Struct biodivine_sketchbook::sketchbook::observations::_manager::ObservationManager

pub struct ObservationManager {
    datasets: HashMap<DatasetId, Dataset>,
}

Class to manage all observations and datasets.

ObservationManager can be managed through its classical Rust API, as well as through the external events (as it implements the SessionState event).

Fields

datasets: HashMap<DatasetId, Dataset>

Implementations

impl ObservationManager

Methods for safely generating new valid (unique) instances of identifiers for the current ObservationManager.

pub fn generate_dataset_id( &self, ideal_id: &str, start_index: Option<usize>, ) -> DatasetId

Generate valid DatasetId that’s currently not used by any dataset in this ObservationManager.

First, the given ideal_id or its transformation by replacing invalid characters are tried. If they are both invalid (non-unique), a numerical identifier is added at the end. By specifying start_index, the index search starts directly at that number (e.g., when ideal ID is “d” and start index is 3, search for ID starts with “d_3”, “d_4”, …)

Warning: Do not use this to pre-generate more than one id at a time, as the process is deterministic and might generate the same IDs. Always generate an Id, add that dataset, and then repeat for other datasets.

pub fn generate_obs_id( &self, dataset_id: &DatasetId, ideal_obs_id: &str, start_index: Option<usize>, ) -> ObservationId

Generate valid ObservationId that’s currently not used by any observation in a particular dataset of this ObservationManager.

For more, see super::Dataset::generate_obs_id.

Assumes that dataset_id was checked beforehand.

pub fn generate_var_id( &self, dataset_id: &DatasetId, ideal_var_id: &str, start_index: Option<usize>, ) -> VarId

Generate valid VarId that’s currently not used by any variable in a particular dataset of this ObservationManager.

Assumes that dataset_id was checked beforehand.

impl ObservationManager

pub fn load_dataset(name: &str, csv_path: &str) -> Result<Dataset, String>

Load a dataset from given CSV file. The header line specifies variables, following lines represent individual observations (id and values).

The resulting dataset has empty annotation string (same for all its observations).

For example, the following might be a valid CSV file for a dataset with 2 observations: ID,YOX1,CLN3,YHP1,ACE2,SWI5,MBF Observation1,0,1,0,1,0,1 Observation2,1,0,,1,0,

pub fn load_and_add_dataset( &mut self, csv_path: &str, id: &str, ) -> Result<(), String>

Load a dataset from given CSV file, and add it to this ObservationManager. The header line specifies variables, following lines represent individual observations (id and values).

See Self::load_dataset for details.

impl ObservationManager

Creating instances of ObservationManager.

pub fn new_empty() -> ObservationManager

Instantiate ObservationManager with empty list of datasets.

pub fn from_datasets( datasets: Vec<(&str, Dataset)>, ) -> Result<ObservationManager, String>

Instantiate ObservationManager with given list of ID-dataset pairs.

impl ObservationManager

Editing ObservationManager.

pub fn add_dataset( &mut self, id: DatasetId, dataset: Dataset, ) -> Result<(), String>

Add a new dataset with given id to this ObservationManager.

The ID must be valid identifier that is not already used by some other dataset. Returns Err in case the id is already being used.

pub fn add_dataset_by_str( &mut self, id: &str, dataset: Dataset, ) -> Result<(), String>

Add a new dataset with given string id to this ObservationManager.

The ID must be valid identifier that is not already used by some other dataset. Returns Err in case the id is already being used.

pub fn add_multiple_datasets( &mut self, id_name_pairs: Vec<(&str, Dataset)>, ) -> Result<(), String>

Shorthand to add a list of new datasets with given string IDs to this manager.

The ID must be valid identifier that is not already used by some other dataset. Returns Err in case the id is already being used.

pub fn swap_dataset_content( &mut self, id: &DatasetId, new_content: Dataset, ) -> Result<(), String>

Swap content of a dataset with given id. The ID must be valid identifier.

pub fn swap_dataset_content_by_str( &mut self, id: &str, new_content: Dataset, ) -> Result<(), String>

Swap content of a dataset with given id. The ID must be valid identifier.

pub fn set_dataset_name( &mut self, id: &DatasetId, name: &str, ) -> Result<(), String>

Set name of a dataset with given id. The name must be valid name string.

pub fn set_dataset_name_by_str( &mut self, id: &str, name: &str, ) -> Result<(), String>

Set name of a dataset with given string id. The name must be valid name string.

