env vars for admin username, fix for decoding string

CHANGELOG.md

@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [v2.15-1.2.1]
+
+### Added
+- Environment vars for sparql endpoint and db admin username.
+
+### Fixed
+- String decode error for 'file' type vocabularies.
+
 ## [v2.15-1.2.0]
 
 ### Added
@@ -32,3 +40,4 @@ Initial version
 [v2.15-1.0.0]: https://github.com/knaw-huc/sd-skosmos/releases/tag/v2.15-1.0-RC4
 [v2.15-1.1.0]: https://github.com/knaw-huc/sd-skosmos/releases/tag/v2.15-1.1.0
 [v2.15-1.2.0]: https://github.com/knaw-huc/sd-skosmos/releases/tag/v2.15-1.2.0
+[v2.15-1.2.1]: https://github.com/knaw-huc/sd-skosmos/releases/tag/v2.15-1.2.1

config-docker-compose.ttl

@@ -19,8 +19,8 @@
     # SPARQL endpoint
     # a local Fuseki server is usually on localhost:3030
     # skosmos:sparqlEndpoint <http://host.docker.internal:7200/repositories/test-skosmos> ;
-    skosmos:sparqlEndpoint <http://host.docker.internal:7200/repositories/skosmos> ;
-    # skosmos:sparqlEndpoint <${SPARQL_ENDPOINT}> ;
+#    skosmos:sparqlEndpoint <http://host.docker.internal:7200/repositories/skosmos> ;
+     skosmos:sparqlEndpoint <${SPARQL_ENDPOINT}> ;
     # use the dev.finto.fi endpoint where the example vocabularies reside
     # skosmos:sparqlEndpoint <http://api.dev.finto.fi/sparql> ;
     # sparql-query extension, or "Generic" for plain SPARQL 1.1

src/graphdb.py

@@ -9,6 +9,7 @@
 from SPARQLWrapper import SPARQLWrapper, JSON, POST, DIGEST
 
 admin_password = os.environ.get("ADMIN_PASSWORD", '')
+admin_username = os.environ.get("ADMIN_USERNAME", 'admin')
 endpoint = os.environ.get("SPARQL_ENDPOINT", '')
 
 
@@ -29,7 +30,7 @@ def setup_graphdb() -> None:
                 f"{endpoint}",
                 headers=headers,
                 data=fp,
-                auth=('admin', admin_password),
+                auth=(admin_username, admin_password),
                 timeout=60
             )
         print(f"CREATED GRAPHDB[{endpoint}] DB[skosmos.tdb]")
@@ -72,7 +73,7 @@ def set_timestamp(graph_name: str, timestamp: int) -> None:
     """
     sparql = SPARQLWrapper(f"{endpoint}/statements")
     sparql.setHTTPAuth(DIGEST)
-    sparql.setCredentials("admin", admin_password)
+    sparql.setCredentials(admin_username, admin_password)
     sparql.setMethod(POST)
     q = """INSERT DATA {{
         <{graph}> <http://purl.org/dc/terms/modified> {timestamp} .
@@ -92,7 +93,7 @@ def update_timestamp(graph_name: str, timestamp: int) -> None:
     """
     sparql = SPARQLWrapper(f"{endpoint}/statements")
     sparql.setHTTPAuth(DIGEST)
-    sparql.setCredentials("admin", admin_password)
+    sparql.setCredentials(admin_username, admin_password)
     sparql.setMethod(POST)
     q = """
     DELETE {{
@@ -139,7 +140,7 @@ def add_vocabulary(graph: TextIO, graph_name: str, extension: str) -> None:
         f"{endpoint}/statements",
         data=graph.read(),
         headers=headers,
-        auth=('admin', admin_password),
+        auth=(admin_username, admin_password),
         params={'context': f"<{graph_name}>"},
         timeout=60,
     )

src/vocabularies.py

@@ -76,7 +76,7 @@ def get_graph(fp: IO) -> str:
     for line in fp:
         try:
             line = line.decode('utf-8')
-        except UnicodeDecodeError:
+        except (UnicodeDecodeError, AttributeError):
             # Already decoded
             pass
         if re.search("sparqlGraph", line):