pysodafair 0.1.62__py3-none-any.whl

pysoda/schema/dataset_description.json

@@ -0,0 +1,295 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "type": "object",
+  "properties": {
+    "metadata_version": {
+      "type": "string",
+      "description": "The version of the metadata schema used."
+    },
+    "type": {
+      "type": "string",
+      "description": "The type of the dataset. For example, experimental."
+    },
+    "standards_information": {
+      "type": "object",
+      "properties": {
+        "data_standard": {
+          "type": "string",
+          "description": "The name of the standard used in the project."
+        },
+        "data_standard_version": {
+          "type": "string",
+          "description": "The version of the standard used in the project."
+        }
+      },
+      "required": []
+    },
+    "basic_information": {
+      "type": "object",
+      "properties": {
+        "title": {
+          "type": "string",
+          "description": "The title of the project."
+        },
+        "subtitle": {
+          "type": "string",
+          "description": "The subtitle of the project."
+        },
+        "description": {
+          "type": "string",
+          "description": "A detailed description of the project."
+        },
+        "keywords": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "A list of keywords related to the project."
+        },
+        "funding": {
+          "type": "string",
+          "description": "Funding awards for the project."
+        },
+        "acknowledgments": {
+          "type": "string",
+          "description": "Acknowledgments for the project."
+        },
+        "license": {
+          "type": "string",
+          "description": "The license under which the project is released."
+        }
+      },
+      "required": []
+    },
+    "funding_information": {
+      "type": "object",
+      "properties": {
+        "funding_consortium": {
+          "type": "string",
+          "description": "The name of the funding consortium."
+        },
+        "funding_agency": {
+          "type": "string",
+          "description": "The name of the funding agency."
+        },
+        "award_number": {
+          "type": "string",
+          "description": "The award number for the funding."
+        }
+      }
+    },
+    "study_information": {
+      "type": "object",
+      "properties": {
+        "study_purpose": {
+          "type": "string",
+          "description": "The purpose of the study."
+        },
+        "study_data_collection": {
+          "type": "string",
+          "description": "The data collection methods used in the study."
+        },
+        "study_primary_conclusion": {
+          "type": "string",
+          "description": "The primary conclusion of the study."
+        },
+        "study_organ_system": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "The organ system(s) studied in the research."
+        },
+        "study_approach": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "The approach used in the study. E.g., electrophysiology"
+        },
+        "study_technique": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "The technique(s) used in the study. E.g., patch clamp, whole cell recording"
+        },
+        "study_collection_title": {
+          "type": "string",
+          "description": "The title of the study collection this dataset belongs to, if one exists."
+        }
+      },
+      "required": []
+    },
+    "contributor_information": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "contributor_orcid_id": {
+            "type": "string",
+            "description": "The ORCiD for this contributor."
+          },
+          "contributor_affiliation": {
+            "type": "string",
+            "description": "The institutional affiliation for this contributor."
+          },
+          "contributor_name": {
+            "type": "string",
+            "pattern": "^[A-Za-z]+, [A-Za-z]+( [A-Za-z]+)?$",
+            "description": "The name of the contributor. The format should be 'Last Name, First Name'."
+          },
+          "contributor_role": {
+            "type": "string",
+            "enum": [
+              "PrincipalInvestigator",
+              "Creator",
+              "CoInvestigator",
+              "CorrespondingAuthor",
+              "DataCollector",
+              "DataCurator",
+              "DataManager",
+              "Distributor",
+              "Editor",
+              "Producer",
+              "ProjectLeader",
+              "ProjectManager",
+              "ProjectMember",
+              "RelatedPerson",
+              "Researcher",
+              "ResearchGroup",
+              "Sponsor",
+              "Supervisor",
+              "WorkPackageLeader",
+              "Other"
+            ],
+            "description": "The role of the contributor in the project. There must be at least one PrincipalInvestigator."
+          }
+        }
+      }
+    },
+    "related_resource_information": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "identifier_description": {
+            "type": "string"
+          },
+          "relation_type": {
+            "type": "string",
+            "enum": [
+              "IsProtocolFor",
+              "HasProtocol",
+              "IsSoftwareFor",
+              "HasSoftware",
+              "SharesEntitiesWithDataset",
+              "IsCitedBy",
+              "Cites",
+              "IsSupplementTo",
+              "IsSupplementedBy",
+              "IsContinuedBy",
+              "Continues",
+              "IsDescribedBy",
+              "Describes",
+              "HasMetadata",
+              "IsMetadataFor",
+              "HasVersion",
+              "IsVersionOf",
+              "IsNewVersionOf",
+              "IsPreviousVersionOf",
+              "IsPartOf",
+              "HasPart",
+              "IsPublishedIn",
+              "IsReferencedBy",
+              "References",
+              "IsDocumentedBy",
+              "Documents",
+              "IsCompiledBy",
+              "Compiles",
+              "IsVariantFormOf",
+              "IsOriginalFormOf",
+              "IsIdenticalTo",
+              "IsReviewedBy",
+              "Reviews",
+              "IsDerivedFrom",
+              "IsSourceOf",
+              "IsRequiredBy",
+              "Requires",
+              "IsObsoletedBy",
+              "Obsoletes"
+            ],
+            "description": "The relationship that this dataset has to the related identifier. For example, the originating article would be this dataset IsDescribedBy originating article."
+          },
+          "identifier": {
+            "type": "string"
+          },
+          "identifier_type": {
+            "type": "string",
+            "enum": [
+              "ARK",
+              "arXiv",
+              "bibcode",
+              "DOI",
+              "EAN13",
+              "EISSN",
+              "Handle",
+              "IGSN",
+              "ISBN",
+              "ISSN",
+              "ISTC",
+              "LISSN",
+              "LSID",
+              "PMID",
+              "PURL",
+              "UPC",
+              "URL",
+              "URN",
+              "w3id"
+            ]
+          }
+        },
+        "required": []
+      }
+    },
+    "participant_information": {
+      "type": "object",
+      "properties": {
+        "number_of_subjects": {
+          "type": "number",
+          "description": "The number of subjects in the study."
+        },
+        "number_of_samples": {
+          "type": "number",
+          "description": "The number of samples in the study."
+        },
+        "number_of_sites": {
+          "type": "number",
+          "description": "The number of sites in the study."
+        },
+        "number_of_performances": {
+          "type": "number",
+          "description": "The number of performance in the study."
+        }
+      },
+      "required": []
+    },
+    "data_dictionary_information": {
+      "type": "object",
+      "properties": {
+        "data_dictionary_path": {
+          "type": "string",
+          "description": "The path to the data dictionary file."
+        },
+        "data_dictionary_type": {
+          "type": "string",
+          "description": "The type of the data dictionary. E.g., json-schema"
+        },
+        "data_dictionary_description": {
+          "type": "string",
+          "description": "A descrption of the data dictionary."
+        }
+      }
+    }
+  }
+}

