medrecords.medrecord.MedRecord#

class MedRecord[source]#

Bases: object

A GraphRecord with built-in medical data handling.

__init__()[source]#: Initializes an empty MedRecord.

Methods

`__init__`()	Initializes an empty MedRecord.
`add_edge`(source_node_index, ...)	Adds a single edge with the given attributes.
`add_edge_in_group`(source_node_index, ...)	Adds a single edge with the given attributes to a group.
`add_edges`(source)	Adds the edges of the given source.
`add_edges_in_group`(source, group_index)	Adds the edges of the given source to a group.
`add_edges_to_group`(edge_indices, group_index)	Adds the selected edges to a group.
`add_group`(group_index)	Adds an empty group.
`add_node`(node_index, attributes)	Adds a single node with the given attributes.
`add_node_in_group`(node_index, attributes, ...)	Adds a single node with the given attributes to a group.
`add_nodes`(source)	Adds the nodes of the given source.
`add_nodes_in_group`(source, group_index)	Adds the nodes of the given source to a group.
`add_nodes_to_group`(node_indices, group_index)	Adds the selected nodes to a group.
`add_plugin`(name, plugin)	Attaches a plugin under the given name.
`clear`()	Removes all nodes, edges and groups, keeping the schema and the plugins.
`compact`()	Reclaims the space that removed nodes and edges still occupy.
`contains_edge`(edge_index)	Checks whether the MedRecord holds an edge with the given index.
`contains_group`(group_index)	Checks whether the MedRecord holds a group with the given index.
`contains_node`(node_index)	Checks whether the MedRecord holds a node with the given index.
`difference`(other)	Removes everything the other MedRecord also holds.
`edge`(edge_index)	Views a single edge.
`edge_count`()	Counts the edges of the MedRecord.
`edge_indices`()	Lists the indices of all edges.
`edges`()	Starts a query over the edges of the MedRecord.
`export`(writer)	Exports the MedRecord through a writer.
`freeze_schema`()	Stops the schema from growing with the data written to the MedRecord.
`from_graphrecord`(graphrecord)	Creates a MedRecord around an existing GraphRecord.
`from_ron`(path)	Reads a MedRecord from a RON file.
`group`(group_index)	Views a single group.
`group_count`()	Counts the groups of the MedRecord.
`group_indices`()	Lists the indices of all groups.
`group_overview`(group_index[, truncate_details])	Summarizes the contents of a single group.
`groups`()	Starts a query over the groups of the MedRecord.
`intersect`(other)	Keeps what this MedRecord and the other one have in common.
`keep_edges`(edge_indices)	Keeps only the selected edges.
`keep_groups`(group_indices)	Keeps only the selected groups and their members.
`keep_nodes`(node_indices)	Keeps only the selected nodes and the edges between them.
`merge`(other[, on_conflict])	Merges the other MedRecord into this one.
`node`(node_index)	Views a single node.
`node_count`()	Counts the nodes of the MedRecord.
`node_indices`()	Lists the indices of all nodes.
`nodes`()	Starts a query over the nodes of the MedRecord.
`overview`([truncate_details])	Summarizes the contents of the MedRecord.
`query`(expression)	Binds an expression to the MedRecord.
`remove_edge_attributes`(edge_indices, ...)	Removes the named attributes from the selected edges.
`remove_edges`(edge_indices)	Removes the selected edges.
`remove_edges_from_group`(edge_indices, ...)	Removes the selected edges from a group, keeping the edges themselves.
`remove_groups`(group_indices)	Removes the selected groups, keeping their members ungrouped.
`remove_node_attributes`(node_indices, ...)	Removes the named attributes from the selected nodes.
`remove_nodes`(node_indices)	Removes the selected nodes and the edges attached to them.
`remove_nodes_from_group`(node_indices, ...)	Removes the selected nodes from a group, keeping the nodes themselves.
`remove_plugin`(name)	Detaches the plugin attached under the given name.
`replace_edge_attributes`(edge_indices, attributes)	Replaces all attributes of the selected edges with the given ones.
`replace_node_attributes`(node_indices, attributes)	Replaces all attributes of the selected nodes with the given ones.
`set_edge_attributes`(edge_indices, attributes)	Sets the given attributes on the selected edges, keeping the others.
`set_node_attributes`(node_indices, attributes)	Sets the given attributes on the selected nodes, keeping the others.
`set_schema`(schema)	Validates the MedRecord against the given schema and adopts it.
`to_arrow`()	Exports the MedRecord to Arrow record batches, partitioned by group.
`to_pandas`()	Exports the MedRecord to Pandas DataFrames, partitioned by group.
`to_polars`()	Exports the MedRecord to Polars DataFrames, partitioned by group.
`to_ron`(path)	Writes the MedRecord to a RON file.
`unfreeze_schema`()	Lets the schema grow with the data written to the MedRecord again.
`with_schema`(schema)	Creates an empty MedRecord that validates against the given schema.

