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-rw-r--r--.guix-deploy2
-rwxr-xr-xscripts/update_virtuoso/check_for_updates.py14
2 files changed, 10 insertions, 6 deletions
diff --git a/.guix-deploy b/.guix-deploy
index f79340d..af4c83f 100644
--- a/.guix-deploy
+++ b/.guix-deploy
@@ -8,5 +8,5 @@ export GUILE_LOAD_COMPILED_PATH=$GUIX_PROFILE/share/guile/site/3.0/
ls $GUILE_LOAD_PATH
-env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_RUN_PORT=5067 FLASK_APP=bh20simplewebuploader/main.py flask run
+env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ $GUIX_PROFILE/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-redis python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_RUN_PORT=5067 FLASK_APP=bh20simplewebuploader/main.py flask run
diff --git a/scripts/update_virtuoso/check_for_updates.py b/scripts/update_virtuoso/check_for_updates.py
index 939a575..f32d0df 100755
--- a/scripts/update_virtuoso/check_for_updates.py
+++ b/scripts/update_virtuoso/check_for_updates.py
@@ -19,6 +19,10 @@ fn = sys.argv[1]
user = sys.argv[2]
pwd = sys.argv[3]
+force = False
+if fn== "--force":
+ force = True
+
no_cache = False
if fn == "--no-cache":
no_cache = True
@@ -51,12 +55,12 @@ def upload(fn):
print(out,err)
assert(p.returncode == 0)
-url = 'https://download.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/_/mergedmetadata.ttl'
+url = 'https://collections.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:
+if not force and not no_cache:
print(r.headers['Last-Modified'])
# --- Convert/validate time stamp
@@ -72,7 +76,7 @@ if os.path.isfile(fn):
stamp = file.read()
file.close
-if no_cache or stamp != last_modified_str:
+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))
@@ -85,7 +89,7 @@ if no_cache or stamp != last_modified_str:
upload(basedir+"/semantic_enrichment/labels.ttl")
upload(basedir+"/semantic_enrichment/countries.ttl")
- if not no_cache:
+ if force or not no_cache:
print("Fetch metadata TTL")
r = requests.get(url)
assert(r.status_code == 200)
@@ -93,7 +97,7 @@ if no_cache or stamp != last_modified_str:
f.write(r.text)
f.close
upload("metadata.ttl")
- if not no_cache:
+ if not force and not no_cache:
with open(fn,"w") as f:
f.write(last_modified_str)
else: