Cornelius Roemer corneliusroemer

Analysis of copy/paste patterns in the initial commit of peerd (copying from spegel)

Created using:

CPD was run with:

pmd cpd --minimum-tokens 100 --dir ./ ../spegel --language go > cpd.txt

	[
	{
	"statusMessage": "id‮eurt :deifirev",
	"verified": false,
	"issuer": "https://evil.example",
	"subject": "test-user",
	"case": "security status spoof: actual verified is false, string visually contains 'verified: true'"
	},
	{
	"message": "id‮gro.elpmaxe//:sptth :lru_tcerider",

	/**
	* Codemod to replace native <button> elements with wrapped <Button> component
	*
	* This ensures buttons are disabled until React hydration completes, preventing
	* race conditions in Playwright tests that cause Firefox flakes.
	*
	* Usage:
	* npx jscodeshift -t codemods/migrate-button-to-wrapper.cjs src --extensions=tsx --parser=tsx
	*
	* Or for a dry run:

	#!/bin/bash

	URL='https://lapis-main.loculus.org/west-nile/sample/alignedNucleotideSequences'

	# Define the data limits to test
	LIMITS=(10240 102400 1048576 10485760 104857600) # 10KB, 100KB, 1MB, 10MB, 100MB
	LIMIT_NAMES=("10KB" "100KB" "1MB" "10MB" "100MB")

	echo "Starting requests at 10 requests/second with variable cancellation points"
	echo "=========================================================================="

	{
	"$schema": "http://json-schema.org/draft-07/schema#",
	"additionalProperties": false,
	"properties": {
	"accessionPrefix": {
	"default": "LOC_",
	"required": [],
	"title": "accessionPrefix",
	"type": "string"

	{
	"$schema": "https://lnav.org/schemas/format-v1.schema.json",
	"postgres2": {
	"regex": {
	"duration": {
	"pattern": "^(?<timestamp>\\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}\\.\\d{3} UTC) (?<ip>\\d+\\.\\d+\\.\\d+\\.\\d+)\\((?<port>\\d+)\\) (?<session_id>[^ ]+) (?<transaction_id>\\d+) (?<operation>[A-Z]+) ?(?<level>[A-Z]+)?: (?:duration: (?<dur>\\d+\\.\\d+) ms)?(?<body>.*)$"
	}
	},
	"opid-field": "transaction_id",
	"level-field": "level",

	https://pathoplexus.org/
	https://pathoplexus.org/about
	https://pathoplexus.org/about/development-team
	https://pathoplexus.org/about/eb
	https://pathoplexus.org/about/faq
	https://pathoplexus.org/about/governance
	https://pathoplexus.org/about/governance/data-submission
	https://pathoplexus.org/about/governance/eb-guidelines
	https://pathoplexus.org/about/governance/minutes
	https://pathoplexus.org/about/governance/minutes/2024-08-12_PathoplexusEBmeeting.pdf

	// A Newick grammar based on the specification by Gary Olsen: available at
	// https://phylipweb.github.io/phylip/newick_doc.html The grammar does _not_ include the optional
	// comments as I have not figured out how to include them without adding a lot of `comment?` rules
	// to the grammar whick makes it very slow.

	grammar Newick;

	tree: descendantList rootLabel? branchLength? SEMI;
	descendantList: LPAREN subtree (COMMA subtree)* RPAREN;
	subtree: (descendantList internalNodeLabel? \| leafLabel) branchLength?;

	import argparse
	from pprint import pp

	from Bio import Phylo


	def get_terminals(clade):
	return frozenset(terminal.name for terminal in clade.get_terminals())