Attributes

`graphrecord`	The GraphRecord the MedRecord holds.
`plugin_entries`	The plugins attached to the MedRecord, by the name they are attached under.
`plugins`	The names of the plugins attached to the MedRecord.
`schema`	The schema the MedRecord validates against.

__copy__()[source]#

Copies the MedRecord.

Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding the same contents.

__deepcopy__(memo=None)[source]#

Deep copies the MedRecord.

Parameters:: memo (Optional[Dict[int, object]]) – The objects copied so far.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding the same contents.

__eq__(other)[source]#

Compares the MedRecord with another one by its contents.

Parameters:

other (object) – The object to compare against.

Return type:

bool

Returns:

bool –

True if both hold the same nodes, edges and groups, otherwise: False.

__reduce__()[source]#

Reduces the MedRecord to what pickle needs to restore it.

Return type:

Tuple[Callable[[GraphRecord], MedRecord], Tuple[GraphRecord]]

Returns:

Tuple[Callable[[GraphRecord], MedRecord], Tuple[GraphRecord]] –

The: callable that restores the MedRecord and its arguments.

__repr__()[source]#

Returns the string representation of the MedRecord.

Return type:: str
Returns:: str – The overview of the MedRecord.

add_edge(source_node_index, target_node_index, attributes)[source]#

Adds a single edge with the given attributes.

Parameters:

source_node_index (SingleNodeSelection) – The node the edge starts at.
target_node_index (SingleNodeSelection) – The node the edge ends at.
attributes (Attributes) – The attributes of the edge.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added edge.

add_edge_in_group(source_node_index, target_node_index, attributes, group_index)[source]#

Adds a single edge with the given attributes to a group.

Parameters:

source_node_index (SingleNodeSelection) – The node the edge starts at.
target_node_index (SingleNodeSelection) – The node the edge ends at.
attributes (Attributes) – The attributes of the edge.
group_index (SingleGroupSelection) – The group the edge is added in.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added edge.

add_edges(source)[source]#

Adds the edges of the given source.

Parameters:: source (EdgeSource) – The edges to add.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord containing the added edges.

add_edges_in_group(source, group_index)[source]#

Adds the edges of the given source to a group.

Parameters:

source (EdgeSource) – The edges to add.
group_index (SingleGroupSelection) – The group the edges are added in.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added edges.

add_edges_to_group(edge_indices, group_index)[source]#

Adds the selected edges to a group.

Parameters:

edge_indices (MultipleEdgeSelection) – The edges to add.
group_index (SingleGroupSelection) – The group the edges join.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with those edges in the group.

add_group(group_index)[source]#

Adds an empty group.

Parameters:: group_index (SingleGroupSelection) – The index of the group to add.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord containing the added group.

add_node(node_index, attributes)[source]#

Adds a single node with the given attributes.

Parameters:

node_index (SingleNodeSelection) – The index of the node to add.
attributes (Attributes) – The attributes of the node.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added node.

add_node_in_group(node_index, attributes, group_index)[source]#

Adds a single node with the given attributes to a group.

Parameters:

node_index (SingleNodeSelection) – The index of the node to add.
attributes (Attributes) – The attributes of the node.
group_index (SingleGroupSelection) – The group the node is added in.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added node.

add_nodes(source)[source]#

Adds the nodes of the given source.

