.github/workflows/release.yml

@@ -1,46 +0,0 @@
-name: Create release and upload assets
-
-on:
-  push:
-    tags:
-      - 'v*'
-
-jobs:
-  linuxbuild:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
-    steps:
-      - uses: actions/checkout@v4
-      - name: Run tests
-        run: cargo test --verbose
-      - run: make linux-package
-      - name: Release
-        uses: softprops/action-gh-release@v2
-        if: startsWith(github.ref, 'refs/tags/')
-        with:
-          draft: 'true'
-          make_latest: 'true'
-          generate_release_notes: 'true'
-          files: |
-            *linux.tar.gz
-  windowsbuild:
-    runs-on: windows-latest
-    defaults:
-      run:
-        shell: bash
-    steps:
-      - uses: actions/checkout@v4
-      - name: Run tests
-        run: cargo test --verbose
-      - run: make win-package
-      - name: Release
-        uses: softprops/action-gh-release@v2
-        if: startsWith(github.ref, 'refs/tags/')
-        with:
-          draft: 'true'
-          make_latest: 'true'
-          generate_release_notes: 'true'
-          files: |
-            *win64.zip

.github/workflows/test.yml

@@ -1,22 +0,0 @@
-name: "Run Tests"
-
-on:
-  push:
-    branches: [ "master" ]
-  pull_request:
-    branches: [ "master" ]
-
-env:
-  CARGO_TERM_COLOR: always
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Build
-        run: cargo build --verbose
-      - name: Run tests
-        run: cargo test --verbose

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bzkf-rwdp-check"
-version = "0.4.0"
+version = "0.2.0"
 edition = "2021"
 authors = ["Paul-Christian Volkmer <volkmer_p@ukw.de>"]
 description = "Anwendung zur Durchführung einer Plausibilitätsprüfung anhand der Daten für die BZKF Real World Data Platform."
@@ -11,11 +11,11 @@ clap = { version = "4.5", features = ["std", "help", "usage", "derive", "error-c
 console = "0.15"
 csv = "1.3"
 dialoguer = "0.11"
-itertools = "0.14"
+itertools = "0.12"
-mysql = "25.0"
+mysql = "24.0"
 serde = { version = "1.0", features = ["derive"] }
 urlencoding = "2.1"
-regex = "1.11"
+regex = "1.10"
 
 [profile.release]
 opt-level = "s"

Makefile

@@ -16,8 +16,7 @@ win-package: win-binary-x86_64
 	cp target/x86_64-pc-windows-gnu/release/$(PROG_NAME).exe $(PROG_NAME)/
 	cp README.md $(PROG_NAME)/
 	cp LICENSE $(PROG_NAME)/
-	# first try (linux) zip command, then powershell sub command to create ZIP file
+	zip $(PROG_NAME)-$(TAG)_win64.zip $(PROG_NAME)/*
-	zip $(PROG_NAME)-$(TAG)_win64.zip $(PROG_NAME)/* || powershell Compress-ARCHIVE $(PROG_NAME) $(PROG_NAME)-$(TAG)_win64.zip
 	rm -rf $(PROG_NAME) || true
 
 .PHONY: linux-package

README.md

@@ -2,9 +2,6 @@
 
 Anwendung zur Durchführung einer Plausibilitätsprüfung anhand der Daten für die BZKF Real World Data Platform.
 
-**Hinweis:** Dies ist eine Weiterführung des ursprünglichen
-Projekts [bzkf-rwdp-check](https://github.com/CCC-MF/bzkf-rwdp-check)
-
 ## Aufbau der ETL-Strecke an den Standorten
 
 Die Daten werden aus der Onkostar-Datenbank ausgelesen und in Apache-Kafka eingespeist.
@@ -25,9 +22,6 @@ flowchart LR
 Die Anwendung gibt für die möglichen Quellen der Kennzahlen die Anzahl der _Conditions_, gruppiert nach ICD-10 Gruppen,
 aus.
 
