Merge branch 'bids-standard:master' into master

Author: bclenet

bids_prov/utils.py

@@ -5,6 +5,7 @@
 import shutil
 import uuid
 from typing import Mapping, Union, Tuple
+import re
 
 CONTEXT_URL = "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json"
 
@@ -120,6 +121,44 @@ def compute_sha_256_entity(entities: dict):
         shutil.rmtree(directory)
 
 
+def simplify_urns(graph: str) -> str:
+    """
+    Replace URNs of a json-ld graph with simpler (not random) values defined by their order of appearance in the graph.
+
+    Parameters
+    ----------
+    graph : str
+        The json-ld graph dumped as a string
+
+    Returns
+    -------
+    str
+        The input string with simplified urns.
+    """
+
+    # Get all occurrences of ("urn:" + 36 following chars)
+    urn_occurrences = [i for i in re.finditer(r'urn:[a-zA-Z0-9\-]{36}', graph)]
+
+    # Prepare a dict in which :
+    #     - key is an urn as present in the original graph
+    #     - value is an id corresponding to the order of appearance of the urn in the graph.
+    known_urns = dict()
+    counter = 0
+
+    # Assign one simpler id to each urn
+    for urn in urn_occurrences:
+        if urn.group() not in known_urns:
+            known_urns[urn.group()] = f"urn:{str(counter).zfill(36)}"
+            counter += 1
+
+    # Replace all urns in the input graph with their assigned id
+    output_graph = graph
+    for key, value in known_urns.items():
+        output_graph = output_graph.replace(key, value)
+
+    return output_graph
+
+
 def writing_jsonld(graph, indent, output_file):
     """
     Write a json-ld in memory unless it already exists and contains the same content
@@ -140,10 +179,12 @@ def writing_jsonld(graph, indent, output_file):
     """
     if os.path.isfile(output_file):
         with open(output_file, "r") as f:
-            existing_content = f.read()
+            existing_content = simplify_urns(f.read())
+
+        new_content = simplify_urns(json.dumps(graph, indent=indent))
 
-            if existing_content == json.dumps(graph, indent=indent):
-                return True
+        if existing_content == new_content:
+            return True
 
     with open(output_file, "w") as fd:
         json.dump(graph, fd, indent=indent)

examples/from_parsers/context_2024_06_13_07h55m05s.txt

@@ -0,0 +1,72 @@
+Date : 2024_06_13_07h55m05s
+Processing files...
+    file= nidmresults-examples/afni_alt_onesided_proc.sub_001
+    file= nidmresults-examples/afni_alt_onesided_proc.sub_001
+    file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
+    file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
+    file= nidmresults-examples/afni_clustconn_18_proc.sub_001
+    file= nidmresults-examples/afni_clustconn_18_proc.sub_001
+    file= nidmresults-examples/afni_clustconn_26_proc.sub_001
+    file= nidmresults-examples/afni_clustconn_26_proc.sub_001
+    file= nidmresults-examples/afni_con_f_proc.sub_001
+    file= nidmresults-examples/afni_con_f_proc.sub_001
+    file= nidmresults-examples/afni_default_proc.sub_001
+    file= nidmresults-examples/afni_default_proc.sub_001
+    file= nidmresults-examples/afni_gam_proc.sub_001
+    file= nidmresults-examples/afni_gam_proc.sub_001
+    file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
+    file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
+    file= nidmresults-examples/afni_hrf_tent_proc.sub_001
+    file= nidmresults-examples/afni_hrf_tent_proc.sub_001
+    file= nidmresults-examples/afni_other_template_proc.sub_001
+    file= nidmresults-examples/afni_other_template_proc.sub_001
+    file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
+    file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
+    file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
+    file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
+    file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
+    file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
+    file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+    file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+    file= nidmresults-examples/fsl_con_f_multiple_report_log.html
+    file= nidmresults-examples/fsl_con_f_report_log.html
+    file= nidmresults-examples/fsl_contrast_mask_report_log.html
+    file= nidmresults-examples/fsl_default_report_log.html
+    file= nidmresults-examples/fsl_full_examples001_report_log.html
+    file= nidmresults-examples/fsl_gamma_basis_report_log.html
+    file= nidmresults-examples/fsl_gaussian_report_log.html
+    file= nidmresults-examples/fsl_group_btw_report_log.html
+    file= nidmresults-examples/fsl_group_ols_report_log.html
+    file= nidmresults-examples/fsl_group_wls_report_log.html
+    file= nidmresults-examples/fsl_hrf_fir_report_log.html
+    file= nidmresults-examples/fsl_hrf_gammadiff_report_log.html
+    file= nidmresults-examples/fsl_motion_reg_der_report_log.html
+    file= nidmresults-examples/fsl_motion_reg_report_log.html
+    file= nidmresults-examples/fsl_thr_clustfwep05_report_log.html
+    file= nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
+    file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
+    file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
+    file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
+    file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
+    file= nidmresults-examples/narps_do_13_view_zoom.tcsh
+    file= nidmresults-examples/narps_do_13_view_zoom.tcsh
+    file= nidmresults-examples/spm_2_t_test_batch.m
+    file= nidmresults-examples/spm_HRF_informed_basis_batch.m
+    file= nidmresults-examples/spm_con_f_batch.m
+    file= nidmresults-examples/spm_conjunction_batch.m
+    file= nidmresults-examples/spm_contrast_mask_batch.m
+    file= nidmresults-examples/spm_covariate_batch.m
+    file= nidmresults-examples/spm_default_batch.m
+    file= nidmresults-examples/spm_explicit_mask_batch.m
+    file= nidmresults-examples/spm_group_ols_batch.m
+    file= nidmresults-examples/spm_group_wls_batch.m
+    file= nidmresults-examples/spm_hrf_fir_batch.m
+    file= nidmresults-examples/spm_non_sphericity_batch.m
+    file= nidmresults-examples/spm_partial_conjunction_batch.m
+    file= nidmresults-examples/spm_temporal_derivative_batch.m
+    file= nidmresults-examples/spm_thr_clustfwep05_batch.m
+    file= nidmresults-examples/spm_thr_clustunck10_batch.m
+    file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
+    file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
+    file= nidmresults-examples/spm_thr_voxelunct4_batch.m
+End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.365113