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Adds query to pull unreleased files. #110

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Adds query to pull unreleased files. #110

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9 changes: 6 additions & 3 deletions ENCODE_is_complete.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,15 +113,18 @@ def main():
results['status issues'] = status_issues

# Inspect files
query = "/search/?type=File&dataset=/experiments/"+obj['accession']+'/'
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Think we can use @id here and string formatting.
query = '/search/?type=File&dataset={}'.format(obj['@id'])

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')]
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