-Unterstützt wird eien OPAL-CSV-Datei (wie für BZKF vorgesehen) und eine Onkostar-Datenbank, basierend auf MariaDB oder
-MySQL.
-
 ![Ausgabe](docs/screenshot.png)
 
 ## Kennzahlen aus der CSV-Datei
@@ -43,8 +37,8 @@ Die Anwendung gibt nun eine Liste der ICD-10-Gruppen mit Anzahl der _Conditions_
 
 ## Kennzahlen aus der Onkostar-Datenbank
 
-Die Anzahl der _Conditions_, gruppiert nach ICD-10-Gruppe, kann auch mit dem Befehl `database` aus der
+Die Anzahl der _Conditions_, gruppiert nach ICD-10-Gruppe, kann auch mit dem Befehl `database` aus der Onkostar-Datenbank
-Onkostar-Datenbank abgerufen werden.
+abgerufen werden.
 
 ```
 bzkf-rwdp-check database --user me --year 2024
@@ -68,16 +62,6 @@ Der zusätzliche Parameter `--ignore-exports-since` ist optional.
 Wird er angegeben, werden keine Einträge mit Exportdatum ab diesem Datum verwendet.
 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
@@ -89,32 +73,18 @@ Die Anwendung ist in der Lage, mit dem Befehl `export` die Spalten
 
 in eine CSV-Datei zum Abgleich mit der OPAL-CSV-Datei zu exportieren.
 
-Hierbei gelten die gleichen Datenbank-Parameter wie
+Hierbei gelten die gleichen Datenbank-Parameter wie unter [Kennzahlen aus der Onkostar-Datenbank](#kennzahlen-aus-der-onkostar-datenbank),
-unter [Kennzahlen aus der Onkostar-Datenbank](#kennzahlen-aus-der-onkostar-datenbank), zusätzlich gibt es noch die
+zusätzlich gibt es noch die folgenden Parameter:
-folgenden Parameter:
 
