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Merge pull request #4 from pcvolkmer/issue_1

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feat: show schema versions and change extern detection
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Paul-Christian Volkmer 2024-06-13 16:22:41 +02:00 committed by GitHub
commit 7fc724db6a
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8 changed files with 218 additions and 36 deletions
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4
README.md
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@ -67,10 +67,14 @@ Dies eignet sich um nachträglich Zahlen zu einem bestimmten Datum zu ermitteln.
Der optionale Parameter `--include-extern` schließt Meldungen mit externer Diagnosestellung ein.
Diese sind normalerweise nicht enthalten.
Die Entscheidung, ob eine Meldung intern oder extern gemeldet wird, wird anhand der `Melder_ID` getroffen.
Enthält diese die Zeichenkette `9999` wird von einer externen Meldung ausgegangen.
Der optionale Parameter `--include-histo-zyto` schließt Meldungen mit Meldeanlass `histologhie_zytologie` ein.
Diese sind normalerweise ebenfalls nicht enthalten.
Mit dem optionalen Parameter `--schema-versions` werden die Angaben zudem noch oBDS-Schema-Version getrennt ausgegeben.
## Export aus der Onkostar-Datenbank
Die Anwendung ist in der Lage, mit dem Befehl `export` die Spalten

2
src/cli.rs
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@ -69,6 +69,8 @@ pub enum SubCommand {
help = "Meldungen mit Meldeanlass 'histologie_zytologie' einschließen"
)]
include_histo_zyto: bool,
#[arg(long, help = "Meldungen mit oBDS-Schema-version anzeigen")]
schema_versions: bool,
},
#[command(
about = "Erstellt eine (reduzierte) CSV-Datei zum direkten Vergleich mit der OPAL-CSV-Datei"

2
src/common.rs
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@ -23,6 +23,7 @@ use serde::{Deserialize, Serialize};
pub struct Icd10GroupSize {
pub name: String,
pub schema_version: Option<String>,
pub size: usize,
}
@ -68,6 +69,7 @@ impl Check {
.map(|(icd10, group)| (icd10, group.collect::<Vec<_>>()))
.map(|record| Icd10GroupSize {
name: record.0,
schema_version: None,
size: record.1.len(),
})
.collect::<Vec<_>>();

50
src/database.rs
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@ -24,7 +24,23 @@ use mysql::prelude::Queryable;
use mysql::{params, Pool};
use crate::common::{ExportData, Icd10GroupSize};
use crate::resources::{EXPORTED_TO_LKR, EXPORT_QUERY, SQL_QUERY};
use crate::resources::{EXPORTED_TO_LKR, EXPORT_QUERY, SQL_QUERY, SQL_QUERY_WITH_SCHEMA_VERSION};
fn result_mapper() -> fn((String, String, usize)) -> Icd10GroupSize {
|(icd10_group, _, count)| Icd10GroupSize {
name: icd10_group,
schema_version: None,
size: count,
}
}
fn result_mapper_with_schema_version() -> fn((String, String, usize)) -> Icd10GroupSize {
|(icd10_group, schema_version, count)| Icd10GroupSize {
name: icd10_group,
schema_version: Some(schema_version),
size: count,
}
}
pub struct DatabaseSource(String);
@ -41,25 +57,31 @@ impl DatabaseSource {
ignore_exports_since: &str,
include_extern: bool,
include_histo_zyto: bool,
schema_versions: bool,
) -> Result<Vec<Icd10GroupSize>, ()> {
let params = params! {
"year" => year,
"ignore_exports_since" => ignore_exports_since,
"include_extern" => if include_extern { 1 } else { 0 },
"include_histo_zyto" => if include_histo_zyto { 1 } else { 0 }
};
match Pool::new(self.0.as_str()) {
Ok(pool) => {
if let Ok(mut connection) = pool.try_get_conn(Duration::from_secs(3)) {
return match connection.exec_map(
SQL_QUERY,
params! {
"year" => year,
"ignore_exports_since" => ignore_exports_since,
"include_extern" => if include_extern { 1 } else { 0 },
"include_histo_zyto" => if include_histo_zyto { 1 } else { 0 }
return match schema_versions {
true => match connection.exec_map(
SQL_QUERY_WITH_SCHEMA_VERSION,
params,
result_mapper_with_schema_version(),
) {
Ok(result) => Ok(result),
Err(_) => Err(()),
},
|(icd10_group, count)| Icd10GroupSize {
name: icd10_group,
size: count,
false => match connection.exec_map(SQL_QUERY, params, result_mapper()) {
Ok(result) => Ok(result),
Err(_) => Err(()),
},
) {
Ok(result) => Ok(result),
Err(_) => Err(()),
};
}
}

24
src/main.rs
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@ -67,26 +67,34 @@ fn print_items(items: &[Icd10GroupSize]) {
.to_string(),
);
items.iter().for_each(|item| {
let _ = term.write_line(&format!("{:<20}={:>6}", item.name, item.size));
let _ = term.write_line(&format!(
"{:<20} {:<6} ={:>6}",
item.name,
item.schema_version.as_ref().unwrap_or(&String::new()),
item.size
));
});
let sum: usize = items
.iter()
.filter(|item| item.name != "Other")
.map(|item| item.size)
.sum();
let _ = term.write_line(&style("─".repeat(27)).dim().to_string());
let _ = term.write_line(&style("─".repeat(35)).dim().to_string());
let _ = term.write_line(
&style(format!("{:<20}={:>6}", "Summe (C**.*/D**.*)", sum))
.dim()
.to_string(),
&style(format!(
"{:<20} {:<6} ={:>6}",
"Summe (C**.*/D**.*)", "", sum
))
.dim()
.to_string(),
);
let sum: usize = items.iter().map(|item| item.size).sum();
let _ = term.write_line(
&style(format!("{:<20}={:>6}", "Gesamtsumme", sum))
&style(format!("{:<20} {:<6} ={:>6}", "Gesamtsumme", "", sum))
.dim()
.to_string(),
);
let _ = term.write_line(&style("─".repeat(27)).dim().to_string());
let _ = term.write_line(&style("─".repeat(35)).dim().to_string());
}
fn print_extern_notice(include_extern: bool) {
@ -123,6 +131,7 @@ fn main() -> Result<(), Box<dyn Error>> {
ignore_exports_since,
include_extern,
include_histo_zyto,
schema_versions,
} => {
let password = request_password_if_none(password);
let year = sanitize_year(year);
@ -141,6 +150,7 @@ fn main() -> Result<(), Box<dyn Error>> {
&ignore_exports_since.unwrap_or("9999-12-31".into()),
include_extern,
include_histo_zyto,
schema_versions,
)
.map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;

2
src/resources/mod.rs
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@ -20,6 +20,8 @@
pub const SQL_QUERY: &str = include_str!("query.sql");
pub const SQL_QUERY_WITH_SCHEMA_VERSION: &str = include_str!("query_with_schema_version.sql");
pub const EXPORT_QUERY: &str = include_str!("export.sql");
pub const EXPORTED_TO_LKR: &str = include_str!("exported-to-lkr.sql");

30
src/resources/query.sql
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@ -107,34 +107,34 @@ SELECT CASE
ELSE 'Other'
END AS ICD10_GROUP,
'' AS schema_version,
COUNT(*) as COUNT
FROM (
SELECT DISTINCT
lme.lkr_meldung,
EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID') AS pid,
EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') AS schema_version,
lme.versionsnummer,
SHA2(CONCAT('https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-condition-id|', EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID'), 'condition', EXTRACTVALUE(lme.xml_daten, '//Diagnose/@Tumor_ID')), 256) AS cond_id,
SUBSTRING_INDEX(EXTRACTVALUE(lm.xml_daten, '//Primaertumor_ICD_Code'), ' ', 1) AS condcodingcode,
SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lm.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) AS diagnosejahr
SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Primaertumor_ICD_Code'), ' ', 1) AS condcodingcode,
SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) AS diagnosejahr
FROM lkr_meldung_export lme
JOIN lkr_meldung lm ON (lm.id = lme.lkr_meldung AND lme.typ <> '-1' AND lm.extern <= :include_extern)
WHERE lme.xml_daten LIKE '%ICD_Version%'
AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lm.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
AND (lm.xml_daten LIKE '%<cTNM%' OR lm.xml_daten LIKE '%<pTNM%' OR lm.xml_daten LIKE '%<Menge_Histologie>%' OR lm.xml_daten LIKE '%<Menge_Weitere_Klassifikation>%')
AND (lm.xml_daten NOT LIKE '%histologie_zytologie%' OR 1 = :include_histo_zyto)
) o1
LEFT OUTER JOIN (
AND lme.typ <> -1
AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
AND (lme.xml_daten LIKE '%<cTNM%' OR lme.xml_daten LIKE '%<pTNM%' OR lme.xml_daten LIKE '%<Menge_Histologie>%' OR lme.xml_daten LIKE '%<Menge_Weitere_Klassifikation>%')
AND (lme.xml_daten NOT LIKE '%histologie_zytologie%' OR 1 = :include_histo_zyto)
AND (EXTRACTVALUE(lme.xml_daten, '//Meldende_Stelle') NOT LIKE '%9999%' OR 1 <= :include_extern)
) o1
LEFT OUTER JOIN (
SELECT DISTINCT
lme.lkr_meldung,
SHA2(CONCAT('https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-condition-id|', EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID'), 'condition', EXTRACTVALUE(lme.xml_daten, '//Diagnose/@Tumor_ID')), 256) AS cond_id,
CASE WHEN le.exportiert_am < :ignore_exports_since THEN MAX(versionsnummer) ELSE ~0 END AS max_version
CASE WHEN STR_TO_DATE(EXTRACTVALUE(lme.xml_daten, '//Meldedatum'), '%d.%c.%Y') < :ignore_exports_since THEN MAX(versionsnummer) ELSE ~0 END AS max_version
FROM lkr_meldung_export lme
JOIN lkr_export le ON (lme.lkr_export = le.id)
WHERE SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
GROUP BY cond_id ORDER BY cond_id
) o2
) o2
ON (o1.cond_id = o2.cond_id AND o1.versionsnummer < max_version)
WHERE diagnosejahr = :year AND o2.cond_id IS NULL
GROUP BY ICD10_GROUP;

