pysodafair 0.1.66__py3-none-any.whl → 0.1.68__py3-none-any.whl

pysoda/schema/code_description.json

@@ -13,7 +13,8 @@
       "type": "array",
       "items": {
         "type": "string",
-        "description": "The identifier used to identify the resource in the RRID database."
+        "description": "The identifier used to identify the resource in the RRID database.",
+        "pattern": "^$|^RRID:"
       }
     },
     "ontology_term": {
@@ -40,8 +41,13 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
-              "description": "The URL or DOI of the publication that describes the tool or method."
+              "description": "The URL or DOI of the publication that describes the tool or method.",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ]
             },
             "Rating": {
               "type": "string",
@@ -73,7 +79,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -106,7 +117,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -139,33 +155,44 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR3c": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR4": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -198,7 +225,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -231,7 +263,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -264,7 +301,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -297,59 +339,76 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR7c": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR7d": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR7e": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR8a": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -382,20 +441,28 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         },
         "TSR9": {
           "type": "object",
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -428,7 +495,12 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             },
             "Rating": {
@@ -461,13 +533,16 @@
           "properties": {
             "Link": {
               "type": "string",
-              "pattern": "^(https?://(?:www\\.)?|doi:)[\\w\\d./?=#]+$",
+              "anyOf": [
+                {
+                  "pattern": "^https://doi.org/10\\.[0-9]{4,9}[-._;()/:a-zA-Z0-9]+$"
+                },
+                { "pattern": "^https://[wd-._~:/?#[]@!$&'()*+,;=%]+$" }
+              ],
               "description": "The URL or DOI of the publication that describes the tool or method."
             }
           },
-          "required": [
-            "Link"
-          ]
+          "required": ["Link"]
         }
       },
       "required": [
@@ -609,12 +684,7 @@
           }
         }
       },
-      "required": [
-        "number_of_inputs",
-        "inputs",
-        "number_of_outputs",
-        "outputs"
-      ]
+      "required": ["number_of_inputs", "inputs", "number_of_outputs", "outputs"]
     }
   },
   "required": [
@@ -626,4 +696,4 @@
     "ontology_term",
     "ontology_identifier"
   ]
-}
+}

