Data Models (indra_network_search.data_models)

This module contains all data models used in the repository. They are all built around the the Pydantic BaseModel.

This file contains data models for queries, results and arguments to algorithm functions.

pydantic model indra_network_search.data_models.__init__.ApiOptions

Options that determine API behaviour

Show JSON schema

{
   "title": "ApiOptions",
   "description": "Options that determine API behaviour",
   "type": "object",
   "properties": {
      "sign": {
         "title": "Sign",
         "type": "integer"
      },
      "fplx_expand": {
         "title": "Fplx Expand",
         "default": false,
         "type": "boolean"
      },
      "user_timeout": {
         "title": "User Timeout",
         "default": false,
         "anyOf": [
            {
               "type": "number"
            },
            {
               "type": "boolean"
            }
         ]
      },
      "two_way": {
         "title": "Two Way",
         "default": false,
         "type": "boolean"
      },
      "shared_regulators": {
         "title": "Shared Regulators",
         "default": false,
         "type": "boolean"
      },
      "format": {
         "title": "Format",
         "default": "json",
         "type": "string"
      }
   }
}

Fields:

• format (Optional[str])

• fplx_expand (Optional[bool])

• shared_regulators (Optional[bool])

• sign (Optional[int])

• two_way (Optional[bool])

• user_timeout (Optional[Union[float, bool]])

field format: Optional[str] = 'json'

field fplx_expand: Optional[bool] = False

field shared_regulators: Optional[bool] = False

field sign: Optional[int] = None

field two_way: Optional[bool] = False

field user_timeout: Union[float, bool, None] = False

pydantic model indra_network_search.data_models.__init__.BreadthFirstSearchOptions

Arguments for indra.explanation.pathfinding.bfs_search

Show JSON schema

{
   "title": "BreadthFirstSearchOptions",
   "description": "Arguments for indra.explanation.pathfinding.bfs_search",
   "type": "object",
   "properties": {
      "source_node": {
         "title": "Source Node",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "reverse": {
         "title": "Reverse",
         "default": false,
         "type": "boolean"
      },
      "depth_limit": {
         "title": "Depth Limit",
         "default": 2,
         "type": "integer"
      },
      "path_limit": {
         "title": "Path Limit",
         "type": "integer"
      },
      "max_per_node": {
         "title": "Max Per Node",
         "default": 5,
         "type": "integer"
      },
      "node_filter": {
         "title": "Node Filter",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "node_blacklist": {
         "title": "Node Blacklist",
         "type": "array",
         "items": {
            "type": "string"
         },
         "uniqueItems": true
      },
      "terminal_ns": {
         "title": "Terminal Ns",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "sign": {
         "title": "Sign",
         "type": "integer"
      },
      "max_memory": {
         "title": "Max Memory",
         "default": 536870912,
         "type": "integer"
      },
      "hashes": {
         "title": "Hashes",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "strict_mesh_id_filtering": {
         "title": "Strict Mesh Id Filtering",
         "default": false,
         "type": "boolean"
      }
   },
   "required": [
      "source_node"
   ]
}

Fields:

• allow_edge (Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]])

• depth_limit (Optional[int])

• edge_filter (Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]])

• hashes (Optional[List[int]])

• max_memory (Optional[int])

• max_per_node (Optional[int])

• node_blacklist (Optional[Set[str]])

• node_filter (Optional[List[str]])

• path_limit (Optional[int])

• reverse (Optional[bool])

• sign (Optional[int])

• source_node (Union[str, Tuple[str, int]])

• strict_mesh_id_filtering (Optional[bool])

• terminal_ns (Optional[List[str]])

field allow_edge: Optional[Callable[[DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]] = None

field depth_limit: Optional[int] = 2

field edge_filter: Optional[Callable[[DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]] = None

field hashes: Optional[List[int]] = None

field max_memory: Optional[int] = 536870912

field max_per_node: Optional[int] = 5

field node_blacklist: Optional[Set[str]] = None

field node_filter: Optional[List[str]] = None

field path_limit: Optional[int] = None

field reverse: Optional[bool] = False

field sign: Optional[int] = None

field source_node: Union[str, Tuple[str, int]] [Required]

field strict_mesh_id_filtering: Optional[bool] = False

field terminal_ns: Optional[List[str]] = None

pydantic model indra_network_search.data_models.__init__.DijkstraOptions

Arguments for open_dijkstra_search

Show JSON schema

{
   "title": "DijkstraOptions",
   "description": "Arguments for open_dijkstra_search",
   "type": "object",
   "properties": {
      "start": {
         "title": "Start",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "reverse": {
         "title": "Reverse",
         "default": false,
         "type": "boolean"
      },
      "path_limit": {
         "title": "Path Limit",
         "type": "integer"
      },
      "hashes": {
         "title": "Hashes",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "ignore_nodes": {
         "title": "Ignore Nodes",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "ignore_edges": {
         "title": "Ignore Edges",
         "type": "array",
         "items": {
            "type": "array",
            "minItems": 2,
            "maxItems": 2,
            "items": [
               {
                  "type": "string"
               },
               {
                  "type": "string"
               }
            ]
         }
      },
      "terminal_ns": {
         "title": "Terminal Ns",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "weight": {
         "title": "Weight",
         "type": "string"
      },
      "const_c": {
         "title": "Const C",
         "default": 1,
         "type": "integer"
      },
      "const_tk": {
         "title": "Const Tk",
         "default": 10,
         "type": "integer"
      }
   },
   "required": [
      "start"
   ]
}

Fields:

• const_c (Optional[int])

• const_tk (Optional[int])

• hashes (Optional[List[int]])

• ignore_edges (Optional[List[Tuple[str, str]]])

• ignore_nodes (Optional[List[str]])

• path_limit (Optional[int])

• ref_counts_function (Optional[Callable])

• reverse (Optional[bool])

• start (Union[str, Tuple[str, int]])

• terminal_ns (Optional[List[str]])

