Merge pull request #1 from xgaia/release_1.1.0_federated

Release 1.1.0
askomics · Oct 8, 2019 · 3a659f1 · 3a659f1
2 parents 5d2b2f0 + ff1b8da
commit 3a659f1
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Showing 3 changed files with 16 additions and 14 deletions.
diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ First, clone the git repo
 
 ```bash
 # clone
-git clone https://github.com/xgaia/abstractor.git
+git clone https://github.com/askomics/abstractor.git
 # cd
 cd abstractor
 ```
@@ -70,4 +70,4 @@ abstractor -e <endpoint_url> -p <entity_prefix> -o <output_file>
 abstractor -e "https://sparql.nextprot.org" -p "http://nextprot.org/rdf#" -o "abstraction.ttl"
 ```
 
-Obtained TTL file can be used with [AskOmics](https://github.com/xgaia/flaskomics)
+Obtained TTL file can be used with [AskOmics](https://github.com/askomics/flaskomics)
diff --git a/abstractor b/abstractor
@@ -16,7 +16,8 @@ class Abstractor(object):
         parser = argparse.ArgumentParser(description="Generate AskOmics abstraction from a SPARQL endpoint")
 
         parser.add_argument("-e", "--endpoint", type=str, help="SPARQL enpoint url", required=True)
-        parser.add_argument("-p", "--prefix", type=str, help="SPARQL prefix uri for :", required=True)
+        parser.add_argument("-p", "--endpoint-prefix", type=str, help="Endpoint prefix", required=True)
+        parser.add_argument("--askomics-prefix", type=str, help="AskOmics prefix", default="http://www.semanticweb.org/user/ontologies/2018/1#")
         parser.add_argument("-o", "--output", type=str, help="Output ttl file", default="abstraction.ttl")
 
         self.args = parser.parse_args()
@@ -29,7 +30,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
+        sparql = SparqlQuery(self.args.endpoint, self.args.askomics_prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?rel ?valueType
@@ -55,7 +56,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
+        sparql = SparqlQuery(self.args.endpoint, self.args.askomics_prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?attr
@@ -79,7 +80,7 @@ class Abstractor(object):
         list, list
             header and results
         """
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
+        sparql = SparqlQuery(self.args.endpoint, self.args.askomics_prefix)
 
         query = textwrap.dedent('''
         SELECT DISTINCT ?entity ?attr
@@ -98,7 +99,7 @@ class Abstractor(object):
 
     def main(self):
         """main"""
-        sparql = SparqlQuery(self.args.endpoint, self.args.prefix)
+        sparql = SparqlQuery(self.args.endpoint, self.args.askomics_prefix)
 
         with open(self.args.output, "w") as file:
 
@@ -119,7 +120,7 @@ class Abstractor(object):
                 relation = result["rel"] if "rel" in result else None
                 relation_range = result["valueType"] if "valueType" in result else None
 
-                if not entity.startswith(self.args.prefix):
+                if not entity.startswith(self.args.endpoint_prefix):
                     continue
 
                 # Write ttl for entities
@@ -129,6 +130,7 @@ class Abstractor(object):
                     <{}> a :entity ,
                             :startPoint ,
                             owl:Class ;
+                            :instancesHaveNoLabels true ;
                         rdfs:label "{}" .
                     '''.format(
                         entity,
@@ -137,7 +139,7 @@ class Abstractor(object):
 
                     file.write(ttl)
 
-                if not relation.startswith(self.args.prefix):
+                if not relation.startswith(self.args.endpoint_prefix):
                     continue
 
                 # write ttl for relations
@@ -168,7 +170,7 @@ class Abstractor(object):
                 entity = result["entity"]
                 attribute = result["attr"] if "attr" in result else None
 
-                if not entity.startswith(self.args.prefix) and attribute.startswith(self.args.prefix):
+                if not entity.startswith(self.args.endpoint_prefix) and attribute.startswith(self.args.endpoint_prefix):
                     continue
 
                 if attribute:
@@ -195,7 +197,7 @@ class Abstractor(object):
                 entity = result["entity"]
                 attribute = result["attr"] if "attr" in result else None
 
-                if not entity.startswith(self.args.prefix) and attribute.startswith(self.args.prefix):
+                if not entity.startswith(self.args.endpoint_prefix) and attribute.startswith(self.args.endpoint_prefix):
                     continue
 
                 if attribute:

diff --git a/setup.py b/setup.py
@@ -2,12 +2,12 @@
 
 setup(
     name='abstractor',
-    version='1.0.5',
+    version='1.1.0',
     description='Abstraction generator for AskOmics, from a distant SPARQL endpoint',
     author='Xavier Garnier',
     author_email='[email protected]',
-    url='https://github.com/xgaia/abstractor',
-    download_url='https://github.com/xgaia/abstractor/archive/1.0.5.tar.gz',
+    url='https://github.com/askomics/abstractor',
+    download_url='https://github.com/askomics/abstractor/archive/1.1.0.tar.gz',
     install_requires=['SPARQLWrapper'],
     packages=find_packages(),
     license='AGPL',