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Reimplement the CLI in TypeScript #172

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Reimplement the CLI in TypeScript #172

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Commits on Jun 17, 2024

  1. remove unneeded files

    @bmesuere
    bmesuere committed Jun 17, 2024
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  2. require node 22 to use fetch

    @bmesuere
    bmesuere committed Jun 17, 2024
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  3. yarn init

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    bmesuere committed Jun 17, 2024
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  4. get basic version working

    @bmesuere
    bmesuere committed Jun 17, 2024
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  5. move to bin folder

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    bmesuere committed Jun 17, 2024
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  6. move to typescript

    @bmesuere
    bmesuere committed Jun 17, 2024
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  7. cleanup

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    bmesuere committed Jun 17, 2024
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  8. add uniprot run command

    @bmesuere
    bmesuere committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. Merge pull request #173 from unipept/next-uniprot 

    Port the uniprot command
    @bmesuere
    bmesuere authored Jun 18, 2024
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  2. refactor

    @bmesuere
    bmesuere committed Jun 18, 2024
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  3. add eslint

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    bmesuere committed Jun 18, 2024
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  4. add github action

    @bmesuere
    bmesuere committed Jun 18, 2024
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  5. refactor

    @bmesuere
    bmesuere committed Jun 18, 2024
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  6. add tests

    @bmesuere
    bmesuere committed Jun 18, 2024
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  7. add CI

    @bmesuere
    bmesuere committed Jun 18, 2024
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  8. add a bit more comments

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    bmesuere committed Jun 18, 2024
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Commits on Jun 20, 2024

  1. Merge pull request #174 from unipept/next-testing 

    Add linting, testing and type checks
    @bmesuere
    bmesuere authored Jun 20, 2024
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  2. implement peptfilter

    @bmesuere
    bmesuere committed Jun 20, 2024
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  3. write tests

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    bmesuere committed Jun 20, 2024
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  4. optimize performance

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    bmesuere committed Jun 20, 2024
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  5. fix tests

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    bmesuere committed Jun 20, 2024
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  6. lint

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    bmesuere committed Jun 20, 2024
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  7. add comments

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    bmesuere committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. implement prot2pept

    @bmesuere
    bmesuere committed Jun 21, 2024
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  2. add tests

    @bmesuere
    bmesuere committed Jun 21, 2024
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  3. Merge pull request #175 from unipept/next-peptfilter 

    Port peptfilter to typescript
    @bmesuere
    bmesuere authored Jun 21, 2024
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  4. Update lib/commands/prot2pept.ts 

    Co-authored-by: Pieter Verschaffelt <[email protected]>
    @bmesuere @pverscha
    bmesuere and pverscha authored Jun 21, 2024
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  5. Merge pull request #176 from unipept/next-prot2pept 

    Port prot2pept to typescript
    @bmesuere
    bmesuere authored Jun 21, 2024
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Commits on Jul 2, 2024

  1. implement basic version of the pept2lca command

    @bmesuere
    bmesuere committed Jul 2, 2024
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  2. use post and set headers

    @bmesuere
    bmesuere committed Jul 2, 2024
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  3. move processing loop to the super class

    @bmesuere
    bmesuere committed Jul 2, 2024
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  4. implement input batches

    @bmesuere
    bmesuere committed Jul 2, 2024
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  5. use different input options if available

    @bmesuere
    bmesuere committed Jul 2, 2024
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  6. parse more parameters

    @bmesuere
    bmesuere committed Jul 2, 2024
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  7. add a few utility methods

    @bmesuere
    bmesuere committed Jul 2, 2024
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Commits on Jul 8, 2024

  1. add basic csv formatter

    @bmesuere
    bmesuere committed Jul 8, 2024
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  2. write to file if needed

    @bmesuere
    bmesuere committed Jul 8, 2024
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  3. support no-header

    @bmesuere
    bmesuere committed Jul 8, 2024
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  4. fix lint

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    bmesuere committed Jul 8, 2024
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Commits on Jul 30, 2024

  1. add test for unipept

    @bmesuere
    bmesuere committed Jul 30, 2024
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  2. add formatter tests