Parameters:: source (NodeSource) – The nodes to add.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord containing the added nodes.

add_nodes_in_group(source, group_index)[source]#

Adds the nodes of the given source to a group.

Parameters:

source (NodeSource) – The nodes to add.
group_index (SingleGroupSelection) – The group the nodes are added in.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord containing the added nodes.

add_nodes_to_group(node_indices, group_index)[source]#

Adds the selected nodes to a group.

Parameters:

node_indices (MultipleNodeSelection) – The nodes to add.
group_index (SingleGroupSelection) – The group the nodes join.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with those nodes in the group.

add_plugin(name, plugin)[source]#

Attaches a plugin under the given name.

Parameters:

name (PluginName) – The name to attach the plugin under.
plugin (Plugin) – The plugin to attach.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with the plugin attached.

clear()[source]#

Removes all nodes, edges and groups, keeping the schema and the plugins.

Return type:: MedRecord
Returns:: MedRecord – An empty MedRecord.

compact()[source]#

Reclaims the space that removed nodes and edges still occupy.

Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding the same contents, compacted.

contains_edge(edge_index)[source]#

Checks whether the MedRecord holds an edge with the given index.

Parameters:: edge_index (EdgeIndex) – The index to look for.
Return type:: bool
Returns:: bool – True if the edge exists, otherwise False.

contains_group(group_index)[source]#

Checks whether the MedRecord holds a group with the given index.

Parameters:: group_index (GroupIndex) – The index to look for.
Return type:: bool
Returns:: bool – True if the group exists, otherwise False.

contains_node(node_index)[source]#

Checks whether the MedRecord holds a node with the given index.

Parameters:: node_index (NodeIndex) – The index to look for.
Return type:: bool
Returns:: bool – True if the node exists, otherwise False.

difference(other)[source]#

Removes everything the other MedRecord also holds.

Parameters:: other (MedRecord) – The MedRecord to subtract.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding what only this one held.

edge(edge_index)[source]#

Views a single edge.

Parameters:: edge_index (EdgeIndex) – The index of the edge to view.
Return type:: EdgeView
Returns:: EdgeView – A view of the edge as this MedRecord holds it.

edge_count()[source]#

Counts the edges of the MedRecord.

Return type:: int
Returns:: int – The number of edges.

edge_indices()[source]#

Lists the indices of all edges.

Return type:: List[EdgeIndex]
Returns:: List[EdgeIndex] – The index of every edge.

edges()[source]#

Starts a query over the edges of the MedRecord.

Return type:: Expression[Bound, Indexed[EdgeIndex, Unit], Multiple[Unordered]]
Returns:: EdgesSeries – A series of all edges, bound to this MedRecord.

export(writer)[source]#

Exports the MedRecord through a writer.

Parameters:: writer (Writer[T]) – The writer to export through.
Return type:: TypeVar(T)
Returns:: T – What the writer handed back.

freeze_schema()[source]#

Stops the schema from growing with the data written to the MedRecord.

Return type:: MedRecord
Returns:: MedRecord – A MedRecord with a frozen schema.

classmethod from_graphrecord(graphrecord)[source]#

Creates a MedRecord around an existing GraphRecord.

Parameters:: graphrecord (GraphRecord) – The GraphRecord to wrap.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding the contents of the GraphRecord.

classmethod from_ron(path)[source]#

Reads a MedRecord from a RON file.

Parameters:: path (Union[str, os.PathLike[str]]) – The path of the file to read.
Return type:: MedRecord
Returns:: MedRecord – The MedRecord stored in the file.

property graphrecord: GraphRecord#

The GraphRecord the MedRecord holds.

Returns:: GraphRecord – The GraphRecord holding the contents of the MedRecord.

group(group_index)[source]#

Views a single group.

Parameters:: group_index (GroupIndex) – The index of the group to view.
Return type:: GroupView
Returns:: GroupView – A view of the group as this MedRecord holds it.

group_count()[source]#

Counts the groups of the MedRecord.

Return type:: int
Returns:: int – The number of groups.

group_indices()[source]#

Lists the indices of all groups.

