#!/bin/bash  

# define resource
resource=glyconnect

# add the time stamped folder
cd /data/projects/glygen/downloads/$resource/

new_dir=$(date +%Y_%m_%d)
mkdir $new_dir

# download files to new folder
cd /data/projects/glygen/downloads/$resource/$new_dir

wget https://glyconnect.expasy.org/api/glycosylations?taxonomy=Homo%20sapiens
wget https://glyconnect.expasy.org/api/glycosylations?taxonomy=Rattus%20norvegicus
wget https://glyconnect.expasy.org/api/glycosylations?taxonomy=Mus%20musculus
wget 'https://glyconnect.expasy.org/api/glycosylations?taxonomy=Severe%20acute%20respiratory%20syndrome%20coronavirus%202%20(2019-nCoV)'
wget https://glyconnect.expasy.org/api/glycosylations?taxonomy=Drosophila%20melanogaster
wget https://glyconnect.expasy.org/api/glycosylations?taxonomy=Saccharomyces%20cerevisiae

# create symbolic links to the files according to species
cd /data/projects/glygen/downloads/$resource/$new_dir

ln -s "glycosylations?taxonomy=Drosophila melanogaster" glyconnect_fruitfly.json
ln -s "glycosylations?taxonomy=Homo sapiens" glyconnect_human.json
ln -s "glycosylations?taxonomy=Mus musculus" glyconnect_mouse.json
ln -s "glycosylations?taxonomy=Rattus norvegicus" glyconnect_rat.json
ln -s "glycosylations?taxonomy=Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)" glyconnect_sarscov2.json
ln -s "glycosylations?taxonomy=Saccharomyces cerevisiae" glyconnect_yeast.json

# update new folder permissions
chmod -R 775 /data/shared/glygen/downloads/$resource/$new_dir/

# create symbolic link
cd /data/projects/glygen/downloads/$resource/
rm current
ln -s $new_dir current