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authorPjotr Prins2020-11-10 05:02:57 -0600
committerPjotr Prins2020-11-10 05:24:14 -0600
commit11812bbf95ddf1771a159b7ef6580a9179c0cad1 (patch)
tree5ffdd9e857e5cbba8a6a946061d79a3b42f7a514 /scripts
parent74d46196ae69c0c557f64593910ada48d84b3654 (diff)
downloadbh20-seq-resource-11812bbf95ddf1771a159b7ef6580a9179c0cad1.tar.gz
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bh20-seq-resource-11812bbf95ddf1771a159b7ef6580a9179c0cad1.zip
virtuoso: Added a --no-cache option
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/update_virtuoso/check_for_updates.py34
1 files changed, 25 insertions, 9 deletions
diff --git a/scripts/update_virtuoso/check_for_updates.py b/scripts/update_virtuoso/check_for_updates.py
index 8761c8a..a63f4d1 100755
--- a/scripts/update_virtuoso/check_for_updates.py
+++ b/scripts/update_virtuoso/check_for_updates.py
@@ -4,7 +4,7 @@
#
# You can run this in a Guix container with
#
-# ~/opt/guix/bin/guix environment -C guix --ad-hoc python python-requests curl --network -- python3 ./scripts/update_virtuoso/check_for_updates.py cache.txt dba dba
+# ~/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.
#
@@ -19,6 +19,11 @@ 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))
@@ -29,6 +34,15 @@ def upload(fn):
# 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)
@@ -39,6 +53,7 @@ def upload(fn):
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)
print(r.headers['Last-Modified'])
@@ -49,14 +64,14 @@ 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
+# 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 stamp != last_modified_str:
+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))
@@ -69,12 +84,13 @@ if stamp != last_modified_str:
upload(basedir+"/semantic_enrichment/labels.ttl")
upload(basedir+"/semantic_enrichment/countries.ttl")
- 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
+ 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")
with open(fn,"w") as f:
f.write(last_modified_str)