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add logging with log struct into codelist-rs lib #100

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125 changes: 75 additions & 50 deletions rust/codelist-rs/src/codelist.rs
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Original file line number Diff line number Diff line change
@@ -1,20 +1,17 @@
//! This file contains the core functionality for the codelist

// External imports
use std::{
collections::{BTreeMap, HashSet},
io::Write,
str::FromStr,
};

use csv::Writer;
use serde::{Deserialize, Serialize};

// Internal imports
use crate::{
codelist_options::CodeListOptions, errors::CodeListError, metadata::Metadata,
types::CodeListType,
logging::{LogEntry, LogType},
};
use crate::logging::{AddType, CodelistLog, RemoveType, EditType};

/// Struct to represent a codelist
///
Expand All @@ -23,15 +20,15 @@ use crate::{
/// * `entries` - The set of code entries
/// * `codelist_type` - The type of codelist
/// * `metadata` - Metadata about the codelist
/// * `logs` - Logs of anything that happened during the codelist creation
/// * `log` - log of anything that happened during the codelist creation
/// * `codelist_options` - Options for the codelist
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
pub struct CodeList {
pub name: String,
pub entries: BTreeMap<String, (Option<String>, Option<String>)>,
pub codelist_type: CodeListType,
pub metadata: Metadata,
pub logs: Vec<String>, // We will want to make this a struct with more info at some point
pub log: CodelistLog,
pub codelist_options: CodeListOptions,
}

Expand All @@ -42,7 +39,7 @@ impl CodeList {
/// * `name` - The name of the codelist
/// * `codelist_type` - The type of codelist
/// * `metadata` - Metadata describing the codelist
/// * `logs` - Logs of anything that happened during the codelist creation
/// * `log` - log of anything that happened during the codelist creation
/// * `options` - Customisable options for the codelist
///
/// # Returns
Expand All @@ -58,7 +55,7 @@ impl CodeList {
entries: BTreeMap::new(),
codelist_type,
metadata,
logs: Vec::new(),
log: CodelistLog::default(),
codelist_options: options.unwrap_or_default(),
}
}
Expand Down Expand Up @@ -86,10 +83,18 @@ impl CodeList {
if code.is_empty() {
return Err(CodeListError::empty_code("Empty code supplied"));
}
self.entries.insert(code, (term, comment));

let log_msg = format!(
"Added entry with code: {code}, term: {:?}, comment: {:?}",
term, comment
);

self.entries.insert(code.clone(), (term, comment));
self.log.add_entry(LogEntry::new(LogType::Add(AddType::Code), log_msg));
Ok(())
}


/// Remove an entry from the codelist
///
/// # Arguments
Expand All @@ -101,6 +106,10 @@ impl CodeList {
pub fn remove_entry(&mut self, code: &str) -> Result<(), CodeListError> {
let removed = self.entries.remove(code);
if removed.is_some() {
self.log.add_entry(LogEntry::new(
LogType::Remove(RemoveType::Code),
format!("Removed entry with code: {code}"),
));
Ok(())
} else {
Err(CodeListError::entry_not_found(code))
Expand Down Expand Up @@ -141,7 +150,7 @@ impl CodeList {
///
/// # Errors
/// * `CodeListError::IOError` - If an error occurs when writing to the file
pub fn save_to_csv(&self, file_path: &str) -> std::result::Result<(), CodeListError> {
pub fn save_to_csv(&mut self, file_path: &str) -> Result<(), CodeListError> {
let mut wtr = Writer::from_path(file_path)?;
// use column names from options
wtr.write_record([
Expand All @@ -152,6 +161,10 @@ impl CodeList {
wtr.write_record([code, term.as_deref().unwrap_or("")])?;
}
wtr.flush()?;
self.log.add_entry(LogEntry::new(
LogType::Save,
format!("Saved codelist to CSV file: {file_path}"),
));
Ok(())
}

Expand All @@ -162,33 +175,38 @@ impl CodeList {
///
/// # Errors
/// * `CodeListError::IOError` - If an error occurs when writing to the file
pub fn save_to_json(&self, file_path: &str) -> Result<(), CodeListError> {
pub fn save_to_json(&mut self, file_path: &str) -> Result<(), CodeListError> {
let json = serde_json::to_string_pretty(self)?;
std::fs::write(file_path, json)?;
self.log.add_entry(LogEntry::new(
LogType::Save,
format!("Saved codelist to JSON file: {file_path}"),
));
Ok(())
}

