aboutsummaryrefslogtreecommitdiff
path: root/scripts/update_virtuoso
diff options
context:
space:
mode:
authorPjotr Prins2020-11-11 17:24:18 +0000
committerPjotr Prins2020-11-11 17:24:18 +0000
commit7f3c8b8486cd215b63f6d7c493ff40d0f0106b9f (patch)
tree5a1b7f923633c5bca2e803d2cc81a2bcbd97e774 /scripts/update_virtuoso
parent7fe362b6d9ee21bc585b618f9de468254aa5f4d7 (diff)
downloadbh20-seq-resource-7f3c8b8486cd215b63f6d7c493ff40d0f0106b9f.tar.gz
bh20-seq-resource-7f3c8b8486cd215b63f6d7c493ff40d0f0106b9f.tar.lz
bh20-seq-resource-7f3c8b8486cd215b63f6d7c493ff40d0f0106b9f.zip
Conflict in guix-deploy
Diffstat (limited to 'scripts/update_virtuoso')
-rwxr-xr-xscripts/update_virtuoso/check_for_updates.py8
1 files changed, 5 insertions, 3 deletions
diff --git a/scripts/update_virtuoso/check_for_updates.py b/scripts/update_virtuoso/check_for_updates.py
index f32d0df..9cb98b4 100755
--- a/scripts/update_virtuoso/check_for_updates.py
+++ b/scripts/update_virtuoso/check_for_updates.py
@@ -14,6 +14,8 @@ import sys
import os.path
import subprocess
+HOST="http://127.0.0.1:8890/"
+
assert(len(sys.argv)==4)
fn = sys.argv[1]
user = sys.argv[2]
@@ -36,7 +38,7 @@ 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(" ")
+ # cmd = ("curl --digest --user dba:%s --verbose --url -G http://xsparql.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}"
@@ -48,7 +50,7 @@ def upload(fn):
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)) )
+ cmd = (f"curl -X PUT --digest -u dba:%s -H Content-Type:text/turtle -T %s -G {HOST}/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()
@@ -79,7 +81,7 @@ if os.path.isfile(fn):
if force or 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))
+ cmd = (f"curl --digest -u dba:%s --verbose --url {HOST}/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]