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Examples fail to run #2

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jimrybarski opened this issue Nov 16, 2021 · 2 comments · May be fixed by #13
Open

Examples fail to run #2

jimrybarski opened this issue Nov 16, 2021 · 2 comments · May be fixed by #13
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bug Something isn't working

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@jimrybarski
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Description

Running the example code from the documentation fails with this exception:
TypeError: batches_support_wrapper() missing 1 required positional argument: 'collection'

Reproduce

Run this code with easy_entrez 0.3.0:

from easy_entrez import EntrezAPI

entrez_api = EntrezAPI(
    'test',
    '[email protected]'
)

print(entrez_api.link(database=None, ids=[15718680, 157427902], database_from='protein', command='acheck'))

Expected behavior

It should return results instead of throwing this exception.

Context

OS: Ubuntu 18.04.6 LTS
Python: 3.6.9
easy_entrez 0.3.0 was installed in a virtualenv.
@jimrybarski jimrybarski added the bug Something isn't working label Nov 16, 2021
@krassowski
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krassowski commented Nov 16, 2021 •
edited
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Thank you for reporting the issue. The ids should be the first positional argument.

print(entrez_api.link([15718680, 157427902], database=None, database_from='protein', command='acheck'))

or keyed as a collection=:

print(entrez_api.link(database=None, collection=[15718680, 157427902], database_from='protein', command='acheck'))

The documentation needs updating.

@krassowski krassowski linked a pull request Jan 7, 2023 that will close this issue
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@dodoflyy
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Hey, this bug still exist in v0.3.6? still can't use ids=.

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Fix misalignment in signatures for methods with @support_batches krassowski/easy-entrez
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@jimrybarski @krassowski @dodoflyy