Merge pull request #364 from incf-nidash/fstrs

Improve string formatting syntax

docker/rest-server.py

@@ -17,7 +17,7 @@ class NIDMRest(Resource):
     def get(self, all):  # noqa: A002
         query_bits = []
         for a in request.args.keys():
-            query_bits.append("{}={}".format(a, request.args.get(a)))
+            query_bits.append(f"{a}={request.args.get(a)}")
         query = "&".join(query_bits)
 
         files = getTTLFiles()
@@ -29,9 +29,7 @@ def get(self, all):  # noqa: A002
             output_format=RestParser.OBJECT_FORMAT, verbosity_level=5
         )
 
-        json_str = json.dumps(
-            restParser.run(files, "{}?{}".format(all, query)), indent=2
-        )
+        json_str = json.dumps(restParser.run(files, f"{all}?{query}"), indent=2)
         response = app.response_class(
             response=json_str, status=200, mimetype="application/json"
         )
@@ -42,9 +40,7 @@ def get(self, all):  # noqa: A002
 class Instructions(Resource):
     def get(self):
         return {
-            "message": "You probably want to start at {}projects  See instructions at PyNIDM/docker/README.md for details on the API and loading data.".format(
-                request.url_root
-            )
+            "message": f"You probably want to start at {request.url_root}projects  See instructions at PyNIDM/docker/README.md for details on the API and loading data."
         }
 
 

src/nidm/core/dot.py

@@ -221,7 +221,7 @@
 def htlm_link_if_uri(value):
     try:
         uri = value.uri
-        return '<a href="%s">%s</a>' % (uri, str(value))
+        return f'<a href="{uri}">{value}</a>'
     except AttributeError:
         return str(value)
 
@@ -279,7 +279,7 @@ def _attach_attribute_annotation(node, record):
                 % (
                     attr.uri,
                     escape(str(attr)),
-                    ' href="%s"' % value.uri if isinstance(value, Identifier) else "",
+                    f' href="{value.uri}"' if isinstance(value, Identifier) else "",
                     escape(
                         str(value)
                         if not isinstance(value, datetime)
@@ -291,66 +291,58 @@ def _attach_attribute_annotation(node, record):
             ann_rows.append(ANNOTATION_END_ROW)
             count[3] += 1
             annotations = pydot.Node(
-                "ann%d" % count[3], label="\n".join(ann_rows), **ANNOTATION_STYLE
+                f"ann{count[3]}", label="\n".join(ann_rows), **ANNOTATION_STYLE
             )
             dot.add_node(annotations)
             dot.add_edge(pydot.Edge(annotations, node, **ANNOTATION_LINK_STYLE))
 
         def _add_bundle(bundle):
             count[2] += 1
             subdot = pydot.Cluster(
-                graph_name="c%d" % count[2], URL='"%s"' % bundle.identifier.uri
+                graph_name=f"c{count[2]}", URL=f'"{bundle.identifier.uri}"'
             )
             if use_labels:
                 if bundle.label == bundle.identifier:
-                    bundle_label = '"%s"' % str(bundle.label)
+                    bundle_label = f'"{bundle.label}"'
                 else:
                     # Fancier label if both are different. The label will be
                     # the main node text, whereas the identifier will be a
                     # kind of subtitle.
                     bundle_label = (
-                        "<%s<br />"
+                        f"<{bundle.label}<br />"
                         '<font color="#333333" point-size="10">'
-                        "%s</font>>"
+                        f"{bundle.identifier}</font>>"
                     )
-                    bundle_label = bundle_label % (
-                        str(bundle.label),
-                        str(bundle.identifier),
-                    )
-                subdot.set_label('"%s"' % str(bundle_label))
+                subdot.set_label(f'"{bundle_label}"')
             else:
-                subdot.set_label('"%s"' % str(bundle.identifier))
+                subdot.set_label(f'"{bundle.identifier}"')
             _bundle_to_dot(subdot, bundle)
             dot.add_subgraph(subdot)
             return subdot
 
         def _add_node(record):
             count[0] += 1
-            node_id = "n%d" % count[0]
+            node_id = f"n{count[0]}"
             if use_labels:
                 if record.label == record.identifier:
-                    node_label = '"%s"' % str(record.label)
+                    node_label = f'"{record.label}"'
                 else:
                     # Fancier label if both are different. The label will be
                     # the main node text, whereas the identifier will be a
                     # kind of subtitle.
                     node_label = (
-                        "<%s<br />"
+                        f"<{record.label}<br />"
                         '<font color="#333333" point-size="10">'
-                        "%s</font>>"
-                    )
-                    node_label = node_label % (
-                        str(record.label),
-                        str(record.identifier),
+                        f"{record.identifier}</font>>"
                     )
             else:
-                node_label = '"%s"' % str(record.identifier)
+                node_label = f'"{record.identifier}"'
 
             uri = record.identifier.uri
             print("record type: ", record.get_type())
             style = DOT_PROVONE_STYLE[record.get_type()]
             print("style: ", style)
-            node = pydot.Node(node_id, label=node_label, URL='"%s"' % uri, **style)
+            node = pydot.Node(node_id, label=node_label, URL=f'"{uri}"', **style)
             node_map[uri] = node
             dot.add_node(node)
 