Return type:: List[Union[str, int]]
Returns:: List[GroupIndex] – The index of every group.

group_overview(group_index, truncate_details=80)[source]#

Summarizes the contents of a single group.

Parameters:

group_index (GroupIndex) – The group to summarize.
truncate_details (Optional[int]) – The width detail columns are truncated to. No truncation if None. Defaults to DEFAULT_TRUNCATE_DETAILS.

Return type:

GroupOverview

Returns:

GroupOverview – The summary of the group.

groups()[source]#

Starts a query over the groups of the MedRecord.

Return type:: Expression[Bound, Indexed[GroupIndex, Unit], Multiple[Unordered]]
Returns:: GroupsSeries – A series of all groups, bound to this MedRecord.

intersect(other)[source]#

Keeps what this MedRecord and the other one have in common.

Parameters:: other (MedRecord) – The MedRecord to intersect with.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding the shared nodes, edges and groups.

keep_edges(edge_indices)[source]#

Keeps only the selected edges.

Parameters:: edge_indices (MultipleEdgeSelection) – The edges to keep.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding only those edges.

keep_groups(group_indices)[source]#

Keeps only the selected groups and their members.

Parameters:: group_indices (MultipleGroupSelection) – The groups to keep.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding only those groups.

keep_nodes(node_indices)[source]#

Keeps only the selected nodes and the edges between them.

Parameters:: node_indices (MultipleNodeSelection) – The nodes to keep.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord holding only those nodes.

merge(other, on_conflict=OnConflict.Raise)[source]#

Merges the other MedRecord into this one.

Parameters:

other (MedRecord) – The MedRecord to merge in.
on_conflict (OnConflict) – How attributes both MedRecords define are resolved. Defaults to OnConflict.Raise.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord holding both.

node(node_index)[source]#

Views a single node.

Parameters:: node_index (NodeIndex) – The index of the node to view.
Return type:: NodeView
Returns:: NodeView – A view of the node as this MedRecord holds it.

node_count()[source]#

Counts the nodes of the MedRecord.

Return type:: int
Returns:: int – The number of nodes.

node_indices()[source]#

Lists the indices of all nodes.

Return type:: List[Union[str, int]]
Returns:: List[NodeIndex] – The index of every node.

nodes()[source]#

Starts a query over the nodes of the MedRecord.

Return type:: Expression[Bound, Indexed[NodeIndex, Unit], Multiple[Unordered]]
Returns:: NodesSeries – A series of all nodes, bound to this MedRecord.

overview(truncate_details=80)[source]#

Summarizes the contents of the MedRecord.

Parameters:: truncate_details (Optional[int]) – The width detail columns are truncated to. No truncation if None. Defaults to DEFAULT_TRUNCATE_DETAILS.
Return type:: Overview
Returns:: Overview – The summary of every group and of the ungrouped part.

property plugin_entries: Dict[str | int, Plugin]#

The plugins attached to the MedRecord, by the name they are attached under.

Returns:: Dict[PluginName, Plugin] – Every attached plugin, by its name.

property plugins: List[str | int]#

The names of the plugins attached to the MedRecord.

Returns:: List[PluginName] – The name of every attached plugin.

query(expression)[source]#

Binds an expression to the MedRecord.

Parameters:: expression (Expression[Unbound, S, C, Unpack[Levels]]) – The expression to bind.
Return type:: Series[TypeVar(S, bound= Shape, covariant=True), TypeVar(C, bound= Container), Unpack[TypeVarTuple]]
Returns:: Series[S, C, Unpack[Levels]] – The expression, bound to this MedRecord.

remove_edge_attributes(edge_indices, attribute_names)[source]#

Removes the named attributes from the selected edges.

Parameters:

edge_indices (MultipleEdgeSelection) – The edges to remove the attributes from.
attribute_names (Iterable[AttributeName]) – The names of the attributes to remove.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord without those attributes.

remove_edges(edge_indices)[source]#

Removes the selected edges.

Parameters:: edge_indices (MultipleEdgeSelection) – The edges to remove.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord without those edges.

remove_edges_from_group(edge_indices, group_index)[source]#

Removes the selected edges from a group, keeping the edges themselves.

