Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

1 files changed, 47 insertions, 17 deletions

diff --git a/scripts/db_enrichment/country_enrichment.py b/scripts/db_enrichment/country_enrichment.py
index 8dcf5f2..37329fb 100644
--- a/scripts/db_enrichment/country_enrichment.py
+++ b/scripts/db_enrichment/country_enrichment.py
@@ -1,3 +1,12 @@
+# This script by @LLTommy queries the main SPARQL end point to find what
+# collections are missing country information for GPS coordinates, such
+#
+# <http://www.wikidata.org/entity/Q657004> rdfs:label "Canterbury Region" ;
+#    ns1:P17 <http://www.wikidata.org/entity/Q664> ;
+#    ns1:P625 "Point(172.0 -43.6)" .
+#
+# See also the ./readme.md
+
 import requests
 import csv
 from rdflib import Graph, Literal, RDF, URIRef
@@ -30,30 +39,49 @@ def callSPARQL(query):
 
 g = Graph()
 
+test_query="""
+# Use with https://query.wikidata.org/
+SELECT DISTINCT ?a ?label ?country ?continent ?coor WHERE {
+    BIND (XXX as ?a) .
+    OPTIONAL {
+        ?a wdt:P625 ?coor.
+    }
+    ?a rdfs:label ?label .
+    ?a wdt:P17 ?country.
+    ?country rdfs:label ?country_label .
+    OPTIONAL {
+        ?country wdt:P30 ?continent.
+        ?continent rdfs:label ?continent_label
+        FILTER (lang(?continent_label)='en')
+    }
+    FILTER (lang(?country_label)='en')
+    FILTER (lang(?label)='en')
+}
+"""
 
+# wdt:P625 are GEO coordinates
 
 query = """
 construct {
-    ?a wdt:P625 ?c. 
+    ?a wdt:P625 ?c.
     ?a rdfs:label ?label .
-    ?a wdt:P17 ?country.      
-    ?country rdfs:label ?country_label . 
-    ?country wdt:P30 ?continent. 
-    ?continent rdfs:label ?continent_label   
-} WHERE 
-{ 
-    BIND (XXX as ?a) . 
-    ?a wdt:P625 ?c. 
+    ?a wdt:P17 ?country.
+    ?country rdfs:label ?country_label .
+    ?country wdt:P30 ?continent .
+    ?continent rdfs:label ?continent_label .
+} WHERE
+{
+    BIND (XXX as ?a) .
     ?a rdfs:label ?label .
-    ?a wdt:P17 ?country.      
-    ?country rdfs:label ?country_label .    
-    ?country wdt:P30 ?continent. 
+    ?a wdt:P17 ?country.
+    ?country rdfs:label ?country_label .
+    ?country wdt:P30 ?continent.
     ?continent rdfs:label ?continent_label
-    FILTER (lang(?continent_label)='en')           
+    FILTER (lang(?continent_label)='en')
     FILTER (lang(?country_label)='en')
-    FILTER (lang(?label)='en') 
-
-}  
+    FILTER (lang(?label)='en')
+    OPTIONAL { ?a wdt:P625 ?c }
+}
 """""
 
 outputFile = 'input_location.csv'
@@ -65,6 +93,8 @@ with open(outputFile, 'r') as csvfile:
         counter=counter+1
 
         try:
+            testq = test_query.replace("XXX", "<"+row[0]+">")
+            print(testq)
             tmpquery=query.replace("XXX", "<"+row[0]+">")
             print(tmpquery)
 
@@ -88,4 +118,4 @@ with open(outputFile, 'r') as csvfile:
             raise
 
 print(g.serialize(format='n3').decode("utf-8"))
-g.serialize(destination='enriched_ouput.txt', format='turtle')
\ No newline at end of file
+g.serialize(destination='enriched_output.txt', format='turtle')