@@ -360,19 +352,19 @@ def _add_node(record):
 
         def _add_generic_node(qname):
             count[0] += 1
-            node_id = "n%d" % count[0]
-            node_label = '"%s"' % str(qname)
+            node_id = f"n{count[0]}"
+            node_label = f'"{qname}"'
 
             uri = qname.uri
             style = DOT_PROVONE_STYLE[0]
-            node = pydot.Node(node_id, label=node_label, URL='"%s"' % uri, **style)
+            node = pydot.Node(node_id, label=node_label, URL=f'"{uri}"', **style)
             node_map[uri] = node
             dot.add_node(node)
             return node
 
         def _get_bnode():
             count[1] += 1
-            bnode_id = "b%d" % count[1]
+            bnode_id = f"b{count[1]}"
             bnode = pydot.Node(bnode_id, label='""', shape="point", color="gray")
             dot.add_node(bnode)
             return bnode

src/nidm/core/serializers/__init__.py

@@ -73,4 +73,4 @@ def get(format_name):
     try:
         return Registry.serializers[format_name]
     except KeyError:
-        raise DoNotExist('No serializer available for the format "%s"' % format_name)
+        raise DoNotExist(f'No serializer available for the format "{format_name}"')

src/nidm/core/serializers/provonerdf.py

@@ -62,7 +62,7 @@ def __init__(self):
     def get_anon_id(self, obj, local_prefix="id"):
         if obj not in self._cache:
             self._count += 1
-            self._cache[obj] = pm.Identifier("_:%s%d" % (local_prefix, self._count)).uri
+            self._cache[obj] = pm.Identifier(f"_:{local_prefix}{self._count}").uri
         return self._cache[obj]
 
 
@@ -178,7 +178,7 @@ def decode_rdf_representation(self, literal, graph):
             if datatype == XSD["gYearMonth"]:
                 parsed_info = dateutil.parser.parse(literal)
                 return pm.Literal(
-                    "{0}-{1:02d}".format(parsed_info.year, parsed_info.month),
+                    f"{parsed_info.year}-{parsed_info.month:02d}",
                     datatype=self.valid_identifier(datatype),
                 )
             else:

src/nidm/experiment/CDE.py

@@ -12,7 +12,7 @@ def download_cde_files():
     cde_dir = tempfile.gettempdir()
 
     for url in Constants.CDE_FILE_LOCATIONS:
-        urlretrieve(url, "{}/{}".format(cde_dir, url.split("/")[-1]))
+        urlretrieve(url, f"{cde_dir}/{url.split('/')[-1]}")
 
     return cde_dir
 
@@ -25,7 +25,7 @@ def getCDEs(file_list=None):
     hasher.update(str(file_list).encode("utf-8"))
     h = hasher.hexdigest()
 
-    cache_file_name = tempfile.gettempdir() + "/cde_graph.{}.pickle".format(h)
+    cache_file_name = tempfile.gettempdir() + f"/cde_graph.{h}.pickle"
 
     if path.isfile(cache_file_name):
         with open(cache_file_name, "rb") as fp:
@@ -50,7 +50,7 @@ def getCDEs(file_list=None):
 
         file_list = []
         for f in ["ants_cde.ttl", "fs_cde.ttl", "fsl_cde.ttl"]:
-            fname = "{}/{}".format(cde_dir, f)
+            fname = f"{cde_dir}/{f}"
             if path.isfile(fname):
                 file_list.append(fname)
 

src/nidm/experiment/Core.py

@@ -250,8 +250,9 @@ def addLiteralAttribute(
                 )
         except KeyError as e:
             print(
-                '\nPredicate namespace identifier " %s " not found! \n'
-                % (str(e).split("'")[1])
+                '\nPredicate namespace identifier "',
+                str(e).split("'")[1],
+                '" not found! \n',
             )
             print(
                 "Use addNamespace method to add namespace before adding literal attribute \n"
@@ -364,7 +365,7 @@ def get_metadata_dict(self, NIDM_TYPE):
             uri = s
 
         if uri is None:
-            print("Error finding %s in NIDM-Exp Graph" % NIDM_TYPE)
+            print(f"Error finding {NIDM_TYPE} in NIDM-Exp Graph")
             return metadata
 
         # Cycle through metadata and add to json
@@ -531,7 +532,7 @@ def save_DotGraph(self, filename, format=None):  # noqa: A002
         """
         qres = rdf_graph.query(query)
         for row in qres:
-            print("project uuid = %s" % row)
+            print(f"project uuid = {row}")
             # parse uuid from project URI
             # project_uuid = str(row[0]).rsplit('/', 1)[-1]
             project_uuid = str(row[0])
@@ -557,7 +558,7 @@ def save_DotGraph(self, filename, format=None):  # noqa: A002
                         dot.obj_dict["nodes"][key][0]["attributes"]["URL"]
                     ):
                         session_node = key
-                        # print("session node = %s" %key)
+                        # print(f"session node = {key}")
 
                         # add to DOT structure edge between project_node and session_node
                         dot.add_edge(Edge(session_node, project_node, **style))
@@ -574,7 +575,7 @@ def save_DotGraph(self, filename, format=None):  # noqa: A002
                                         ]
                                     ):
                                         acquisition_node = key
-                                        # print("acquisition node = %s" %key)
+                                        # print(f"acquisition node = {key}")
 
                                         dot.add_edge(
                                             Edge(

src/nidm/experiment/Navigate.py

@@ -538,7 +538,7 @@ def GetDataelementDetails(nidm_files_tuple, dataelement):
                             if d in rdf_graph.subjects(
                                 predicate=isa, object=Constants.NIDM["Project"]
                             ):
-                                result["inProjects"].add("{} ({})".format(str(d), file))
+                                result["inProjects"].add(f"{d} ({file})")
 
             return result  # found it, we are done