WIP: load-qebil-downloaded-studies#3112
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scripts/qiita-load-qebil-downloads
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| SLEEP_TIME = 10 | ||
| EBIDIR = '/panfs/panfs1.ucsd.edu/panscratch/qiita/qebil/vertebrates/' |
scripts/qiita-load-qebil-downloads
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| # note necessry but nice for debugging | ||
| print(f'\n\n\n+++> Processing {folder}, you have {SLEEP_TIME} ' | ||
| 'seconds to ctrl-c') | ||
| sleep(10) |
| qebil_status_fp = [f for f in files if f.endswith('qebil_status')][0] | ||
| with open(qebil_status_fp, 'r') as fp: | ||
| qebil_status = fp.readlines()[0] |
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How is qebil being executed? The filebased process communication may represent a pain point in the future.
| continue | ||
| files_used.append(qebil_status_fp) | ||
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| title_fp = [f for f in files if f.endswith('_study_title.txt')][0] |
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Would it be erroneous if there were zero _study_title.txt files, or more than 1?
scripts/qiita-load-qebil-downloads
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| st = study.sample_template | ||
| sample_info = load_sample_template_from_cmd(sample_fp, study.id) | ||
| st.ebi_sample_accessions = st.get_category('secondary_sample_accession') | ||
| st.biosample_accessions = st.get_category('sample_accession') |
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Out of curiosity, would it be valuable to test if the accessions were observed already in qiita in addition to the study title? although, I'm not sure what action it would suggest if they were :/
scripts/qiita-load-qebil-downloads
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| filepaths = [] | ||
| for rp in run_prefixes: | ||
| matches = sorted([f for f in files if rp in f]) |
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should this be if f.startswith(rp)?
| prep_template=pt, move_files=False) | ||
| notes = '' | ||
| if warnings: | ||
| notes = '<b>Warnings</b>:<ol>%s</ol>\n' % ''.join( |
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html formatting here feeeeels like it should be done at the visualization layer on template render, but I would understand why doing so here is pragmatic
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