Merge pull request #124 from bids-standard/fix_key_soft

Fix key for Software + Version
bids-standard · Sep 19, 2023 · 3fb2379 · 3fb2379
2 parents abcbc33 + 6a26142
commit 3fb2379
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Showing 72 changed files with 15,965 additions and 15,965 deletions.
diff --git a/bids_prov/tests/test_utils.py b/bids_prov/tests/test_utils.py
@@ -32,14 +32,14 @@ def test_get_default_graph():
     # Test the default arguments
     graph, agent_id = get_default_graph(label)
     assert graph["@context"] == CONTEXT_URL
-    assert graph["Records"]["prov:Agent"][0]["Label"] == label
+    assert graph["Records"]["Software"][0]["Label"] == label
     assert agent_id is not None
 
     # Test custom arguments
     graph, agent_id = get_default_graph(label, context_url, spm_ver)
     assert graph["@context"] == context_url
-    assert graph["Records"]["prov:Agent"][0]["Label"] == label
-    assert graph["Records"]["prov:Agent"][0]["version"] == spm_ver
+    assert graph["Records"]["Software"][0]["Label"] == label
+    assert graph["Records"]["Software"][0]["Version"] == spm_ver
     assert agent_id is not None
 
 

diff --git a/bids_prov/utils.py b/bids_prov/utils.py
@@ -20,13 +20,13 @@ def get_default_graph(label: str, context_url: str = CONTEXT_URL, soft_ver: str
                "@context": context_url,
                "BIDSProvVersion": "dev",  # TODO ?
                "Records": {
-                   "prov:Agent": [
+                   "Software": [
                        {
                            "@id": "urn:" + agent_id,
                            "RRID": "RRID:SCR_007037",
                            "@type": "prov:SoftwareAgent",
                            "Label": label,
-                           "version": soft_ver
+                           "Version": soft_ver
                        }
                    ],
                    "Activities": [],

diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_bloc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_bloc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_bloc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_bloc.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_con_f_proc.jsonld b/examples/from_parsers/afni/afni_con_f_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_con_f_proc_bloc.jsonld b/examples/from_parsers/afni/afni_con_f_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_default_proc.jsonld b/examples/from_parsers/afni/afni_default_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_default_proc_bloc.jsonld b/examples/from_parsers/afni/afni_default_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_gam_proc.jsonld b/examples/from_parsers/afni/afni_gam_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_gam_proc_bloc.jsonld b/examples/from_parsers/afni/afni_gam_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_bloc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_bloc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_other_template_proc.jsonld b/examples/from_parsers/afni/afni_other_template_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_other_template_proc_bloc.jsonld b/examples/from_parsers/afni/afni_other_template_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_bloc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_bloc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_bloc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_bloc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_bloc.jsonld
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
@@ -2,126 +2,126 @@
   "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
   "BIDSProvVersion": "dev",
   "Records": {
-    "prov:Agent": [
+    "Software": [
       {
-        "@id": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+        "@id": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
-        "version": "afni24"
+        "Version": "afni24"
       }
     ],
     "Activities": [
       {
-        "@id": "urn:aab53304-9b12-437b-806d-49e31efb24d7",
+        "@id": "urn:b30cc606-6137-447b-b28e-0fae2ef7dd42",
         "Label": "3dpc",
-        "AssociatedWith": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
         "Parameters": {},
         "Used": [
-          "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e",
-          "urn:869adb8d-9320-4314-abe1-6b6d044a5c59"
+          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4",
+          "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b"
         ]
       },
       {
-        "@id": "urn:0b7aab45-33e6-4933-87bf-1f8f951f1bb1",
+        "@id": "urn:70d7cd80-32f6-4994-a4d4-c3fed4e02383",
         "Label": "3dresample",
-        "AssociatedWith": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
         "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
         "Parameters": {},
         "Used": [
-          "urn:1eef669f-661f-4568-8142-004f40d9ce57",
-          "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e"
+          "urn:af9b4299-4373-4423-8478-02481413a92c",
+          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4"
         ]
       },
       {
-        "@id": "urn:46658bb2-25a3-4c69-a644-fecd3b60b9ca",
+        "@id": "urn:f0664c49-ddd6-4d24-a5ba-c6bbf6b11662",
         "Label": "3dMatch",
-        "AssociatedWith": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
         "Command": "3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED",
         "Parameters": {},
         "Used": [
-          "urn:f6e52004-da13-4dda-b778-6622f666c503",
-          "urn:6d3d46ee-7e37-43d2-8ba4-a2bb416a4b5f",
-          "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e"
+          "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
+          "urn:b04ba5a4-7187-414c-bf95-ec135e792a53",
+          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4"
         ]
       },
       {
-        "@id": "urn:6845abf4-4f03-4e1e-9fb4-e47350f39fe1",
+        "@id": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
         "Label": "3dcalc",
-        "AssociatedWith": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
         "Command": "3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
         "Parameters": {},
         "Used": [
-          "urn:6d3d46ee-7e37-43d2-8ba4-a2bb416a4b5f"
+          "urn:b04ba5a4-7187-414c-bf95-ec135e792a53"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e",
+        "@id": "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:869adb8d-9320-4314-abe1-6b6d044a5c59",
+        "@id": "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:bca7fdff-cf83-4ed5-86ca-ce6de993d731",
+        "@id": "urn:7f8dcb20-fc81-454b-bfd1-236e9f7c0c4f",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:aab53304-9b12-437b-806d-49e31efb24d7",
+        "GeneratedBy": "urn:b30cc606-6137-447b-b28e-0fae2ef7dd42",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:1eef669f-661f-4568-8142-004f40d9ce57",
+        "@id": "urn:af9b4299-4373-4423-8478-02481413a92c",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:f6e52004-da13-4dda-b778-6622f666c503",
+        "@id": "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
         "Label": "tmp_REF_DSET.nii.gz",
         "AtLocation": "tmp_REF_DSET.nii.gz",
-        "GeneratedBy": "urn:0b7aab45-33e6-4933-87bf-1f8f951f1bb1",
+        "GeneratedBy": "urn:70d7cd80-32f6-4994-a4d4-c3fed4e02383",
         "digest": {
           "sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
         }
       },
       {
-        "@id": "urn:6d3d46ee-7e37-43d2-8ba4-a2bb416a4b5f",
+        "@id": "urn:b04ba5a4-7187-414c-bf95-ec135e792a53",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:8b71facf-7122-43cf-b438-a8fe71f1eb30",
+        "@id": "urn:39cc23bc-4f4d-4709-9250-e84f23fea27f",
         "Label": "tmp_MATCHED",
         "AtLocation": "tmp_MATCHED",
-        "GeneratedBy": "urn:46658bb2-25a3-4c69-a644-fecd3b60b9ca",
+        "GeneratedBy": "urn:f0664c49-ddd6-4d24-a5ba-c6bbf6b11662",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:74ad9995-210a-4a09-96c1-021ac291fc78",
+        "@id": "urn:5d71ef67-fdc3-4c22-b0ce-a46353f96da6",
         "Label": "PC_hyp${num}_sign0.nii.gz",
         "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "GeneratedBy": "urn:6845abf4-4f03-4e1e-9fb4-e47350f39fe1",
+        "GeneratedBy": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }

diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld
@@ -2,104 +2,104 @@
   "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
   "BIDSProvVersion": "dev",
   "Records": {
-    "prov:Agent": [
+    "Software": [
       {
-        "@id": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
+        "@id": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
-        "version": "afni24"
+        "Version": "afni24"
       }
     ],
     "Activities": [
       {
-        "@id": "urn:3ebb9f9c-0f46-4208-9d6b-8e296d89ad87",
+        "@id": "urn:f9d9798b-3574-4575-9644-32356a2670e4",
         "Label": "",
-        "AssociatedWith": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
+        "AssociatedWith": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
         "Used": [
-          "urn:c0771e58-a6ad-4067-a247-994db5d57566",
-          "urn:d751aff5-d3ee-485c-be17-647730723212"
+          "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+          "urn:fe638e60-c25e-4ea2-9402-d0a17266edce"
         ]
       },
       {
-        "@id": "urn:768bdff7-fc79-48ed-b4be-76ffa67c22a7",
+        "@id": "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
         "Label": "bloc ...",
-        "AssociatedWith": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
+        "AssociatedWith": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
         "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ",
         "Used": [
-          "urn:eb38131d-32b2-4cbf-9b65-bb40b299df05",
-          "urn:c0771e58-a6ad-4067-a247-994db5d57566",
-          "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd",
-          "urn:c0771e58-a6ad-4067-a247-994db5d57566",
-          "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
+          "urn:4a3af7a0-3036-4378-9a44-c64d83423ba4",
+          "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+          "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4",
+          "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+          "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:c0771e58-a6ad-4067-a247-994db5d57566",
+        "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:d751aff5-d3ee-485c-be17-647730723212",
+        "@id": "urn:fe638e60-c25e-4ea2-9402-d0a17266edce",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:0708ea50-1d83-48c9-be2e-3871dfeb2b0a",
+        "@id": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:3ebb9f9c-0f46-4208-9d6b-8e296d89ad87",
+        "GeneratedBy": "urn:f9d9798b-3574-4575-9644-32356a2670e4",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:c0771e58-a6ad-4067-a247-994db5d57566",
+        "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:eb38131d-32b2-4cbf-9b65-bb40b299df05",
+        "@id": "urn:4a3af7a0-3036-4378-9a44-c64d83423ba4",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd",
+        "@id": "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:9c0f5dac-fd86-459b-b326-320b070d354c",
+        "@id": "urn:74a19541-23cc-4447-9e24-964b612c2b15",
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