#!/bin/bash  

# define resource
resource=export_files

# add the glyconnect 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

echo "Copying compiled files to new directory..."

cp /data/projects/glygen/generated/datasets/compiled/glycan_synthesized.csv .
cp /data/projects/glygen/generated/datasets/compiled/hcv1a_proteoform_glycosylation_sites_literature.csv .
cp /data/projects/glygen/generated/datasets/compiled/human_proteoform_glycosylation_sites_o-gluc.csv .
cp /data/projects/glygen/generated/datasets/compiled/sarscov1_proteoform_glycosylation_sites_literature.csv .
cp /data/projects/glygen/generated/datasets/compiled/diabetes_glycomic_mapping.csv .

echo "Generating protein masterlist file..."

cd /software/glygen
python dump_protein_masterlist.py
mv /data/shared/glygen/downloads/$resource/glygen_protein_masterlist.csv /data/shared/glygen/downloads/$resource/$new_dir/

echo "Updating permissions and creating symbolic link..."

# 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

echo "Download Complete"