    @bmesuere
    bmesuere committed Jul 30, 2024
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  3. linter

    @bmesuere
    bmesuere committed Jul 30, 2024
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  4. refactor passing arguments programatically

    @bmesuere
    bmesuere committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. add basic command runner tests

    @bmesuere
    bmesuere committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Merge pull request #177 from unipept/next-unipept-1 

    Add pept2lca
    @bmesuere
    bmesuere authored Aug 1, 2024
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  2. implement json formatter

    @bmesuere
    bmesuere committed Aug 1, 2024
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  3. add tests for json formatter

    @bmesuere
    bmesuere committed Aug 1, 2024
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  4. add xml formatter

    @bmesuere
    bmesuere committed Aug 1, 2024
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  5. add tests for xml formatter

    @bmesuere
    bmesuere committed Aug 1, 2024
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  6. fix linter

    @bmesuere
    bmesuere committed Aug 1, 2024
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  7. Merge pull request #178 from unipept/next-unipept-2 

    implement xml and json formatters
    @bmesuere
    bmesuere authored Aug 1, 2024
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Commits on Aug 5, 2024

  1. refactor existing code

    @bmesuere
    bmesuere committed Aug 5, 2024
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  2. add fasta support

    @bmesuere
    bmesuere committed Aug 5, 2024
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  3. add tests

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    bmesuere committed Aug 5, 2024
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  4. Merge pull request #179 from unipept/next-unipept-fasta 

    Add fasta support
    @bmesuere
    bmesuere authored Aug 5, 2024
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Commits on Aug 6, 2024

  1. implement pept2ec

    @bmesuere
    bmesuere committed Aug 6, 2024
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  2. add pept2lca test

    @bmesuere
    bmesuere committed Aug 6, 2024
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  3. add pept2ec test

    @bmesuere
    bmesuere committed Aug 6, 2024
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  4. fix linter

    @bmesuere
    bmesuere committed Aug 6, 2024
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  5. add pept2funct

    @bmesuere
    bmesuere committed Aug 6, 2024
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  6. add pept2go

    @bmesuere
    bmesuere committed Aug 6, 2024
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  7. add pept2interpro

    @bmesuere
    bmesuere committed Aug 6, 2024
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  8. add pept2prot

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    bmesuere committed Aug 6, 2024
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  9. add pept2taxa

    @bmesuere
    bmesuere committed Aug 6, 2024
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  10. add peptinfo

    @bmesuere
    bmesuere committed Aug 6, 2024
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  11. add protinfo

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    bmesuere committed Aug 6, 2024
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  12. add taxa2lca

    @bmesuere
    bmesuere committed Aug 6, 2024
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  13. add taxonomy command

    @bmesuere
    bmesuere committed Aug 6, 2024
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  14. fix strings

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    bmesuere committed Aug 6, 2024
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  15. Merge pull request #180 from unipept/next-unipept-subcommands 

    Implement all unipept subcommands and tests
    @bmesuere
    bmesuere authored Aug 6, 2024
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Commits on Aug 7, 2024

  1. filter results

    @bmesuere
    bmesuere committed Aug 7, 2024
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  2. always flatten the results for csv so select fields works

    @bmesuere
    bmesuere committed Aug 7, 2024
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  3. don't crash on empty response

    @bmesuere
    bmesuere committed Aug 7, 2024
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  4. don't crash if the server doesn't return valid json

    @bmesuere
    bmesuere committed Aug 7, 2024
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  5. retry requests and log errors

    @bmesuere
    bmesuere committed Aug 7, 2024
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  6. linter

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    bmesuere committed Aug 7, 2024
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  7. add comments

    @bmesuere
    bmesuere committed Aug 7, 2024
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  8. Merge pull request #181 from unipept/next-rest 

    Finalize implementation
    @bmesuere
    bmesuere authored Aug 7, 2024
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  9. prepare to publish on npm

    @bmesuere
    bmesuere committed Aug 7, 2024
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  10. fix relative file paths

    @bmesuere
    bmesuere committed Aug 7, 2024
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