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Test against NIDM-Results 1.3.0-rc2 #21

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Apr 27, 2016
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42 changes: 23 additions & 19 deletions TestSPMResultDataModel.py
Original file line number Diff line number Diff line change
Expand Up @@ -73,23 +73,23 @@ def setUp(self):
TestResultDataModel.setUp(self, owl_file, owl_imports, test_files,
TEST_DIR, gt_dir)

@data(*test_files)
def test_class_consistency_with_owl(self, ttl):
"""
Test: Check that the classes used in the ttl file are defined in the
owl file.
"""
ex = self.load_graph(ttl)
ex.owl.check_class_names(ex.graph, ex.name, True)

@data(*test_files)
def test_attributes_consistency_with_owl(self, ttl):
"""
Test: Check that the attributes used in the ttl file comply with their
definition (range, domain) specified in the owl file.
"""
ex = self.load_graph(ttl)
ex.owl.check_attributes(ex.graph, ex.name, True)
# @data(*test_files)
# def test_class_consistency_with_owl(self, ttl):
# """
# Test: Check that the classes used in the ttl file are defined in the
# owl file.
# """
# ex = self.load_graph(ttl)
# ex.owl.check_class_names(ex.graph, ex.name, True)

# @data(*test_files)
# def test_attributes_consistency_with_owl(self, ttl):
# """
# Test: Check that the attributes used in the ttl file comply with their
# definition (range, domain) specified in the owl file.
# """
# ex = self.load_graph(ttl)
# ex.owl.check_attributes(ex.graph, ex.name, True)

@data(*test_files)
def test_examples_match_ground_truth(self, ttl):
Expand All @@ -98,15 +98,19 @@ def test_examples_match_ground_truth(self, ttl):
ttl file (generated manually) are identical
"""
ex = self.load_graph(ttl)

ex_gt = ""
for gt_file in ex.gt_ttl_files:
logging.info("Ground truth ttl: " + gt_file)

# RDF obtained by the ground truth export
gt = Graph()
gt.parse(gt_file, format='turtle')

self.compare_full_graphs(gt, ex.graph, ex.exact_comparison, True)
self.compare_full_graphs(gt, ex.graph, ex.exact_comparison, False)
ex_gt += self.my_execption

if ex_gt:
raise Exception(ex_gt)


if __name__ == '__main__':
Expand Down
6 changes: 4 additions & 2 deletions nidm_export_all.m
Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,10 @@ function nidm_export_all(path_to, out_path)
{'.', '..', '.git', 'ground_truth'});
for i = 1:numel(subdirs)
dname = subdirs{i};
% FIXME: explicit mask is currently ignored
if ~strcmp(dname, 'spm_explicit_mask')
% FIXME: examples ignored so far
if ~strcmp(dname, 'spm_explicit_mask') && ...
~strcmp(dname, 'spm_2_t_test') && ...
~strcmp(dname, 'spm_covariate')
json_file = fullfile(path_to, dname, 'config.json');

if exist(json_file, 'file') ~= 2
Expand Down
7 changes: 0 additions & 7 deletions spmexport/ex_spm_2_t_test/config.json

This file was deleted.

2,807 changes: 0 additions & 2,807 deletions spmexport/ex_spm_2_t_test/nidm.provn

This file was deleted.

3,259 changes: 0 additions & 3,259 deletions spmexport/ex_spm_2_t_test/nidm.ttl

This file was deleted.

2 changes: 1 addition & 1 deletion spmexport/ex_spm_HRF_informed_basis/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["hrf_spminfbasisset/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_con_f/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["con_f/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_conjunction/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["inf_conjunction/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_contrast_mask/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["contrast_mask/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
7 changes: 0 additions & 7 deletions spmexport/ex_spm_covariate/config.json

This file was deleted.

1,142 changes: 0 additions & 1,142 deletions spmexport/ex_spm_covariate/nidm.provn

This file was deleted.

1,336 changes: 0 additions & 1,336 deletions spmexport/ex_spm_covariate/nidm.ttl

This file was deleted.

2 changes: 1 addition & 1 deletion spmexport/ex_spm_default/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_voxeluncp001/nidm.ttl", "hrf_spmcanonical/nidm.ttl", "con_t/nidm.ttl", "clusterconn_18/nidm.ttl", "alt_onetailed/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
4 changes: 2 additions & 2 deletions spmexport/ex_spm_group_ols/config.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

{
"software": "spm",
"ground_truth": ["errmodel_ols/nidm.ttl"],
"ground_truth": ["errmodel_ols/nidm.ttl", "group/nidm.ttl", "space_spm12mni/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
4 changes: 2 additions & 2 deletions spmexport/ex_spm_group_wls/config.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

