Code

fix: Add pubmlst utils#192

Code

Merged

karlnyr merged 39 commits intomasterClinical-Genomics/microSALT:masterfrom add-pubmlst-utilsClinical-Genomics/microSALT:add-pubmlst-utilsCopy head branch name to clipboardJan 8, 2025

+1,023-750

Commits

Commits on Dec 6, 2024

• PubMLST authentication utilities

  ahdamin

  committed
  45ff7d7

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• Refactor PubMLST data fetching

  ahdamin

  committed
  a2864c6

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Commits on Dec 7, 2024

• Add quotations

  ahdamin

  authored
  4ed5881

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Commits on Dec 9, 2024

• Add rauth v0.7.3

  ahdamin

  committed
  4802515

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Commits on Dec 11, 2024

• Add pubmlst config

  ahdamin

  committed
  7ea4aa9

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• Add pubmlst config loader

  ahdamin

  committed
  b740bde

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• Add session token validation

  ahdamin

  committed
  279c3bc

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• Improve OAuth credentials usage

  ahdamin

  committed
  705dbdc

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• Read credentials from config

  ahdamin

  committed
  60a3cde

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• dd OAuth header generation

  ahdamin

  committed
  1c0c62c

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• Refactor PubMLST fetch process

  ahdamin

  committed
  9265ee0

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Commits on Dec 12, 2024

• Update database query checks

  ahdamin

  committed
  1a00339

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• Add logger to authentication

  ahdamin

  committed
  b98b2d3

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• Handle nested db entries and kip non-sequence dbs

  ahdamin

  committed
  882d0c8

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• Remove credentials file

  ahdamin

  committed
  1dc4c91

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• Replace print with logger

  ahdamin

  committed
  d7567a0

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• Add reusable path resolver

  ahdamin

  committed
  bb8b172

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• Enhance logging for Auth

  ahdamin

  committed
  cd51465

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• Match organisms

  ahdamin

  committed
  f27b9f7

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Commits on Dec 13, 2024

• Handle MLST profiles in CSV format

  ahdamin

  committed
  f1de77f

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• Add PubMLST congis and improve config path checks

  ahdamin

  committed
  817bd90

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• Improve config path handling

  ahdamin

  committed
  826bfec

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• Replace f-strings with format

  ahdamin

  committed
  95c4ba2

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• Refactor path handling functions

  ahdamin

  committed
  d01cc5a

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• Improve exception handling

  ahdamin

  committed
  5e129f9

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• Ensure directories exist

  ahdamin

  committed
  f8c8c04

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• Add check_database_metadata

  ahdamin

  committed
  2b87fca

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• Fix methods position

  ahdamin

  committed
  1235c6a

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• Fix logger

  ahdamin

  committed
  f70e836

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Commits on Dec 16, 2024

• Add client, constants, and exceptions

  ahdamin

  committed
  8268a3f

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• Fix checks for pubmlst config

  ahdamin

  committed
  21e3094

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Commits on Dec 17, 2024

• Add URL rules for pubmlst db

  ahdamin

  committed
  941bd53

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• Add InvalidURLError

  ahdamin

  committed
  d7a7c92

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• Add URL parsing helper

  ahdamin

  committed
  9325d01

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• Add MLST scheme retrieval & URL parsing helper

  ahdamin

  committed
  a5f4c71

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• Replace manual HTTP requests with PubMLSTClient

  ahdamin

  committed
  977a240

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• Remove client object

  ahdamin

  committed
  d36ba0d

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• Fix tests

  Vince-janv

  committed
  6153cff

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Commits on Jan 8, 2025

• Merge branch 'master' into add-pubmlst-utils

  karlnyr

  authored
  2d13f27

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