Delint

docker/rest-blaze.py

@@ -17,7 +17,7 @@ def getTTLFiles():
 
 
 class NIDMRest(Resource):
-    def get(self, all):
+    def get(self, all):  # noqa: A002
         query_bits = []
         for a in request.args.keys():
             query_bits.append("{}={}".format(a, request.args.get(a)))

docs/source/conf.py

@@ -53,7 +53,7 @@
 
 # General information about the project.
 project = "PyNIDM"
-copyright = "2018, [email protected], [email protected], [email protected], [email protected]"
+copyright = "2018, [email protected], [email protected], [email protected], [email protected]"  # noqa: A001
 author = "[email protected], [email protected], [email protected], [email protected]"
 
 # The version info for the project you're documenting, acts as replacement for

nidm/__init__.py

@@ -1,6 +1,3 @@
-from __future__ import absolute_import, division, print_function
-import __main__
-
 __version__ = "3.9.7"
 
 try:

nidm/core/BIDS_Constants.py

@@ -42,7 +42,7 @@
 }
 # JSON file keys
 json_keys = {
-    ##Image terms
+    # Image terms
     "run": Constants.NIDM_ACQUISITION_ENTITY,
     "ImageType": Constants.DICOM["ImageType"],
     "ManufacturerModelName": Constants.DICOM["ManufacturerModelName"],
@@ -108,7 +108,7 @@
     "NumberDiscardedVolumesByUser": Constants.NIDM["NumberDiscardedVolumesByUser"],
     "DelayTime": Constants.NIDM["DelayTime"],
     "PulseSequenceType": Constants.DICOM["PulseSequenceName"],
-    ###Task Stuff
+    # Task Stuff
     "TaskName": Constants.NIDM_MRI_FUNCTION_TASK
     # "CogAtlasID" :
     # "CogPOID" :

nidm/core/Constants.py

@@ -7,7 +7,7 @@
     Added Python provtoolbox  support
     10/3/17 Modified Namespace to be QualifiedName for provtoolbox support...left most of the NIDM-Results Namespaces the same
 @author: Sanu Ann Abraham <[email protected]>
-	05/04/2018 Added python ProvONE support
+        05/04/2018 Added python ProvONE support
 """
 from collections import namedtuple
 from prov.constants import PROV_ATTRIBUTE_LITERALS, PROV_ATTRIBUTE_QNAMES, PROV_N_MAP
@@ -604,7 +604,7 @@ def __init__(self, namespaces=None):
 )
 
 
-####ADDED BY DBK to make searching NIDM-Experiment Terms easier...temporary, should be done in the OWL file#####
+# ADDED BY DBK to make searching NIDM-Experiment Terms easier...temporary, should be done in the OWL file #
 nidm_experiment_terms = [
     NIDM_PROJECT,
     NIDM_PROJECT_IDENTIFIER,

nidm/core/dot.py

@@ -19,7 +19,6 @@
     from cgi import escape
 
 from datetime import datetime
-from prov.dot import DOT_PROV_STYLE
 from prov.model import (
     PROV_ACTIVITY,
     PROV_AGENT,
@@ -47,7 +46,28 @@
 )
 import pydot
 import six
-from .Constants import *
+from .Constants import (
+    PROVONE_ATTRIBUTE_QNAMES,
+    PROVONE_CLTODESTP,
+    PROVONE_DATA,
+    PROVONE_DATALINK,
+    PROVONE_DATAONLINK,
+    PROVONE_DLTOINPORT,
+    PROVONE_DLTOOUTPORT,
+    PROVONE_HASINPORT,
+    PROVONE_HASOUTPORT,
+    PROVONE_HASSUBPROCESS,
+    PROVONE_INPORTTODL,
+    PROVONE_INPUTPORT,
+    PROVONE_ISPARTOF,
+    PROVONE_OUTPORTTODL,
+    PROVONE_OUTPUTPORT,
+    PROVONE_PROCESS,
+    PROVONE_PROCESSEXEC,
+    PROVONE_SEQCTRLLINK,
+    PROVONE_SOURCEPTOCL,
+    PROVONE_USER,
+)
 
