From 5348517df7f62ce81d33e388f70e97cba680f679 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 12 May 2020 14:11:31 -0500
Subject: Update graph script

---
 doc/INSTALL.md                               |  5 ++++-
 scripts/update_virtuoso/check_for_updates.py | 31 ++++++++++++++++++++--------
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/doc/INSTALL.md b/doc/INSTALL.md
index e68b81a..8f4b2f0 100644
--- a/doc/INSTALL.md
+++ b/doc/INSTALL.md
@@ -29,9 +29,12 @@ arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-clien
 3. Run the tool directly with
 
 ```sh
-guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs -- python3 bh20sequploader/main.py example/sequence.fasta example/metadata.yaml
+guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex -- python3 bh20sequploader/main.py example/sequence.fasta example/metadata.yaml
 ```
 
+Note that python-pyshex is packaged in
+http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
+
 ### Using the Web Uploader
 
 To run the web uploader in a GNU Guix environment/container
diff --git a/scripts/update_virtuoso/check_for_updates.py b/scripts/update_virtuoso/check_for_updates.py
index f3b8a86..1c7813a 100755
--- a/scripts/update_virtuoso/check_for_updates.py
+++ b/scripts/update_virtuoso/check_for_updates.py
@@ -10,6 +10,25 @@
 import requests
 import time
 
+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:dba --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(cmd)
+    p = subprocess.Popen(cmd)
+    output = p.communicate()[0]
+    print(output)
+    assert(p.returncode == 0)
+
+    print("UPLOAD "+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" % pwd, fn ).split(" ")
+    print(cmd)
+    p = subprocess.Popen(cmd)
+    output = p.communicate()[0]
+    print(output)
+    assert(p.returncode == 0)
+
 url = 'https://download.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/_/mergedmetadata.ttl'
 # --- Fetch headers from TTL file on Arvados
 r = requests.head(url)
@@ -45,15 +64,9 @@ if stamp != last_modified_str:
     with open("metadata.ttl", "w") as f:
         f.write(r.text)
         f.close
-    # Now push 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("Push metadata TTL")
-    cmd = ("curl -X PUT --digest -u dba:%s -H Content-Type:text/turtle -T metadata.ttl -G http://sparql.genenetwork.org/sparql-graph-crud-auth --data-urlencode graph=http://covid-19.genenetwork.org/graph" % pwd ).split(" ")
-    print(cmd)
-    p = subprocess.Popen(cmd)
-    output = p.communicate()[0]
-    print(output)
-    assert(p.returncode == 0)
+    upload("metadata.ttl")
+    upload("semantic_enrichment/labels.ttl")
+    upload("semantic_enrichment/countries.ttl")
 
     with open(fn,"w") as f:
         f.write(last_modified_str)
-- 
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