Struct MSVocabulary 

pub struct MSVocabulary();

A global facade for interacting with the PSI-MS controlled vocabulary.

This requires the cv feature which uses the mzcv library to work with OBO files, runtime caching and embed static compile-time embedding of controlled vocabulary data.

This type is a singleton guarded by a OnceLock wrapping a mzcv::CVIndex that lets the caller fetch MSTerm entries by accession CURIE or name. It also lets the caller traverse the controlled vocabulary tree.

let term = MSVocabulary::get(curie!(MS:1000044)).unwrap();
assert_eq!(term.name.as_ref(), "dissociation method");
assert!(!MSVocabulary::children_of(term.accession()).expect("this term is defined!").is_empty());

Data Source

Alternatively, you can take a reference to the global instance with MSVocabulary::init, which first checks the on-disk cache and then uses the statically embedded copy of the controlled vocabulary if it isn’t available. Using MSVocabulary::init_static directly uses the fixed, pre-compiled version if it is the first call. Finally, you can choose to update the cached on-disk version using MSVocabulary::update_from_obo, see the method documentation for more details.

Implementations

impl MSVocabulary

pub fn version() -> &'static CVVersion

Get the version metadata of the vocabulary

pub fn update_from_obo<P>(obo_path: P) -> Result<(), Box<dyn Error>>

where P: AsRef<Path>,

Update the PSI-MS vocabulary to the version at the provided path. This will update the parsed cache on disk and attempt to set the global in-memory representation to use this version.

Warning

If the controlled vocabulary is already loaded, this will fail to update the current version in memory, but should still update the version on disk so that it will be read from when the a new process starts.

This does not update the compile time static version embedded in the binary used by Self::init_static. That can only be upgraded at build time.

pub fn init() -> &'static CVIndex<MSVocabulary>

Get or create the global instance of the mzcv::CVIndex for MSVocabulary

pub fn init_static() -> &'static CVIndex<MSVocabulary>

Get or create the global instance of the mzcv::CVIndex for MSVocabulary using only the statically embedded data.

pub fn get(curie: CURIE) -> Option<Arc<MSTerm>>

Get a term by its CURIE

pub fn get_by_name(name: &str) -> Option<Arc<MSTerm>>

Get a term by its human-readable name in a case-insensitive manner.

pub fn get_by_name_or_synonym(name: &str) -> Option<(bool, Arc<MSTerm>)>

Load a term by name or if that fails by synonym, names are matched in a case insensitive manner. Returns a boolean indicating if it matches a name true or a synonym false

pub fn parents_of(curie: CURIE) -> Option<HashSet<Compat<CURIE>>>

Get the immediate parents of this term

This follows the is_a OBO relationship.

pub fn parents_of_recursive(curie: CURIE) -> HashSet<Compat<CURIE>>

Get all parents of this term, recursively querying the graph

This follows the is_a OBO relationship.

pub fn children_of(curie: CURIE) -> Option<&'static [Compat<CURIE>]>

Get the immediate children of this term

This follows the is_a OBO relationship.

pub fn is_child_of(child: CURIE, parent: CURIE) -> bool

Test if child is derived from parent along a transitive is_a relationship

pub fn children_of_recursive(curie: CURIE) -> HashSet<Compat<CURIE>>

Get all children of this term, recursively querying the graph

This follows the is_a OBO relationship.

Trait Implementations

impl CVSource for MSVocabulary

type Data = MSTerm

The data item that is stored in the CV

type Structure = VocabularyData<MSTerm>

The type of the main data structure to keep all data items (used to build any kind of hierarchy necessary)

fn cv_name() -> &'static str

The name of the CV, used to create the paths to store intermediate files and caches so has to be valid in that context

fn files() -> &'static [CVFile]

The source files for the CV

fn static_data() -> Option<(CVVersion, <MSVocabulary as CVSource>::Structure)>

The static data of this CV

fn parse( reader: impl Iterator<Item = HashBufReader<Box<dyn Read>, impl Digest>>, ) -> Result<(CVVersion, <MSVocabulary as CVSource>::Structure, Vec<BoxedError<'static, CVError>>), Vec<BoxedError<'static, CVError>>>

Parse the textual representation of this CV. Return the version, the data, and possibly a list of warnings or noncritical errors encountered while parsing.

const AUTOMATICALLY_WRITE_UNCOMPRESSED: bool = false

Set this constant to true to enable automatic writing of the CV when the cache is updated

fn cv_label() -> &'static str

The label of the CV, the identifier that is used at the start of CURIEs. Defaults to the name.

fn default_stem() -> PathBuf

The default file stem (no extension).

fn write_uncompressed<W>( _writer: W, _version: &CVVersion, _data: impl Iterator<Item = Arc<Self::Data>>, ) -> Result<(), BoxedError<'static, CVError>>

where W: Write,

Write out the data to the standard file, only need to implement this if AUTOMATICALLY_WRITE_UNCOMPRESSED is set to true. This is used to write out data when the main way of interacting with this structure is via the crate::CVIndex::update method. So for custom modification CVs for example.

impl CVTraversal<MSVocabulary> for CVIndex<MSVocabulary>

fn child_map( &self, ) -> &HashMap<Compat<<MSTerm as CVData>::Index>, Vec<Compat<<MSTerm as CVData>::Index>>>

fn children_of( &self, curie: CURIE, ) -> Option<&[Compat<<<MSVocabulary as CVSource>::Data as CVData>::Index>]>

Get the immediate children of this term

fn parents_of( &self, curie: CURIE, ) -> Option<HashSet<Compat<<<MSVocabulary as CVSource>::Data as CVData>::Index>>>

Get the immediate parents of this term

fn get_by_index( &self, key: <<MSVocabulary as CVSource>::Data as CVData>::Index, ) -> Option<Arc<<MSVocabulary as CVSource>::Data>>

Helper method to mirror mzcv::CVIndex::get_by_index

fn parents_of_recursive( &self, curie: <<T as CVSource>::Data as CVData>::Index, ) -> HashSet<Compat<<<T as CVSource>::Data as CVData>::Index>>

Get all parents of this term, recursively querying the graph

fn children_of_recursive( &self, curie: <<T as CVSource>::Data as CVData>::Index, ) -> HashSet<Compat<<<T as CVSource>::Data as CVData>::Index>>

Get all children of this term, recursively querying the graph

fn is_child_of( &self, child: <<T as CVSource>::Data as CVData>::Index, parent: <<T as CVSource>::Data as CVData>::Index, ) -> bool

Test if child is derived from parent along a transitive is_a relationship

impl Debug for MSVocabulary

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

Formats the value using the given formatter.