ENH:Allow for missing features in feature metadata #734
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Allows for feature metadata to not include some of the features represented in the ordination. The errors and warnings have been updated to properly refer to either features or samples. I've added a couple of tests to validate the error/warning messages. Fixes biocore#730 Fixes biocore#733
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| @@ -250,7 +251,7 @@ def __init__(self, ordination, mapping_file, feature_mapping_file=None, | |||
| self.feature_mf = \ | |||
| self._validate_metadata(feature_mapping_file, | |||
| self.ordination.features, | |||
| ignore_missing_samples=False) | |||
| ignore_missing_samples, kind='feature') | |||
emperor/core.py
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| "file. Override this error by using the " | ||
| "`ignore_missing_samples` argument. Offending " | ||
| "samples: %s" | ||
| % ', '.join(sorted([str(i) for i in difference]))) | ||
| "%ss: %s" % (kind, kind, kind, elements)) |
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Not necessary for this PR, but py3.6 has f-strings that look pretty cool
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This PR is ready for review if anyone would like to have a look. |
emperor/core.py
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| if difference and not ignore_missing_samples: | ||
| raise KeyError("There are samples not included in the mapping " | ||
| elements = ', '.join(sorted([str(i) for i in difference])) |
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Can this be a truncated list? If thousands of features are missing, the output will be substantial especially if they're sOTUs
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I think it's ok since QIIME2 would hide the list of features by default and only if the user uses --verbose the full text will be displayed. What do you think?
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Does it...? I ran q2-emperor from 2019.7 recently with malformed metadata and got a buffer full of output on the terminal :/
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Got it, just addressed this 👍
The output is truncated to 5 missing elements.
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👍 |
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Thanks so much @wasade!
…On (Oct-22-19|11:10), Daniel McDonald wrote:
Merged #734 into new-api.
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#734 (comment)
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Allows for feature metadata to not include some of the features
represented in the ordination. The errors and warnings have been updated
to properly refer to either features or samples. I've added a couple of
tests to validate the error/warning messages.
Fixes #730 and #733