• weight (Optional[str])

field const_c: Optional[int] = 1

field const_tk: Optional[int] = 10

field hashes: Optional[List[int]] = None

field ignore_edges: Optional[List[Tuple[str, str]]] = None

field ignore_nodes: Optional[List[str]] = None

field path_limit: Optional[int] = None

field ref_counts_function: Optional[Callable] = None

field reverse: Optional[bool] = False

field start: Union[str, Tuple[str, int]] [Required]

field terminal_ns: Optional[List[str]] = None

field weight: Optional[str] = None

pydantic model indra_network_search.data_models.__init__.EdgeData

Data for one single edge

Show JSON schema

{
   "title": "EdgeData",
   "description": "Data for one single edge",
   "type": "object",
   "properties": {
      "edge": {
         "title": "Edge",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "statements": {
         "title": "Statements",
         "type": "object",
         "additionalProperties": {
            "$ref": "#/definitions/StmtTypeSupport"
         }
      },
      "belief": {
         "title": "Belief",
         "minimum": 0,
         "maximum": 1,
         "type": "number"
      },
      "weight": {
         "title": "Weight",
         "minimum": 0,
         "type": "number"
      },
      "context_weight": {
         "title": "Context Weight",
         "default": "N/A",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "number",
               "exclusiveMinimum": 0
            },
            {
               "enum": [
                  "N/A"
               ],
               "type": "string"
            }
         ]
      },
      "z_score": {
         "title": "Z Score",
         "type": "number"
      },
      "corr_weight": {
         "title": "Corr Weight",
         "exclusiveMinimum": 0.0,
         "type": "number"
      },
      "sign": {
         "title": "Sign",
         "minimum": 0,
         "maximum": 1,
         "type": "integer"
      },
      "db_url_edge": {
         "title": "Db Url Edge",
         "type": "string"
      },
      "source_counts": {
         "title": "Source Counts",
         "default": {},
         "type": "object",
         "additionalProperties": {
            "type": "integer"
         }
      }
   },
   "required": [
      "edge",
      "statements",
      "belief",
      "weight",
      "db_url_edge"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      }
   }
}

Fields:

• belief (indra_network_search.data_models.__init__.ConstrainedFloatValue)

• context_weight (Union[str, indra_network_search.data_models.__init__.ConstrainedFloatValue, typing_extensions.Literal[N/A]])

• corr_weight (Optional[indra_network_search.data_models.__init__.ConstrainedFloatValue])

• db_url_edge (str)

• edge (List[indra_network_search.data_models.__init__.Node])

• sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])

• source_counts (Dict[str, int])

• statements (Dict[str, indra_network_search.data_models.__init__.StmtTypeSupport])

• weight (indra_network_search.data_models.__init__.ConstrainedFloatValue)

• z_score (Optional[float])

field belief: ConstrainedFloatValue [Required]

Constraints:

• minimum = 0

• maximum = 1

field context_weight: Union[str, ConstrainedFloatValue, Literal['N/A']] = 'N/A'

field corr_weight: Optional[ConstrainedFloatValue] = None

Constraints:

• exclusiveMinimum = 0.0

field db_url_edge: str [Required]

field edge: List[Node] [Required]

field sign: Optional[ConstrainedIntValue] = None

Constraints:

• minimum = 0

• maximum = 1

field source_counts: Dict[str, int] = {}

field statements: Dict[str, StmtTypeSupport] [Required]

field weight: ConstrainedFloatValue [Required]

Constraints:

• minimum = 0

field z_score: Optional[float] = None

is_empty()

Return True if len(statements) == 0

Return type:

bool

set_source_counts()

Updates the source count from the contained data in self.statements

pydantic model indra_network_search.data_models.__init__.EdgeDataByHash

Data for one single edge, with data keyed by hash

Show JSON schema

{
   "title": "EdgeDataByHash",
   "description": "Data for one single edge, with data keyed by hash",
   "type": "object",
   "properties": {
      "edge": {
         "title": "Edge",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "stmts": {
         "title": "Stmts",
         "type": "object",
         "additionalProperties": {
            "$ref": "#/definitions/StmtData"
         }
      },
      "belief": {
         "title": "Belief",
         "type": "number"
      },
      "weight": {
         "title": "Weight",
         "type": "number"
      },
      "db_url_edge": {
         "title": "Db Url Edge",
         "type": "string"
      },
      "url_by_type": {
         "title": "Url By Type",
         "type": "object",
         "additionalProperties": {
            "type": "string"
         }
      }
   },
   "required": [
      "edge",
      "stmts",
      "belief",
      "weight",
      "db_url_edge",
      "url_by_type"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      }
   }
}

Fields:

• belief (float)

• db_url_edge (str)

• edge (List[indra_network_search.data_models.__init__.Node])

• stmts (Dict[int, indra_network_search.data_models.__init__.StmtData])

• url_by_type (Dict[str, str])

• weight (float)

field belief: float [Required]

field db_url_edge: str [Required]

field edge: List[Node] [Required]

field stmts: Dict[int, StmtData] [Required]

field url_by_type: Dict[str, str] [Required]

field weight: float [Required]

pydantic model indra_network_search.data_models.__init__.FilterOptions

Options for filtering out nodes or edges

Show JSON schema

{
   "title": "FilterOptions",
   "description": "Options for filtering out nodes or edges",
   "type": "object",
   "properties": {
      "stmt_filter": {
         "title": "Stmt Filter",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "allowed_ns": {
         "title": "Allowed Ns",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "node_blacklist": {
         "title": "Node Blacklist",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "path_length": {
         "title": "Path Length",
         "type": "integer"
      },
      "belief_cutoff": {
         "title": "Belief Cutoff",
         "default": 0.0,
         "type": "number"
      },
      "curated_db_only": {
         "title": "Curated Db Only",
         "default": false,
         "type": "boolean"
      },
      "max_paths": {
         "title": "Max Paths",
         "default": 50,
         "type": "integer"
      },
      "cull_best_node": {
         "title": "Cull Best Node",
         "type": "integer"
      },
      "weighted": {
         "title": "Weighted",
         "enum": [
            "weight",
            "context_weight",
            "corr_weight"
         ],
         "type": "string"
      },
      "context_weighted": {
         "title": "Context Weighted",
         "default": false,
         "type": "boolean"
      },
      "overall_weighted": {
         "title": "Overall Weighted",
         "default": false,
         "type": "boolean"
      }
   }
}

Fields:

• allowed_ns (List[indra_network_search.data_models.__init__.ConstrainedStrValue])

• belief_cutoff (float)

• context_weighted (bool)

• cull_best_node (Optional[int])

• curated_db_only (bool)

• max_paths (int)

• node_blacklist (List[str])

• overall_weighted (bool)

• path_length (Optional[int])

• stmt_filter (List[indra_network_search.data_models.__init__.ConstrainedStrValue])

• weighted (Optional[typing_extensions.Literal[weight, context_weight, corr_weight]])

field allowed_ns: List[ConstrainedStrValue] = []

field belief_cutoff: float = 0.0

field context_weighted: bool = False

field cull_best_node: Optional[int] = None

field curated_db_only: bool = False

field max_paths: int = 50

field node_blacklist: List[str] = []

field overall_weighted: bool = False

field path_length: Optional[int] = None

field stmt_filter: List[ConstrainedStrValue] = []

field weighted: Optional[Literal['weight', 'context_weight', 'corr_weight']] = None

no_filters()

Return True if all filter options are set to defaults

Return type:

bool

no_node_filters()

Return True if the node filter options allow all nodes

no_stmt_filters()