 __author__ = "Sanu Ann Abraham"
 __email__ = "[email protected]"
@@ -381,8 +401,8 @@ def _get_node(qname):
                 relations.append(rec)
 
         if not bundle.is_bundle():
-            for bundle in bundle.bundles:
-                _add_bundle(bundle)
+            for b in bundle.bundles:
+                _add_bundle(b)
 
         for rec in relations:
             args = rec.args

nidm/core/provone.py

@@ -57,7 +57,6 @@
     PROVONE_ATTR_PLAN,
     PROVONE_ATTR_PROCESS,
     PROVONE_ATTR_PROCESSEXEC,
-    PROVONE_ATTR_RELATED_PREXEC,
     PROVONE_ATTR_SEQCTRLLINK,
     PROVONE_ATTR_USED_DATA,
     PROVONE_ATTR_USED_PREXEC,
@@ -76,7 +75,6 @@
     PROVONE_INPORTTODL,
     PROVONE_INPUTPORT,
     PROVONE_ISPARTOF,
-    PROVONE_MEMBERSHIP,
     PROVONE_N_MAP,
     PROVONE_OUTPORTTODL,
     PROVONE_OUTPUTPORT,
@@ -882,7 +880,7 @@ def parameterization(
             other_attributes,
         )
 
-    def serialize(self, destination=None, format="json", **args):
+    def serialize(self, destination=None, format="json", **args):  # noqa: A002
         """
         Serialize the :py:class:`ProvDocument` to the destination.
 

