ferritin_plms/esm/tokenization/
sequence_tokenizer.rs

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use crate::esm::utils::constants::esm3::SEQUENCE_VOCAB;
use anyhow::Result;
use std::collections::HashMap;
use std::sync::Arc;
use tokenizers::models::bpe::{BpeBuilder, BPE};
use tokenizers::processors::template::{Template, TemplateProcessing};
use tokenizers::processors::PostProcessorWrapper;
use tokenizers::{AddedToken, Tokenizer};

pub trait EsmTokenizerBase {
    fn encode(&self) -> Result<()>;
    fn decode(&self) -> Result<()>;
    fn mask_token(&self) -> &str;
    fn mask_token_id(&self) -> u32;
    fn bos_token(&self) -> &str;
    fn bos_token_id(&self) -> u32;
    fn eos_token(&self) -> &str;
    fn eos_token_id(&self) -> u32;
    fn pad_token(&self) -> &str;
    fn pad_token_id(&self) -> u32;
    fn chain_break_token(&self) -> &str;
    fn chain_break_token_id(&self) -> u32;
    fn all_token_ids(&self) -> Vec<u32>;
    fn special_token_ids(&self) -> Vec<u32>;
}

pub struct EsmSequenceTokenizer {
    tokenizer: Arc<Tokenizer>,
    cb_token: String,
}

impl EsmSequenceTokenizer {
    pub fn new(
        unk_token: &str,
        cls_token: &str,
        pad_token: &str,
        mask_token: &str,
        eos_token: &str,
        chain_break_token: &str,
    ) -> Result<Self> {
        let mut token_to_id = HashMap::new();
        for (i, tok) in SEQUENCE_VOCAB.iter().enumerate() {
            token_to_id.insert(tok.to_string(), i);
        }
        let bpe_builder = BpeBuilder::new();
        let bpe: BPE = bpe_builder
            .unk_token(unk_token.to_string())
            .build()
            .map_err(|e| anyhow::anyhow!("Failed to build BPE tokenizer: {}", e))?;

        let mut tokenizer = Tokenizer::new(bpe);
        let special_tokens = vec![
            AddedToken::from(cls_token, true),
            AddedToken::from(pad_token, true),
            AddedToken::from(mask_token, true),
            AddedToken::from(eos_token, true),
            AddedToken::from(chain_break_token, true),
        ];

        tokenizer.add_special_tokens(&special_tokens);

        let post_processor = TemplateProcessing::builder()
            .try_single(Template::try_from(format!("{} $A {}", cls_token, eos_token)).unwrap())?
            .special_tokens(vec![
                (cls_token, tokenizer.token_to_id(cls_token).unwrap()),
                (eos_token, tokenizer.token_to_id(eos_token).unwrap()),
            ])
            .build()?;

        tokenizer.with_post_processor(Some(PostProcessorWrapper::Template(post_processor)));

        Ok(Self {
            tokenizer: Arc::new(tokenizer),
            cb_token: chain_break_token.to_string(),
        })
    }
}
impl Default for EsmSequenceTokenizer {
    fn default() -> Self {
        Self::new("<unk>", "<cls>", "<pad>", "<mask>", "<eos>", "|")
            .expect("Failed to create default tokenizer")
    }
}

impl EsmTokenizerBase for EsmSequenceTokenizer {
    fn encode(&self) -> Result<()> {
        todo!()
    }

    fn decode(&self) -> Result<()> {
        todo!()
    }

    fn mask_token(&self) -> &str {
        "mask"
    }

    fn mask_token_id(&self) -> u32 {
        self.tokenizer.token_to_id("mask").unwrap_or(0)
    }

    fn bos_token(&self) -> &str {
        unimplemented!()
        // self.cls_token()
    }

    fn bos_token_id(&self) -> u32 {
        unimplemented!()
        // self.cls_token_id()
    }

    fn eos_token(&self) -> &str {
        "eos"
    }

    fn eos_token_id(&self) -> u32 {
        self.tokenizer.token_to_id("eos").unwrap_or(0)
    }

    fn pad_token(&self) -> &str {
        "pad"
    }

    fn pad_token_id(&self) -> u32 {
        self.tokenizer.token_to_id("pad").unwrap_or(0)
    }

    fn chain_break_token(&self) -> &str {
        &self.cb_token
    }

    fn chain_break_token_id(&self) -> u32 {
        self.tokenizer.token_to_id(&self.cb_token).unwrap_or(0)
    }

    fn all_token_ids(&self) -> Vec<u32> {
        unimplemented!()
        // (0..self.vocab_size()).collect()
    }

    fn special_token_ids(&self) -> Vec<u32> {
        unimplemented!()
        // self.tokenizer.get_special_token_ids()
    }
}