Code

Add pubmlst utils#188

Code

Merged

diitaz93 merged 38 commits intorc410Clinical-Genomics/microSALT:rc410from add-pubmlst-utilsClinical-Genomics/microSALT:add-pubmlst-utilsCopy head branch name to clipboardDec 18, 2024

+1,025-750

Commits

Commits on Dec 6, 2024

• PubMLST authentication utilities

  ahdamin

  committed
  45ff7d7

  Copy full SHA for 45ff7d7

• Refactor PubMLST data fetching

  ahdamin

  committed
  a2864c6

  Copy full SHA for a2864c6

Commits on Dec 7, 2024

• Add quotations

  ahdamin

  authored
  4ed5881

  Copy full SHA for 4ed5881

Commits on Dec 9, 2024

• Add rauth v0.7.3

  ahdamin

  committed
  4802515

  Copy full SHA for 4802515

Commits on Dec 11, 2024

• Add pubmlst config

  ahdamin

  committed
  7ea4aa9

  Copy full SHA for 7ea4aa9

• Add pubmlst config loader

  ahdamin

  committed
  b740bde

  Copy full SHA for b740bde

• Add session token validation

  ahdamin

  committed
  279c3bc

  Copy full SHA for 279c3bc

• Improve OAuth credentials usage

  ahdamin

  committed
  705dbdc

  Copy full SHA for 705dbdc

• Read credentials from config

  ahdamin

  committed
  60a3cde

  Copy full SHA for 60a3cde

• dd OAuth header generation

  ahdamin

  committed
  1c0c62c

  Copy full SHA for 1c0c62c

• Refactor PubMLST fetch process

  ahdamin

  committed
  9265ee0

  Copy full SHA for 9265ee0

Commits on Dec 12, 2024

• Update database query checks

  ahdamin

  committed
  1a00339

  Copy full SHA for 1a00339

• Add logger to authentication

  ahdamin

  committed
  b98b2d3

  Copy full SHA for b98b2d3

• Handle nested db entries and kip non-sequence dbs

  ahdamin

  committed
  882d0c8

  Copy full SHA for 882d0c8

• Remove credentials file

  ahdamin

  committed
  1dc4c91

  Copy full SHA for 1dc4c91

• Replace print with logger

  ahdamin

  committed
  d7567a0

  Copy full SHA for d7567a0

• Add reusable path resolver

  ahdamin

  committed
  bb8b172

  Copy full SHA for bb8b172

• Enhance logging for Auth

  ahdamin

  committed
  cd51465

  Copy full SHA for cd51465

• Match organisms

  ahdamin

  committed
  f27b9f7

  Copy full SHA for f27b9f7

Commits on Dec 13, 2024

• Handle MLST profiles in CSV format

  ahdamin

  committed
  f1de77f

  Copy full SHA for f1de77f

• Add PubMLST congis and improve config path checks

  ahdamin

  committed
  817bd90

  Copy full SHA for 817bd90

• Improve config path handling

  ahdamin

  committed
  826bfec

  Copy full SHA for 826bfec

• Replace f-strings with format

  ahdamin

  committed
  95c4ba2

  Copy full SHA for 95c4ba2

• Refactor path handling functions

  ahdamin

  committed
  d01cc5a

  Copy full SHA for d01cc5a

• Improve exception handling

  ahdamin

  committed
  5e129f9

  Copy full SHA for 5e129f9

• Ensure directories exist

  ahdamin

  committed
  f8c8c04

  Copy full SHA for f8c8c04

• Add check_database_metadata

  ahdamin

  committed
  2b87fca

  Copy full SHA for 2b87fca

• Fix methods position

  ahdamin

  committed
  1235c6a

  Copy full SHA for 1235c6a

• Fix logger

  ahdamin

  committed
  f70e836

  Copy full SHA for f70e836

Commits on Dec 16, 2024

• Add client, constants, and exceptions

  ahdamin

  committed
  8268a3f

  Copy full SHA for 8268a3f

• Fix checks for pubmlst config

  ahdamin

  committed
  21e3094

  Copy full SHA for 21e3094

Commits on Dec 17, 2024

• Add URL rules for pubmlst db

  ahdamin

  committed
  941bd53

  Copy full SHA for 941bd53

• Add InvalidURLError

  ahdamin

  committed
  d7a7c92

  Copy full SHA for d7a7c92

• Add URL parsing helper

  ahdamin

  committed
  9325d01

  Copy full SHA for 9325d01

• Add MLST scheme retrieval & URL parsing helper

  ahdamin

  committed
  a5f4c71

  Copy full SHA for a5f4c71

• Replace manual HTTP requests with PubMLSTClient

  ahdamin

  committed
  977a240

  Copy full SHA for 977a240

• Remove client object

  ahdamin

  committed
  d36ba0d

  Copy full SHA for d36ba0d

• Fix tests

  Vince-janv

  committed
  6153cff

  Copy full SHA for 6153cff