biolib 1.3.301

BioLib client library and CLI for running applications on BioLib
Documentation 
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use super::utils::IndexableBuffer;

pub struct StreamSeeker<'a> {
    upstream_buffer: &'a dyn IndexableBuffer,
    files_data_end: u64,
    max_chunk_size: u64,
    buffer_start: u64,
    buffer: Vec<u8>,
}

impl<'a> StreamSeeker<'a> {
    pub fn new(
        upstream_buffer: &'a dyn IndexableBuffer,
        files_data_start: u64,
        files_data_end: u64,
        max_chunk_size: u64,
    ) -> Self {
        Self {
            upstream_buffer,
            files_data_end,
            max_chunk_size,
            buffer_start: files_data_start,
            buffer: Vec::new(),
        }
    }

    pub fn seek_and_write<W: std::io::Write>(
        &mut self,
        file_start: u64,
        file_length: u64,
        read_ahead_bytes: u64,
        writer: &mut W,
    ) -> crate::Result<()> {
        assert!(file_start >= self.buffer_start);
        let skip = (file_start - self.buffer_start) as usize;
        self.buffer = self.buffer[skip..].to_vec();
        self.buffer_start = file_start;

        loop {
            let file_byte_count_remaining =
                file_length as i64 - (self.buffer_start - file_start) as i64;
            if file_byte_count_remaining <= 0 {
                return Ok(());
            }
            let file_byte_count_remaining = file_byte_count_remaining as u64;

            if !self.buffer.is_empty() {
                let take = std::cmp::min(file_byte_count_remaining as usize, self.buffer.len());
                writer.write_all(&self.buffer[..take])?;
                self.buffer = self.buffer[take..].to_vec();
                self.buffer_start += take as u64;
            } else {
                let start_of_fetch = self.buffer_start + self.buffer.len() as u64;
                let bytes_left_in_stream = self.files_data_end as i64 - start_of_fetch as i64;
                if bytes_left_in_stream <= 0 {
                    crate::logging::error(&format!(
                        "StreamSeeker: no bytes left upstream (start_of_fetch={}, files_data_end={})",
                        start_of_fetch, self.files_data_end
                    ));
                    return Ok(());
                }
                let bytes_left_in_stream = bytes_left_in_stream as u64;

                let mut fetch_size = std::cmp::min(
                    self.max_chunk_size,
                    file_byte_count_remaining + read_ahead_bytes,
                );
                if fetch_size > bytes_left_in_stream {
                    crate::logging::error(&format!(
                        "StreamSeeker: fetch_size ({}) > bytes_left_in_stream ({}); clamping",
                        fetch_size, bytes_left_in_stream
                    ));
                    fetch_size = bytes_left_in_stream;
                }

                let fetched_data = self.upstream_buffer.get_data(start_of_fetch, fetch_size)?;
                self.buffer.extend_from_slice(&fetched_data);
            }
        }
    }
}