mtholder

#!/bin/bash

# 
# Master script using MTH's hard-coded paths used to create darwin core
#   archives
# Requires do-dwca-export.sh available from https://gist.github.com/mtholder/f733a75fe1616af1841ded62aadb4f04
# See also https://github.com/SpeciesFileGroup/2025_workshop_on_taxon_names 

set -x
od=ott3.7.2-dwca

mtholder

#!/bin/bash
# 
# This requires a build of otcetera that from any branch that incorporates:
#  https://github.com/OpenTreeOfLife/otcetera/commit/f29521709b60ee2a4a8e754a7c3a111b22761718
# As of the writing of this gist that is only the dwca-dump of otcetera
# See also https://github.com/SpeciesFileGroup/2025_workshop_on_taxon_names 

set -x
od="${1}"
inp="${2}"

mtholder

#!/bin/sh
set -x
d=prev-`date +"%d-%b-%Y"`
if ! test -d "$d" ; then
	mkdir "$d" || exit
fi
if ! test -d "${d}/results" ; then
	mkdir "${d}/results" || exit
fi
if ! test -d "${d}/wrappers" ; then

mtholder

#!/bin/bash
curl 'http://www.timetree.org/references' > studies.html
grep citation_data studies.html | sed -E 's:.*citation_data/::' | sed -E 's/".*//' > ids.txt
for i in `cat ids.txt` ; do
    echo $i
    if ! test -f "${i}.tre" ; then
        python grab.py "$i" > "${i}.tre" || exit 1
    fi
    sleep 2
done

mtholder

#!/usr/bin/env python
import requests
import sys
durl = 'http://www.timetree.org/ajax/newick/publishedtree/download'
for i in sys.argv[1:]:
    url = 'http://www.timetree.org/api/widget/citation_data/{i}'.format(i=i)
    s = requests.Session()
    r = s.get(url)
    nr = s.post(durl, data={'export': 'newick', 'rank': 'na'})
    nr.raise_for_status()

mtholder

#!/bin/bash
if ! test -d cruft ; then
    mkdir cruft
fi
for i in ott*.tre ; do
    j=`echo ${i} | sed -E 's/^ott//' | sed -E 's/\.tre//'`
    echo $j >&2
    tail -n1 ${i} > cruft/tax.tre
    ntax=`otc-degree-distribution cruft/tax.tre 2>&1 | tail -n2 | head -n1 | awk '{print $1}'`
    nsoln=`otc-degree-distribution ../subproblem_solutions/${i} 2>&1 | tail -n2 | head -n1 | awk '{print $1}'`

mtholder

#!/usr/bin/env python3
"""Tool to compress tree_slice_comparison JSON

otc-explain-phylo-diffs writes a form of this JSON in which multiple
    adjacent slices of the tree can have the same topology for each
    of the two trees that were compared.
This tool merges adjacent slices that are not differing in topology
    to produces a terser representation that is easier to display

Roughly speaking, the schema of the JSON is:

mtholder

#!/bin/bash
n="$1"
if test -z $n ; then
	echo "Expecting a machine name for the opentreeoflife.org domain as first arg"
	exit 1
fi
if test -z $2 ; then
	u=admin
else
	u="${2}"

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"