Return True if the stmt filter options allow all statements

pydantic model indra_network_search.data_models.__init__.MultiInteractorsOptions

Multi interactors options

Show JSON schema

{
   "title": "MultiInteractorsOptions",
   "description": "Multi interactors options",
   "type": "object",
   "properties": {
      "nodes": {
         "title": "Nodes",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "downstream": {
         "title": "Downstream",
         "type": "boolean"
      },
      "allowed_ns": {
         "title": "Allowed Ns",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "stmt_types": {
         "title": "Stmt Types",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "source_filter": {
         "title": "Source Filter",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "max_results": {
         "title": "Max Results",
         "default": 50,
         "type": "integer"
      },
      "hash_blacklist": {
         "title": "Hash Blacklist",
         "type": "array",
         "items": {
            "type": "integer"
         },
         "uniqueItems": true
      },
      "node_blacklist": {
         "title": "Node Blacklist",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "belief_cutoff": {
         "title": "Belief Cutoff",
         "default": 0.0,
         "type": "number"
      },
      "curated_db_only": {
         "title": "Curated Db Only",
         "default": false,
         "type": "boolean"
      }
   },
   "required": [
      "nodes",
      "downstream"
   ]
}

Fields:

• allowed_ns (Optional[List[str]])

• belief_cutoff (float)

• curated_db_only (bool)

• downstream (bool)

• hash_blacklist (Optional[Set[int]])

• max_results (int)

• node_blacklist (Optional[List[str]])

• nodes (List[str])

• source_filter (Optional[List[str]])

• stmt_types (Optional[List[str]])

field allowed_ns: Optional[List[str]] = None

field belief_cutoff: float = 0.0

field curated_db_only: bool = False

field downstream: bool [Required]

field hash_blacklist: Optional[Set[int]] = None

field max_results: int = 50

field node_blacklist: Optional[List[str]] = None

field nodes: List[str] [Required]

field source_filter: Optional[List[str]] = None

field stmt_types: Optional[List[str]] = None

pydantic model indra_network_search.data_models.__init__.MultiInteractorsRestQuery

Multi interactors rest query

Show JSON schema

{
   "title": "MultiInteractorsRestQuery",
   "description": "Multi interactors rest query",
   "type": "object",
   "properties": {
      "nodes": {
         "title": "Nodes",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "downstream": {
         "title": "Downstream",
         "type": "boolean"
      },
      "allowed_ns": {
         "title": "Allowed Ns",
         "type": "array",
         "items": {
            "type": "string",
            "minLength": 1
         }
      },
      "stmt_types": {
         "title": "Stmt Types",
         "type": "array",
         "items": {
            "type": "string",
            "minLength": 1
         }
      },
      "source_filter": {
         "title": "Source Filter",
         "type": "array",
         "items": {
            "type": "string",
            "minLength": 1
         }
      },
      "max_results": {
         "title": "Max Results",
         "default": 50,
         "type": "integer"
      },
      "node_blacklist": {
         "title": "Node Blacklist",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "belief_cutoff": {
         "title": "Belief Cutoff",
         "default": 0.0,
         "type": "number"
      },
      "curated_db_only": {
         "title": "Curated Db Only",
         "default": false,
         "type": "boolean"
      },
      "timeout": {
         "title": "Timeout",
         "default": 30,
         "minimum": 5.0,
         "maximum": 120.0,
         "type": "number"
      }
   },
   "required": [
      "nodes",
      "downstream"
   ]
}

Fields:

• allowed_ns (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])

• belief_cutoff (float)

• curated_db_only (bool)

• downstream (bool)

• max_results (int)

• node_blacklist (Optional[List[str]])

• nodes (List[str])

• source_filter (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])

• stmt_types (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])

• timeout (indra_network_search.data_models.__init__.ConstrainedFloatValue)

field allowed_ns: Optional[List[ConstrainedStrValue]] = None

field belief_cutoff: float = 0.0

field curated_db_only: bool = False

field downstream: bool [Required]

field max_results: int = 50

field node_blacklist: Optional[List[str]] = None

field nodes: List[str] [Required]

field source_filter: Optional[List[ConstrainedStrValue]] = None

field stmt_types: Optional[List[ConstrainedStrValue]] = None

field timeout: ConstrainedFloatValue = 30

Constraints:

• minimum = 5.0

• maximum = 120.0

pydantic model indra_network_search.data_models.__init__.MultiInteractorsResults

Results post direct_multi_interactors

Show JSON schema

{
   "title": "MultiInteractorsResults",
   "description": "Results post direct_multi_interactors",
   "type": "object",
   "properties": {
      "targets": {
         "title": "Targets",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "regulators": {
         "title": "Regulators",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "edge_data": {
         "title": "Edge Data",
         "default": [],
         "type": "array",
         "items": {
            "$ref": "#/definitions/EdgeData"
         }
      }
   },
   "required": [
      "targets",
      "regulators"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      },
      "EdgeData": {
         "title": "EdgeData",
         "description": "Data for one single edge",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtTypeSupport"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0,
               "maximum": 1,
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "minimum": 0,
               "type": "number"
            },
            "context_weight": {
               "title": "Context Weight",
               "default": "N/A",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "number",
                     "exclusiveMinimum": 0
                  },
                  {
                     "enum": [
                        "N/A"
                     ],
                     "type": "string"
                  }
               ]
            },
            "z_score": {
               "title": "Z Score",
               "type": "number"
            },
            "corr_weight": {
               "title": "Corr Weight",
               "exclusiveMinimum": 0.0,
               "type": "number"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "edge",
            "statements",
            "belief",
            "weight",
            "db_url_edge"
         ]
      }
   }
}

Fields:

• edge_data (List[indra_network_search.data_models.__init__.EdgeData])

• regulators (List[indra_network_search.data_models.__init__.Node])

• targets (List[indra_network_search.data_models.__init__.Node])

field edge_data: List[EdgeData] = []

field regulators: List[Node] [Required]

field targets: List[Node] [Required]