{
"software": "spm",
"ground_truth": ["errmodel_wls/nidm.ttl"],
"ground_truth": ["errmodel_wls/nidm.ttl", "group/nidm.ttl", "space_spm12mni/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_hrf_fir/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["hrf_fir/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_non_sphericity/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["errmodel_unstruct/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_partial_conjunction/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["inf_partialconj/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_temporal_derivative/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["hrf_spmtempoderiv/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_thr_clustfwep05/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_clustfwep05/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_thr_clustunck10/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_clustunck10/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_thr_voxelfdrp05/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_voxelfdrp05/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_thr_voxelfwep05/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_voxelfwep05/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
2 changes: 1 addition & 1 deletion spmexport/ex_spm_thr_voxelunct4/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@
"software": "spm",
"ground_truth": ["thr_voxelunct4/nidm.ttl"],
"inclusive": true,
"versions": ["1.2.0"]
"versions": ["1.3.0-rc2"]
}
12 changes: 12 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/alt_onetailed/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_Inference: <http://purl.org/nidash/nidm#NIDM_0000049> .
@prefix nidm_hasAlternativeHypothesis: <http://purl.org/nidash/nidm#NIDM_0000097> .
@prefix nidm_OneTailedTest: <http://purl.org/nidash/nidm#NIDM_0000060> .


niiri:inference_id a prov:Activity , nidm_Inference: ;
nidm_hasAlternativeHypothesis: nidm_OneTailedTest: .
13 changes: 13 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/clusterconn_18/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_ClusterDefinitionCriteria: <http://purl.org/nidash/nidm#NIDM_0000007> .
@prefix nidm_hasConnectivityCriterion: <http://purl.org/nidash/nidm#NIDM_0000099> .
@prefix nidm_voxel18connected: <http://purl.org/nidash/nidm#NIDM_0000128> .


niiri:cluster_definition_criteria_id a prov:Entity , nidm_ClusterDefinitionCriteria: ;
rdfs:label "Cluster Connectivity Criterion: 18" ;
nidm_hasConnectivityCriterion: nidm_voxel18connected: .
13 changes: 13 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/con_f/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_statisticType: <http://purl.org/nidash/nidm#NIDM_0000123> .
@prefix nidm_contrastName: <http://purl.org/nidash/nidm#NIDM_0000085> .
@prefix obo_contrastweightmatrix: <http://purl.obolibrary.org/obo/STATO_0000323> .
@prefix obo_fstatistic: <http://purl.obolibrary.org/obo/STATO_0000282> .


niiri:contrast_id a prov:Entity , obo_contrastweightmatrix: ;
nidm_statisticType: obo_fstatistic: .
13 changes: 13 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/con_t/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_statisticType: <http://purl.org/nidash/nidm#NIDM_0000123> .
@prefix nidm_contrastName: <http://purl.org/nidash/nidm#NIDM_0000085> .
@prefix obo_contrastweightmatrix: <http://purl.obolibrary.org/obo/STATO_0000323> .
@prefix obo_tstatistic: <http://purl.obolibrary.org/obo/STATO_0000176> .


niiri:contrast_id a prov:Entity , obo_contrastweightmatrix: ;
nidm_statisticType: obo_tstatistic: .
13 changes: 13 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/contrast_mask/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix crypto: <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#> .
@prefix dct: <http://purl.org/dc/terms/> .

@prefix nidm_DisplayMaskMap: <http://purl.org/nidash/nidm#NIDM_0000020> .
@prefix nidm_inCoordinateSpace: <http://purl.org/nidash/nidm#NIDM_0000104> .


niiri:display_map_id a prov:Entity , nidm_DisplayMaskMap: ;
dct:format "image/nifti"^^xsd:string .
20 changes: 20 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/errmodel_ols/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_ErrorModel: <http://purl.org/nidash/nidm#NIDM_0000023> .
@prefix nidm_hasErrorDistribution: <http://purl.org/nidash/nidm#NIDM_0000101> .
@prefix nidm_errorVarianceHomogeneous: <http://purl.org/nidash/nidm#NIDM_0000094> .
@prefix nidm_varianceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000126> .
@prefix nidm_hasErrorDependence: <http://purl.org/nidash/nidm#NIDM_0000100> .
@prefix nidm_dependenceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000089> .
@prefix nidm_IndependentParameter: <http://purl.org/nidash/nidm#NIDM_0000073> .
@prefix nidm_IndependentError: <http://purl.org/nidash/nidm#NIDM_0000048> .
@prefix obo_normaldistribution: <http://purl.obolibrary.org/obo/STATO_0000227> .

