From 01c49901aac2a41e5c06a5c5c0c508ebf69e0922 Mon Sep 17 00:00:00 2001
From: xgaia <xgaia@gmx.com>
Date: Wed, 24 Jul 2019 09:25:31 +0200
Subject: [PATCH] remove json file and store prefix in SparqlQuery

---
 abstractor                   | 16 ++++------------
 libabstractor/SparqlQuery.py | 15 +++++++++++++--
 prefixes.json                | 11 -----------
 setup.py                     |  4 ++--
 4 files changed, 19 insertions(+), 27 deletions(-)
 delete mode 100644 prefixes.json

diff --git a/abstractor b/abstractor
index ca38cb8..a066bff 100644
--- a/abstractor
+++ b/abstractor
@@ -1,7 +1,6 @@
 #! /usr/bin/python3
 
 import argparse
-import json
 import textwrap
 from libabstractor.SparqlQuery import SparqlQuery
 
@@ -22,13 +21,6 @@ class Abstractor(object):
 
         self.args = parser.parse_args()
 
-        # Get common prefix from the json file
-        with open("prefixes.json", "r") as file:
-            file_content = file.read()
-
-        self.prefixes = json.loads(file_content)
-        self.prefixes[":"] = self.args.prefix
-
     def get_entities_and_relations(self):
         """Get all entities and relations
 
@@ -37,7 +29,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix, self.prefixes)
+        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?rel ?valueType
@@ -63,7 +55,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix, self.prefixes)
+        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?attr
@@ -87,7 +79,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix, self.prefixes)
+        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?attr
@@ -106,7 +98,7 @@ class Abstractor(object):
 
     def main(self):
         """main"""
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix, self.prefixes)
+        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
 
         with open(self.args.output, "w") as file:
 
diff --git a/libabstractor/SparqlQuery.py b/libabstractor/SparqlQuery.py
index dac5018..b9b81c3 100644
--- a/libabstractor/SparqlQuery.py
+++ b/libabstractor/SparqlQuery.py
@@ -4,7 +4,7 @@
 class SparqlQuery(object):
     """SPARQL methods"""
 
-    def __init__(self, endpoint, prefix, prefixes):
+    def __init__(self, endpoint, prefix):
         """Init
 
         Parameters
@@ -18,7 +18,18 @@ def __init__(self, endpoint, prefix, prefixes):
         """
         self.endpoint = endpoint
         self.prefix = prefix
-        self.prefixes = prefixes
+        self.prefixes = {
+            "owl:": "http://www.w3.org/2002/07/owl#",
+            "rdf:": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+            "rdfs:": "http://www.w3.org/2000/01/rdf-schema#",
+            "dc:": "http://purl.org/dc/elements/1.1/",
+            "prov:": "http://www.w3.org/ns/prov#",
+            "xsd:": "http://www.w3.org/2001/XMLSchema#",
+            "skos:": "http://www.w3.org/2004/02/skos/core#",
+            "chebi:": "http://purl.obolibrary.org/obo/",
+            "drugbankdrugs:": "http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugs/",
+            ":": self.prefix
+        }
 
     def get_sparl_prefix(self):
         """Get a SPARQL prefix string
diff --git a/prefixes.json b/prefixes.json
deleted file mode 100644
index b0a9c9e..0000000
--- a/prefixes.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
-    "owl:": "http://www.w3.org/2002/07/owl#",
-    "rdf:": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
-    "rdfs:": "http://www.w3.org/2000/01/rdf-schema#",
-    "dc:": "http://purl.org/dc/elements/1.1/",
-    "prov:": "http://www.w3.org/ns/prov#",
-    "xsd:": "http://www.w3.org/2001/XMLSchema#",
-    "skos:": "http://www.w3.org/2004/02/skos/core#",
-    "chebi:": "http://purl.obolibrary.org/obo/",
-    "drugbankdrugs:": "http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugs/"
-}
diff --git a/setup.py b/setup.py
index ce0b602..e556b6c 100644
--- a/setup.py
+++ b/setup.py
@@ -2,12 +2,12 @@
 
 setup(
     name='abstractor',
-    version='1.0.4',
+    version='1.0.5',
     description='Abstraction generator for AskOmics, from a distant SPARQL endpoint',
     author='Xavier Garnier',
     author_email='xavier.garnier@irisa.fr',
     url='https://github.com/xgaia/abstractor',
-    download_url='https://github.com/xgaia/abstractor/archive/1.0.4.tar.gz',
+    download_url='https://github.com/xgaia/abstractor/archive/1.0.5.tar.gz',
     install_requires=['SPARQLWrapper'],
     packages=find_packages(),
     license='AGPL',