pydantic model indra_network_search.data_models.__init__.NetworkSearchQuery

The query model for network searches

Show JSON schema

{
   "title": "NetworkSearchQuery",
   "description": "The query model for network searches",
   "type": "object",
   "properties": {
      "source": {
         "title": "Source",
         "default": "",
         "type": "string"
      },
      "target": {
         "title": "Target",
         "default": "",
         "type": "string"
      },
      "stmt_filter": {
         "title": "Stmt Filter",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "filter_curated": {
         "title": "Filter Curated",
         "default": true,
         "type": "boolean"
      },
      "allowed_ns": {
         "title": "Allowed Ns",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "node_blacklist": {
         "title": "Node Blacklist",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "path_length": {
         "title": "Path Length",
         "type": "integer"
      },
      "depth_limit": {
         "title": "Depth Limit",
         "default": 2,
         "type": "integer"
      },
      "sign": {
         "title": "Sign",
         "minimum": 0,
         "maximum": 1,
         "type": "integer"
      },
      "weighted": {
         "title": "Weighted",
         "default": "unweighted",
         "enum": [
            "belief",
            "context",
            "z_score",
            "unweighted"
         ],
         "type": "string"
      },
      "belief_cutoff": {
         "title": "Belief Cutoff",
         "default": 0.0,
         "anyOf": [
            {
               "type": "number"
            },
            {
               "type": "boolean"
            }
         ]
      },
      "curated_db_only": {
         "title": "Curated Db Only",
         "default": false,
         "type": "boolean"
      },
      "fplx_expand": {
         "title": "Fplx Expand",
         "default": false,
         "type": "boolean"
      },
      "k_shortest": {
         "title": "K Shortest",
         "default": 50,
         "type": "integer"
      },
      "max_per_node": {
         "title": "Max Per Node",
         "default": 5,
         "type": "integer"
      },
      "cull_best_node": {
         "title": "Cull Best Node",
         "type": "integer"
      },
      "mesh_ids": {
         "title": "Mesh Ids",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "strict_mesh_id_filtering": {
         "title": "Strict Mesh Id Filtering",
         "default": false,
         "type": "boolean"
      },
      "const_c": {
         "title": "Const C",
         "default": 1,
         "type": "integer"
      },
      "const_tk": {
         "title": "Const Tk",
         "default": 10,
         "type": "integer"
      },
      "user_timeout": {
         "title": "User Timeout",
         "default": 30,
         "anyOf": [
            {
               "type": "number"
            },
            {
               "type": "boolean"
            }
         ]
      },
      "two_way": {
         "title": "Two Way",
         "default": false,
         "type": "boolean"
      },
      "shared_regulators": {
         "title": "Shared Regulators",
         "default": false,
         "type": "boolean"
      },
      "terminal_ns": {
         "title": "Terminal Ns",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "format": {
         "title": "Format",
         "default": "json",
         "type": "string"
      }
   },
   "additionalProperties": false
}

Config:

• allow_mutation: bool = False

• extra: Extra = forbid

Fields:

• allowed_ns (List[indra_network_search.data_models.__init__.ConstrainedStrValue])

• belief_cutoff (Union[float, bool])

• const_c (int)

• const_tk (int)

• cull_best_node (Optional[int])

• curated_db_only (bool)

• depth_limit (int)

• filter_curated (bool)

• format (str)

• fplx_expand (bool)

• k_shortest (int)

• max_per_node (int)

• mesh_ids (List[str])

• node_blacklist (List[str])

• path_length (Optional[int])

• shared_regulators (bool)

• sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])

• source (indra_network_search.data_models.__init__.ConstrainedStrValue)

• stmt_filter (List[indra_network_search.data_models.__init__.ConstrainedStrValue])

• strict_mesh_id_filtering (bool)

• target (indra_network_search.data_models.__init__.ConstrainedStrValue)

• terminal_ns (List[str])

• two_way (bool)

• user_timeout (Union[float, bool])

• weighted (typing_extensions.Literal[belief, context, z_score, unweighted])

Validators:

• is_int_gt2 » cull_best_node

• is_pos_int » max_per_node

• is_positive_int » path_length

field allowed_ns: List[ConstrainedStrValue] = []

field belief_cutoff: Union[float, bool] = 0.0

field const_c: int = 1

field const_tk: int = 10

field cull_best_node: Optional[int] = None

Validated by:

• is_int_gt2

field curated_db_only: bool = False

field depth_limit: int = 2

field filter_curated: bool = True

field format: str = 'json'

field fplx_expand: bool = False

field k_shortest: int = 50

field max_per_node: int = 5

Validated by:

• is_pos_int

field mesh_ids: List[str] = []

field node_blacklist: List[str] = []

field path_length: Optional[int] = None

Validated by:

• is_positive_int

field shared_regulators: bool = False

field sign: Optional[ConstrainedIntValue] = None

Constraints:

• minimum = 0

• maximum = 1

field source: ConstrainedStrValue = ''

field stmt_filter: List[ConstrainedStrValue] = []

field strict_mesh_id_filtering: bool = False

field target: ConstrainedStrValue = ''

field terminal_ns: List[str] = []

field two_way: bool = False

field user_timeout: Union[float, bool] = 30

field weighted: Literal['belief', 'context', 'z_score', 'unweighted'] = 'unweighted'

get_filter_options()

Returns the filter options

Return type:

FilterOptions

get_hash()

Get the corresponding query hash of the query

get_int_sign()

Return the integer representation of the sign

Return type:

Optional[int]

is_context_weighted()

Return True if this query is context weighted

validator is_int_gt2  »  cull_best_node

Validate cull_best_node >= 2

is_overall_weighted()

Return True if this query is weighted

This method is used to determine if a weighted search needs to be done using either of shortest_simple_paths and open_dijkstra_search.

The exception to self.weighted not being None but still be unweighted is strict mesh id search.

Return type:

bool

validator is_pos_int  »  max_per_node

Validate max_per_node >= 1 if given

validator is_positive_int  »  path_length

Validate path_length >= 1 if given

reverse_search()

Return a copy of the query with source and target switched

pydantic model indra_network_search.data_models.__init__.Node

Data for a node

Show JSON schema

{
   "title": "Node",
   "description": "Data for a node",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "minLength": 1,
         "type": "string"
      },
      "namespace": {
         "title": "Namespace",
         "minLength": 1,
         "type": "string"
      },
      "identifier": {
         "title": "Identifier",
         "minLength": 1,
         "type": "string"
      },
      "lookup": {
         "title": "Lookup",
         "minLength": 1,
         "type": "string"
      },
      "sign": {
         "title": "Sign",
         "minimum": 0,
         "maximum": 1,
         "type": "integer"
      }
   },
   "required": [
      "namespace",
      "identifier"
   ]
}

Fields:

• identifier (indra_network_search.data_models.__init__.ConstrainedStrValue)

• lookup (Optional[indra_network_search.data_models.__init__.ConstrainedStrValue])

• name (Optional[indra_network_search.data_models.__init__.ConstrainedStrValue])

• namespace (indra_network_search.data_models.__init__.ConstrainedStrValue)

• sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])

field identifier: ConstrainedStrValue [Required]

Constraints:

• minLength = 1

field lookup: Optional[ConstrainedStrValue] = None

Constraints:

• minLength = 1

field name: Optional[ConstrainedStrValue] = None

Constraints:

• minLength = 1

field namespace: ConstrainedStrValue [Required]

Constraints:

• minLength = 1

field sign: Optional[ConstrainedIntValue] = None

Constraints:

• minimum = 0

• maximum = 1

get_unsigned_node()

Get unsigned version of this node instance

signed_node_tuple()

Get a signed node tuple of node name and node sign

Return type:

Tuple[str, int]

Returns:

A name, sign tuple

Raises:

TypeError – If sign is not defined, a TypeError

pydantic model indra_network_search.data_models.__init__.OntologyOptions

Arguments for indra_network_search.pathfinding.shared_parents

Show JSON schema

{
   "title": "OntologyOptions",
   "description": "Arguments for indra_network_search.pathfinding.shared_parents",
   "type": "object",
   "properties": {
      "source_ns": {
         "title": "Source Ns",
         "type": "string"
      },
      "source_id": {
         "title": "Source Id",
         "type": "string"
      },
      "target_ns": {
         "title": "Target Ns",
         "type": "string"
      },
      "target_id": {
         "title": "Target Id",
         "type": "string"
      },
      "max_paths": {
         "title": "Max Paths",
         "default": 50,
         "type": "integer"
      },
      "immediate_only": {
         "title": "Immediate Only",
         "default": false,
         "type": "boolean"
      },
      "is_a_part_of": {
         "title": "Is A Part Of",
         "type": "array",
         "items": {
            "type": "string"
         },
         "uniqueItems": true
      }
   },
   "required": [
      "source_ns",
      "source_id",
      "target_ns",
      "target_id"
   ]
}

Fields:

• immediate_only (Optional[bool])

• is_a_part_of (Optional[Set[str]])

• max_paths (int)

• source_id (str)

• source_ns (str)

• target_id (str)

• target_ns (str)

field immediate_only: Optional[bool] = False

field is_a_part_of: Optional[Set[str]] = None

field max_paths: int = 50

field source_id: str [Required]

field source_ns: str [Required]

field target_id: str [Required]

field target_ns: str [Required]

pydantic model indra_network_search.data_models.__init__.OntologyResults

Results for shared_parents

Show JSON schema

{
   "title": "OntologyResults",
   "description": "Results for shared_parents",
   "type": "object",
   "properties": {
      "source": {
         "$ref": "#/definitions/Node"
      },
      "target": {
         "$ref": "#/definitions/Node"
      },
      "parents": {
         "title": "Parents",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      }
   },
   "required": [
      "source",
      "target",
      "parents"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      }
   }
}

Fields:

• parents (List[indra_network_search.data_models.__init__.Node])

• source (indra_network_search.data_models.__init__.Node)

• target (indra_network_search.data_models.__init__.Node)

field parents: List[Node] [Required]

field source: Node [Required]

field target: Node [Required]

is_empty()

Return True if parents list is empty

Return type:

bool

pydantic model indra_network_search.data_models.__init__.Path

Results for a single path

Show JSON schema

{
   "title": "Path",
   "description": "Results for a single path",
   "type": "object",
   "properties": {
      "path": {
         "title": "Path",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "edge_data": {
         "title": "Edge Data",
         "type": "array",
         "items": {
            "$ref": "#/definitions/EdgeData"
         }
      }
   },
   "required": [
      "path",
      "edge_data"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      },
      "EdgeData": {
         "title": "EdgeData",
         "description": "Data for one single edge",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtTypeSupport"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0,
               "maximum": 1,
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "minimum": 0,
               "type": "number"
            },
            "context_weight": {
               "title": "Context Weight",
               "default": "N/A",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "number",
                     "exclusiveMinimum": 0
                  },
                  {
                     "enum": [
                        "N/A"
                     ],
                     "type": "string"
                  }
               ]
            },
            "z_score": {
               "title": "Z Score",
               "type": "number"
            },
            "corr_weight": {
               "title": "Corr Weight",
               "exclusiveMinimum": 0.0,
               "type": "number"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "edge",
            "statements",
            "belief",
            "weight",
            "db_url_edge"
         ]
      }
   }
}

Fields:

• edge_data (List[indra_network_search.data_models.__init__.EdgeData])

• path (List[indra_network_search.data_models.__init__.Node])

field edge_data: List[EdgeData] [Required]

field path: List[Node] [Required]

is_empty()

Return True if len(path) == 0 or len(edge_data) == 0

Return type:

bool

pydantic model indra_network_search.data_models.__init__.PathResultData

Results for any of the path algorithms

Show JSON schema

{
   "title": "PathResultData",
   "description": "Results for any of the path algorithms",
   "type": "object",
   "properties": {
      "source": {
         "$ref": "#/definitions/Node"
      },
      "target": {
         "$ref": "#/definitions/Node"
      },
      "paths": {
         "title": "Paths",
         "type": "object",
         "additionalProperties": {
            "type": "array",
            "items": {
               "$ref": "#/definitions/Path"
            }
         }
      }
   },
   "required": [
      "paths"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      },
      "EdgeData": {
         "title": "EdgeData",
         "description": "Data for one single edge",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtTypeSupport"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0,
               "maximum": 1,
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "minimum": 0,
               "type": "number"
            },
            "context_weight": {
               "title": "Context Weight",
               "default": "N/A",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "number",
                     "exclusiveMinimum": 0
                  },
                  {
                     "enum": [
                        "N/A"
                     ],
                     "type": "string"
                  }
               ]
            },
            "z_score": {
               "title": "Z Score",
               "type": "number"
            },
            "corr_weight": {
               "title": "Corr Weight",
               "exclusiveMinimum": 0.0,
               "type": "number"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "edge",
            "statements",
            "belief",
            "weight",
            "db_url_edge"
         ]
      },
      "Path": {
         "title": "Path",
         "description": "Results for a single path",
         "type": "object",
         "properties": {
            "path": {
               "title": "Path",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "edge_data": {
               "title": "Edge Data",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/EdgeData"
               }
            }
         },
         "required": [
            "path",
            "edge_data"
         ]
      }
   }
}

Fields:

• paths (Dict[int, List[indra_network_search.data_models.__init__.Path]])

• source (Optional[indra_network_search.data_models.__init__.Node])

• target (Optional[indra_network_search.data_models.__init__.Node])

field paths: Dict[int, List[Path]] [Required]

field source: Optional[Node] = None

field target: Optional[Node] = None

is_empty()

