use crate::entities::protein::{Protein, ProteinSearchResult};
use crate::sources::uniprot::UniProtRecord;
pub fn from_uniprot_search_record(record: UniProtRecord) -> ProteinSearchResult {
let accession = record.primary_accession.clone();
ProteinSearchResult {
accession: accession.clone(),
uniprot_id: accession,
name: record.display_name(),
gene_symbol: record.primary_gene_symbol(),
species: record
.organism
.as_ref()
.and_then(|o| o.scientific_name.as_deref())
.map(str::trim)
.map(str::to_string)
.filter(|v| !v.is_empty()),
}
}
pub fn from_uniprot_record_base(record: UniProtRecord) -> Protein {
let accession = record.primary_accession.clone();
let entry_id = record.uni_prot_kb_id.clone();
let name = record.display_name();
let gene_symbol = record.primary_gene_symbol();
let organism = record
.organism
.as_ref()
.and_then(|o| o.scientific_name.as_deref())
.map(str::trim)
.map(str::to_string)
.filter(|v| !v.is_empty());
let length = record.sequence.as_ref().and_then(|s| s.length);
let function = record.function_summary();
Protein {
accession,
entry_id,
name,
gene_symbol,
organism,
length,
function,
structures: Vec::new(),
structure_count: None,
domains: Vec::new(),
interactions: Vec::new(),
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::sources::uniprot::{
UniProtComment, UniProtCrossReference, UniProtGene, UniProtNameContainer, UniProtOrganism,
UniProtProteinDescription, UniProtSequence, UniProtTextValue,
};
fn sample_record() -> UniProtRecord {
UniProtRecord {
primary_accession: "P15056".to_string(),
uni_prot_kb_id: Some("BRAF_HUMAN".to_string()),
protein_description: Some(UniProtProteinDescription {
recommended_name: Some(UniProtNameContainer {
full_name: Some(UniProtTextValue {
value: "Serine/threonine-protein kinase B-raf".to_string(),
}),
}),
submission_names: None,
}),
genes: vec![UniProtGene {
gene_name: Some(UniProtTextValue {
value: "BRAF".to_string(),
}),
}],
organism: Some(UniProtOrganism {
scientific_name: Some("Homo sapiens".to_string()),
}),
sequence: Some(UniProtSequence { length: Some(766) }),
comments: vec![UniProtComment {
comment_type: Some("FUNCTION".to_string()),
texts: vec![UniProtTextValue {
value: "Protein kinase involved in MAPK signaling.".to_string(),
}],
}],
uni_prot_kb_cross_references: vec![UniProtCrossReference {
database: Some("PDB".to_string()),
id: Some("6PP9".to_string()),
properties: Vec::new(),
}],
}
}
#[test]
fn from_uniprot_search_record_maps_fields() {
let out = from_uniprot_search_record(sample_record());
assert_eq!(out.accession, "P15056");
assert_eq!(out.uniprot_id, "P15056");
assert_eq!(out.name, "Serine/threonine-protein kinase B-raf");
assert_eq!(out.gene_symbol.as_deref(), Some("BRAF"));
assert_eq!(out.species.as_deref(), Some("Homo sapiens"));
}
#[test]
fn from_uniprot_record_base_maps_fields() {
let out = from_uniprot_record_base(sample_record());
assert_eq!(out.accession, "P15056");
assert_eq!(out.entry_id.as_deref(), Some("BRAF_HUMAN"));
assert_eq!(out.name, "Serine/threonine-protein kinase B-raf");
assert_eq!(out.gene_symbol.as_deref(), Some("BRAF"));
assert_eq!(out.organism.as_deref(), Some("Homo sapiens"));
assert_eq!(out.length, Some(766));
assert!(
out.function
.as_deref()
.is_some_and(|v| v.contains("MAPK signaling"))
);
assert!(out.domains.is_empty());
assert!(out.interactions.is_empty());
assert!(out.structures.is_empty());
}
#[test]
fn from_uniprot_search_record_handles_missing_organism() {
let mut record = sample_record();
record.organism = None;
let out = from_uniprot_search_record(record);
assert_eq!(out.species, None);
}
#[test]
fn from_uniprot_record_base_handles_missing_sequence() {
let mut record = sample_record();
record.sequence = None;
let out = from_uniprot_record_base(record);
assert_eq!(out.length, None);
}
#[test]
fn protein_sections_maps_egfr() {
let mut record = sample_record();
record.primary_accession = "P00533".to_string();
record.uni_prot_kb_id = Some("EGFR_HUMAN".to_string());
record.protein_description = Some(UniProtProteinDescription {
recommended_name: Some(UniProtNameContainer {
full_name: Some(UniProtTextValue {
value: "Epidermal growth factor receptor".to_string(),
}),
}),
submission_names: None,
});
record.genes = vec![UniProtGene {
gene_name: Some(UniProtTextValue {
value: "EGFR".to_string(),
}),
}];
let out = from_uniprot_record_base(record);
assert_eq!(out.accession, "P00533");
assert_eq!(out.gene_symbol.as_deref(), Some("EGFR"));
assert!(out.name.contains("growth factor receptor"));
}
#[test]
fn protein_sections_maps_tp53() {
let mut record = sample_record();
record.primary_accession = "P04637".to_string();
record.uni_prot_kb_id = Some("P53_HUMAN".to_string());
record.protein_description = Some(UniProtProteinDescription {
recommended_name: Some(UniProtNameContainer {
full_name: Some(UniProtTextValue {
value: "Cellular tumor antigen p53".to_string(),
}),
}),
submission_names: None,
});
record.genes = vec![UniProtGene {
gene_name: Some(UniProtTextValue {
value: "TP53".to_string(),
}),
}];
let out = from_uniprot_search_record(record);
assert_eq!(out.accession, "P04637");
assert_eq!(out.gene_symbol.as_deref(), Some("TP53"));
assert!(out.name.contains("p53"));
}
}