/// Save the logs to a file
/// Save the log to a file
///
/// # Arguments
/// * `file_path` - The path to the file to save the logs to
/// * `file_path` - The path to the file to save the log to
///
/// # Errors
/// * `CodeListError::IOError` - If an error occurs when writing to the file
pub fn save_log(&self, file_path: &str) -> std::result::Result<(), CodeListError> {
let mut file = std::fs::File::create(file_path)?;
for log in &self.logs {
writeln!(file, "{log}")?;
}
Ok(())
pub fn save_log(&self, file_path: &str) -> Result<(), CodeListError> {
self.log.write_to_file(file_path).map_err(|e| {
CodeListError::IOError(e)
})
}

/// Add a log message to the codelist
///
/// # Arguments
/// * `message` - The message to add to the log
pub fn add_log(&mut self, message: String) {
self.logs.push(message);
self.log.add_entry(LogEntry::new(
LogType::Note,
message.clone(),
));
}

/// Get the metadata
Expand Down Expand Up @@ -220,7 +238,12 @@ impl CodeList {
"Please use update comment instead",
))
} else {
self.log.add_entry(LogEntry::new(
LogType::Add(AddType::Comment),
format!("Added comment to entry with code: {code}, comment: {comment}"),
));
*comment_opt = Some(comment);

Ok(())
}
}
Expand All @@ -244,7 +267,13 @@ impl CodeList {
match self.entries.get_mut(&code) {
Some((_, comment_opt)) => {
if comment_opt.is_some() {
// Move `comment` into a temporary variable so we can use it for both logging and assignment
let log_msg = format!(
"Updated comment for entry with code: {code}, comment: {:?}",
comment
);
*comment_opt = Some(comment);
self.log.add_entry(LogEntry::new(LogType::Edit(EditType::Comment), log_msg));
Ok(())
} else {
Err(CodeListError::code_entry_comment_does_not_exist(
Expand All @@ -257,6 +286,7 @@ impl CodeList {
}
}


/// Remove the comment from the code entry
///
/// # Arguments
Expand All @@ -273,6 +303,10 @@ impl CodeList {
Some((_, comment_opt)) => {
if comment_opt.is_some() {
*comment_opt = None;
self.log.add_entry(LogEntry::new(
LogType::Remove(RemoveType::Comment),
format!("Removed comment from entry with code: {code}"),
));
Ok(())
} else {
Err(CodeListError::code_entry_comment_does_not_exist(
Expand Down Expand Up @@ -545,7 +579,6 @@ mod tests {

assert_eq!(codelist.codelist_type(), &CodeListType::ICD10);
assert_eq!(codelist.entries.len(), 2);
assert_eq!(codelist.logs.len(), 0);
assert_eq!(&codelist.codelist_options, &CodeListOptions::default());

assert_eq!(codelist.metadata().provenance.source, Source::ManuallyCreated);
Expand Down Expand Up @@ -620,7 +653,7 @@ mod tests {

assert_eq!(codelist.codelist_type(), &CodeListType::ICD10);
assert_eq!(codelist.entries.len(), 0);
assert_eq!(codelist.logs.len(), 0);
assert_eq!(codelist.log.len(), 0);

Ok(())
}
Expand Down Expand Up @@ -746,7 +779,7 @@ mod tests {
let file_path_str = file_path
.to_str()
.ok_or(CodeListError::invalid_file_path("Path contains invalid Unicode characters"))?;
let codelist = create_test_codelist()?;
let mut codelist = create_test_codelist()?;
codelist.save_to_csv(file_path_str)?;
let content = std::fs::read_to_string(file_path_str)?;
let lines: Vec<&str> = content.lines().collect();
Expand All @@ -767,31 +800,26 @@ mod tests {
.to_str()
.ok_or(CodeListError::invalid_file_path("Path contains invalid Unicode characters"))?;

let original_codelist = create_test_codelist()?;
let mut original_codelist = create_test_codelist()?;
original_codelist.save_to_json(file_path_str)?;
let json_content = std::fs::read_to_string(file_path_str)?;
let loaded_codelist: CodeList = serde_json::from_str(&json_content)?;

assert_eq!(original_codelist, loaded_codelist);

Ok(())
}
assert_eq!(original_codelist.name, loaded_codelist.name);
assert_eq!(original_codelist.codelist_type, loaded_codelist.codelist_type);
assert_eq!(original_codelist.entries, loaded_codelist.entries);

#[test]
fn test_add_to_log() -> Result<(), CodeListError> {
let mut codelist = create_test_codelist()?;
codelist.add_log("Test log message".to_string());

assert_eq!(codelist.logs.len(), 1);
assert_eq!(codelist.logs[0], "Test log message".to_string());
// Note we are not testing log here because saving a log in of itself creates
// a new log entry, and since we are writing to a temporary file, the log will
// not match the original log and is not guessable.

