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Rdf output adapter #338

Merged
merged 29 commits into from
Apr 24, 2024
Merged

Rdf output adapter #338

merged 29 commits into from
Apr 24, 2024

Commits on Jun 22, 2023

  1. First minimal working version for rdf conversion

    @supermaxiste
    supermaxiste committed Jun 22, 2023
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Commits on Apr 4, 2024

  1. Bump pillow from 10.0.1 to 10.3.0 

    Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.1 to 10.3.0.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.0.1...10.3.0)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
    @dependabot
    dependabot[bot] committed Apr 4, 2024
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  2. Merge pull request #1 from thehyve/dependabot/pip/pillow-10.3.0 

    Bump pillow from 10.0.1 to 10.3.0
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 4, 2024
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  3. Merge remote-tracking branch 'origin/main' into rdf

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. update the RDF writer to be compatible with latest changes of Biocypher.

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 5, 2024
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Commits on Apr 8, 2024

  1. add triples with URIs instead of strings. also add properties of the … 

    …nodes.
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. include some namespaces. Currently it's hardcoded but it should be in… 

    …tegrated with the config file.
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 9, 2024
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Commits on Apr 11, 2024

  1. write files for every node and relationship type , instead of one big… 

    … file
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 11, 2024
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  2. remove redundant code from rdfwriter which is already defined in batc… 

    …h_writer
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 11, 2024
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Commits on Apr 17, 2024

  1. add edges as nodes. attach the properties of the edge to the created … 

    …node
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 17, 2024
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  2. create basic unit test. add dummy nodes and edges and check nr of nod… 

    …es and edges written to xml file
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 17, 2024
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  3. add namespaces to the rdf output

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. Merge remote-tracking branch 'origin/main' into rdf

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  2. resolve merge conflict

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  3. use example data from fixtures and assert every node and 'edge' has a… 

    … type relationship and that all nodes have property "id".
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  4. run precommit, align with pep8 naming convention

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  5. #106: fix integration test

    @nilskre
    nilskre committed Apr 18, 2024
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  6. add some doc

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  7. small changes

    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 18, 2024
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  8. Merge pull request #337 from thehyve/rdf 

    first version of RDF conversion
    @slobentanzer
    slobentanzer committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. #106: minor fixes; link rdf docs from main output docs page

    @nilskre
    nilskre committed Apr 19, 2024
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Commits on Apr 22, 2024

  1. expand tests to check every triple individually. needed to rearrange/… 

    …change code in the _RDFWriter
    @LoesvdBiggelaar
    LoesvdBiggelaar committed Apr 22, 2024
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Commits on Apr 24, 2024

  1. docs format and phrasing

    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  2. move output in TOC

    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  3. output page index formatting

    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  4. pre-commit

    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  5. bump action version due to deprecation warning

    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  6. move python versions to 3.10-3.12 due to 

    support issue of 3.9 with the latest macOS on GitHub runners
    @slobentanzer
    slobentanzer committed Apr 24, 2024
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  7. #342: temporary cicd fix (set macos version to last macos version on … 

    …amd64)
    @nilskre
    nilskre committed Apr 24, 2024
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