niiri:error_model_id a prov:Entity , nidm_ErrorModel: ;
nidm_hasErrorDistribution: obo_normaldistribution: ;
nidm_errorVarianceHomogeneous: "true"^^xsd:boolean ;
nidm_varianceMapWiseDependence: nidm_IndependentParameter: ;
nidm_hasErrorDependence: nidm_IndependentError: .
23 changes: 23 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/errmodel_unstruct/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_ErrorModel: <http://purl.org/nidash/nidm#NIDM_0000023> .
@prefix nidm_hasErrorDistribution: <http://purl.org/nidash/nidm#NIDM_0000101> .
@prefix nidm_errorVarianceHomogeneous: <http://purl.org/nidash/nidm#NIDM_0000094> .
@prefix nidm_varianceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000126> .
@prefix nidm_hasErrorDependence: <http://purl.org/nidash/nidm#NIDM_0000100> .
@prefix nidm_dependenceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000089> .
@prefix nidm_IndependentParameter: <http://purl.org/nidash/nidm#NIDM_0000073> .
@prefix nidm_ConstantParameter: <http://purl.org/nidash/nidm#NIDM_0000072> .
@prefix obo_normaldistribution: <http://purl.obolibrary.org/obo/STATO_0000227> .
@prefix obo_unstructuredcovariancestructure: <http://purl.obolibrary.org/obo/STATO_0000405> .


niiri:error_model_id a prov:Entity , nidm_ErrorModel: ;
nidm_hasErrorDistribution: obo_normaldistribution: ;
nidm_errorVarianceHomogeneous: "false"^^xsd:boolean ;
nidm_varianceMapWiseDependence: nidm_IndependentParameter: ;
nidm_hasErrorDependence: obo_unstructuredcovariancestructure: ;
nidm_dependenceMapWiseDependence: nidm_ConstantParameter: .
20 changes: 20 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/errmodel_wls/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix nidm_ErrorModel: <http://purl.org/nidash/nidm#NIDM_0000023> .
@prefix nidm_hasErrorDistribution: <http://purl.org/nidash/nidm#NIDM_0000101> .
@prefix nidm_errorVarianceHomogeneous: <http://purl.org/nidash/nidm#NIDM_0000094> .
@prefix nidm_varianceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000126> .
@prefix nidm_hasErrorDependence: <http://purl.org/nidash/nidm#NIDM_0000100> .
@prefix nidm_dependenceMapWiseDependence: <http://purl.org/nidash/nidm#NIDM_0000089> .
@prefix nidm_IndependentParameter: <http://purl.org/nidash/nidm#NIDM_0000073> .
@prefix nidm_IndependentError: <http://purl.org/nidash/nidm#NIDM_0000048> .
@prefix obo_normaldistribution: <http://purl.obolibrary.org/obo/STATO_0000227> .

niiri:error_model_id a prov:Entity , nidm_ErrorModel: ;
nidm_hasErrorDistribution: obo_normaldistribution: ;
nidm_errorVarianceHomogeneous: "false"^^xsd:boolean ;
nidm_varianceMapWiseDependence: nidm_IndependentParameter: ;
nidm_hasErrorDependence: nidm_IndependentError: .
12 changes: 12 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/group/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

@prefix obo_studygrouppopulation: <http://purl.obolibrary.org/obo/STATO_0000193> .
@prefix nidm_Data: <http://purl.org/nidash/nidm#NIDM_0000169> .

niiri:group_id a prov:Entity , obo_studygrouppopulation: .

niiri:data_id a prov:Entity , nidm_Data: , prov:Collection ;
prov:wasAttributedTo niiri:group_id .
14 changes: 14 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/hrf_fir/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nfo: <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#> .

@prefix nidm_DesignMatrix: <http://purl.org/nidash/nidm#NIDM_0000019> .
@prefix nidm_hasHRFBasis: <http://purl.org/nidash/nidm#NIDM_0000102> .
@prefix nidm_FiniteImpulseResponseBasisSet: <http://purl.org/nidash/nidm#NIDM_0000028> .


niiri:first_level_design_matrix_id a prov:Entity , nidm_DesignMatrix: ;
nidm_hasHRFBasis: nidm_FiniteImpulseResponseBasisSet: .
16 changes: 16 additions & 0 deletions spmexport/ground_truth/1.3.0-rc2/hrf_spmcanonical/nidm.ttl
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix niiri: <http://iri.nidash.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix nfo: <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#> .

@prefix nidm_DesignMatrix: <http://purl.org/nidash/nidm#NIDM_0000019> .
@prefix nidm_regressorNames: <http://purl.org/nidash/nidm#NIDM_0000021> .
@prefix nidm_hasHRFBasis: <http://purl.org/nidash/nidm#NIDM_0000102> .
@prefix nidm_hasDriftModel: <http://purl.org/nidash/nidm#NIDM_0000088> .
@prefix spm_SPMsCanonicalHRF: <http://purl.org/nidash/spm#SPM_0000004> .


niiri:first_level_design_matrix_id a prov:Entity , nidm_DesignMatrix: ;
nidm_hasHRFBasis: spm_SPMsCanonicalHRF: .
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