tdb/elife_upload: Update assay_date parsing #146
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Pull out assay_date parsing from filename into a separate method `parse_assay_date_from_filename`. This is done in preparation to update the assay date parsing for VIDRL flat files.
The assay date is the same for all measurement records from the same fstem, so only parse the assay date once.
Use regex to find all matches for the expected date format 'YYYYMMDD'. Then use the datetime module to validate the date string and check that the date is earlier than the date we are parsing the file. I made the decision to use the latest date if there are multiple matches with the expectation that we would be parsing files not long after the assay date.
Only fill in with the assay date parsed from the fstem when the measurment does not have an assay date. This is done in preparation for parsing the flat VIDRL files which will include assay date as a column.¹ This ensures that the fstem date is only a backup to the date that is set within `format_date`.² ¹ https://bedfordlab.slack.com/archives/C03KWDET9/p1699914235686809 ² https://github.com/nextstrain/fauna/blob/8088646ce0ba438310cdc9f919080950d0767c46/tdb/upload.py#L328
huddlej
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This is so much cleaner, @joverlee521! I had a question about the third logical case in parsing assay dates from file names, but I don't think it's blocking.
tdb/elife_upload.py
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| sorted_dates = list(map(lambda x: datetime.datetime.strftime(x, '%Y-%m-%d'), sorted(valid_dates))) | ||
| assay_date = sorted_dates[-1] | ||
| print(f"Found multiple potential assay dates in filename {fstem!r}: {sorted_dates}.", | ||
| f"Using the last valid date as the assay date: {assay_date!r}") |
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Does this case ever happen? Are we sure that we want to pick the latest date as the assay date when we do find multiple dates or do we want to throw an error so the user has a chance to fix the file name before the upload happens?
As a minor aesthetic note, you could also sort the dates with a list comprehension to avoid using list, map, and lambda:
sorted_dates = [datetime.datetime.strftime(valid_date, '%Y-%m-%d') for valid_date in sorted(valid_dates)]There was a problem hiding this comment.
Does this case ever happen? Are we sure that we want to pick the latest date as the assay date when we do find multiple dates or do we want to throw an error so the user has a chance to fix the file name before the upload happens?
Not yet 😄 You're right that it would probably be better to throw an error here and manually fix the filename. I was thinking we would want the latest date if the file had an updated date appended, but better to be explicit about having one date in the filename.
It's unclear if we'll ever run into the case where there are multiple assay dates in the filename, but if we do, raise an exception to alert the user to manually fix the filename before upload.
Description of proposed changes
Updates to the assay date parsing in tdb/elife_upload:
Motivated by the latest discussion on ingesting the VIDRL flat files.
Checklist