Code

Reimplement the CLI in TypeScript#172

Code

Merged

bmesuere merged 86 commits intomainunipept/unipept-cli:mainfrom nextunipept/unipept-cli:nextCopy head branch name to clipboardNov 28, 2024

+7,105-6,513

Commits

Commits on Jun 17, 2024

• remove unneeded files

  bmesuere

  committed
  a0a7c6a

• require node 22 to use fetch

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• yarn init

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  02c2af5

• get basic version working

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• move to bin folder

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• move to typescript

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• cleanup

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• add uniprot run command

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  committed
  dcaee59

Commits on Jun 18, 2024

• Merge pull request #173 from unipept/next-uniprot

  Show description for 4fc9216
  bmesuere

  authored
  4fc9216

• refactor

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  committed
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• add eslint

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• add github action

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• refactor

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• add tests

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• add CI

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• add a bit more comments

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Commits on Jun 20, 2024

• Merge pull request #174 from unipept/next-testing

  Show description for b0c9868
  bmesuere

  authored
  b0c9868

• implement peptfilter

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  committed
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• write tests

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• optimize performance

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• fix tests

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• lint

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• add comments

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Commits on Jun 21, 2024

• implement prot2pept

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• add tests

  bmesuere

  committed
  c24382a

• Merge pull request #175 from unipept/next-peptfilter

  Show description for b071301
  bmesuere

  authored
  b071301

• Update lib/commands/prot2pept.ts

  Show description for f0346d3
  

  bmesuere

  and

  pverscha

  authored
  f0346d3

• Merge pull request #176 from unipept/next-prot2pept

  Show description for ad82132
  bmesuere

  authored
  ad82132

Commits on Jul 2, 2024

• implement basic version of the pept2lca command

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  committed
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• use post and set headers

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• move processing loop to the super class

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• implement input batches

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• use different input options if available

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• parse more parameters

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• add a few utility methods

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Commits on Jul 8, 2024

• add basic csv formatter

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• write to file if needed

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• support no-header

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• fix lint

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  committed
  beb414c

Commits on Jul 30, 2024

• add test for unipept

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  committed
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• add formatter tests

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• linter

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• refactor passing arguments programatically

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Commits on Jul 31, 2024

• add basic command runner tests

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  committed
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Commits on Aug 1, 2024

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

  Show description for 0e377b2
  bmesuere

  authored
  0e377b2

• implement json formatter

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  committed
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• add tests for json formatter

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• add xml formatter

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• add tests for xml formatter

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• fix linter

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  committed
  ed97bab

• Merge pull request #178 from unipept/next-unipept-2

  Show description for c9aa3aa
  bmesuere

  authored
  c9aa3aa

Commits on Aug 5, 2024

• refactor existing code

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  committed
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• add fasta support

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• add tests

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  committed
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• Merge pull request #179 from unipept/next-unipept-fasta

  Show description for eac4282
  bmesuere

  authored
  eac4282

Commits on Aug 6, 2024

• implement pept2ec

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  committed
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• add pept2lca test

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  committed
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• add pept2ec test

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  committed
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• fix linter

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  committed
  d7ed283

• add pept2funct

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  committed
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• add pept2go

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• add pept2interpro

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• add pept2prot

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• add pept2taxa

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• add peptinfo

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• add protinfo

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• add taxa2lca

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• add taxonomy command

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• fix strings

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  committed
  e7c2365

• Merge pull request #180 from unipept/next-unipept-subcommands

  Show description for cc21dad
  bmesuere

  authored
  cc21dad

Commits on Aug 7, 2024

• filter results

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  committed
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• always flatten the results for csv so select fields works

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• don't crash on empty response

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• don't crash if the server doesn't return valid json

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• retry requests and log errors

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• linter

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  committed
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• add comments

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  committed
  0579bec

• Merge pull request #181 from unipept/next-rest

  Show description for 0dd1b12
  bmesuere

  authored
  0dd1b12

• prepare to publish on npm

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  committed
  e66da23

• fix relative file paths

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  2472da2

Commits on Nov 27, 2024

• typo

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  authored
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• minor tweaks

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• Merge branch 'next' of github.com:unipept/unipept-cli into next

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Commits on Nov 28, 2024

• more flexible test matching

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• use integevers as input for taxa2lca and taxonomy

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• bump version

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