 ```
 Options:
       --pat-id               Export mit Klartext-Patienten-ID
   -o, --output <OUTPUT>      Ausgabedatei
-      --xls-csv              Export mit Trennzeichen ';' für Excel
 ```
 
 ## Vergleich CSV-Datei für OPAL und Onkostar-Datenbank
 
 Die Anwendung kann auch die Conditions in der CSV-Datei mit der Onkostar-Datenbank direkt vergleichen.
 
-Hierzu kann der Befehl `compare` genutzt werden. Dieser verwendet alle Optionen für die Datenbank und die
+Hierzu kann der Befehl `compare` genutzt werden. Dieser verwendet alle Optionen für die Datenbank und die Option `--file`
-Option `--file` für die CSV-Datei und gibt eine Übersicht auf der Konsole aus.
+für die CSV-Datei und gibt eine Übersicht auf der Konsole aus.
-
-## Vergleich der XML-basierten LKR-Export-Protokolldatei mit der Datenbank
-
-Mithilfe dieser Anwendung kann auch der aktuelle Inhalt der Datenbank gegen die LKR-Export-Protokolldatei für einen
-Export verglichen werden.
-
-Der Befehl `check-export` kann zusammen mit der Angabe der Protokolldatei (`--file`) und der Angabe des
-Exports (`--package=...` bzw. `--export-package=...`) und den Optionen für den Datenbankzugriff ausgeführt werden.
-
-Zur Überprüfung werden irrelevante Leerzeichen und Zeilenumbrüche entfernt und _Self-Closed-Tags_ ersetzt
-(`<Meldeanlass />` => `<Meldeanlass></Meldeanlass>`),
-da in Onkostar in der Datenbank und der LKR-Export-Protokolldatei verschiedene Formatierungen verwendet werden (können).

src/cli.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -20,7 +20,6 @@
 
 use clap::{Parser, Subcommand};
 use regex::Regex;
-use std::path::PathBuf;
 
 #[derive(Parser)]
 #[command(author, version, about)]
@@ -35,7 +34,7 @@ pub enum SubCommand {
     #[command(about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL")]
     OpalFile {
         #[arg(short, long, help = "CSV-File für Opal")]
-        file: PathBuf,
+        file: String,
     },
     #[command(about = "Ermittelt die Prüfwerte aus der Onkostar-Datenbank")]
     Database {
@@ -62,17 +61,6 @@ pub enum SubCommand {
         year: String,
         #[arg(long, value_parser = value_is_date, help = "Ignoriere LKR-Exporte seit Datum")]
         ignore_exports_since: Option<String>,
-        #[arg(long, help = "Ignoriere Meldungen, die nicht im oBDS 2.x Format sind")]
-        ignore_non_obds_2: bool,
-        #[arg(long, help = "Meldungen mit externer Diagnose einschließen")]
-        include_extern: bool,
-        #[arg(
-            long,
-            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"
@@ -100,22 +88,11 @@ pub enum SubCommand {
         #[arg(short = 'u', long, help = "Benutzername")]
         user: String,
         #[arg(short = 'o', long, help = "Ausgabedatei")]
-        output: PathBuf,
+        output: String,
         #[arg(short = 'y', long, help = "Jahr der Diagnose")]
         year: String,
         #[arg(long, value_parser = value_is_date, help = "Ignoriere LKR-Exporte seit Datum")]
         ignore_exports_since: Option<String>,
-        #[arg(long, help = "Ignoriere Meldungen, die nicht im oBDS 2.x Format sind")]
-        ignore_non_obds_2: bool,
-        #[arg(long, help = "Export mit Trennzeichen ';' für Excel")]
-        xls_csv: bool,
-        #[arg(long, help = "Meldungen mit externer Diagnose einschließen")]
-        include_extern: bool,
-        #[arg(
-            long,
-            help = "Meldungen mit Meldeanlass 'histologie_zytologie' einschließen"
-        )]
-        include_histo_zyto: bool,
     },
     #[command(about = "Abgleich zwischen CSV-Datei für OPAL und Onkostar-Datenbank")]
     Compare {
@@ -141,51 +118,11 @@ pub enum SubCommand {
         #[arg(short = 'u', long, help = "Benutzername")]
         user: String,
         #[arg(short, long, help = "CSV-File für Opal")]
-        file: PathBuf,
+        file: String,
         #[arg(short = 'y', long, help = "Jahr der Diagnose")]
         year: String,
         #[arg(long, value_parser = value_is_date, help = "Ignoriere LKR-Exporte seit Datum")]
         ignore_exports_since: Option<String>,
-        #[arg(long, help = "Ignoriere Meldungen, die nicht im oBDS 2.x Format sind")]
-        ignore_non_obds_2: bool,
-        #[arg(long, help = "Meldungen mit externer Diagnose einschließen")]
-        include_extern: bool,
-        #[arg(
-            long,
-            help = "Meldungen mit Meldeanlass 'histologie_zytologie' einschließen"
-        )]
-        include_histo_zyto: bool,
