Add ONT FCs to bioinfo tab #446
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taca/utils/bioinfo_tab.py
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| flowcell_info = ( | ||
| couch_connection["nanopore_runs"].view("info/lims")[flowcell_id].rows[0] | ||
| ) | ||
| if flowcell_info.value and "sample_data" in flowcell_info.value["loading"][0]: |
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I think I would like to see a case that catches the case where "loading" is not inside value and if it's an empty list. Even if it's "always" supposed to be there, I think it would be a shame if it broke the entire script run if it wasn't there.
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In the case where the db .json has a "lims" nest, there should always be a subnest of "loading", and possibly "reloading". The db .json will not contain the "lims" nest until the LIMS step has been completed though.
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Easy enough to add a check that the key exists here I think.
taca/utils/bioinfo_tab.py
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| elif inst_brand == "ont": | ||
| base_name = os.path.basename(os.path.abspath(run_dir)) | ||
| # Skip archived, no_backup, nosync and qc folders | ||
| if base_name in ["archived", "no_backup", "nosync", "qc"]: |
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Wouldn't base_name here be the name of the run, and not the dir in which it resides?
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Oh, I see now. We are passing everything in the datadir into this function, including subdirs like nosyncand qc. I think it would be cleaner if we have some ealier logic to make sure only folders that look like ONT run dirs are passed into this function. The ONT run regex is available in the repo.
taca/utils/bioinfo_tab.py
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| couch_connection["nanopore_runs"].view("info/lims")[flowcell_id].rows[0] | ||
| ) | ||
| if flowcell_info.value and "sample_data" in flowcell_info.value["loading"][0]: | ||
| samples = flowcell_info.value["loading"][0]["sample_data"] |
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I think the index should be [-1], not [0]. If the LIMS script is re-run manually, we should use the latest values.
Forgot to commit fix in PR: Add ONT FCs to bioinfo tab #446
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