pysoda/schema/manifest.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "type": "array",
+  "items": [
+    {
+      "type": "object",
+      "properties": {
+        "filename": {
+          "type": "string",
+          "description": "File path to the data file. This should be a valid file path relative to the root of the dataset."
+        },
+        "timestamp": {
+          "type": "string",
+          "description": "Timestamp of when the data was created or last modified. This should be in ISO 8601 format."
+        },
+        "description": {
+          "type": "string",
+          "description": "Description of the data file. This should provide a brief overview of the contents of the file."
+        },
+        "file_type": {
+          "type": "string",
+          "description": "Type of the data file. This should be the extension of the data file, such as .txt, .csv, .json, etc."
+        },
+        "entity": {
+          "type": "string",
+          "description": "Each ID should be taken from the subject.xlsx, samples.xlsx, sites.xlsx, or performances.xlsx files."
+        },
+        "data_modality": {
+          "type": "string",
+          "description": "Modality of the data. This should describe the type of data contained in the file, such as 'image', 'text', 'audio', etc."
+        },
+        "also_in_dataset": {
+          "type": "string",
+          "description": "DOI to the dataset this data is also part of."
+        },
+        "also_in_dataset_path": {
+          "type": "string",
+          "description": "Path to the dataset that this data file is part of. This should be a valid file path in the system where the manifest is being used."
+        },
+        "data_dictionary_path": {
+          "type": "string",
+          "description": "Path to the data dictionary for this data file. This should be a valid file path in the system where the manifest is being used."
+        },
+        "entity_is_transitive": {
+          "type": "string",
+          "description": "Indicates whether the entity represented in this data file is transitive. This should be either true or false."
+        },
+        "additional_metadata": {
+          "type": "string",
+          "description": "Additional metadata about the data file. This can include any other relevant information that does not fit into the other categories."
+        }
+      },
+      "required": ["filename"],
+      "additionalProperties": {
+        "type": "string",
+        "description": "Additional properties for the manifest file. This can include any other relevant information about the subject that is not covered by the predefined fields."
+      }
+    }
+  ]
+}

pysoda/schema/performances.json

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+{
+  "$schema": "https://json.schemastore.org/performances.json",
+  "type": "array",
+  "items": {
+    "type": "object",
+    "properties": {
+      "performance_id": {
+        "type": "string",
+        "description": "Unique identifier for the performance"
+      },
+      "protocol_url_or_doi": {
+        "type": "string",
+        "description": "URL or DOI of the protocol associated with the performance",
+        "pattern": "^$|^(https?://|doi:).+"
+      },
+      "date": {
+        "type": "string",
+        "format": "date",
+        "description": "Date of the performance in YYYY-MM-DD format"
+      },
+      "start_datetime": {
+        "type": "string",
+        "format": "date-time",
+        "description": "Start date and time of the performance in ISO 8601 format"
+      },
+      "end_datetime": {
+        "type": "string",
+        "format": "date-time",
+        "description": "End date and time of the performance in ISO 8601 format"
+      },
+      "participants": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        }
+      },
+      "additional_metadata": {
+        "type": "string",
+        "description": "Any additional metadata related to the performance"
+      }
+    },
+    "required": ["performance_id"]
+  }
+}