Ok(())
}

#[test]
fn test_save_log() -> Result<(), CodeListError> {
let temp_dir = TempDir::new()?;
let file_path = temp_dir.path().join("test.log");
let file_path = temp_dir.path().join("test.txt");
let file_path_str = file_path
.to_str()
.ok_or(CodeListError::invalid_file_path("Path contains invalid Unicode characters"))?;
Expand All @@ -801,7 +829,10 @@ mod tests {
codelist.save_log(file_path_str)?;
let content = std::fs::read_to_string(file_path_str)?;

assert_eq!(content, "Test log message\n");
assert!(content.contains("Add(Code): Added entry with code: R65.2, term: None, comment: None"));
assert!(content.contains("Add(Code): Added entry with code: A48.51, term: Some(\"Infant botulism\"), comment: Some(\"test comment\")"));
assert!(content.contains("Note: Test log message"));


Ok(())
}
Expand Down Expand Up @@ -1020,7 +1051,7 @@ mod tests {

observed_codelist.truncate_to_3_digits(TermManagement::DropTerm)?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand Down Expand Up @@ -1053,7 +1084,7 @@ mod tests {

observed_codelist.truncate_to_3_digits(TermManagement::DropTerm)?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand Down Expand Up @@ -1081,7 +1112,7 @@ mod tests {

observed_codelist.truncate_to_3_digits(TermManagement::First)?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand Down Expand Up @@ -1114,7 +1145,7 @@ mod tests {

observed_codelist.truncate_to_3_digits(TermManagement::First)?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand All @@ -1134,22 +1165,16 @@ mod tests {
Some("Typhoid and paratyphoid fevers".to_string()),
None,
)?;

expected_codelist.add_entry("B0111".to_string(), Some("TB".to_string()), None)?;

let mut observed_codelist = expected_codelist.clone();

expected_codelist.add_entry("A10X".to_string(), Some("Cholera".to_string()), None)?;

expected_codelist.add_entry(
"B01X".to_string(),
Some("Typhoid and paratyphoid fevers".to_string()),
None,
)?;

observed_codelist.add_x_codes()?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand Down Expand Up @@ -1184,7 +1209,7 @@ mod tests {

observed_codelist.add_x_codes()?;

assert_eq!(observed_codelist, expected_codelist);
assert_eq!(observed_codelist.entries, expected_codelist.entries);

Ok(())
}
Expand Down
8 changes: 4 additions & 4 deletions rust/codelist-rs/src/codelist_factory.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -366,9 +366,9 @@ impl CodeListFactory {
pub fn save_codelists_to_json(
&self,
folder_path: &str,
codelists: Vec<CodeList>,
mut codelists: Vec<CodeList>,
) -> Result<(), CodeListError> {
for (index, codelist) in codelists.iter().enumerate() {
for (index, codelist) in codelists.iter_mut().enumerate() {
let filename = format!("{}.json", index + 1);
let full_path = std::path::Path::new(folder_path).join(filename);
let path_str = full_path.to_str().ok_or_else(|| {
Expand Down Expand Up @@ -396,9 +396,9 @@ impl CodeListFactory {
pub fn save_codelists_to_csv(
&self,
folder_path: &str,
codelists: Vec<CodeList>,
mut codelists: Vec<CodeList>,
) -> Result<(), CodeListError> {
for (index, codelist) in codelists.iter().enumerate() {
for (index, codelist) in codelists.iter_mut().enumerate() {
let filename = format!("{}.csv", index + 1);
let full_path = std::path::Path::new(folder_path).join(filename);
let path_str = full_path.to_str().ok_or_else(|| {
Expand Down
1 change: 1 addition & 0 deletions rust/codelist-rs/src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ pub mod codelist_options;
pub mod errors;
pub mod metadata;
pub mod types;
pub mod logging;
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