Problems with Serializing deserialized data

I have defined a struct to store data generated by the code. Since it takes a lot of time to generate it each time, I wanted it to be written out - used serde (1.0, derive feature enabled).

pub struct TrgWorld {
    pub atlas: Vec<(String, TrgLink)>

type TrgLink = Arc<Mutex<TrgNode>>;

#[derive(Debug, Serialize, Deserialize)]
pub struct TrgNode {
    pub seq: String,
    pub id_score: Vec<f32>,
    pub sim_score: Vec<Vec<f32>>,
    pub sim_seq: Vec<Vec<TrgLink>>,
    pub valid_trg: bool

I've enabled #[serde(skip)] on one of the fields which is by default non-SerDe, and unnecessary once I've generated the data once.

Once the necessary operations are complete, I collect the TrgNode struct into vector for export.

       let out = trgmap.atlas.into_iter().map(|(_, node)| 
                    Arc::try_unwrap(node).expect("Strong counts not released.")
                                  .into_inner().expect("Could not lock")

I then use serde_json (v1.0.73) to Deserialize the struct into json, and write the string to a file.

            let outdump = serde_json::to_string(&out).unwrap();
            let output_printer = io::BufWriter::new(File::create(format!("{}/{}_exported_files.json", outdir, outname))
                    .expect("Could not prepare output summary file"));
            serde_json::to_writer(output_printer, &outdump).unwrap();

I also need another piece of information - lineages: Vec<String> to be exported along with this.

            let outdump = serde_json::to_string(&lineages).unwrap();
            let output_printer = io::BufWriter::new(File::create(format!("{}/{}_exported_lineages.json", outdir, outname))
                     .expect("Could not prepare output summary file"));
            serde_json::to_writer(output_printer, &outdump).unwrap();

Both of these are exported without any issue, but it fails to Serialized when I try the following

        // Serialize a Vec<String>
        let mut temp_str = String::new();
        let mut file = std::fs::File::open(&path_to_lineages).unwrap();
        file.read_to_string(&mut temp_str).unwrap();
        let lineages: Vec<String> = serde_json::from_str(&temp_str).unwrap();

        // Serialize Vec<TrgNode>
        let mut file = std::fs::File::open(&path_to_import).unwrap();
        file.read_to_string(&mut tmp_str).unwrap();
        let out: Vec<TrgNode> = serde_json::from_str(&temp_str).unwrap();

Where I get the following error:

thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: 
Error("invalid type: string \"[\\\"denv_0\\\",\\\"denv_1\\\",\\\"denv_2\\\",\\\"denv_3\\\",\\\"denv_4\\\"]\",
 expected a sequence", line: 1, column: 58)', src/

Even when I uncomment the Vec<String> serialization part, I get a similar error with the Vec<TrgNode> part. I'm not sure where I am going wrong here, please help me out.

Thanks in advance! Let me know if you need any more information from my side.

You are unnecessarily wrapping the values in two levels of JSON. First, you call serde_json::to_string(), and then you call serde_json::to_writer() on that already-JSON-serialized string. Remove one of them.

1 Like

Thanks a ton! I removed serde_json::to_string(); it works perfectly! I poured over so many threads on serde, but I didn't get this obvious issue.

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