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#! /usr/bin/env python3
#
# Check for updates on Arvados, pull the TTL and push into Virtuoso
#
# You can run this in a Guix container with
#
# ~/opt/guix/bin/guix environment -C guix --ad-hoc raptor2 python python-requests curl --network -- python3 ./scripts/update_virtuoso/check_for_updates.py cache.txt dba dba
#
# Note you'll need to run from the root dir. Remove the ./cache.txt file if you want to force an update.
#
import requests
import time
import sys
import os.path
import subprocess
assert(len(sys.argv)==4)
fn = sys.argv[1]
user = sys.argv[2]
pwd = sys.argv[3]
no_cache = False
if fn == "--no-cache":
no_cache = True
print("Skipping cache check and download of metadata.ttl")
scriptdir = os.path.dirname(os.path.realpath(__file__))
print(scriptdir)
basedir = os.path.dirname(os.path.dirname(scriptdir))
def upload(fn):
# Upload into Virtuoso using CURL
# cmd = "curl -X PUT --digest -u dba:dba -H Content-Type:text/turtle -T metadata.ttl -G http://localhost:8890/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph".split(" ")
# print("DELETE "+fn)
# cmd = ("curl --digest --user dba:%s --verbose --url -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph -X DELETE" % pwd).split(" ")
print("VALIDATE "+fn)
cmd = f"rapper -i turtle {fn}"
print(cmd)
p = subprocess.Popen(cmd.split(" "),stdout=subprocess.PIPE,stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
print(out,err)
assert(p.returncode == 0)
print("UPLOADING "+fn)
cmd = ("curl -X PUT --digest -u dba:%s -H Content-Type:text/turtle -T %s -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph/%s" % (pwd, fn, os.path.basename(fn)) )
print(cmd)
p = subprocess.Popen(cmd.split(" "),stdout=subprocess.PIPE,stderr=subprocess.PIPE)
out, err = p.communicate()
print(out,err)
assert(p.returncode == 0)
url = 'https://download.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/_/mergedmetadata.ttl'
# --- Fetch headers from TTL file on Arvados
# curl --head https://download.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/_/mergedmetadata.ttl
r = requests.head(url)
print(r.headers)
if not no_cache:
print(r.headers['Last-Modified'])
# --- Convert/validate time stamp
# ValueError: time data 'Tue, 21 Apr 2020 23:47:43 GMT' does not match format '%a %b %d %H:%M:%S %Y'
last_modified_str = r.headers['Last-Modified']
t_stamp = time.strptime(last_modified_str,"%a, %d %b %Y %H:%M:%S %Z" )
print(t_stamp)
# OK, it works, now check last stored value in the cache
stamp = None
if os.path.isfile(fn):
file = open(fn,"r")
stamp = file.read()
file.close
if no_cache or stamp != last_modified_str:
print("Delete graphs")
for graph in ["labels.ttl", "metadata.ttl", "countries.ttl"]:
cmd = ("curl --digest -u dba:%s --verbose --url http://127.0.0.1:8890/sparql-graph-crud-auth?graph=http://covid-19.genenetwork.org/graph/%s -X DELETE" % (pwd, graph))
print(cmd)
p = subprocess.Popen(cmd.split(" "))
output = p.communicate()[0]
print(output)
# assert(p.returncode == 0) -> may prevent update
upload(basedir+"/semantic_enrichment/labels.ttl")
upload(basedir+"/semantic_enrichment/countries.ttl")
if not no_cache:
print("Fetch metadata TTL")
r = requests.get(url)
assert(r.status_code == 200)
with open("metadata.ttl", "w") as f:
f.write(r.text)
f.close
upload("metadata.ttl")
if not no_cache:
with open(fn,"w") as f:
f.write(last_modified_str)
else:
print("Metadata is up to date")
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