nidm/core/serializers/provonerdf.py

@@ -29,7 +29,6 @@
     PROV_DERIVATION,
     PROV_END,
     PROV_GENERATION,
-    PROV_ID_ATTRIBUTES_MAP,
     PROV_INVALIDATION,
     PROV_LOCATION,
     PROV_MENTION,
@@ -258,7 +257,7 @@ def encode_container(self, bundle, container=None, identifier=None):
                     record.attributes
                 )
                 formal_qualifiers = False
-                for attrid, (attr, value) in enumerate(list(record.formal_attributes)):
+                for attrid, (_, value) in enumerate(list(record.formal_attributes)):
                     if (identifier is not None and value is not None) or (
                         identifier is None and value is not None and attrid > 1
                     ):
@@ -284,10 +283,7 @@ def encode_container(self, bundle, container=None, identifier=None):
                             if identifier is None and subj is not None:
                                 try:
                                     obj_val = record.formal_attributes[1][1]
-                                    obj_attr = URIRef(
-                                        record.formal_attributes[1][0].uri
-                                    )
-                                    # TODO: Why is obj_attr above not used anywhere?
+                                    URIRef(record.formal_attributes[1][0].uri)
                                 except IndexError:
                                     obj_val = None
                                 if obj_val and (
@@ -478,7 +474,7 @@ def decode_container(self, graph, bundle):
         PROV_CLS_MAP = {}
         formal_attributes = {}
         unique_sets = {}
-        for key, val in PROV_BASE_CLS.items():
+        for key, _ in PROV_BASE_CLS.items():
             PROV_CLS_MAP[key.uri] = PROV_BASE_CLS[key]
         relation_mapper = {
             URIRef(PROV["alternateOf"].uri): "alternate",
@@ -511,11 +507,14 @@ def decode_container(self, graph, bundle):
         }
         other_attributes = {}
         for stmt in graph.triples((None, RDF.type, None)):
-            id = six.text_type(stmt[0])
+            id_ = six.text_type(stmt[0])
             obj = six.text_type(stmt[2])
             if obj in PROV_CLS_MAP:
-                if not isinstance(stmt[0], BNode) and self.valid_identifier(id) is None:
-                    prefix, iri, _ = graph.namespace_manager.compute_qname(id)
+                if (
+                    not isinstance(stmt[0], BNode)
+                    and self.valid_identifier(id_) is None
+                ):
+                    prefix, iri, _ = graph.namespace_manager.compute_qname(id_)
                     self.document.add_namespace(prefix, iri)
                 try:
                     prov_obj = PROV_CLS_MAP[obj]
@@ -528,53 +527,53 @@ def decode_container(self, graph, bundle):
                     or pm.PROV["PrimarySource"].uri in stmt[2]
                 )
                 if (
-                    id not in ids
+                    id_ not in ids
                     and prov_obj
                     and (
                         prov_obj.uri == obj
                         or isderivation
                         or isinstance(stmt[0], BNode)
                     )
                 ):
-                    ids[id] = prov_obj
+                    ids[id_] = prov_obj
                     klass = pm.PROV_REC_CLS[prov_obj]
-                    formal_attributes[id] = OrderedDict(
+                    formal_attributes[id_] = OrderedDict(
                         [(key, None) for key in klass.FORMAL_ATTRIBUTES]
                     )
-                    unique_sets[id] = OrderedDict(
+                    unique_sets[id_] = OrderedDict(
                         [(key, []) for key in klass.FORMAL_ATTRIBUTES]
                     )
                     add_attr = False or (
                         (isinstance(stmt[0], BNode) or isderivation)
                         and prov_obj.uri != obj
                     )
                 if add_attr:
-                    if id not in other_attributes:
-                        other_attributes[id] = []
+                    if id_ not in other_attributes:
+                        other_attributes[id_] = []
                     obj_formatted = self.decode_rdf_representation(stmt[2], graph)
-                    other_attributes[id].append((pm.PROV["type"], obj_formatted))
+                    other_attributes[id_].append((pm.PROV["type"], obj_formatted))
             else:
-                if id not in other_attributes:
-                    other_attributes[id] = []
+                if id_ not in other_attributes:
+                    other_attributes[id_] = []
                 obj = self.decode_rdf_representation(stmt[2], graph)
-                other_attributes[id].append((pm.PROV["type"], obj))
-        for id, pred, obj in graph:
-            id = six.text_type(id)
-            if id not in other_attributes:
-                other_attributes[id] = []
+                other_attributes[id_].append((pm.PROV["type"], obj))
+        for id_, pred, obj in graph:
+            id_ = six.text_type(id_)
+            if id_ not in other_attributes:
+                other_attributes[id_] = []
             if pred == RDF.type:
                 continue
             if pred in relation_mapper:
                 if "alternateOf" in pred:
-                    getattr(bundle, relation_mapper[pred])(obj, id)
+                    getattr(bundle, relation_mapper[pred])(obj, id_)
                 elif "mentionOf" in pred:
                     mentionBundle = None
                     for stmt in graph.triples(
-                        (URIRef(id), URIRef(pm.PROV["asInBundle"].uri), None)
+                        (URIRef(id_), URIRef(pm.PROV["asInBundle"].uri), None)
                     ):
                         mentionBundle = stmt[2]
                     getattr(bundle, relation_mapper[pred])(
-                        id, six.text_type(obj), mentionBundle
+                        id_, six.text_type(obj), mentionBundle
                     )
                 elif "actedOnBehalfOf" in pred or "wasAssociatedWith" in pred:
                     qualifier = (
@@ -584,83 +583,83 @@ def decode_container(self, graph, bundle):
                     )
                     qualifier_bnode = None
                     for stmt in graph.triples(
-                        (URIRef(id), URIRef(pm.PROV[qualifier].uri), None)
