From ca63eaaf22589d6376da7d0253bc0105a1cb3dc1 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 4 Sep 2023 14:30:37 -0400
Subject: [PATCH] fix tests after merge from main

---
 +bids/+util/create_scans_tsv.m            |  8 ++++++--
 tests/data/reports/ds000117_anat.md       |  6 ++++--
 tests/tests_utils/test_create_scans_tsv.m | 24 +++++++++++------------
 tests/utils/validate_dataset.m            |  2 +-
 4 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/+bids/+util/create_scans_tsv.m b/+bids/+util/create_scans_tsv.m
index 79f3071f..24f53424 100644
--- a/+bids/+util/create_scans_tsv.m
+++ b/+bids/+util/create_scans_tsv.m
@@ -74,7 +74,11 @@
   %%
   output_filenames = {};
 
-  layout = bids.layout(layout_or_path, 'use_schema', use_schema);
+  layout = bids.layout(layout_or_path, ...
+                       'use_schema', use_schema, ...
+                       'index_dependencies', false, ...
+                       'tolerant', tolerant, ...
+                       'verbose', verbose);
 
   subjects_list = bids.query(layout, 'subjects');
 
@@ -126,7 +130,7 @@
                        'acq_time', {cell(numel(data), 1)}, ...
                        'comments', {cell(numel(data), 1)});
 
-      output_filenames{end + 1} = scans_file; %#ok<AGROW>
+      output_filenames{end + 1} = scans_file;
 
       bids.util.tsvwrite(fullfile(layout.pth, scans_file), content);
 
diff --git a/tests/data/reports/ds000117_anat.md b/tests/data/reports/ds000117_anat.md
index 72e86b9c..dbd27395 100644
--- a/tests/data/reports/ds000117_anat.md
+++ b/tests/data/reports/ds000117_anat.md
@@ -4,7 +4,7 @@
 
 ### Anatomical Magnetic Resonance Imaging data
 
-#### T1-weighted image
+#### Fast-Low-Angle-Shot image
 
 The data acquisition was performed in the {{InstitutionName}}, {{InstitutionalDepartmentName}},
 {{InstitutionAddress}}.
@@ -15,10 +15,12 @@ The software version was {{SoftwareVersions}}.
 
 {{PulseSequenceType}} {{ScanningSequence}} {{SequenceVariant}} FLASH structural
 MRI data were collected ({{nb_slices}} slices; repetition time, TR= {{RepetitionTime}}
-s; echo time, TE= {{echo_time}} ms; flip angle, FA= {{FlipAngle}} deg; field
+s; echo time, TE= {{echo_time}} s; flip angle, FA= {{FlipAngle}} deg; field
 of view, FOV= {{fov}} mm; matrix size= {{mat_size}}; voxel size= {{vox_size}}
 mm).
 
+#### T1-weighted image
+
 The data acquisition was performed in the MRC Cognition and Brain Sciences Unit,
 {{InstitutionalDepartmentName}}, 15 Chaucer Road, Cambridge CB2 7EF, UK.
 
diff --git a/tests/tests_utils/test_create_scans_tsv.m b/tests/tests_utils/test_create_scans_tsv.m
index 89222c22..1424cf84 100644
--- a/tests/tests_utils/test_create_scans_tsv.m
+++ b/tests/tests_utils/test_create_scans_tsv.m
@@ -8,7 +8,11 @@
 
 function test_create_scans_tsv_basic_no_session()
 
-  bids_path = fullfile(get_test_data_dir(), 'asl001');
+  source_ds = fullfile(get_test_data_dir(), 'asl001');
+  tmp_path = temp_dir();
+  copyfile(source_ds, tmp_path);
+
+  bids_path = fullfile(tmp_path);
 
   validate_dataset(bids_path);
 
@@ -21,31 +25,25 @@ function test_create_scans_tsv_basic_no_session()
 
   validate_dataset(bids_path);
 
-  teardown(bids_path, output_filenames);
-
 end
 
 function test_create_scans_tsv_basic()
 
-  bids_path = fullfile(get_test_data_dir(), 'ds000117');
+  source_ds = fullfile(get_test_data_dir(), 'ds006');
+  tmp_path = temp_dir();
+  copyfile(source_ds, tmp_path);
+
+  bids_path = fullfile(tmp_path);
 
   validate_dataset(bids_path);
 
   output_filenames = bids.util.create_scans_tsv(bids_path, 'verbose', false);
 
-  assertEqual(numel(output_filenames), 16);
+  assertEqual(numel(output_filenames), 28);
   assertEqual(exist(fullfile(bids_path, output_filenames{1}), 'file'), 2);
   content = bids.util.tsvread(fullfile(bids_path, output_filenames{1}));
   assertEqual(fieldnames(content), {'filename'; 'acq_time'; 'comments'});
 
   validate_dataset(bids_path);
 
-  teardown(bids_path, output_filenames);
-
-end
-
-function teardown(pth, filelist)
-  for i = 1:numel(filelist)
-    delete(fullfile(pth, filelist{i}));
-  end
 end
diff --git a/tests/utils/validate_dataset.m b/tests/utils/validate_dataset.m
index b5c71e07..ef23a27f 100644
--- a/tests/utils/validate_dataset.m
+++ b/tests/utils/validate_dataset.m
@@ -5,6 +5,6 @@ function validate_dataset(bids_path)
   end
 
   [sts, msg] = bids.validate(bids_path,  '--config.ignore=99 --ignoreNiftiHeaders');
-  assertEqual(sts, 0);
+  assert(sts == 0, msg);
 
 end