pysoda/schema/dataset_description.json

@@ -4,7 +4,8 @@
   "properties": {
     "metadata_version": {
       "type": "string",
-      "description": "The version of the metadata schema used."
+      "description": "The version of the metadata schema used.",
+      "enum": ["3.0.0", "3.0.1", "3.0.2"]
     },
     "type": {
       "type": "string",
@@ -148,36 +149,39 @@
             "pattern": "^(([Vv]an|[Vv]an [Dd]e[rn]?|[Vv]an [Tt]|[Vv]ander|[Vv]on|[Vv]on [Dd]e[rn]?|[Zz]u|[Zz]ur|[Vv]om|[Dd]e|[Dd]es|[Dd]u|[Dd]e [Ll]a|[Dd]e [Ll]es|[Dd]e [Ll]os|[Ll]e|[Ll]a|[Ll]es|[Dd]el|[Dd]e [Ll]os|[Dd]e [Ll]a|[Dd]e [Ll]as|[Dd]a|[Dd]o|[Dd]i|[Dd]ell[ao]|[Dd]ell[ei]|[Dd]ai|[Dd]al|[Dd]alle|[Oo]'|[Mm]c|[Mm]ac|[Aa]l|[Ee]l|[Aa]bd [Aa]l|[Aa]bu|[Ii]bn|[Ff]itz|[Aa]p|[Bb]en|[Bb]ar|[Bb]at) )?[^, ]+, [^,]+$",
             "description": "The name of the contributor. The format should be 'Last Name, First Name'. Supports international family name prefixes (van, von, de, del, etc.)."
           },
-          "contributor_role": {
-            "type": "string",
-            "enum": [
-              "CorrespondingAuthor",
-              "ContactPerson",
-              "Creator",
-              "DataCollector",
-              "DataCurator",
-              "DataManager",
-              "Distributor",
-              "Editor",
-              "HostingInstitution",
-              "PrincipalInvestigator",
-              "CoInvestigator",
-              "Producer",
-              "ProjectLeader",
-              "ProjectManager",
-              "ProjectMember",
-              "RegistrationAgency",
-              "RegistrationAuthority",
-              "RelatedPerson",
-              "Researcher",
-              "ResearchGroup",
-              "RightsHolder",
-              "Sponsor",
-              "Supervisor",
-              "WorkPackageLeader",
-              "Other"
-            ],
-            "description": "The role of the contributor in the project. There must be at least one PrincipalInvestigator."
+          "contributor_roles": {
+            "type": "array",
+            "items": {
+              "type": "string",
+              "enum": [
+                "CorrespondingAuthor",
+                "ContactPerson",
+                "Creator",
+                "DataCollector",
+                "DataCurator",
+                "DataManager",
+                "Distributor",
+                "Editor",
+                "HostingInstitution",
+                "PrincipalInvestigator",
+                "CoInvestigator",
+                "Producer",
+                "ProjectLeader",
+                "ProjectManager",
+                "ProjectMember",
+                "RegistrationAgency",
+                "RegistrationAuthority",
+                "RelatedPerson",
+                "Researcher",
+                "ResearchGroup",
+                "RightsHolder",
+                "Sponsor",
+                "Supervisor",
+                "WorkPackageLeader",
+                "Other"
+              ]
+            },
+            "description": "The roles of the contributor in the project. There must be at least one PrincipalInvestigator. The Creator role requires an additional role to accompany it."
           }
         }
       }

pysoda/schema/manifest.json

@@ -12,7 +12,7 @@
         "timestamp": {
           "type": "string",
           "description": "Timestamp of when the data was created or last modified. This should be in ISO 8601 format. Per the SDS guidelines, commas are to be used for separating fractional seconds. Empty string for when it does not apply.",
-          "pattern": "^([0-9]{4}-[0-1][0-9]-[0-3][0-9]T[0-2][0-9]:[0-6][0-9](:[0-6][0-9](,[0-9]{1,9})?)?(Z|[+-][0-2][0-9]:[0-6][0-9])?)?$"
+          "pattern": "^([0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[12][0-9]|3[01])T([01][0-9]|2[0-3]):[0-5][0-9](:[0-5][0-9]([.,][0-9]{1,9})?)?(Z|[+-]([01][0-9]|2[0-3]):[0-5][0-9]))?$"
         },
         "description": {
           "type": "string",

pysoda/schema/performances.json

@@ -1,17 +1,25 @@
 {
-  "$schema": "https://json.schemastore.org/performances.json",
+  "$schema": "http://json-schema.org/draft-07/schema#",
   "type": "array",
   "items": {
     "type": "object",
     "properties": {
       "performance_id": {
         "type": "string",
-        "description": "Unique identifier for the performance"
+        "description": "Unique identifier for the performance",
+        "pattern": "^(pop-)?perf-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
       },
       "protocol_url_or_doi": {
         "type": "string",
-        "description": "URL or DOI of the protocol associated with the performance",
-        "pattern": "^$|^(https?://|doi:).+"
+        "description": "URL or DOI of the protocol used for the subject.",
+        "anyOf": [
+          { "pattern": "^$" },
+          { "pattern": "^https://[A-Za-z0-9.-]+[A-Za-z0-9](:[0-9]+)?(/.*)?$" },
+          { "pattern": "^10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$" },
+          {
+            "pattern": "^https://doi\\.org/10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$"
+          }
+        ]
       },
       "date": {
         "type": "string",
@@ -21,12 +29,14 @@
       "start_datetime": {
         "type": "string",
         "format": "date-time",
-        "description": "Start date and time of the performance in ISO 8601 format"
+        "description": "Start date and time of the performance in ISO 8601 format",
+        "pattern": "^([0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[12][0-9]|3[01])T([01][0-9]|2[0-3]):[0-5][0-9](:[0-5][0-9]([.,][0-9]{1,9})?)?(Z|[+-]([01][0-9]|2[0-3]):[0-5][0-9]))?$"
       },
       "end_datetime": {
         "type": "string",
         "format": "date-time",
-        "description": "End date and time of the performance in ISO 8601 format"
+        "description": "End date and time of the performance in ISO 8601 format",
+        "pattern": "^([0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[12][0-9]|3[01])T([01][0-9]|2[0-3]):[0-5][0-9](:[0-5][0-9]([.,][0-9]{1,9})?)?(Z|[+-]([01][0-9]|2[0-3]):[0-5][0-9]))?$"
       },
       "participants": {
         "type": "array",

