compatibility fixes for input dataset in BIDSVersion > 1.3

fmridenoise/interfaces/bids.py

@@ -1,4 +1,6 @@
 # Interface for loading preprocessed fMRI data and confounds table
+from os.path import exists
+
 from bids import BIDSLayout
 from nipype.interfaces.io import IOBase
 from nipype.utils.filemanip import copyfile
@@ -228,16 +230,29 @@ def validate_derivatives(bids_dir: str,
         for derivative_path in derivatives_valid:
             dataset_desc_path = os.path.join(derivative_path,
                                              'dataset_description.json')
-            try:
+            if exists(dataset_desc_path):
                 with open(dataset_desc_path, 'r') as f:
                     dataset_desc = json.load(f)
-                scope.append(dataset_desc['PipelineDescription']['Name'])
-            except FileNotFoundError as e:
+            else:
                 raise MissingFile(f"{derivative_path} should contain" +
-                                " dataset_description.json file") from e
-            except KeyError as e:
-                raise MissingFile(f"Key 'PipelineDescription.Name' is " +
-                                "required in {dataset_desc_path} file") from e
+                                  " dataset_description.json file")
+            try:
+                major, minor, patch = (int(element) for element in str(dataset_desc['BIDSVersion']).split('.'))
+            except Exception:
+                raise Exception(f"Unable to parse bids version ({dataset_desc['BIDSVersion']}) into 3 parts")
+            if major == 1 and minor <= 3:
+                try:
+                    scope.append(dataset_desc['PipelineDescription']['Name'])
+                except KeyError as e:
+                    raise KeyError("Key 'PipelineDescription.Name' is "
+                                      f"required in {dataset_desc_path} file") from e
+            else:
+                pipeline = None
+                try:
+                    for pipeline in dataset_desc['GeneratedBy']:
+                        scope.append(pipeline['Name'])
+                except KeyError as e:
+                    raise KeyError(f"Unable to extract Name from GeneratedBy: {pipeline} in file {dataset_desc_path}")
 
         return derivatives_valid, scope
 
@@ -321,10 +336,10 @@ def get_entity_files(include_no_aroma: bool, include_aroma: bool, entity: dict)
 
             return False, entity_files
 
+        subjects_to_exclude = []
         # Select interface behavior depending on user behavior
         if not tasks and not sessions and not subjects:
             raise_missing = False
-            subjects_to_exclude = []
         else:
             raise_missing = True
 
@@ -362,7 +377,7 @@ def get_entity_files(include_no_aroma: bool, include_aroma: bool, entity: dict)
     def _run_interface(self, runtime):
 
         # Validate derivatives argument
-        derivatives, scope = BIDSValidate.validate_derivatives(
+        derivatives, _ = BIDSValidate.validate_derivatives(
             bids_dir=self.inputs.bids_dir,
             derivatives=self.inputs.derivatives
         )

requirements.txt

@@ -1,6 +1,8 @@
 nibabel>=2.0
+matplotlib<=3.2.1
 seaborn>=0.9.0
-numpy>=1.11
+numpy>=1.11,<1.16.5
+scipy>=1.4,<=1.5
 nilearn>=0.4.0
 pandas>=0.19,<1.2
 jsonschema>=3.0.1

tests/interfaces/bids/test_bids_validate.py

@@ -1,11 +1,14 @@
+import json
+import os
+import shutil
+import tempfile
 from bids import BIDSLayout
 from fmridenoise.interfaces.bids import BIDSValidate, MissingFile, _lists_to_entities
 import fmridenoise.pipelines as pipe
 import unittest as ut
 from os.path import join, dirname
 from typing import List
 
-
 # Data sets
 testDir = dirname(__file__)
 dummyDataPath = join(testDir, "dummy_complete")
@@ -54,7 +57,6 @@ def test_no_sessions_content(self):
 
 
 class BidsValidateBasicPropertiesOnCompleteDataTestCase(ut.TestCase):
-
     derivatives = ["fmriprep"]
     tasks = ["audionback", "dualnback", "rest", "spatialnback"]
     sessions = ["1", "2", "3", "4"]
@@ -125,9 +127,9 @@ def test_noAromaFiles(self):
 
     def test_conf_raw_files(self):
         filesCount = len(self.subjects) \
-                         * (len(self.sessions) if self.sessions else 1) \
-                         * len(self.tasks) \
-                         * (len(self.runs) if self.runs else 1)
+                     * (len(self.sessions) if self.sessions else 1) \
+                     * len(self.tasks) \
+                     * (len(self.runs) if self.runs else 1)
         self.assertEqual(filesCount, len(self.bidsValidate._results['conf_raw']))
 
     def test_conf_raw_json(self):
@@ -303,3 +305,64 @@ class BidsValidateOnRunsTestCase(BidsValidateBasicPropertiesOnCompleteDataTestCa
     pipelinesDicts = list(map(pipe.load_pipeline_from_json, pipelines))
     bids_dir = dummyRuns
     maxDiff = None
+
+
+class BidsValidate_validate_derivatives_TestCase(ut.TestCase):
+    bids_validate_1_3_content = {
+        "Name": "definitely not a fmriprep",
+        "BIDSVersion": "1.1.1",
+        "PipelineDescription": {
+            "Name": "NotAFmriprep",
+            "Version": "666",
+            "CodeURL": "https://no_url_there.com"
+        },
+        "CodeURL": "https://no_url_there.com",
+        "HowToAcknowledge": "Do not cite this",
+        "SourceDatasetsURLs": [
+            "https://no_url_there.com"
+        ],
+        "License": "CC0"
+    }
+
+    bids_validate_1_4_content = {
+        "Name": "fMRIDenoise",
+        "BIDSVersion": "1.4.1",
+        "GeneratedBy": [
+            {
+                "Name": "fMRIDenoise",
+                "Version": "some version",
+                "CodeURL": "NO URL, DEVELOPMENT BUILD"
+            },
+            {
+                "Name": "Test",
+                "Version": "test_version",
+                "CodeURL": "NO URL"
+            }
+        ]
+    }
+
+    def setUp(self) -> None:
+        self.bids_dir = tempfile.TemporaryDirectory()
+        self.derivatives_dir = join(self.bids_dir.name, 'derivatives')
+        self.derivative_name = 'test'
+        self.derivative_dir = join(self.derivatives_dir, self.derivative_name)
+        os.makedirs(self.derivative_dir)
+        self.derivatives_json_path = join(self.derivative_dir, 'dataset_description.json')
+
+    def tearDown(self) -> None:
+        self.bids_dir.cleanup()
+
+    def test_valid_old(self) -> None:
+        with open(self.derivatives_json_path, 'w') as f:
+            json.dump(self.bids_validate_1_3_content, f)
+        derivatives_valid, scope = BIDSValidate.validate_derivatives(self.bids_dir.name, self.derivative_name)
+        self.assertEqual([self.derivative_dir], derivatives_valid)
+        self.assertEqual(['NotAFmriprep'], scope)
+
+    def test_valid_new(self) -> None:
+        with open(self.derivatives_json_path, 'w') as f:
+            json.dump(self.bids_validate_1_4_content, f)
+        derivatives_valid, scope = BIDSValidate.validate_derivatives(self.bids_dir.name, self.derivative_name)
+        self.assertEqual([self.derivative_dir], derivatives_valid)
+        self.assertEqual(['fMRIDenoise', "Test"], scope)
+