fix #1236 #1644
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fix #1236 #1644
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qiita_db/analysis.py
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| from biom.util import biom_open | ||
| import pandas as pd | ||
| from skbio.util import find_duplicates | ||
| from skbio.util import flatten |
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flatten has been removed in later versions of skbio. In other parts of the code, we have been using the construction below to use flatten:
from itertools import chain
list(chain.from_iterable(ITERABLE))
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thanks @antgonza - some comments |
qiita_db/analysis.py
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| # different stages and possible errors. | ||
| samples = self.samples | ||
| # figuring out if we are going to have duplicated samples, again | ||
| # doing it here cause it's computetional cheaper |
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computetional -> computational
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Super minor typos. 👍 otherwise. |
qiita_db/analysis.py
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| to_concat = [] | ||
| for aid, samps in viewitems(samples): | ||
| qdb.sql_connection.TRN.add(sql, [aid]) | ||
| qm_fp = qdb.sql_connection.TRN.execute_fetchindex()[0][1] |
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Just realized - if you are accession only to [0][1], doesn't it mean that the above query is retrieving more info than needed? I think it should only be SELECT filepath and then here you can use execute_fetchlast. I think it will make the code cleaner and also removes the magic numbers.
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Few minor comments. |
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👍 given tests pass |
josenavas
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This fixes #1236 as discussed in there and during the last call. The best way to test this was to add a new biom artifact in a study that already had one => added in populate_test_db.sql (artifact 5). This change will also be helpful as we move to test more than one artifact at the time. However, this change also make some scripts to failed and I'm fixing them. I check all errors in my laptop and flake8 so we should be OK to review ASAP.