pysoda/schema/resources.json

@@ -0,0 +1,39 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "type": "array",
+  "items": {
+    "type": "object",
+    "properties": {
+      "rrid": {
+        "type": "string",
+        "description": "Unique identifier for the site, typically an RRID"
+      },
+      "name": {
+        "type": "string",
+        "description": "The resources name"
+      },
+      "url": {
+        "type": "string",
+        "description": "URL to the resource.",
+        "pattern": "^(https?://)?.*$"
+      },
+      "vendor": {
+        "type": "string",
+        "description": "The vendor or provider of the resource"
+      },
+      "version": {
+        "type": "string",
+        "description": "Version of the resource, if applicable"
+      },
+      "id_in_protocol": {
+        "type": "string",
+        "description": "Identifier for the resource within a specific protocol or experiment"
+      },
+      "additional_metadata": {
+        "type": "string",
+        "description": "Additional metadata about the resource, such as usage notes or specific details"
+      }
+    },
+    "required": ["rrid", "name", "url", "vendor", "version", "id_in_protocol"]
+  }
+}

pysoda/schema/samples.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "type": "array",
+  "maxItems": 19,
+  "items": [
+    {
+      "type": "object",
+      "properties": {
+        "sample_id": {
+          "type": "string",
+          "description": "Unique identifier for the sample within the dataset."
+        },
+        "subject_id": {
+          "type": "string",
+          "description": "Unique identifier for the subject from which the sample was derived."
+        },
+        "was_derived_from": {
+          "type": "string",
+          "description": "Unique identifier for the sample from which this sample was derived."
+        },
+        "pool_id": {
+          "type": "string",
+          "description": "Unique identifier for the pool to which this sample belongs."
+        },
+        "sample_experimental_group": {
+          "type": "string",
+          "description": "Experimental group associated with the sample."
+        },
+        "sample_type": {
+          "type": "string",
+          "description": "Type of sample (e.g., blood, tissue, etc.)."
+        },
+        "sample_anatomical_location": {
+          "type": "string",
+          "description": "Anatomical location of the sample."
+        },
+        "also_in_dataset": {
+          "type": "string",
+          "description": "Indicates if the sample is also part of another dataset."
+        },
+        "member_of": {
+          "type": "string",
+          "description": "Group or cohort the sample is a member of."
+        },
+        "metadata_only": {
+          "type": "string",
+          "description": "Indicates whether this sample is metadata only (true or false)."
+        },
+        "laboratory_internal_id": {
+          "type": "string",
+          "description": "Internal identifier used by the laboratory for the sample."
+        },
+        "date_of_derivation": {
+          "type": "string",
+          "description": "Date when the sample was derived."
+        },
+        "experimental_log_file_path": {
+          "type": "string",
+          "description": "Path to the experimental log file for the sample."
+        },
+        "reference_atlas": {
+          "type": "string",
+          "description": "Reference atlas used in the experiment."
+        },
+        "pathology": {
+          "type": "string",
+          "description": "Pathology associated with the sample."
+        },
+        "laterality": {
+          "type": "string",
+          "description": "Laterality of the sample (e.g., left, right, bilateral)."
+        },
+        "cell_type": {
+          "type": "string",
+          "description": "Cell type of the sample."
+        },
+        "plane_of_section": {
+          "type": "string",
+          "description": "Plane of section of the sample."
+        },
+        "protocol_title": {
+          "type": "string",
+          "description": "Title of the protocol used in the experiment."
+        },
+        "protocol_url_or_doi": {
+          "type": "string",
+          "description": "URL or DOI of the protocol used in the experiment."
+        }
+      },
+      "required": ["sample_id", "subject_id"],
+      "additionalProperties": {
+        "type": "string",
+        "description": "Additional properties for the sample. This can include any other relevant information about the sample that is not covered by the predefined fields."
+      }
+    }
+  ]
+}

pysoda/schema/sites.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "type": "array",
+  "items": {
+    "type": "object",
+    "properties": {
+      "site_id": {
+        "type": "string",
+        "description": "Unique identifier for the site"
+      },
+      "specimen_id": {
+        "type": "string",
+        "description": "Unique identifier for the specimen associated with the site"
+      },
+      "site_type": {
+        "type": "string",
+        "description": "Type of the site (e.g., 'tissue', 'cell culture')"
+      },
+      "laboratory_internal_id": {
+        "type": "string",
+        "description": "Internal id for the site"
+      },
+      "coordinate_system": {
+        "type": "string",
+        "description": "Coordinate system used for the site (e.g., 'microns', 'pixels')"
+      },
+      "coordinate_system_position": {
+        "type": "string",
+        "description": "Position in the coordinate system (e.g., 'x,y,z' for 3D coordinates)"
+      },
+      "more...": {
+        "type": "string",
+        "description": "Any additional metadata related to the site"
+      }
+    },
+    "required": ["site_id", "specimen_id"]
+  }
+}