Merge pull request #127 from yarikoptic/enh-used

Make "Used" to contain only unique values and sort them

bids_prov/afni/afni_parser.py

@@ -219,6 +219,9 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
             else:
                 activity["Used"].append(existing_input["@id"])
 
+        # Order does not matter and then makes sense to include only unique values
+        activity["Used"] = sorted(set(activity["Used"]))
+
         for output_path in outputs:
             records["Entities"].append(
                 {

bids_prov/fsl/fsl_parser.py

@@ -502,6 +502,9 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
                 else:
                     a["Used"].append(existing_input["@id"])
 
+            # Order does not matter and then makes sense to include only unique values
+            a["Used"] = sorted(set(a["Used"]))
+
             for output_path in outputs:
                 # output_name = output_path.replace("/", "_") # TODO
                 records["Entities"].append(

bids_prov/spm/spm_parser.py

@@ -381,6 +381,9 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
                 param_value = right_ if not right_.startswith("[") else right_.replace(" ", ", ")
                 params[param_name] = param_value  # example : [4 2] becomes [4, 2]
 
+        # Order does not matter and then makes sense to include only unique values
+        activity["Used"] = sorted(set(activity["Used"]))
+
         if params:
             activity["Parameters"] = params
 

examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld

@@ -4,7 +4,7 @@
   "Records": {
     "Software": [
       {
-        "@id": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+        "@id": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
@@ -13,115 +13,115 @@
     ],
     "Activities": [
       {
-        "@id": "urn:b30cc606-6137-447b-b28e-0fae2ef7dd42",
+        "@id": "urn:90645147-6abd-4c8a-a8a5-517f8a8f21fe",
         "Label": "3dpc",
-        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+        "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
         "Parameters": {},
         "Used": [
-          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4",
-          "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b"
+          "urn:a68d7d7d-2892-4c73-8931-cb493bf3664b",
+          "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451"
         ]
       },
       {
-        "@id": "urn:70d7cd80-32f6-4994-a4d4-c3fed4e02383",
+        "@id": "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
         "Label": "3dresample",
-        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+        "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
         "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
         "Parameters": {},
         "Used": [
-          "urn:af9b4299-4373-4423-8478-02481413a92c",
-          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4"
+          "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
+          "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451"
         ]
       },
       {
-        "@id": "urn:f0664c49-ddd6-4d24-a5ba-c6bbf6b11662",
+        "@id": "urn:31c67e59-a174-4acc-a9db-a84469c666cf",
         "Label": "3dMatch",
-        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+        "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
         "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:8967c63f-5fc7-44a6-a350-10e4d91420e5",
-          "urn:b04ba5a4-7187-414c-bf95-ec135e792a53",
-          "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4"
+          "urn:0aff86a2-c424-420f-8105-3869a44750ba",
+          "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
+          "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04"
         ]
       },
       {
-        "@id": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
+        "@id": "urn:e6b98c73-86e5-4eed-abdd-25d3eb6842f7",
         "Label": "3dcalc",
-        "AssociatedWith": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+        "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
         "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:b04ba5a4-7187-414c-bf95-ec135e792a53"
+          "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4",
+        "@id": "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b",
+        "@id": "urn:a68d7d7d-2892-4c73-8931-cb493bf3664b",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:7f8dcb20-fc81-454b-bfd1-236e9f7c0c4f",
+        "@id": "urn:1d44d844-c4ca-4840-9019-b9b7a5f712e2",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:b30cc606-6137-447b-b28e-0fae2ef7dd42",
+        "GeneratedBy": "urn:90645147-6abd-4c8a-a8a5-517f8a8f21fe",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:af9b4299-4373-4423-8478-02481413a92c",
+        "@id": "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
+        "@id": "urn:0aff86a2-c424-420f-8105-3869a44750ba",
         "Label": "tmp_REF_DSET.nii.gz",
         "AtLocation": "tmp_REF_DSET.nii.gz",
-        "GeneratedBy": "urn:70d7cd80-32f6-4994-a4d4-c3fed4e02383",
+        "GeneratedBy": "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
         "digest": {
           "sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
         }
       },
       {
-        "@id": "urn:b04ba5a4-7187-414c-bf95-ec135e792a53",
+        "@id": "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:39cc23bc-4f4d-4709-9250-e84f23fea27f",
+        "@id": "urn:a8a1a9f6-ef1a-480d-bdea-a1be759db9ea",
         "Label": "tmp_MATCHED",
         "AtLocation": "tmp_MATCHED",
-        "GeneratedBy": "urn:f0664c49-ddd6-4d24-a5ba-c6bbf6b11662",
+        "GeneratedBy": "urn:31c67e59-a174-4acc-a9db-a84469c666cf",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:5d71ef67-fdc3-4c22-b0ce-a46353f96da6",
+        "@id": "urn:40c7b3b1-aa1b-41ef-b09f-423be7a6600a",
         "Label": "PC_hyp${num}_sign0.nii.gz",
         "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "GeneratedBy": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
+        "GeneratedBy": "urn:e6b98c73-86e5-4eed-abdd-25d3eb6842f7",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }

examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld

@@ -4,7 +4,7 @@
   "Records": {
     "Software": [
       {
-        "@id": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
+        "@id": "urn:b42066b4-1ce6-4ef1-81c8-5b010b7b18a9",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
@@ -13,93 +13,93 @@
     ],
     "Activities": [
       {
-        "@id": "urn:f9d9798b-3574-4575-9644-32356a2670e4",
+        "@id": "urn:66899270-94c2-43f0-a18d-0cc0171d7a9c",
         "Label": "",
-        "AssociatedWith": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
+        "AssociatedWith": "urn:b42066b4-1ce6-4ef1-81c8-5b010b7b18a9",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
         "Used": [
-          "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
-          "urn:fe638e60-c25e-4ea2-9402-d0a17266edce"
+          "urn:3a3f7dc1-b64c-4e37-94ad-ced61e976493",
+          "urn:6bd8a464-c1d1-4ad1-887e-89e4569f4fc5"
         ]
       },
       {
-        "@id": "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
+        "@id": "urn:c5b45432-97f7-4d5d-9cb7-4468389c1014",
         "Label": "bloc ...",
-        "AssociatedWith": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
+        "AssociatedWith": "urn:b42066b4-1ce6-4ef1-81c8-5b010b7b18a9",
         "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: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"
+          "urn:6bd8a464-c1d1-4ad1-887e-89e4569f4fc5",
+          "urn:dbc62c04-7401-4242-bd5f-1e0cd3200344",
+          "urn:6bd8a464-c1d1-4ad1-887e-89e4569f4fc5",
+          "urn:a38e9c6e-092c-4a2a-ad84-77d8ef3aed75",
+          "urn:a38e9c6e-092c-4a2a-ad84-77d8ef3aed75"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+        "@id": "urn:6bd8a464-c1d1-4ad1-887e-89e4569f4fc5",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:fe638e60-c25e-4ea2-9402-d0a17266edce",
+        "@id": "urn:3a3f7dc1-b64c-4e37-94ad-ced61e976493",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+        "@id": "urn:b1c2c519-8550-40ba-9541-f954ae39fb12",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:f9d9798b-3574-4575-9644-32356a2670e4",
+        "GeneratedBy": "urn:66899270-94c2-43f0-a18d-0cc0171d7a9c",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+        "@id": "urn:6bd8a464-c1d1-4ad1-887e-89e4569f4fc5",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:4a3af7a0-3036-4378-9a44-c64d83423ba4",
+        "@id": "urn:dbc62c04-7401-4242-bd5f-1e0cd3200344",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4",
+        "@id": "urn:a38e9c6e-092c-4a2a-ad84-77d8ef3aed75",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:74a19541-23cc-4447-9e24-964b612c2b15",
+        "@id": "urn:0e402105-a625-4b0d-aabb-84565733d38a",
         "Label": "tmp_MATCHED",
         "AtLocation": "tmp_MATCHED",
-        "GeneratedBy": "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
+        "GeneratedBy": "urn:c5b45432-97f7-4d5d-9cb7-4468389c1014",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:ba85afc6-5799-4f95-8ec2-1b938e646d31",
+        "@id": "urn:f077f5e9-1c50-4198-9c92-b9d632ff2e18",
         "Label": "PC_hyp${num}_sign0.nii.gz",
         "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "GeneratedBy": "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
+        "GeneratedBy": "urn:c5b45432-97f7-4d5d-9cb7-4468389c1014",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }