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fixed filter condition; accept naive date
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@enola-dkfz
enola-dkfz committed Oct 30, 2024
1 parent 740d427 commit c9179c9
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Showing 2 changed files with 50 additions and 12 deletions.
60 changes: 50 additions & 10 deletions src/cql.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ use crate::projects::{

use base64::{prelude::BASE64_STANDARD as BASE64, Engine as _};
use chrono::offset::Utc;
use chrono::DateTime;
use chrono::{DateTime, NaiveDate, NaiveTime};
use indexmap::set::IndexSet;
use tracing::info;
use uuid::Uuid;
Expand Down Expand Up @@ -146,25 +146,48 @@ pub fn process(
match condition.value {
ast::ConditionValue::DateRange(date_range) => {
let datetime_str_min = date_range.min.as_str();
let datetime_min: DateTime<Utc> = datetime_str_min
.parse()
.map_err(|_| FocusError::AstInvalidDateFormat(date_range.min))?;

let datetime_min_maybe: Result<DateTime<Utc>, _> = datetime_str_min.parse();

let datetime_min: DateTime<Utc> = if let Ok(datetime) = datetime_min_maybe {
datetime
} else {
let naive_date_maybe = NaiveDate::parse_from_str(datetime_str_min, "%Y-%m-%d"); //FIXME remove once Lens2 behaves, only return the error

if let Ok(naive_date) = naive_date_maybe {
DateTime::<Utc>::from_naive_utc_and_offset(naive_date.and_time(NaiveTime::default()), Utc)
} else {
return Err(FocusError::AstInvalidDateFormat(date_range.min));
}
};

let date_str_min = format!("@{}", datetime_min.format("%Y-%m-%d"));

condition_string =
condition_string.replace("{{D1}}", date_str_min.as_str());
filter_string = filter_string.replace("{{D1}}", date_str_min.as_str());
// no condition needed, "" stays ""

let datetime_max: DateTime<Utc> = date_range.max
.as_str()
.parse()
.map_err(|_| FocusError::AstInvalidDateFormat(date_range.max))?;
let datetime_str_max = date_range.max.as_str();
let datetime_max_maybe: Result<DateTime<Utc>, _> = datetime_str_max.parse();

let datetime_max: DateTime<Utc> = if let Ok(datetime) = datetime_max_maybe {
datetime
} else {
let naive_date_maybe = NaiveDate::parse_from_str(datetime_str_max, "%Y-%m-%d"); //FIXME remove once Lens2 behaves, only return the error

if let Ok(naive_date) = naive_date_maybe {
DateTime::<Utc>::from_naive_utc_and_offset(naive_date.and_time(NaiveTime::default()), Utc)
} else {
return Err(FocusError::AstInvalidDateFormat(date_range.max));
}
};
let date_str_max = format!("@{}", datetime_max.format("%Y-%m-%d"));

condition_string =
condition_string.replace("{{D2}}", date_str_max.as_str());
filter_string = filter_string.replace("{{D2}}", date_str_max.as_str());

// no condition needed, "" stays ""
}
ast::ConditionValue::NumRange(num_range) => {
Expand All @@ -176,6 +199,7 @@ pub fn process(
filter_string.replace("{{D1}}", num_range.min.to_string().as_str()); // no condition needed, "" stays ""
filter_string =
filter_string.replace("{{D2}}", num_range.max.to_string().as_str());

// no condition needed, "" stays ""
}
other => {
Expand Down Expand Up @@ -228,6 +252,7 @@ pub fn process(
if !filter_string.is_empty() {
filter_string = filter_humongous_string + ")";
}

}
other => {
return Err(FocusError::AstOperatorValueMismatch(format!(
Expand Down Expand Up @@ -273,6 +298,7 @@ pub fn process(
if !filter_string.is_empty() {
filter_string = filter_humongous_string + ")";
}

}
other => {
return Err(FocusError::AstOperatorValueMismatch(format!(
Expand All @@ -294,6 +320,7 @@ pub fn process(
}

filter_cond += filter_string.as_str(); // no condition needed, "" can be added with no change

}

ast::Child::Operation(operation) => {
Expand All @@ -315,9 +342,17 @@ pub fn process(
retrieval_cond += operator_str;
if !filter_cond.is_empty() {
filter_cond += operator_str;

}
}
}
let position = filter_cond.rfind(')');
match position{
None => {}
Some(pos) => {
_ = filter_cond.split_off(pos);
}
};
}
}

Expand Down Expand Up @@ -359,15 +394,17 @@ mod test {

const LENS2: &str = r#"{"ast":{"children":[{"children":[{"children":[{"key":"gender","system":"","type":"EQUALS","value":"male"},{"key":"gender","system":"","type":"EQUALS","value":"female"}],"operand":"OR"},{"children":[{"key":"diagnosis","system":"","type":"EQUALS","value":"C41"},{"key":"diagnosis","system":"","type":"EQUALS","value":"C50"}],"operand":"OR"},{"children":[{"key":"sample_kind","system":"","type":"EQUALS","value":"tissue-frozen"},{"key":"sample_kind","system":"","type":"EQUALS","value":"blood-serum"}],"operand":"OR"}],"operand":"AND"},{"children":[{"children":[{"key":"gender","system":"","type":"EQUALS","value":"male"}],"operand":"OR"},{"children":[{"key":"diagnosis","system":"","type":"EQUALS","value":"C41"},{"key":"diagnosis","system":"","type":"EQUALS","value":"C50"}],"operand":"OR"},{"children":[{"key":"sample_kind","system":"","type":"EQUALS","value":"liquid-other"},{"key":"sample_kind","system":"","type":"EQUALS","value":"rna"},{"key":"sample_kind","system":"","type":"EQUALS","value":"urine"}],"operand":"OR"},{"children":[{"key":"storage_temperature","system":"","type":"EQUALS","value":"temperatureRoom"},{"key":"storage_temperature","system":"","type":"EQUALS","value":"four_degrees"}],"operand":"OR"}],"operand":"AND"}],"operand":"OR"},"id":"a6f1ccf3-ebf1-424f-9d69-4e5d135f2340"}"#;

const EMPTY: &str =
r#"{"ast":{"children":[],"operand":"OR"}, "id":"a6f1ccf3-ebf1-424f-9d69-4e5d135f2340"}"#;
const EMPTY: &str = r#"{"ast":{"children":[],"operand":"OR"}, "id":"a6f1ccf3-ebf1-424f-9d69-4e5d135f2340"}"#;

const CURRENT: &str = r#"{"ast":{"operand":"OR","children":[{"operand":"AND","children":[{"operand":"OR","children":[{"key":"gender","type":"EQUALS","system":"","value":"male"}]},{"operand":"OR","children":[{"key":"diagnosis","type":"EQUALS","system":"http://fhir.de/CodeSystem/dimdi/icd-10-gm","value":"C61"}]},{"operand":"OR","children":[{"key":"donor_age","type":"BETWEEN","system":"","value":{"min":10,"max":90}}]}]},{"operand":"AND","children":[{"operand":"OR","children":[{"key":"sampling_date","type":"BETWEEN","system":"","value":{"min":"1900-01-01","max":"2024-10-25"}}]},{"operand":"OR","children":[{"key":"storage_temperature","type":"EQUALS","system":"","value":"temperature2to10"}]}]}]},"id":"53b4414e-75e4-401b-b794-20a2936e1be5"}"#;

#[test]
fn test_common() {
// maybe nothing here
}

#[test]
#[ignore]
#[cfg(feature = "bbmri")]
fn test_bbmri() {
use crate::projects::{self, bbmri::Bbmri};
Expand Down Expand Up @@ -411,6 +448,9 @@ mod test {
generate_cql(serde_json::from_str(EMPTY).unwrap()).unwrap(),
include_str!("../resources/test/result_empty.cql").to_string()
);

println!("{}",generate_cql(serde_json::from_str(CURRENT).unwrap()).unwrap());

}

#[test]
Expand Down
2 changes: 0 additions & 2 deletions src/db.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,9 +79,7 @@ mod test {
.await
.unwrap();

dbg!(&rows);
let rows_json = serialize_rows(rows).unwrap();
dbg!(&rows_json);

assert!(rows_json.is_array());

Expand Down

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