ResSimpy.Nexus.DataModels.NexusFile.NexusFile

class ResSimpy.Nexus.DataModels.NexusFile.NexusFile(location: str | None = None, include_locations: list[str] | None = None, origin: str | None = None, include_objects: list[ResSimpy.Nexus.DataModels.NexusFile.NexusFile] | None = None, file_content_as_list: list[str] | None = None, linked_user: str | None = None, last_modified: datetime | None = None)[source]

Bases: File

Class to deal with origin and structure of Nexus files and preserve origin of include files.

location

Path to the original file being opened. Defaults to None.

Type:: Optional[str]

include_locations

list of file paths that the file contains. Defaults to None.

Type:: Optional[list[str]]

origin

Where the file was opened from. Defaults to None.

Type:: Optional[str]

include_objects

The include files but generated as a NexusFile instance. Defaults to None.

Type:: Optional[list[NexusFile]]

linked_user

user or owner of the file. Defaults to None

Type:: Optional[str]

last_modified

last modified date of the file

Type:: Optional[datetime]

Public Data Attributes:

`include_locations`
`origin`
`include_objects`
`object_locations`
`line_locations`
`linked_user`
`last_modified`
`get_flat_list_str_file`
`get_flat_list_str_file_including_includes`
`input_file_location`
`location`
`file_content_as_list`

Inherited from File

`location`
`file_content_as_list`
`id`	Unique identifier for each Node object.
`file_modified`
`get_flat_list_str_file`

Inherited from FileBase

`location`
`file_content_as_list`
`get_flat_list_str_file`

Methods:

`__init__`([location, include_locations, ...])
`generate_file_include_structure`(file_path[, ...])	Generates a nexus file instance for a provided text file with information storing the included files.
`export_network_lists`()	Exports lists of connections from and to for use in network graphs.
`iterate_line`([file_index, max_depth, ...])	Generator object for iterating over a list of strings with nested NexusFile objects in them.
`get_full_network`([max_depth])	Recursively constructs two lists of from and to nodes representing the connections between files.
`add_object_locations`(obj_uuid, line_indices)	Adds a uuid to the object_locations dictionary.
`find_which_include_file`(flattened_index)	Given a line index that relates to a position within the flattened file_as_list from the method get_flat_file_as_list.
`add_to_file_as_list`(additional_content, index)	To add content to the file as list, also updates object numbers and optionally allows user to add several additional new objects.
`remove_object_from_file_as_list`(...)	Removes all associated lines in the file as well as the object locations relating to a list of objects.
`remove_from_file_as_list`(index[, ...])	Remove an entry from the file as list.
`insert_comments`(additional_content, comments)	Adds comments alongside additional content.
`get_object_locations_for_id`(id)	Gets the number of object locations for a specified id.
`__repr__`()	Return repr(self).
`__eq__`(other)	Return self==value.

Inherited from File

`__init__`([location, file_content_as_list])
`write_to_file`([new_file_path])	Writes to file specified in self.location the strings contained in the list self.file_content_as_list.
`add_object_locations`(obj_uuid, line_indices)
`insert_comments`(additional_content, comments)
`get_object_locations_for_id`(obj_id)
`remove_object_from_file_as_list`(...)
`add_to_file_as_list`(additional_content, index)
`remove_from_file_as_list`(index[, ...])
`find_which_include_file`(flattened_index)
`__repr__`()	Return repr(self).
`__eq__`(other)	Return self==value.

Inherited from FileBase

`write_to_file`()
`add_object_locations`(obj_uuid, line_indices)
`insert_comments`(additional_content, comments)
`get_object_locations_for_id`(obj_id)
`remove_object_from_file_as_list`(...)
`add_to_file_as_list`(additional_content, index)
`remove_from_file_as_list`(index[, ...])
`__init__`([location, file_content_as_list, ...])
`__repr__`()	Return repr(self).
`__eq__`(other)	Return self==value.

__init__(location: str | None = None, include_locations: list[str] | None = None, origin: str | None = None, include_objects: list[ResSimpy.Nexus.DataModels.NexusFile.NexusFile] | None = None, file_content_as_list: list[str] | None = None, linked_user: str | None = None, last_modified: datetime | None = None) → None[source]

classmethod generate_file_include_structure(file_path: str, origin: str | None = None, recursive: bool = True, skip_arrays: bool = True, top_level_file: bool = True) → Self[source]

Generates a nexus file instance for a provided text file with information storing the included files.