pysoda/schema/resources.json

@@ -6,7 +6,8 @@
     "properties": {
       "rrid": {
         "type": "string",
-        "description": "Unique identifier for the site, typically an RRID"
+        "pattern": "^$|^RRID:",
+        "description": "Research Resource Identifier (RRID) for the resource. Accepts RRID:SCR_003070 or RRID:SCR:003070 formats. Also captures legacy format."
       },
       "type": {
         "type": "string",

pysoda/schema/samples.json

@@ -8,11 +8,13 @@
       "properties": {
         "sample_id": {
           "type": "string",
-          "description": "Unique identifier for the sample within the dataset."
+          "description": "Unique identifier for the sample within the dataset.",
+          "pattern": "^(pop-)?sam-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
         },
         "subject_id": {
           "type": "string",
-          "description": "Unique identifier for the subject from which the sample was derived."
+          "description": "Unique identifier for the subject from which the sample was derived.",
+          "pattern": "^(pop-)?sub-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
         },
         "was_derived_from": {
           "type": "string",
@@ -31,8 +33,18 @@
           "description": "Type of sample (e.g., blood, tissue, etc.)."
         },
         "sample_anatomical_location": {
-          "type": "string",
-          "description": "Anatomical location of the sample."
+          "description": "Anatomical location of the sample. Can be a single string or an array of strings.",
+          "oneOf": [
+            {
+              "type": "string"
+            },
+            {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            }
+          ]
         },
         "also_in_dataset": {
           "type": "string",
@@ -84,7 +96,21 @@
         },
         "protocol_url_or_doi": {
           "type": "string",
-          "description": "URL or DOI of the protocol used in the experiment."
+          "description": "URL or DOI of the protocol used for the subject.",
+          "anyOf": [
+            { "pattern": "^$" },
+            {
+              "pattern": "^https://[A-Za-z0-9.-]+[A-Za-z0-9](:[0-9]+)?(/.*)?$"
+            },
+            { "pattern": "^10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$" },
+            {
+              "pattern": "^https://doi\\.org/10\\.\\d{4,9}/[-._;()/:A-Za-z0-9]+$"
+            }
+          ]
+        },
+        "number_of_directly_derived_samples": {
+          "type": "string",
+          "description": "Number of samples directly derived from this sample."
         }
       },
       "required": ["sample_id", "subject_id"],

pysoda/schema/sites.json

@@ -6,11 +6,13 @@
     "properties": {
       "site_id": {
         "type": "string",
-        "description": "Unique identifier for the site"
+        "description": "Unique identifier for the site",
+        "pattern": "^(pop-)?site-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
       },
       "specimen_id": {
         "type": "string",
-        "description": "Unique identifier for the specimen associated with the site"
+        "description": "Unique identifier for the specimen associated with the site",
+        "pattern": "^(pop-)?(sub|sam)-[A-Za-z0-9]([A-Za-z0-9-]*[A-Za-z0-9])?$"
       },
       "site_type": {
         "type": "string",