Code

get_unite_data functions#134

Code

Merged

mikerobeson merged 64 commits intobokulich-lab:masterbokulich-lab/RESCRIPt:masterfrom colinbrislawn:get_unitecolinbrislawn/RESCRIPt:get_uniteCopy head branch name to clipboardNov 13, 2023

+318

Commits

Commits on Apr 10, 2022

• Add _assemble_unite_data_urls and testing code

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Commits on Oct 5, 2023

• update unite url lookup

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Commits on Oct 6, 2023

• add _assemble_unite_data_urls() and DOI dict

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• Delete .vscode/settings.json

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• Add draft _unite_download_targz()'

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• Merge branch 'get_unite' of https://github.com/colinbrislawn/RESCRIPt into get_unite

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Commits on Oct 7, 2023

• Add examples for questions

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Commits on Oct 11, 2023

• add imporing tests

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• revert get_data.py and splint out unite

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• simply _unite_doi_to_url

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Commits on Oct 12, 2023

• unmuddle _get_unite_* functions

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• rename function, again

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• remove old Silva stuff

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• Merge branch 'bokulich-lab:master' into get_unite

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• Add working get_unite_data()!

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• add alt method get_unite_data2()

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Commits on Oct 14, 2023

• major updateto get_unite_data

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Commits on Oct 15, 2023

• linting with flake8

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Commits on Oct 16, 2023

• remove unneeded import

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• remove unitefile.tar.gz and change cluster_id filter

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Commits on Oct 17, 2023

• rename for consistancy

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• flake8 and remove unite v8.0

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• match files by _dev and check for unfinished download

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Commits on Oct 18, 2023

• fix labels

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  e674fde

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• fixes to retry download loop

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Commits on Oct 20, 2023

• major update, rename and reorg functions

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• autoformat with black

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Commits on Oct 21, 2023

• add early testing

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• Add alt tests for get_doi and get_url

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Commits on Oct 23, 2023

• add nilsson2019unite

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• add check to _unite_get_artifacts

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• major update to testing code

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• add global test_get_unite_data and alt

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Commits on Oct 24, 2023

• merge _unite_get_doi into _unite_get_url

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• remove unused code

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• return tuple of Artifacts, without lists

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  f637891

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• update unite citation

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  aed4d06

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• remove extra print lines

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  3f9dafc

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• update unite description and license

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Commits on Oct 25, 2023

• fixing types

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Commits on Oct 26, 2023

• first working build

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Commits on Oct 27, 2023

• test bad URL in _unite_get_tgz

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  42e3ca1

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Commits on Nov 1, 2023

• set all defaults for get_unite_data()

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  2781122

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• removing unneeded / uncommon error handeling in _unite_get_tgz

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• tests

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Commits on Nov 2, 2023

• Update defaults

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Commits on Nov 3, 2023

• remove unneeded import of HTTPError

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  3d4e53e

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Commits on Nov 6, 2023

• Test output types for get_unite_data()

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• formating

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• remove full unite abstract

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• reword error for wrong number of cluster_id files

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Commits on Nov 8, 2023

• update text

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• use one dlfail in _unite_get_tgz

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• use self.assertRaisesRegex

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• Add mock download code

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  4317d77

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• roll back mock download

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  52a9ed1

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• Merge branch 'get_unite' of https://github.com/colinbrislawn/RESCRIPt into get_unite

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• rollback, again

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• rollback, again

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  4e39434

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• add back URL

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• add mocked test_unite_get_tgz2

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Commits on Nov 10, 2023

• use MixedCaseDNAFASTAFormat

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• black format

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Commits on Nov 13, 2023

• test get_tgz with mock

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