Parameters:

file_path (str) – path to a file
origin (Optional[str], optional) – Where the file was opened from. Defaults to None.
recursive (bool) – Whether the method should recursively drill down multiple layers of include_locations.
skip_arrays (bool) – If set True skips the INCLUDE arrays that come after property array and VALUE
top_level_file (bool) – If set to True, the code assumes this is a ‘top level’ file rather than an included
one. –

Returns:

NexusFile – a class instance for NexusFile with knowledge of include files

export_network_lists()[source]

Exports lists of connections from and to for use in network graphs.

Raises:: ValueError – If the from and to lists are not the same length
Returns:: tuple[list] – list of to and from file paths where the equivalent indexes relate to a connection

class FileIndex(index: 'int')[source]

Bases: object

__init__(index: int) → None

iterate_line(file_index: FileIndex | None = None, max_depth: int | None = None, parent: NexusFile | None = None, prefix_line: str | None = None, keep_include_references=False) → Generator[str, None, None][source]

Generator object for iterating over a list of strings with nested NexusFile objects in them.

Yields:: str – sequential line from the file.

get_full_network(max_depth: int | None = None) → tuple[list[str | None], list[str | None]][source]

Recursively constructs two lists of from and to nodes representing the connections between files.

Parameters:: max_depth (Optional[int], optional) – depth of the iteration to construct the network down to. Defaults to None.
Returns:: tuple[list[str | None], list[str | None]] – two lists of from and to nodes where corresponding indices create an edge within a graph network. e.g. (from_list[i], to_list[i]) is a connection between two files.

add_object_locations(obj_uuid: UUID, line_indices: list[int]) → None[source]

Adds a uuid to the object_locations dictionary. Used for storing the line numbers where objects are stored within the flattened file_as_list.

Parameters:

obj_uuid (UUID) – unique identifier of the object being created/stored.
line_indices (list[int]) – line number in the flattened file_content_as_list (i.e. from the get_flat_list_str_file method).

property id: UUID: Unique identifier for each Node object.

write_to_file(new_file_path: str | None = None) → None: Writes to file specified in self.location the strings contained in the list self.file_content_as_list.

find_which_include_file(flattened_index: int) → tuple[ResSimpy.File.File, int][source]

Given a line index that relates to a position within the flattened file_as_list from the method get_flat_file_as_list.

Parameters:: flattened_index (int) – index in the flattened file as list structure
Returns:: tuple[File, int] where the first element is the file that the relevant line is in and the second element is the relative index in that file.

add_to_file_as_list(additional_content: list[str], index: int, additional_objects: dict[uuid.UUID, list[int]] | None = None, comments: str | None = None) → None[source]

To add content to the file as list, also updates object numbers and optionally allows user to add several additional new objects.

Parameters:

additional_content (list[str]) – Additional lines as a list of strings to be added.
index (int) – index to insert the new lines at in the calling flat_file_as_list
additional_objects (Optional[dict[UUID, int]]) – defaults to None. Otherwise, a dictionary keyed with the UUID of the new objects to add as well as the corresponding index of the object in the original calling NexusFile
comments (str | None) – defaults to None. Comments to add in-line to the file.

remove_object_from_file_as_list(objects_to_remove: list[uuid.UUID]) → None[source]: Removes all associated lines in the file as well as the object locations relating to a list of objects.

remove_from_file_as_list(index: int, objects_to_remove: list[uuid.UUID] | None = None, string_to_remove: str | None = None) → None[source]

Remove an entry from the file as list. Also updates existing object locations and removes any specified objects from the object locations dictionary.

Parameters:

index (int) – index n the calling flat_file_as_list to remove the entry from
objects_to_remove (Optional[list[UUID]]) – list of object id’s to remove from the object locations. Defaults to None
string_to_remove (Optional[str]) – if specified will only remove the listed string from the entry at the index. Defaults to None, which removes the entire entry.

static insert_comments(additional_content: list[str], comments: str) → list[str][source]

Adds comments alongside additional content.

Parameters:

additional_content (list[str]) – additional lines of the file to be added with a new entry per line.
comments (str) – comments to be added to all lines

Returns:

list of strings within the content.

get_object_locations_for_id(id: UUID) → list[int][source]: Gets the number of object locations for a specified id.