Return True if paths list is empty

Return type:

bool

pydantic model indra_network_search.data_models.__init__.Results

The model wrapping all results from the NetworkSearchQuery

Show JSON schema

{
   "title": "Results",
   "description": "The model wrapping all results from the NetworkSearchQuery",
   "type": "object",
   "properties": {
      "query_hash": {
         "title": "Query Hash",
         "type": "string"
      },
      "time_limit": {
         "title": "Time Limit",
         "type": "number"
      },
      "timed_out": {
         "title": "Timed Out",
         "type": "boolean"
      },
      "hashes": {
         "title": "Hashes",
         "default": [],
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "path_results": {
         "$ref": "#/definitions/PathResultData"
      },
      "reverse_path_results": {
         "$ref": "#/definitions/PathResultData"
      },
      "ontology_results": {
         "$ref": "#/definitions/OntologyResults"
      },
      "shared_target_results": {
         "$ref": "#/definitions/SharedInteractorsResults"
      },
      "shared_regulators_results": {
         "$ref": "#/definitions/SharedInteractorsResults"
      }
   },
   "required": [
      "query_hash",
      "time_limit",
      "timed_out"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      },
      "EdgeData": {
         "title": "EdgeData",
         "description": "Data for one single edge",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtTypeSupport"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0,
               "maximum": 1,
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "minimum": 0,
               "type": "number"
            },
            "context_weight": {
               "title": "Context Weight",
               "default": "N/A",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "number",
                     "exclusiveMinimum": 0
                  },
                  {
                     "enum": [
                        "N/A"
                     ],
                     "type": "string"
                  }
               ]
            },
            "z_score": {
               "title": "Z Score",
               "type": "number"
            },
            "corr_weight": {
               "title": "Corr Weight",
               "exclusiveMinimum": 0.0,
               "type": "number"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "edge",
            "statements",
            "belief",
            "weight",
            "db_url_edge"
         ]
      },
      "Path": {
         "title": "Path",
         "description": "Results for a single path",
         "type": "object",
         "properties": {
            "path": {
               "title": "Path",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "edge_data": {
               "title": "Edge Data",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/EdgeData"
               }
            }
         },
         "required": [
            "path",
            "edge_data"
         ]
      },
      "PathResultData": {
         "title": "PathResultData",
         "description": "Results for any of the path algorithms",
         "type": "object",
         "properties": {
            "source": {
               "$ref": "#/definitions/Node"
            },
            "target": {
               "$ref": "#/definitions/Node"
            },
            "paths": {
               "title": "Paths",
               "type": "object",
               "additionalProperties": {
                  "type": "array",
                  "items": {
                     "$ref": "#/definitions/Path"
                  }
               }
            }
         },
         "required": [
            "paths"
         ]
      },
      "OntologyResults": {
         "title": "OntologyResults",
         "description": "Results for shared_parents",
         "type": "object",
         "properties": {
            "source": {
               "$ref": "#/definitions/Node"
            },
            "target": {
               "$ref": "#/definitions/Node"
            },
            "parents": {
               "title": "Parents",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            }
         },
         "required": [
            "source",
            "target",
            "parents"
         ]
      },
      "SharedInteractorsResults": {
         "title": "SharedInteractorsResults",
         "description": "Results for shared targets and shared regulators",
         "type": "object",
         "properties": {
            "source_data": {
               "title": "Source Data",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/EdgeData"
               }
            },
            "target_data": {
               "title": "Target Data",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/EdgeData"
               }
            },
            "downstream": {
               "title": "Downstream",
               "type": "boolean"
            }
         },
         "required": [
            "source_data",
            "target_data",
            "downstream"
         ]
      }
   }
}

Fields:

• hashes (List[str])

• ontology_results (Optional[indra_network_search.data_models.__init__.OntologyResults])

• path_results (Optional[indra_network_search.data_models.__init__.PathResultData])

• query_hash (str)

• reverse_path_results (Optional[indra_network_search.data_models.__init__.PathResultData])

• shared_regulators_results (Optional[indra_network_search.data_models.__init__.SharedInteractorsResults])

• shared_target_results (Optional[indra_network_search.data_models.__init__.SharedInteractorsResults])

• time_limit (float)

• timed_out (bool)

field hashes: List[str] = []

field ontology_results: Optional[OntologyResults] = None

field path_results: Optional[PathResultData] = None

field query_hash: str [Required]

field reverse_path_results: Optional[PathResultData] = None

field shared_regulators_results: Optional[SharedInteractorsResults] = None

field shared_target_results: Optional[SharedInteractorsResults] = None

field time_limit: float [Required]

field timed_out: bool [Required]

pydantic model indra_network_search.data_models.__init__.SharedInteractorsOptions

Arguments for indra_network_search.pathfinding.shared_interactors

Show JSON schema

{
   "title": "SharedInteractorsOptions",
   "description": "Arguments for indra_network_search.pathfinding.shared_interactors",
   "type": "object",
   "properties": {
      "source": {
         "title": "Source",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "target": {
         "title": "Target",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "allowed_ns": {
         "title": "Allowed Ns",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "stmt_types": {
         "title": "Stmt Types",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "source_filter": {
         "title": "Source Filter",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "max_results": {
         "title": "Max Results",
         "default": 50,
         "type": "integer"
      },
      "regulators": {
         "title": "Regulators",
         "default": false,
         "type": "boolean"
      },
      "sign": {
         "title": "Sign",
         "type": "integer"
      }
   },
   "required": [
      "source",
      "target"
   ]
}

Fields:

• allowed_ns (Optional[List[str]])

• max_results (Optional[int])

• regulators (Optional[bool])

• sign (Optional[int])

• source (Union[str, Tuple[str, int]])

• source_filter (Optional[List[str]])

• stmt_types (Optional[List[str]])

• target (Union[str, Tuple[str, int]])

field allowed_ns: Optional[List[str]] = None

field max_results: Optional[int] = 50

field regulators: Optional[bool] = False

field sign: Optional[int] = None

field source: Union[str, Tuple[str, int]] [Required]

field source_filter: Optional[List[str]] = None

field stmt_types: Optional[List[str]] = None

field target: Union[str, Tuple[str, int]] [Required]

pydantic model indra_network_search.data_models.__init__.SharedInteractorsResults

Results for shared targets and shared regulators

Show JSON schema

{
   "title": "SharedInteractorsResults",
   "description": "Results for shared targets and shared regulators",
   "type": "object",
   "properties": {
      "source_data": {
         "title": "Source Data",
         "type": "array",
         "items": {
            "$ref": "#/definitions/EdgeData"
         }
      },
      "target_data": {
         "title": "Target Data",
         "type": "array",
         "items": {
            "$ref": "#/definitions/EdgeData"
         }
      },
      "downstream": {
         "title": "Downstream",
         "type": "boolean"
      }
   },
   "required": [
      "source_data",
      "target_data",
      "downstream"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "StmtTypeSupport": {
         "title": "StmtTypeSupport",
         "description": "Data per statement type",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/StmtData"
               }
            }
         },
         "required": [
            "stmt_type",
            "statements"
         ]
      },
      "EdgeData": {
         "title": "EdgeData",
         "description": "Data for one single edge",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "statements": {
               "title": "Statements",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtTypeSupport"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0,
               "maximum": 1,
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "minimum": 0,
               "type": "number"
            },
            "context_weight": {
               "title": "Context Weight",
               "default": "N/A",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "number",
                     "exclusiveMinimum": 0
                  },
                  {
                     "enum": [
                        "N/A"
                     ],
                     "type": "string"
                  }
               ]
            },
            "z_score": {
               "title": "Z Score",
               "type": "number"
            },
            "corr_weight": {
               "title": "Corr Weight",
               "exclusiveMinimum": 0.0,
               "type": "number"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "source_counts": {
               "title": "Source Counts",
               "default": {},
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "edge",
            "statements",
            "belief",
            "weight",
            "db_url_edge"
         ]
      }
   }
}

