automated nidm example computation from github action

bids-standard · Jun 23, 2023 · 520fc64 · 520fc64
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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
@@ -1,11 +1,10 @@
 {
   "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
   "BIDSProvVersion": "dev",
-  "@id": "http://example.org/ds00000X",
   "records": {
     "prov:Agent": [
       {
-        "@id": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+        "@id": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "label": "AFNI",
@@ -14,115 +13,115 @@
     ],
     "prov:Activity": [
       {
-        "@id": "urn:d7a66507-3350-42b8-9e9f-f37d0e3d31f7",
+        "@id": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
         "label": "3dpc",
-        "associatedWith": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+        "associatedWith": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
         "command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
         "parameters": {},
         "used": [
-          "urn:ef69e3aa-d7be-4960-b129-6ad43fc9442c",
-          "urn:abda5291-509b-40dd-b303-74ba3f8fe26f"
+          "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79",
+          "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87"
         ]
       },
       {
-        "@id": "urn:6fd64536-641a-413b-8d77-390f0514fea8",
+        "@id": "urn:a4725cde-22c1-43e1-bb39-8ca323359467",
         "label": "3dresample",
-        "associatedWith": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+        "associatedWith": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
         "command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
         "parameters": {},
         "used": [
-          "urn:598ab807-45ed-4acf-a417-d0bcb23a4959",
-          "urn:ef69e3aa-d7be-4960-b129-6ad43fc9442c"
+          "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+          "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79"
         ]
       },
       {
-        "@id": "urn:74362364-33c0-47db-81df-fe5bc8a25c49",
+        "@id": "urn:a9ba8f6c-c396-418e-a76a-08e1034d485c",
         "label": "3dMatch",
-        "associatedWith": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+        "associatedWith": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
         "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:b60f8029-dace-4def-b134-96c533ed2469",
-          "urn:231336c7-5029-499e-aa70-72035c9d8213",
-          "urn:ef69e3aa-d7be-4960-b129-6ad43fc9442c"
+          "urn:a424e26a-4756-4ebf-aee7-78caa8508f49",
+          "urn:f7b45616-d40f-4f94-9390-20175b6abab7",
+          "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79"
         ]
       },
       {
-        "@id": "urn:9381c42a-f942-49f3-bcf2-577fbb62b05c",
+        "@id": "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772",
         "label": "3dcalc",
-        "associatedWith": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+        "associatedWith": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
         "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:231336c7-5029-499e-aa70-72035c9d8213"
+          "urn:f7b45616-d40f-4f94-9390-20175b6abab7"
         ]
       }
     ],
     "prov:Entity": [
       {
-        "@id": "urn:ef69e3aa-d7be-4960-b129-6ad43fc9442c",
+        "@id": "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79",
         "label": "${dset_mask}",
         "prov:atLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:abda5291-509b-40dd-b303-74ba3f8fe26f",
+        "@id": "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87",
         "label": "${grp_dset}",
         "prov:atLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:6b77283c-0366-4a19-b108-5a6f3bafe64f",
+        "@id": "urn:ac224bd4-b45c-4ad9-a7c7-14bff747481d",
         "label": "PC_hyp${num}",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}",
-        "generatedBy": "urn:d7a66507-3350-42b8-9e9f-f37d0e3d31f7",
+        "generatedBy": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:598ab807-45ed-4acf-a417-d0bcb23a4959",
+        "@id": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
         "label": "\"${ref_dset}\"",
         "prov:atLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:b60f8029-dace-4def-b134-96c533ed2469",
+        "@id": "urn:a424e26a-4756-4ebf-aee7-78caa8508f49",
         "label": "tmp_REF_DSET.nii.gz",
         "prov:atLocation": "tmp_REF_DSET.nii.gz",
-        "generatedBy": "urn:6fd64536-641a-413b-8d77-390f0514fea8",
+        "generatedBy": "urn:a4725cde-22c1-43e1-bb39-8ca323359467",
         "digest": {
           "sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
         }
       },
       {
-        "@id": "urn:231336c7-5029-499e-aa70-72035c9d8213",
+        "@id": "urn:f7b45616-d40f-4f94-9390-20175b6abab7",
         "label": "PC_hyp${num}",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:ceafbca0-7a13-4165-b3bb-60120eef23cb",
