']] fastqs = [f for f in obj['files'] if f['status'] in ['released', 'in progress']] - print("There are files in this experiment:", len(obj['files'])) + print("There are files in this experiment:", len(all_files)) print("There are good files in this experiment:", len(good_files)) # look for unarchived processed files from other labs - processed_files = [f for f in obj['files'] + processed_files = [f for f in all_files if f['file_format'] != 'fastq'] external_files = [f for f in processed_files if ( f['lab']['name'] != 'encode-processing-pipeline')]