pub fn set_dataset_annot( &mut self, id: &DatasetId, annot: &str, ) -> Result<(), String>

Set annotation of a dataset with given id.

pub fn set_dataset_annot_by_str( &mut self, id: &str, annot: &str, ) -> Result<(), String>

Set annotation of a dataset with given string id.

pub fn set_dataset_id( &mut self, original_id: &DatasetId, new_id: DatasetId, ) -> Result<(), String>

Set the id of dataset with original_id to new_id.

pub fn set_dataset_id_by_str( &mut self, original_id: &str, new_id: &str, ) -> Result<(), String>

Set the id of dataset with original_id to new_id.

pub fn set_var_id( &mut self, dataset_id: &DatasetId, original_id: &VarId, new_id: VarId, ) -> Result<(), String>

Set the id of a variable with original_id (in a given dataset) to new_id.

pub fn set_var_id_by_str( &mut self, dataset_id: &str, original_id: &str, new_id: &str, ) -> Result<(), String>

Set the id of a variable with original_id (in a given dataset) to new_id.

pub fn set_all_variables( &mut self, dataset_id: &DatasetId, new_variables_list: Vec<VarId>, ) -> Result<(), String>

Set the list of all variable IDs (in a given dataset), essentially renaming some/all of them. The length of the new list must be the same as existing one (only renaming, not adding/removing variables).

pub fn set_all_variables_by_str( &mut self, dataset_id: &str, new_variables_list: Vec<&str>, ) -> Result<(), String>

Set the list of all variable IDs (in a given dataset), essentially renaming some/all of them. The length of the new list must be the same as existing one (only renaming, not adding/removing variables).

pub fn remove_var( &mut self, dataset_id: &DatasetId, var_id: &VarId, ) -> Result<(), String>

Remove variable and all the values corresponding to it from a dataset (decrementing dimension of the dataset in process).

pub fn remove_var_by_str( &mut self, dataset_id: &str, id: &str, ) -> Result<(), String>

Remove variable and all the values corresponding to it from a dataset (decrementing dimension of the dataset in process).

pub fn add_var( &mut self, dataset_id: &DatasetId, var_id: VarId, ) -> Result<(), String>

Add variable column and fill all its values (in each existing observation) with *.

pub fn add_var_by_str( &mut self, dataset_id: &str, id: &str, ) -> Result<(), String>

Add variable column and fill all its values (in each existing observation) with *.

pub fn remove_dataset(&mut self, id: &DatasetId) -> Result<(), String>

Remove the dataset with given id from this manager. Returns Err in case the id is not a valid dataset’s identifier.

pub fn remove_dataset_by_str(&mut self, id: &str) -> Result<(), String>

Remove the dataset with given string id from this manager. Returns Err in case the id is not a valid dataset’s identifier.

impl ObservationManager

Observing the ObservationManager.

pub fn num_datasets(&self) -> usize

The number of datasets in this ObservationManager.

pub fn is_valid_dataset_id(&self, id: &DatasetId) -> bool

Check if there is a dataset with given Id.

pub fn get_dataset_id(&self, id: &str) -> Result<DatasetId, String>

Return a valid dataset’s DatasetId corresponding to the given str id.

Return Err if such dataset does not exist (and the ID is invalid).

pub fn get_dataset(&self, id: &DatasetId) -> Result<&Dataset, String>

Return a Dataset corresponding to a given DatasetId.

Return Err if such dataset does not exist (the ID is invalid in this context).

pub fn get_dataset_by_str(&self, id: &str) -> Result<&Dataset, String>

Return a Dataset corresponding to a given id given as string.

Return Err if such dataset does not exist (the ID is invalid in this context).

pub fn get_obs_id( &self, dataset_id: &str, obs_id: &str, ) -> Result<ObservationId, String>

Shorthand to get ObservationId from a specified dataset.

Return Err if such dataset does not exist (the ID is invalid in this context).

pub fn get_obs( &self, dataset_id: &DatasetId, obs_id: &ObservationId, ) -> Result<&Observation, String>

Shorthand to get Observation with a given id, from a specified dataset.

Return Err if such dataset does not exist (the ID is invalid in this context).

pub fn get_obs_by_str( &self, dataset_id: &str, obs_id: &str, ) -> Result<&Observation, String>

Shorthand to get Observation with a given string id, from a specified dataset.