+        "@id": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5",
         "label": "tmp_MATCHED",
         "prov:atLocation": "tmp_MATCHED",
-        "generatedBy": "urn:74362364-33c0-47db-81df-fe5bc8a25c49",
+        "generatedBy": "urn:a9ba8f6c-c396-418e-a76a-08e1034d485c",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:cb9a8af7-6454-46d3-8072-d4fb735a7949",
+        "@id": "urn:7ad4dcb0-cec7-4d82-ab67-1da97d0a6e4e",
         "label": "PC_hyp${num}_sign0.nii.gz",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "generatedBy": "urn:9381c42a-f942-49f3-bcf2-577fbb62b05c",
+        "generatedBy": "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772",
         "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
@@ -1,11 +1,10 @@
 {
   "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
   "BIDSProvVersion": "dev",
-  "@id": "http://example.org/ds00000X",
   "records": {
     "prov:Agent": [
       {
-        "@id": "urn:fc4f2b90-f6c6-410a-a8ff-78d8206b5df0",
+        "@id": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "label": "AFNI",
@@ -14,93 +13,93 @@
     ],
     "prov:Activity": [
       {
-        "@id": "urn:4fe9ad80-620c-406c-a242-7f323181a475",
+        "@id": "urn:1e091424-d3b1-4596-b5e1-2b5167927fa1",
         "label": "",
-        "associatedWith": "urn:fc4f2b90-f6c6-410a-a8ff-78d8206b5df0",
+        "associatedWith": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
         "command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
         "used": [
-          "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
-          "urn:5d73a76e-4df1-4fd3-a040-769dac5ac08d"
+          "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
+          "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a"
         ]
       },
       {
-        "@id": "urn:5c602888-1bca-4c78-8710-3274acc87d5e",
+        "@id": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
         "label": "bloc ...",
-        "associatedWith": "urn:fc4f2b90-f6c6-410a-a8ff-78d8206b5df0",
+        "associatedWith": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
         "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:cbc9b629-6395-406a-8661-234f76bf6faa",
-          "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
-          "urn:715350ea-baf9-4e67-af8b-4c223751977f",
-          "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
-          "urn:715350ea-baf9-4e67-af8b-4c223751977f"
+          "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b",
+          "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
+          "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
+          "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
+          "urn:fe7823e7-a7a4-4991-8938-14e7d736a233"
         ]
       }
     ],
     "prov:Entity": [
       {
-        "@id": "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
+        "@id": "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
         "label": "${dset_mask}",
         "prov:atLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:5d73a76e-4df1-4fd3-a040-769dac5ac08d",
+        "@id": "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
         "label": "${grp_dset}",
         "prov:atLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:cf41eab2-9285-40e8-ac6d-f47cd151abb4",
+        "@id": "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21",
         "label": "PC_hyp${num}",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}",
-        "generatedBy": "urn:4fe9ad80-620c-406c-a242-7f323181a475",
+        "generatedBy": "urn:1e091424-d3b1-4596-b5e1-2b5167927fa1",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
+        "@id": "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
         "label": "${dset_mask}",
         "prov:atLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:cbc9b629-6395-406a-8661-234f76bf6faa",
+        "@id": "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b",
         "label": "\"${ref_dset}\"",
         "prov:atLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:715350ea-baf9-4e67-af8b-4c223751977f",
+        "@id": "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
         "label": "PC_hyp${num}",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:cbb044da-cc8b-4ef7-977c-2c3794c9027a",
+        "@id": "urn:6cc92bfd-ba05-4178-9439-f356bb45800e",
         "label": "tmp_MATCHED",
         "prov:atLocation": "tmp_MATCHED",
-        "generatedBy": "urn:5c602888-1bca-4c78-8710-3274acc87d5e",
+        "generatedBy": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:fcf71ded-26d2-4518-a3e8-bb58b66bdb22",
+        "@id": "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315",
         "label": "PC_hyp${num}_sign0.nii.gz",
         "prov:atLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "generatedBy": "urn:5c602888-1bca-4c78-8710-3274acc87d5e",
+        "generatedBy": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }