WIP: load-qebil-downloaded-studies #3112
Conversation
scripts/qiita-load-qebil-downloads
Outdated
|
|
||
|
|
||
| SLEEP_TIME = 10 | ||
| EBIDIR = '/panfs/panfs1.ucsd.edu/panscratch/qiita/qebil/vertebrates/' |
scripts/qiita-load-qebil-downloads
Outdated
| # 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] |
There was a problem hiding this comment.
How is qebil being executed? The filebased process communication may represent a pain point in the future.
| continue | ||
| files_used.append(qebil_status_fp) | ||
|
|
||
| title_fp = [f for f in files if f.endswith('_study_title.txt')][0] |
There was a problem hiding this comment.
Would it be erroneous if there were zero _study_title.txt files, or more than 1?
scripts/qiita-load-qebil-downloads
Outdated
| 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') |
There was a problem hiding this comment.
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
Outdated
|
|
||
| filepaths = [] | ||
| for rp in run_prefixes: | ||
| matches = sorted([f for f in files if rp in f]) |
There was a problem hiding this comment.
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( |
There was a problem hiding this comment.
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
No description provided.