140
src/resources/query_with_schema_version.sql Normal file
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@ -0,0 +1,140 @@
/*
* This file is part of bzkf-rwdp-check
*
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken and contributors.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
SELECT CASE
WHEN condcodingcode LIKE 'C00%'
OR condcodingcode LIKE 'C01%'
OR condcodingcode LIKE 'C02%'
OR condcodingcode LIKE 'C03%'
OR condcodingcode LIKE 'C04%'
OR condcodingcode LIKE 'C05%'
OR condcodingcode LIKE 'C06%'
OR condcodingcode LIKE 'C07%'
OR condcodingcode LIKE 'C08%'
OR condcodingcode LIKE 'C09%'
OR condcodingcode LIKE 'C10%'
OR condcodingcode LIKE 'C11%'
OR condcodingcode LIKE 'C12%'
OR condcodingcode LIKE 'C13%'
OR condcodingcode LIKE 'C14%' THEN 'C00-C14'
WHEN condcodingcode LIKE 'C15%' THEN 'C15'
WHEN condcodingcode LIKE 'C16%' THEN 'C16'
WHEN condcodingcode LIKE 'C18%'
OR condcodingcode LIKE 'C19%'
OR condcodingcode LIKE 'C20%'
OR condcodingcode LIKE 'C21%' THEN 'C18-C21'
WHEN condcodingcode LIKE 'C22%' THEN 'C22'
WHEN condcodingcode LIKE 'C23%'
OR condcodingcode LIKE 'C24%' THEN 'C23-C24'
WHEN condcodingcode LIKE 'C25%' THEN 'C25'
WHEN condcodingcode LIKE 'C32%' THEN 'C32'
WHEN condcodingcode LIKE 'C33%'
OR condcodingcode LIKE 'C34%' THEN 'C33-C34'
WHEN condcodingcode LIKE 'C43%' THEN 'C43'
WHEN condcodingcode LIKE 'C50%'
OR condcodingcode LIKE 'D05%' THEN 'C50, D05'
WHEN condcodingcode LIKE 'C53%'
OR condcodingcode LIKE 'D06%' THEN 'C53, D06'
WHEN condcodingcode LIKE 'C54%'
OR condcodingcode LIKE 'C55%' THEN 'C54-C55'
WHEN condcodingcode LIKE 'C56%'
OR condcodingcode = 'D39.1' THEN 'C56, D39.1'
WHEN condcodingcode LIKE 'C61%' THEN 'C61'
WHEN condcodingcode LIKE 'C62%' THEN 'C62'
WHEN condcodingcode LIKE 'C64%' THEN 'C64'
WHEN condcodingcode LIKE 'C67%'
OR condcodingcode = 'D09.0'
OR condcodingcode = 'D41.4' THEN 'C67, D09.0, D41.4'
WHEN condcodingcode LIKE 'C70%'
OR condcodingcode LIKE 'C71%'
OR condcodingcode LIKE 'C72%' THEN 'C70-C72'
WHEN condcodingcode LIKE 'C73%' THEN 'C73'
WHEN condcodingcode LIKE 'C81%' THEN 'C81'
WHEN condcodingcode LIKE 'C82%'
OR condcodingcode LIKE 'C83%'
OR condcodingcode LIKE 'C84%'
OR condcodingcode LIKE 'C85%'
OR condcodingcode LIKE 'C86%'
OR condcodingcode LIKE 'C87%'
OR condcodingcode LIKE 'C88%'
OR condcodingcode LIKE 'C96%' THEN 'C82-C88, C96'
WHEN condcodingcode LIKE 'C90%' THEN 'C90'
WHEN condcodingcode LIKE 'C91%'
OR condcodingcode LIKE 'C92%'
OR condcodingcode LIKE 'C93%'
OR condcodingcode LIKE 'C94%'
OR condcodingcode LIKE 'C95%' THEN 'C91-C95'
ELSE 'Other'
END AS ICD10_GROUP,
schema_version,
COUNT(*) as COUNT
FROM (
SELECT DISTINCT
lme.lkr_meldung,
EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID') AS pid,
EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') AS schema_version,
lme.versionsnummer,
SHA2(CONCAT('https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-condition-id|', EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID'), 'condition', EXTRACTVALUE(lme.xml_daten, '//Diagnose/@Tumor_ID')), 256) AS cond_id,
SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Primaertumor_ICD_Code'), ' ', 1) AS condcodingcode,
SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) AS diagnosejahr
FROM lkr_meldung_export lme
WHERE lme.xml_daten LIKE '%ICD_Version%'
AND lme.typ <> -1
AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
AND (lme.xml_daten LIKE '%<cTNM%' OR lme.xml_daten LIKE '%<pTNM%' OR lme.xml_daten LIKE '%<Menge_Histologie>%' OR lme.xml_daten LIKE '%<Menge_Weitere_Klassifikation>%')
AND (lme.xml_daten NOT LIKE '%histologie_zytologie%' OR 1 = :include_histo_zyto)
AND (EXTRACTVALUE(lme.xml_daten, '//Meldende_Stelle') NOT LIKE '%9999%' OR 1 <= :include_extern)
) o1
LEFT OUTER JOIN (
SELECT DISTINCT
lme.lkr_meldung,
SHA2(CONCAT('https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-condition-id|', EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID'), 'condition', EXTRACTVALUE(lme.xml_daten, '//Diagnose/@Tumor_ID')), 256) AS cond_id,
CASE WHEN STR_TO_DATE(EXTRACTVALUE(lme.xml_daten, '//Meldedatum'), '%d.%c.%Y') < :ignore_exports_since THEN MAX(versionsnummer) ELSE ~0 END AS max_version
FROM lkr_meldung_export lme
WHERE SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
GROUP BY cond_id ORDER BY cond_id
) o2
ON (o1.cond_id = o2.cond_id AND o1.versionsnummer < max_version)
WHERE diagnosejahr = :year AND o2.cond_id IS NULL
GROUP BY ICD10_GROUP, schema_version;