nu_plugin_dcm 0.1.2

use std::io::{Cursor, Seek, SeekFrom};

use crate::meta::make_row_from_dicom_metadata;

use dicom::object::StandardDataDictionary;
use dicom::object::{self as dicom_object, DefaultDicomObject};
use indexmap::IndexMap;
use nu_errors::ShellError;
use nu_plugin::Plugin;
use nu_protocol::{
    CallInfo, ColumnPath, Primitive, ReturnSuccess, ReturnValue, Signature, SyntaxShape,
    UntaggedValue, Value,
};
use nu_value_ext::get_data_by_column_path;

use crate::dcm;

#[derive(Default)]
pub struct DcmPlugin {
    pub dcm_dictionary: StandardDataDictionary,
    pub source_column: Option<ColumnPath>,
    pub silent_errors: bool,
}

impl Plugin for DcmPlugin {
    fn config(&mut self) -> Result<Signature, ShellError> {
        Ok(Signature::build("dcm")
            .desc("Parse Dicom object from file or binary data. Invalid Dicom objects are reported as errors and excluded from the output.")
            .switch(
                "silent-errors",
                "For each input row generate an output row. If Dicom cannot be read, empty row is output. This makes sure that the number of input and output rows is identical. Useful for merging tables.",
                Some('s')
            )
            .optional(
                "column",
                SyntaxShape::ColumnPath,
                "Optional column name to use as Dicom source",
            )
            .filter())
    }

    fn begin_filter(&mut self, call_info: CallInfo) -> Result<Vec<ReturnValue>, ShellError> {
        // nu makes sure the num of args and type is correct
        if let Some(column) = call_info.args.nth(0) {
            if let UntaggedValue::Primitive(Primitive::ColumnPath(column)) = &column.value {
                self.source_column = Some(column.clone());
            }
        }

        if let Some(index_map) = call_info.args.named {
            self.silent_errors =
                index_map.contains_key("silent-errors") || index_map.contains_key("s");
        }

        Ok(vec![])
    }

    fn filter(&mut self, value: Value) -> Result<Vec<ReturnValue>, ShellError> {
        let result = self.run_filter(&value);

        match (self.silent_errors, &result) {
            (_, Ok(_)) | (false, Err(_)) => result,
            // found an error and we should silence it
            (true, Err(_shell_error)) => {
                let value = Value::new(UntaggedValue::nothing(), value.tag);
                Ok(vec![Ok(ReturnSuccess::Value(value))])
            }
        }
    }
}

impl DcmPlugin {
    fn run_filter(&mut self, value: &Value) -> Result<Vec<ReturnValue>, ShellError> {
        let tag = value.tag();

        // use source column if known
        if let Some(source_column) = &self.source_column {
            // FIXME error handling
            let value = get_data_by_column_path(value, source_column, |_v, _p, e| e)?;

            match &value.value {
                UntaggedValue::Primitive(_) => self.process_value(tag, &value),
                UntaggedValue::Table(ref t) => {
                    let mut result = Vec::with_capacity(t.len());

                    for e in t {
                        result.extend(self.process_value(tag.clone(), e)?);
                    }

                    Ok(result)
                }
                UntaggedValue::Row(_) => todo!("get_data_by_column_path row branch"),
                UntaggedValue::Block(_) => todo!("get_data_by_column_path block branch"),
                UntaggedValue::Error(e) => Err(e.clone()),
            }
        } else {
            // expect a primitive value if column is not known
            self.process_value(tag, value)
        }
    }

    fn process_value(
        &self,
        tag: nu_source::Tag,
        value: &Value,
    ) -> Result<Vec<ReturnValue>, ShellError> {
        match &value.value {
            UntaggedValue::Primitive(Primitive::FilePath(path)) => {
                let obj = dicom_object::open_file(path).map_err(|e| {
                    ShellError::labeled_error(
                        format!("{} [file {}]", e, path.to_string_lossy()),
                        "'dcm' expects a valid Dicom file",
                        tag.span,
                    )
                })?;

                self.process_dicom_object(tag, obj)
            }
            UntaggedValue::Primitive(Primitive::String(path_as_string)) => {
                let obj = dicom_object::open_file(path_as_string).map_err(|e| {
                    ShellError::labeled_error(
                        format!("{} [file {}]", e, path_as_string),
                        "'dcm' expects a valid Dicom file",
                        tag.span,
                    )
                })?;

                self.process_dicom_object(tag, obj)
            }
            UntaggedValue::Primitive(Primitive::Binary(data)) => {
                let mut cursor = Cursor::new(data);

                // FIXME don't assume the preamble
                cursor
                    .seek(SeekFrom::Start(128))
                    .ok()
                    .filter(|new_pos| *new_pos == 128) // Unexpectedly this is true even for binaries < 128 bytes long
                    .ok_or_else(|| {
                        ShellError::labeled_error(
                            "Cannot read Dicom preamble",
                            "'dcm' expects valid Dicom binary data",
                            tag.span,
                        )
                    })?;

                let obj = dicom_object::from_reader(cursor).map_err(|e| {
                    ShellError::labeled_error(
                        e.to_string(),
                        "'dcm' expects valid Dicom binary data",
                        tag.span,
                    )
                })?;

                self.process_dicom_object(tag, obj)
            }
            _ => Err(ShellError::labeled_error(
                "Unrecognized type in stream",
                "'dcm' expects a filepath, binary, string or a column path",
                tag.span,
            )),
        }
    }

    fn process_dicom_object(
        &self,
        tag: nu_source::Tag,
        obj: DefaultDicomObject,
    ) -> Result<Vec<ReturnValue>, ShellError> {
        let dcm_dumper = dcm::DicomDump {
            dcm_dictionary: &self.dcm_dictionary,
        };

        // dump both metadata and data into a single table
        let mut index_map = IndexMap::with_capacity(1000);
        make_row_from_dicom_metadata(&mut index_map, obj.meta());
        dcm_dumper.make_row_from_dicom_object(&mut index_map, &obj);

        let value = Value::new(UntaggedValue::Row(index_map.into()), tag);
        Ok(vec![Ok(ReturnSuccess::Value(value))])
    }
}