Return Err if such dataset (or observation) does not exist (the ID is invalid in this context).

pub fn datasets(&self) -> DatasetIterator<'_>

Return an iterator over all datasets of this model.

fn assert_no_dataset(&self, id: &DatasetId) -> Result<(), String>

(internal) Utility method to ensure there is no dataset with given ID yet.

fn assert_valid_dataset(&self, id: &DatasetId) -> Result<(), String>

(internal) Utility method to ensure there is a dataset with given ID.

impl ObservationManager

Implementation for events related to modifying datasets.

pub(super) fn event_add_dataset( &mut self, event: &Event, ) -> Result<Consumed, DynError>

Perform event of adding a new dataset to this ObservationManager.

pub(super) fn event_add_default_dataset( &mut self, event: &Event, ) -> Result<Consumed, DynError>

Perform event of adding a new DEFAULT (empty) dataset to this ObservationsManager.

pub(super) fn event_load_dataset( &mut self, event: &Event, ) -> Result<Consumed, DynError>

Perform event of loading (and adding) new dataset to this ObservationManager.

pub(super) fn event_modify_dataset( &mut self, event: &Event, at_path: &[&str], dataset_id: DatasetId, ) -> Result<Consumed, DynError>

Perform event of modifying or removing existing dataset component of this ObservationManager.

Trait Implementations

impl Clone for ObservationManager

fn clone(&self) -> ObservationManager

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ObservationManager

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for ObservationManager

fn default() -> ObservationManager

Default manager instance with no datasets.

impl Manager for ObservationManager

fn generate_id<T>( &self, ideal_id: &str, is_taken: &dyn Fn(&Self, &T) -> bool, num_indices: usize, start_index: Option<usize>, ) -> T

where T: FromStr, <T as FromStr>::Err: Debug,

Generate an ID of type T for a certain component of a manager (e.g., generate a VariableId for a Variable in a ModelState).

fn assert_ids_unique_and_used<T>( &self, id_list: &Vec<&str>, assert_id_is_managed: &dyn Fn(&Self, &T) -> Result<(), String>, ) -> Result<(), String>

where T: Eq + Hash + Debug + FromStr, <T as FromStr>::Err: Debug,

Check that the list of (typesafe or string) IDs contains only unique IDs (no duplicates), and check that all of the IDs are already managed by the manager instance (this is important, for instance, when we need to change already existing elements).

fn assert_ids_unique_and_new<T>( &self, id_list: &Vec<&str>, assert_id_is_new: &dyn Fn(&Self, &T) -> Result<(), String>, ) -> Result<(), String>

where T: Eq + Hash + Debug + FromStr, <T as FromStr>::Err: Debug,

Check that the list of (typesafe or string) IDs contains only unique IDs (no duplicates), and check that all of the IDs are NOT yet managed by the manager instance, i.e., they are fresh new values (this is important, for instance, when we need to add several new elements).

impl PartialEq for ObservationManager

fn eq(&self, other: &ObservationManager) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl SessionHelper for ObservationManager

fn starts_with<'a, 'b>( prefix: &str, at_path: &'a [&'b str], ) -> Option<&'a [&'b str]>

A utility function which checks if at_path starts with a specific first segment. If yes, returns the remaining part of the path.

fn matches(expected: &[&str], at_path: &[&str]) -> bool

A utility function which checks if at_path is exactly

fn invalid_path_error_generic<T>(at_path: &[&str]) -> Result<T, DynError>

A utility function which emits a generic “invalid path” error.

fn invalid_path_error_specific<T>( path: &[&str], component: &str, ) -> Result<T, DynError>

A utility function which emits a “invalid path” error mentioning specific state’s component.

fn clone_payload_str(event: &Event, component: &str) -> Result<String, DynError>

A utility function to get and clone a payload of an event. Errors if payload is empty.

fn assert_path_length( path: &[&str], length: usize, component: &str, ) -> Result<(), DynError>

A utility function to assert that path has a given length, or emit a DynError otherwise.

fn assert_payload_empty(event: &Event, component: &str) -> Result<(), DynError>

A utility function to assert that payload is empty - otherwise, DynError is emitted.

impl SessionState for ObservationManager

fn perform_event( &mut self, event: &Event, at_path: &[&str], ) -> Result<Consumed, DynError>

Modify the session state using the provided event. The possible outcomes are described by Consumed.

fn refresh( &self, full_path: &[String], at_path: &[&str], ) -> Result<Event, DynError>

“Read” session state into an event without modifying it.

impl StructuralPartialEq for ObservationManager