mtholder

#!/bin/bash
n=${1}
if test -z $n ; then
	echo "Takes a number argument n that, as ot${n}.opentreeoflife.org should be the machine to update" 
	exit 1
fi
u=${2}
if test -z $u ; then
	u=admin
fi

mtholder

#!/bin/bash
i="${1}"
if test -z $i ; then
	echo "Number like 51 for ot51 needed as an arg"
	exit 1
fi
echo "fetching cert from ot$i to compare to a local copy of a cert from ot50"
if echo | openssl s_client -servername ot${i}.opentreeoflife.org -connect ot${i}.opentreeoflife.org:443 | sed -ne '/-BEGIN CERTIFICATE-/,/-END CERTIFICATE-/p' > ot${i}-certificate.crt 
diff ot50-certificate.crt ot${i}-certificate.crt  ; then
	echo "Success"

mtholder

#!/usr/bin/env python3


def func(arg):
    a_var.append(1)
    loc_a_var = arg
    b_var = list(arg)
    print('func({} with id: {} and ids: {})'.format(repr(arg), id(arg), [id(i) for i in arg]))
    print('  locals: {}'.format({k: id(v) for k, v in locals().items() if not k.startswith('__')}))
    print('  globals: {}'.format({k: id(v) for k, v in globals().items() if not k.startswith('__')}))

mtholder

#!/usr/env python
""" Example of wrapping a call to gnparser from python
See https://gitlab.com/gogna/gnparser#command-line

Adapted based on instructions on
    https://medium.com/learning-the-go-programming-language/calling-go-functions-from-other-languages-4c7d8bcc69bf
"""
import ctypes
import json
lib = ctypes.cdll.LoadLibrary("./libgnparser.so")

mtholder

#!/bin/bash
inpdir=$1
if ! test -d "${inpdir}" ; then
	echo "$0 must be passed in a directory of subproblems (with ott###.tre files)."
	exit 1
fi
rpwd=`realpath .`
rpid=`realpath $inpdir`
if test "${rpwd}" = "${rpid}" ; then
	echo "$0 Cannot be run in place."

mtholder

#!/usr/bin/env python3
'''Reverses the order of the first n-1 lines of a file
and writes it to stdout.
'''
import sys
fp = sys.argv[1]
with open(fp, 'r', encoding='utf-8') as inp:
    lines = inp.readlines()
last = lines.pop(-1)
lines.reverse()

mtholder

#!/bin/env python
import json
import sys
import subprocess
import itertools


inpjson = 'subproblem_size_summary.json'
with open(inpjson, 'r', encoding='utf-8') as inp:
    summary_blob = json.load(inp)

mtholder

#!/bin/env python
import json
import sys
import subprocess
import itertools

DEBUG = False

def count_tips_and_inf_splits(fn):
    out = subprocess.check_output(['otc-degree-distribution', fn], stderr=subprocess.DEVNULL).decode('utf-8')

mtholder

#!/bin/bash

otc-tree-tool --indented-table labelled_supertree/labelled_supertree_simplified_ottnames.tre > subproblems/indented-table.txt
cat subproblems/indented-table.txt | sed -E '/ +mrca/d' | sed -E 's/.* ott([0-9]+) : ([0-9]+)/"ott\1": \2,/' > num_tips_for_ott_internals_in_labelled_tree.json
rm subproblems/indented-table.txt

mtholder

#!/bin/bash
# This needs to be made part of the propinquity process.
# 	MTH ran steps that made up the basis of this before the
#	Jan 2020 SSB workshop. So the resulting file will be in
#	the https://files.opentreeoflife.org/synthesis/opentree12.3/opentree12.3/subproblems/
#	folder, but (perversely enough) not in the tar archive at https://files.opentreeoflife.org/synthesis/opentree12.3/opentree12.3.tgz
# If all goes as planned, we'll start adding this to the tree build process so that it will be in 
#	builds and archives made after 12.3

# This is to be run with the working directory being the propinquity