Parameters:

edge_indices (MultipleEdgeSelection) – The edges to remove.
group_index (SingleGroupSelection) – The group the edges leave.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord without those edges in the group.

remove_groups(group_indices)[source]#

Removes the selected groups, keeping their members ungrouped.

Parameters:: group_indices (MultipleGroupSelection) – The groups to remove.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord without those groups.

remove_node_attributes(node_indices, attribute_names)[source]#

Removes the named attributes from the selected nodes.

Parameters:

node_indices (MultipleNodeSelection) – The nodes to remove the attributes from.
attribute_names (Iterable[AttributeName]) – The names of the attributes to remove.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord without those attributes.

remove_nodes(node_indices)[source]#

Removes the selected nodes and the edges attached to them.

Parameters:: node_indices (MultipleNodeSelection) – The nodes to remove.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord without those nodes.

remove_nodes_from_group(node_indices, group_index)[source]#

Removes the selected nodes from a group, keeping the nodes themselves.

Parameters:

node_indices (MultipleNodeSelection) – The nodes to remove.
group_index (SingleGroupSelection) – The group the nodes leave.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord without those nodes in the group.

remove_plugin(name)[source]#

Detaches the plugin attached under the given name.

Parameters:: name (PluginName) – The name the plugin is attached under.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord without that plugin.

replace_edge_attributes(edge_indices, attributes)[source]#

Replaces all attributes of the selected edges with the given ones.

Parameters:

edge_indices (MultipleEdgeSelection) – The edges to replace the attributes of.
attributes (Attributes) – The attributes the edges end up with.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with the attributes replaced.

replace_node_attributes(node_indices, attributes)[source]#

Replaces all attributes of the selected nodes with the given ones.

Parameters:

node_indices (MultipleNodeSelection) – The nodes to replace the attributes of.
attributes (Attributes) – The attributes the nodes end up with.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with the attributes replaced.

property schema: Schema#

The schema the MedRecord validates against.

Returns:: Schema – The schema of the MedRecord.

set_edge_attributes(edge_indices, attributes)[source]#

Sets the given attributes on the selected edges, keeping the others.

Parameters:

edge_indices (MultipleEdgeSelection) – The edges to set the attributes on.
attributes (Attributes) – The attributes to set.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with the attributes set.

set_node_attributes(node_indices, attributes)[source]#

Sets the given attributes on the selected nodes, keeping the others.

Parameters:

node_indices (MultipleNodeSelection) – The nodes to set the attributes on.
attributes (Attributes) – The attributes to set.

Return type:

MedRecord

Returns:

MedRecord – A MedRecord with the attributes set.

set_schema(schema)[source]#

Validates the MedRecord against the given schema and adopts it.

Parameters:: schema (Schema) – The schema to adopt.
Return type:: MedRecord
Returns:: MedRecord – A MedRecord carrying the schema.

to_arrow()[source]#

Exports the MedRecord to Arrow record batches, partitioned by group.

Return type:

Export[RecordBatch]

Returns:

Export[RecordBatch] –

The node and edge tables of every group and of: the ungrouped part.

to_pandas()[source]#

Exports the MedRecord to Pandas DataFrames, partitioned by group.

Return type:

Export[DataFrame]

Returns:

Export[pd.DataFrame] –

The node and edge tables of every group and of: the ungrouped part.

to_polars()[source]#

Exports the MedRecord to Polars DataFrames, partitioned by group.

Return type:

Export[DataFrame]

Returns:

Export[pl.DataFrame] –

The node and edge tables of every group and of: the ungrouped part.

to_ron(path)[source]#

Writes the MedRecord to a RON file.

Parameters:: path (Union[str, os.PathLike[str]]) – The path of the file to write.
Return type:: None

unfreeze_schema()[source]#

Lets the schema grow with the data written to the MedRecord again.

Return type:: MedRecord
Returns:: MedRecord – A MedRecord with an unfrozen schema.

classmethod with_schema(schema)[source]#

Creates an empty MedRecord that validates against the given schema.

Parameters:: schema (Schema) – The schema the MedRecord validates against.
Return type:: MedRecord
Returns:: MedRecord – An empty MedRecord carrying the schema.