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

	{
	"$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())

	{"seqName":"England/MILK-28D52E2/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/CO-CDPHE-2102374275/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Wales/PHWC-PGY3IH/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Turkey/HSGM-F70/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/WI-CDC-QDX31282160/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"Canada/ON-SHL-21-02331/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"France/BRE-IPP48628/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"USA/CA-CDC-LC0396661/2021","nearestNodes":["B.1.617.2"]}
	{"seqName":"France/OCC-HCL021227635901/2021","nearestNodes":["B.1.617.2"]}

	import argparse
	from math import e
	from Bio import Entrez
	import openai

	def search_latest_papers(faculty_name, source="Pubmed", num_papers=5):
	papers_info = []

	if source == "Pubmed":
	Entrez.email = "[email protected]"