Fields:

• downstream (bool)

• source_data (List[indra_network_search.data_models.__init__.EdgeData])

• target_data (List[indra_network_search.data_models.__init__.EdgeData])

field downstream: bool [Required]

field source_data: List[EdgeData] [Required]

field target_data: List[EdgeData] [Required]

is_empty()

Return True if both source and target data is empty

pydantic model indra_network_search.data_models.__init__.ShortestSimplePathOptions

Arguments for indra.explanation.pathfinding.shortest_simple_paths

Show JSON schema

{
   "title": "ShortestSimplePathOptions",
   "description": "Arguments for indra.explanation.pathfinding.shortest_simple_paths",
   "type": "object",
   "properties": {
      "source": {
         "title": "Source",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "target": {
         "title": "Target",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         ]
      },
      "weight": {
         "title": "Weight",
         "type": "string"
      },
      "ignore_nodes": {
         "title": "Ignore Nodes",
         "type": "array",
         "items": {
            "type": "string"
         },
         "uniqueItems": true
      },
      "ignore_edges": {
         "title": "Ignore Edges",
         "type": "array",
         "items": {
            "type": "array",
            "minItems": 2,
            "maxItems": 2,
            "items": [
               {
                  "type": "string"
               },
               {
                  "type": "string"
               }
            ]
         },
         "uniqueItems": true
      },
      "hashes": {
         "title": "Hashes",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "strict_mesh_id_filtering": {
         "title": "Strict Mesh Id Filtering",
         "default": false,
         "type": "boolean"
      },
      "const_c": {
         "title": "Const C",
         "default": 1,
         "type": "integer"
      },
      "const_tk": {
         "title": "Const Tk",
         "default": 10,
         "type": "integer"
      }
   },
   "required": [
      "source",
      "target"
   ]
}

Fields:

• const_c (Optional[int])

• const_tk (Optional[int])

• hashes (Optional[List[int]])

• ignore_edges (Optional[Set[Tuple[str, str]]])

• ignore_nodes (Optional[Set[str]])

• ref_counts_function (Optional[Callable])

• source (Union[str, Tuple[str, int]])

• strict_mesh_id_filtering (Optional[bool])

• target (Union[str, Tuple[str, int]])

• weight (Optional[str])

field const_c: Optional[int] = 1

field const_tk: Optional[int] = 10

field hashes: Optional[List[int]] = None

field ignore_edges: Optional[Set[Tuple[str, str]]] = None

field ignore_nodes: Optional[Set[str]] = None

field ref_counts_function: Optional[Callable] = None

field source: Union[str, Tuple[str, int]] [Required]

field strict_mesh_id_filtering: Optional[bool] = False

field target: Union[str, Tuple[str, int]] [Required]

field weight: Optional[str] = None

pydantic model indra_network_search.data_models.__init__.StmtData

Data for one statement supporting an edge

Show JSON schema

{
   "title": "StmtData",
   "description": "Data for one statement supporting an edge",
   "type": "object",
   "properties": {
      "stmt_type": {
         "title": "Stmt Type",
         "type": "string"
      },
      "evidence_count": {
         "title": "Evidence Count",
         "minimum": 1,
         "type": "integer"
      },
      "stmt_hash": {
         "title": "Stmt Hash",
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "string",
               "minLength": 1,
               "maxLength": 2083,
               "format": "uri"
            }
         ]
      },
      "source_counts": {
         "title": "Source Counts",
         "type": "object",
         "additionalProperties": {
            "type": "integer"
         }
      },
      "belief": {
         "title": "Belief",
         "minimum": 0.0,
         "maximum": 1.0,
         "type": "number"
      },
      "curated": {
         "title": "Curated",
         "type": "boolean"
      },
      "english": {
         "title": "English",
         "type": "string"
      },
      "weight": {
         "title": "Weight",
         "type": "number"
      },
      "residue": {
         "title": "Residue",
         "default": "",
         "type": "string"
      },
      "position": {
         "title": "Position",
         "default": "",
         "type": "string"
      },
      "initial_sign": {
         "title": "Initial Sign",
         "minimum": 0,
         "maximum": 1,
         "type": "integer"
      },
      "db_url_hash": {
         "title": "Db Url Hash",
         "type": "string"
      }
   },
   "required": [
      "stmt_type",
      "evidence_count",
      "stmt_hash",
      "source_counts",
      "belief",
      "curated",
      "english",
      "db_url_hash"
   ]
}

Fields:

• belief (indra_network_search.data_models.__init__.ConstrainedFloatValue)

• curated (bool)

• db_url_hash (str)

• english (str)

• evidence_count (indra_network_search.data_models.__init__.ConstrainedIntValue)

• initial_sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])

• position (Optional[str])

• residue (Optional[str])

• source_counts (Dict[str, int])

• stmt_hash (Union[int, pydantic.networks.HttpUrl])

• stmt_type (str)

• weight (Optional[float])

field belief: ConstrainedFloatValue [Required]

Constraints:

• minimum = 0.0

• maximum = 1.0

field curated: bool [Required]

field db_url_hash: str [Required]

field english: str [Required]

field evidence_count: ConstrainedIntValue [Required]

Constraints:

• minimum = 1

field initial_sign: Optional[ConstrainedIntValue] = None

Constraints:

• minimum = 0

• maximum = 1

field position: Optional[str] = ''

field residue: Optional[str] = ''

field source_counts: Dict[str, int] [Required]

field stmt_hash: Union[int, HttpUrl] [Required]

field stmt_type: str [Required]

field weight: Optional[float] = None

pydantic model indra_network_search.data_models.__init__.StmtTypeSupport

Data per statement type

Show JSON schema

{
   "title": "StmtTypeSupport",
   "description": "Data per statement type",
   "type": "object",
   "properties": {
      "stmt_type": {
         "title": "Stmt Type",
         "type": "string"
      },
      "source_counts": {
         "title": "Source Counts",
         "default": {},
         "type": "object",
         "additionalProperties": {
            "type": "integer"
         }
      },
      "statements": {
         "title": "Statements",
         "type": "array",
         "items": {
            "$ref": "#/definitions/StmtData"
         }
      }
   },
   "required": [
      "stmt_type",
      "statements"
   ],
   "definitions": {
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      }
   }
}

Fields:

• source_counts (Dict[str, int])

• statements (List[indra_network_search.data_models.__init__.StmtData])

• stmt_type (str)

field source_counts: Dict[str, int] = {}

field statements: List[StmtData] [Required]

field stmt_type: str [Required]

set_source_counts()