-    },
-    #[command(about = "Abgleich zwischen LKR-Export-Protokoll und Onkostar-Datenbank")]
-    CheckExport {
-        #[arg(short = 'D', long, help = "Datenbank-Name", default_value = "onkostar")]
-        database: String,
-        #[arg(
-            short = 'h',
-            long,
-            help = "Datenbank-Host",
-            default_value = "localhost"
-        )]
-        host: String,
-        #[arg(short = 'P', long, help = "Datenbank-Host", default_value = "3306")]
-        port: u16,
-        #[arg(
-            short = 'p',
-            long,
-            help = "Passwort. Wenn nicht angegeben, wird danach gefragt"
-        )]
-        password: Option<String>,
-        #[arg(short = 'u', long, help = "Benutzername")]
-        user: String,
-        #[arg(short, long, help = "LKR-Export-Protokoll-Datei")]
-        file: PathBuf,
-        #[arg(
-            long,
-            alias = "export-package",
-            help = "Exportpaketnummer",
-            default_value = "0"
-        )]
-        package: u16,
     },
 }
 

src/common.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -23,7 +23,6 @@ use serde::{Deserialize, Serialize};
 
 pub struct Icd10GroupSize {
     pub name: String,
-    pub schema_version: Option<String>,
     pub size: usize,
 }
 
@@ -64,12 +63,11 @@ impl Check {
                 icd10_code: Self::map_icd_code(&record.icd10_code),
             })
             .sorted_by_key(|record| record.icd10_code.to_string())
-            .chunk_by(|record| record.icd10_code.to_string())
+            .group_by(|record| record.icd10_code.to_string())
             .into_iter()
             .map(|(icd10, group)| (icd10, group.collect::<Vec<_>>()))
             .map(|record| Icd10GroupSize {
                 name: record.0,
-                schema_version: None,
                 size: record.1.len(),
             })
             .collect::<Vec<_>>();
@@ -118,15 +116,3 @@ impl Check {
         .to_string()
     }
 }
-
-#[cfg(test)]
-mod tests {
-    use crate::common::Check;
-
-    #[test]
-    fn should_map_icd10_code_as_expected() {
-        assert_eq!(Check::map_icd_code("D39.1"), "C56, D39.1");
-        assert_eq!(Check::map_icd_code("C00"), "C00-C14");
-        assert_eq!(Check::map_icd_code("F79.9"), "Other");
-    }
-}

src/database.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -18,29 +18,12 @@
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
 
-use std::time::Duration;
-
 use mysql::prelude::Queryable;
 use mysql::{params, Pool};
+use std::time::Duration;
 
 use crate::common::{ExportData, Icd10GroupSize};
-use crate::resources::{EXPORTED_TO_LKR, EXPORT_QUERY, SQL_QUERY, SQL_QUERY_WITH_SCHEMA_VERSION};
+use crate::resources::{EXPORT_QUERY, SQL_QUERY};
-
-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);
 
@@ -51,39 +34,20 @@ impl DatabaseSource {
         DatabaseSource(url)
     }
 
-    pub fn check(
+    pub fn check(&self, year: &str, ignore_exports_since: &str) -> Result<Vec<Icd10GroupSize>, ()> {
-        &self,
-        year: &str,
-        ignore_exports_since: &str,
-        ignore_non_obds_2: bool,
-        include_extern: bool,
-        include_histo_zyto: bool,
-        schema_versions: bool,
-    ) -> Result<Vec<Icd10GroupSize>, ()> {
-        let params = params! {
-            "year" => year,
-            "ignore_exports_since" => ignore_exports_since,
-            "ignore_non_obds_2" => if ignore_non_obds_2 { 1 } else { 0 },
-            "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 schema_versions {
+                    return match connection.exec_map(
-                        true => match connection.exec_map(
+                        SQL_QUERY,
-                            SQL_QUERY_WITH_SCHEMA_VERSION,
+                        params! {"year" => year, "ignore_exports_since" => ignore_exports_since},
-                            params,
+                        |(icd10_group, count)| Icd10GroupSize {
-                            result_mapper_with_schema_version(),
+                            name: icd10_group,
-                        ) {
+                            size: count,
-                            Ok(result) => Ok(result),
-                            Err(_) => Err(()),
-                        },
-                        false => match connection.exec_map(SQL_QUERY, params, result_mapper()) {
-                            Ok(result) => Ok(result),
-                            Err(_) => Err(()),
