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annotate_metadata_with_index raises ValueError when dtypes don't match #948

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joverlee521 opened this issue May 13, 2022 · 0 comments · May be fixed by #952
Open

annotate_metadata_with_index raises ValueError when dtypes don't match #948

joverlee521 opened this issue May 13, 2022 · 0 comments · May be fixed by #952
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@huddlej
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bug Something isn't working easy problem Requires less work than most issues

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@joverlee521
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Current Behavior
Within annotate_metadata_with_index, the index TSV is read without explicitly set dtypes. This can lead to numerical id strain values to be interpreted as numbers, leading to a ValueError when merging with the metadata.

Additional context
See error reported by user: https://discussion.nextstrain.org/t/value-error-trying-to-merge-on-object-and-int64-columns/1106
@joverlee521 joverlee521 added the bug Something isn't working label May 13, 2022
@joverlee521 joverlee521 mentioned this issue May 13, 2022
Open
@victorlin victorlin moved this from New to Prioritized in Nextstrain planning (archived) May 25, 2022
@huddlej huddlej self-assigned this May 25, 2022
@victorlin victorlin added the easy problem Requires less work than most issues label May 25, 2022
huddlej added a commit that referenced this issue May 25, 2022
@huddlej
Add test for annotating metadata with index with numeric strain names
861840f 
Adds a functional test to cover a use case described in #948.
huddlej added a commit that referenced this issue May 25, 2022
@huddlej
Set dtype of strain column in sequence index
c49a5a6 
Sets the dtype of the strain column in the sequence index to "string"
prior to annotating metadata with that index. This change prevents
pandas from inferring the dtype as numeric when strain names are all
numeric.

Fixes #948
@huddlej huddlej linked a pull request May 25, 2022 that will close this issue
Open
2 tasks
@huddlej huddlej moved this from Prioritized to In Review in Nextstrain planning (archived) May 25, 2022
huddlej added a commit that referenced this issue Aug 5, 2022
@huddlej
Add test for annotating metadata with index with numeric strain names
01a0dd2 
Adds a functional test to cover a use case described in #948.
huddlej added a commit that referenced this issue Aug 5, 2022
@huddlej
Set dtype of strain column in sequence index
38b4d52 
Sets the dtype of the strain column in the sequence index to "string"
prior to annotating metadata with that index. This change prevents
pandas from inferring the dtype as numeric when strain names are all
numeric.

Fixes #948
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@huddlej huddlej

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bug Something isn't working easy problem Requires less work than most issues
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Nextstrain planning (archived)
Status: In Review
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Fix annotate metadata with numeric strains nextstrain/ncov
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@huddlej @victorlin @joverlee521