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fix(cff): doi structure parsing#121

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rmfranken merged 81 commits intomainsdsc-ordes/gimie:mainfrom hotfix-CFF-doisdsc-ordes/gimie:hotfix-CFF-doiCopy head branch name to clipboardDec 17, 2024

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Commits

Commits on Nov 14, 2024

• feat:write goal of cff parser

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• feat: add function body and placeholder

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• refactor: do list(dict) formatting within the function

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• fix: forgot arrow in type annotation

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• chore: black reformat

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Commits on Nov 15, 2024

• feat: update parsers to output graphs instead of property "doubles", output RDF of authors

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• chore: update docstrings

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• fix: remove python <= 3.12 req

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Commits on Nov 18, 2024

• feat: add "affiliation" of authors to output

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• docs: add CFF file (#111)

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• feat: add test for cff author parsing

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• fix: python dependencies in poetry

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• fix: adapt parser tests to graph structure instead of property structure. Update pyshacl, comment out useless pyshacl test throwing errors

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• fix: remove faulty cff function example description

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• Update test_cff.py

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• Merge branch 'main' into cff_parsing

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Commits on Nov 19, 2024

• Merge branch 'main' into cff_parsing

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Commits on Nov 20, 2024

• fix: unused import

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• fix: typo

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• refactor: rename variable

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• docs: add docstring parameter for parser class

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• refactor: rename variable

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• feat: check if orcid is valid before writing

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• refactor: rename variable

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• chore: remove pyshacl

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• fix: typo

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• fix: remove unused imports

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Commits on Nov 22, 2024

• fix: tests for cff, add test for doi, move doi and orcid matchers to utils

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• docs:fix docs of valid_doi_extractor

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• Merge branch 'main' into cff_parsing

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• refactor: doi re matcher

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• chore: remove unneccessary comment

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Commits on Nov 28, 2024

• chore(docker): bump base layer to python 3.13

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• Update gimie/parsers/abstract.py

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• Update gimie/parsers/cff.py

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• chore(docker): use python 3.12 base

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• fix: improve tests, rename some variables

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• Merge branch 'cff_parsing' of github.com:sdsc-ordes/gimie into cff_parsing

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• fix:rename the example in extract_doi_march

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Commits on Dec 16, 2024

• fix: DOI from dict, not flat value

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• fix:make cff example correct

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• docs: adapt docstring example to match real CFF structure

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• fix:docstring still fucked

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• fix:typo docstring

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• fix:chatGPT's suggestion for docstring formatting

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• fix:OK, no multiline, and double escape newlines

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• fix: spelling mistake in run as library docs (#113)

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• fix: unused import

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• fix: typo

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• refactor: rename variable

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• docs: add docstring parameter for parser class

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• refactor: rename variable

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• feat: check if orcid is valid before writing

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• refactor: rename variable

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• chore: remove pyshacl

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• fix: typo

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• fix: remove unused imports

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• fix: tests for cff, add test for doi, move doi and orcid matchers to utils

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• docs:fix docs of valid_doi_extractor

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• Improve authentication error messages (#116)

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• ci: make conventional PR title check optional (#117)

  

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• refactor: doi re matcher

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• chore: remove unneccessary comment

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• fix: improve tests, rename some variables

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• chore(docker): bump base layer to python 3.13

  

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• Update gimie/parsers/abstract.py

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• Update gimie/parsers/cff.py

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• chore(docker): use python 3.12 base

  

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• fix:rename the example in extract_doi_march

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• fix: DOI from dict, not flat value

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• fix:make cff example correct

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• docs: adapt docstring example to match real CFF structure

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• fix:docstring still fucked

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• fix:typo docstring

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• fix:chatGPT's suggestion for docstring formatting

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• fix:OK, no multiline, and double escape newlines

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• Merge branch 'hotfix-CFF-doi' of github.com:sdsc-ordes/gimie into hotfix-CFF-doi

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Commits on Dec 17, 2024

• Merge branch 'main' into hotfix-CFF-doi

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• feat: support multiple DOI's

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• refactor(cff): reduce nesting

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• chore(cff): use type hint for list from python standard collection

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