                         },
+                    ) {
+                        Ok(result) => Ok(result),
+                        Err(_) => Err(()),
                     };
                 }
             }
@@ -99,23 +63,14 @@ impl DatabaseSource {
         &self,
         year: &str,
         ignore_exports_since: &str,
-        ignore_non_obds_2: bool,
         use_pat_id: bool,
-        include_extern: bool,
-        include_histo_zyto: bool,
     ) -> Result<Vec<ExportData>, ()> {
         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(
                         EXPORT_QUERY,
-                        params! {
+                        params! {"year" => year, "ignore_exports_since" => ignore_exports_since},
-                            "year" => year,
-                            "ignore_exports_since" => ignore_exports_since,
-                            "ignore_non_obds_2" => if ignore_non_obds_2 { 1 } else { 0 },
-                            "include_extern" => if include_extern { 1 } else { 0 },
-                            "include_histo_zyto" => if include_histo_zyto { 1 } else { 0 }
-                        },
                         |(condition_id, icd_10_code, diagnosis_date, pat_id)| ExportData {
                             condition_id,
                             icd_10_code,
@@ -137,30 +92,4 @@ impl DatabaseSource {
 
         Err(())
     }
-
-    pub fn exported(&self, package: u16) -> Result<Vec<(String, String)>, ()> {
-        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(
-                        EXPORTED_TO_LKR,
-                        params! {
-                            "export_id" => package,
-                        },
-                        |(id, xml_data)| (id, xml_data),
-                    ) {
-                        Ok(result) => Ok(result),
-                        Err(_) => {
-                            return Err(());
-                        }
-                    };
-                }
-            }
-            Err(_) => {
-                return Err(());
-            }
-        }
-
-        Err(())
-    }
 }

src/lkrexport.rs

@@ -1,270 +0,0 @@
-/*
- * This file is part of bzkf-rwdp-check
- *
- * Copyright (C) 2024 the original author or authors.
- *
- * 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.
- */
-
-use std::fs;
-use std::path::Path;
-use std::str::FromStr;
-
-use itertools::Itertools;
-use regex::Regex;
-
-pub struct LkrExportProtocolFile {
-    pub patients: Vec<Patient>,
-}
-
-impl LkrExportProtocolFile {
-    pub fn parse_file(path: &Path) -> Result<LkrExportProtocolFile, ()> {
-        let xml_file_content = fs::read_to_string(path).map_err(|_| ())?;
-        Self::parse(&xml_file_content)
-    }
-
-    pub fn parse(content: &str) -> Result<LkrExportProtocolFile, ()> {
-        let re = Regex::new(r"(?s)(?<patient><Patient>(.*?)</Patient>)").unwrap();
-
-        if re.is_match(content) {
-            let patients = re
-                .find_iter(content)
-                .map(|m| Patient {
-                    raw_value: m.as_str().to_string(),
-                })
-                .collect_vec();
-            return Ok(LkrExportProtocolFile { patients });
-        }
-
-        Err(())
-    }
-
-    pub fn meldungen(&self) -> Vec<Meldung> {
-        self.patients
-            .iter()
-            .flat_map(|patient| patient.meldungen())
-            .collect_vec()
-    }
-}
-
-pub struct Patient {
-    pub raw_value: String,
-}
-
-impl Patient {
-    pub fn meldungen(&self) -> Vec<Meldung> {
-        let re = Regex::new(r"(?s)(?<meldung><Meldung(.*?)</Meldung>)").unwrap();
-
-        if re.is_match(&self.raw_value) {
-            return re
-                .find_iter(&self.raw_value)
-                .map(|m| Meldung {
-                    raw_value: m.as_str().to_string(),
-                })
-                .collect_vec();
-        }
-        vec![]
-    }
-}
-
-pub struct Meldung {
-    pub raw_value: String,
-}
-
-impl FromStr for Meldung {
-    type Err = ();
-
-    fn from_str(s: &str) -> Result<Self, Self::Err> {
-        Ok(Meldung {
-            raw_value: s.to_string(),
-        })
-    }
-}
-
-#[allow(unused)]
-impl Meldung {
-    pub fn id(&self) -> Option<String> {
-        let re = Regex::new(r#"Meldung_ID="(?<meldung_id>(.*?))""#).unwrap();
-
-        if re.is_match(&self.raw_value) {
-            let caps = re.captures(&self.raw_value).unwrap();
-            return Some(caps["meldung_id"].to_string());