+                        (URIRef(id_), URIRef(pm.PROV[qualifier].uri), None)
                     ):
                         qualifier_bnode = stmt[2]
                     if qualifier_bnode is None:
-                        getattr(bundle, relation_mapper[pred])(id, six.text_type(obj))
+                        getattr(bundle, relation_mapper[pred])(id_, six.text_type(obj))
                     else:
                         fakeys = list(
                             formal_attributes[six.text_type(qualifier_bnode)].keys()
                         )
                         formal_attributes[six.text_type(qualifier_bnode)][
                             fakeys[0]
-                        ] = id
+                        ] = id_
                         formal_attributes[six.text_type(qualifier_bnode)][
                             fakeys[1]
                         ] = six.text_type(obj)
                 else:
-                    getattr(bundle, relation_mapper[pred])(id, six.text_type(obj))
-            elif id in ids:
+                    getattr(bundle, relation_mapper[pred])(id_, six.text_type(obj))
+            elif id_ in ids:
                 obj1 = self.decode_rdf_representation(obj, graph)
                 if obj is not None and obj1 is None:
                     raise ValueError(("Error transforming", obj))
                 pred_new = pred
                 if pred in predicate_mapper:
                     pred_new = predicate_mapper[pred]
-                if ids[id] == PROV_COMMUNICATION and "activity" in six.text_type(
+                if ids[id_] == PROV_COMMUNICATION and "activity" in six.text_type(
                     pred_new
                 ):
                     pred_new = PROV_ATTR_INFORMANT
-                if ids[id] == PROV_DELEGATION and "agent" in six.text_type(pred_new):
+                if ids[id_] == PROV_DELEGATION and "agent" in six.text_type(pred_new):
                     pred_new = PROV_ATTR_RESPONSIBLE
-                if ids[id] in [PROV_END, PROV_START] and "entity" in six.text_type(
+                if ids[id_] in [PROV_END, PROV_START] and "entity" in six.text_type(
                     pred_new
                 ):
                     pred_new = PROV_ATTR_TRIGGER
-                if ids[id] in [PROV_END] and "activity" in six.text_type(pred_new):
+                if ids[id_] in [PROV_END] and "activity" in six.text_type(pred_new):
                     pred_new = PROV_ATTR_ENDER
-                if ids[id] in [PROV_START] and "activity" in six.text_type(pred_new):
+                if ids[id_] in [PROV_START] and "activity" in six.text_type(pred_new):
                     pred_new = PROV_ATTR_STARTER
-                if ids[id] == PROV_DERIVATION and "entity" in six.text_type(pred_new):
+                if ids[id_] == PROV_DERIVATION and "entity" in six.text_type(pred_new):
                     pred_new = PROV_ATTR_USED_ENTITY
                 if six.text_type(pred_new) in [
-                    val.uri for val in formal_attributes[id]
+                    val.uri for val in formal_attributes[id_]
                 ]:
                     qname_key = self.valid_identifier(pred_new)
-                    formal_attributes[id][qname_key] = obj1
-                    unique_sets[id][qname_key].append(obj1)
-                    if len(unique_sets[id][qname_key]) > 1:
-                        formal_attributes[id][qname_key] = None
+                    formal_attributes[id_][qname_key] = obj1
+                    unique_sets[id_][qname_key].append(obj1)
+                    if len(unique_sets[id_][qname_key]) > 1:
+                        formal_attributes[id_][qname_key] = None
                 else:
                     if "qualified" not in six.text_type(
                         pred_new
                     ) and "asInBundle" not in six.text_type(pred_new):
-                        other_attributes[id].append((six.text_type(pred_new), obj1))
+                        other_attributes[id_].append((six.text_type(pred_new), obj1))
             local_key = six.text_type(obj)
             if local_key in ids:
                 if "qualified" in pred:
                     formal_attributes[local_key][
                         list(formal_attributes[local_key].keys())[0]
-                    ] = id
-        for id in ids:
+                    ] = id_
+        for id_ in ids:
             attrs = None
-            if id in other_attributes:
-                attrs = other_attributes[id]
+            if id_ in other_attributes:
+                attrs = other_attributes[id_]
             items_to_walk = []
-            for qname, values in unique_sets[id].items():
+            for qname, values in unique_sets[id_].items():
                 if values and len(values) > 1:
                     items_to_walk.append((qname, values))
             if items_to_walk:
                 for subset in list(walk(items_to_walk)):
                     for key, value in subset.items():
-                        formal_attributes[id][key] = value
-                    bundle.new_record(ids[id], id, formal_attributes[id], attrs)
+                        formal_attributes[id_][key] = value
+                    bundle.new_record(ids[id_], id_, formal_attributes[id_], attrs)
             else:
-                bundle.new_record(ids[id], id, formal_attributes[id], attrs)
-            ids[id] = None
+                bundle.new_record(ids[id_], id_, formal_attributes[id_], attrs)
+            ids[id_] = None
             if attrs is not None:
-                other_attributes[id] = []
+                other_attributes[id_] = []
         for key, val in other_attributes.items():
             if val:
                 ids[key].add_attributes(val)

nidm/core/tests/test_provone.py

@@ -1,5 +1,4 @@
 # from nidm.core.provone import ProvONEDocument
-from nidm.core import Constants
 from nidm.core.dot import provone_to_dot
 import pytest
 
@@ -11,6 +10,8 @@
 @pytest.fixture(scope="module")
 def doc():
     # Create new provone document with namespaces
+    from nidm.core.provone import ProvONEDocument
+
     d1 = ProvONEDocument()
     d1.add_namespace("dcterms", "http://purl.org/dc/terms/")
     d1.add_namespace("wfms", "http://www.wfms.org/registry/")

nidm/experiment/Acquisition.py

@@ -1,9 +1,4 @@
-import os
-import sys
 import prov.model as pm
-import rdflib as rdf
-
-# sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 from ..core import Constants
 from ..experiment import Core
 from ..experiment.Core import getUUID