Updates the source count field from the set statement data

pydantic model indra_network_search.data_models.__init__.SubgraphOptions

Argument for indra_network_search.pathfinding.get_subgraph_edges

Show JSON schema

{
   "title": "SubgraphOptions",
   "description": "Argument for indra_network_search.pathfinding.get_subgraph_edges",
   "type": "object",
   "properties": {
      "nodes": {
         "title": "Nodes",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      }
   },
   "required": [
      "nodes"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      }
   }
}

Fields:

• nodes (List[indra_network_search.data_models.__init__.Node])

field nodes: List[Node] [Required]

pydantic model indra_network_search.data_models.__init__.SubgraphRestQuery

Subgraph query

Show JSON schema

{
   "title": "SubgraphRestQuery",
   "description": "Subgraph query",
   "type": "object",
   "properties": {
      "nodes": {
         "title": "Nodes",
         "minItems": 1,
         "maxItems": 4000,
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "timeout": {
         "title": "Timeout",
         "default": 590,
         "minimum": 1,
         "maximum": 590,
         "type": "number"
      }
   },
   "required": [
      "nodes"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      }
   }
}

Fields:

• nodes (types.ConstrainedListValue[indra_network_search.data_models.__init__.Node])

• timeout (indra_network_search.data_models.__init__.ConstrainedFloatValue)

field nodes: ConstrainedListValue[Node] [Required]

Constraints:

• minItems = 1

• maxItems = 4000

field timeout: ConstrainedFloatValue = 590

Constraints:

• minimum = 1

• maximum = 590

pydantic model indra_network_search.data_models.__init__.SubgraphResults

Results for get_subgraph_edges

Show JSON schema

{
   "title": "SubgraphResults",
   "description": "Results for get_subgraph_edges",
   "type": "object",
   "properties": {
      "input_nodes": {
         "title": "Input Nodes",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "not_in_graph": {
         "title": "Not In Graph",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "available_nodes": {
         "title": "Available Nodes",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Node"
         }
      },
      "edges": {
         "title": "Edges",
         "type": "array",
         "items": {
            "$ref": "#/definitions/EdgeDataByHash"
         }
      }
   },
   "required": [
      "input_nodes",
      "not_in_graph",
      "available_nodes",
      "edges"
   ],
   "definitions": {
      "Node": {
         "title": "Node",
         "description": "Data for a node",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "minLength": 1,
               "type": "string"
            },
            "namespace": {
               "title": "Namespace",
               "minLength": 1,
               "type": "string"
            },
            "identifier": {
               "title": "Identifier",
               "minLength": 1,
               "type": "string"
            },
            "lookup": {
               "title": "Lookup",
               "minLength": 1,
               "type": "string"
            },
            "sign": {
               "title": "Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            }
         },
         "required": [
            "namespace",
            "identifier"
         ]
      },
      "StmtData": {
         "title": "StmtData",
         "description": "Data for one statement supporting an edge",
         "type": "object",
         "properties": {
            "stmt_type": {
               "title": "Stmt Type",
               "type": "string"
            },
            "evidence_count": {
               "title": "Evidence Count",
               "minimum": 1,
               "type": "integer"
            },
            "stmt_hash": {
               "title": "Stmt Hash",
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "string",
                     "minLength": 1,
                     "maxLength": 2083,
                     "format": "uri"
                  }
               ]
            },
            "source_counts": {
               "title": "Source Counts",
               "type": "object",
               "additionalProperties": {
                  "type": "integer"
               }
            },
            "belief": {
               "title": "Belief",
               "minimum": 0.0,
               "maximum": 1.0,
               "type": "number"
            },
            "curated": {
               "title": "Curated",
               "type": "boolean"
            },
            "english": {
               "title": "English",
               "type": "string"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "residue": {
               "title": "Residue",
               "default": "",
               "type": "string"
            },
            "position": {
               "title": "Position",
               "default": "",
               "type": "string"
            },
            "initial_sign": {
               "title": "Initial Sign",
               "minimum": 0,
               "maximum": 1,
               "type": "integer"
            },
            "db_url_hash": {
               "title": "Db Url Hash",
               "type": "string"
            }
         },
         "required": [
            "stmt_type",
            "evidence_count",
            "stmt_hash",
            "source_counts",
            "belief",
            "curated",
            "english",
            "db_url_hash"
         ]
      },
      "EdgeDataByHash": {
         "title": "EdgeDataByHash",
         "description": "Data for one single edge, with data keyed by hash",
         "type": "object",
         "properties": {
            "edge": {
               "title": "Edge",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Node"
               }
            },
            "stmts": {
               "title": "Stmts",
               "type": "object",
               "additionalProperties": {
                  "$ref": "#/definitions/StmtData"
               }
            },
            "belief": {
               "title": "Belief",
               "type": "number"
            },
            "weight": {
               "title": "Weight",
               "type": "number"
            },
            "db_url_edge": {
               "title": "Db Url Edge",
               "type": "string"
            },
            "url_by_type": {
               "title": "Url By Type",
               "type": "object",
               "additionalProperties": {
                  "type": "string"
               }
            }
         },
         "required": [
            "edge",
            "stmts",
            "belief",
            "weight",
            "db_url_edge",
            "url_by_type"
         ]
      }
   }
}

Fields:

• available_nodes (List[indra_network_search.data_models.__init__.Node])

• edges (List[indra_network_search.data_models.__init__.EdgeDataByHash])

• input_nodes (List[indra_network_search.data_models.__init__.Node])

• not_in_graph (List[indra_network_search.data_models.__init__.Node])

field available_nodes: List[Node] [Required]

field edges: List[EdgeDataByHash] [Required]

field input_nodes: List[Node] [Required]

field not_in_graph: List[Node] [Required]

indra_network_search.data_models.__init__.basemodel_in_iterable(basemodel, iterable, any_item, exclude=None)

Test if a basemodel object is part of a collection

Parameters:

• basemodel (BaseModel) – A BaseModel to test membership in iterable for

• iterable (Iterable) – An iterable that contains objects to test for equality with basemodel

• any_item (bool) – If True, use any() when testing collections for equality, otherwise use all(), i.e. the collections must match exactly

• exclude (Optional[Set[str]]) – A set of field names to exclude from the basemodels

Return type:

bool

Returns:

True if basemodel is found in the collection

indra_network_search.data_models.__init__.basemodels_equal(basemodel, other_basemodel, any_item, exclude=None)

Wrapper to test two basemodels for equality, can exclude irrelevant keys

Parameters:

• basemodel (BaseModel) – BaseModel to test against other_basemodel

• other_basemodel (BaseModel) – BaseModel to test against basemodel

• any_item (bool) – If True, use any() when testing collections for equality, otherwise use all(), i.e. the collections must match exactly

• exclude (Optional[Set[str]]) – A set of field names to exclude from the basemodels

Return type:

bool

Returns:

True if the two models are equal