-        }
-
-        None
-    }
-
-    pub fn icd10(&self) -> Option<String> {
-        let re = Regex::new(r"(?s)<Primaertumor_ICD_Code>(?<icd10>(.*?))</Primaertumor_ICD_Code>")
-            .unwrap();
-
-        if re.is_match(&self.raw_value) {
-            let caps = re.captures(&self.raw_value).unwrap();
-            return Some(caps["icd10"].to_string());
-        }
-
-        None
-    }
-
-    pub fn database_id(&self) -> Option<String> {
-        match self.id() {
-            Some(id) => to_database_id(&id),
-            _ => None,
-        }
-    }
-
-    pub fn sanitized_xml_string(&self) -> String {
-        let re = Regex::new(r"[\r|\n]+\s*").unwrap();
-        let content = re.replace_all(&self.raw_value, "").trim().to_string();
-
-        let re = Regex::new(r"<[^>]+/>").unwrap();
-        if re.is_match(&content) {
-            let mut c = content.to_string();
-            re.find_iter(&content)
-                .map(|m| m.as_str().to_string().replace('<', "").replace("/>", ""))
-                .for_each(|tag| {
-                    c = c.replace(&format!("<{}/>", tag), &format!("<{}></{}>", tag, tag));
-                });
-            return c;
-        }
-
-        content
-    }
-}
-
-pub fn to_database_id(id: &str) -> Option<String> {
-    let re1 = Regex::new(r"^(?<id>[0-9A-F]+)").unwrap();
-    let re2 = Regex::new(r"(?<id>[0-9]+)$").unwrap();
-
-    if re1.is_match(id) {
-        match re1.find(id).map(|m| m.as_str().to_string()) {
-            Some(val) => match u64::from_str_radix(&val, 16) {
-                Ok(val) => Some(val.to_string()),
-                _ => None,
-            },
-            _ => None,
-        }
-    } else if re2.is_match(id) {
-        re2.find(id).map(|m| m.as_str().to_string())
-    } else {
-        None
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use crate::lkrexport::{LkrExportProtocolFile, Meldung};
-
-    #[test]
-    fn should_read_xml_file_content() {
-        let actual = LkrExportProtocolFile::parse(include_str!("../testdaten/testdaten_1.xml"));
-
-        assert!(actual.is_ok());
-        assert_eq!(actual.unwrap().patients.len(), 2);
-    }
-
-    #[test]
-    fn should_get_meldungen() {
-        let actual = LkrExportProtocolFile::parse(include_str!("../testdaten/testdaten_1.xml"));
-
-        assert!(actual.is_ok());
-
-        let patients = actual.unwrap().patients;
-
-        assert_eq!(patients[0].meldungen().len(), 1);
-        assert_eq!(patients[1].meldungen().len(), 1);
-    }
-
-    #[test]
-    fn should_get_meldung_id() {
-        let actual = LkrExportProtocolFile::parse(include_str!("../testdaten/testdaten_1.xml"));
-
-        assert!(actual.is_ok());
-
-        let patients = actual.unwrap().patients;
-
-        assert_eq!(
-            patients[0].meldungen()[0].id(),
-            Some("TEST1727528".to_string())
-        );
-        assert_eq!(
-            patients[1].meldungen()[0].id(),
-            Some("001A5D50-TEST".to_string())
-        );
-    }
-
-    #[test]
-    fn should_get_meldung_database_id() {
-        let actual = LkrExportProtocolFile::parse(include_str!("../testdaten/testdaten_1.xml"));
-
-        assert!(actual.is_ok());
-
-        let patients = actual.unwrap().patients;
-
-        assert_eq!(
-            patients[0].meldungen()[0].database_id(),
-            Some("1727528".to_string())
-        );
-        assert_eq!(
-            patients[1].meldungen()[0].database_id(),
-            Some("1727824".to_string())
-        );
-    }
-
-    #[test]
-    fn should_get_meldung_icd10() {
-        let actual = LkrExportProtocolFile::parse(include_str!("../testdaten/testdaten_1.xml"));
-
-        assert!(actual.is_ok());
-
-        let patients = actual.unwrap().patients;
-
-        assert_eq!(
-            patients[0].meldungen()[0].icd10(),
-            Some("C17.1".to_string())
-        );
-        assert_eq!(
-            patients[1].meldungen()[0].icd10(),
-            Some("C17.2".to_string())
-        );
-    }
-
-    #[test]
-    fn should_get_meldung_with_trimmed_margin() {
-        let meldung = Meldung {
-            raw_value: "  <Test>\n  <Test2>TestInhalt 3</Test2>\n</Test>\n".into(),
-        };
-
-        assert_eq!(
-            meldung.sanitized_xml_string(),
-            "<Test><Test2>TestInhalt 3</Test2></Test>".to_string()
-        );
-    }
-
-    #[test]
-    fn should_get_meldung_without_self_closing_tags() {
-        let meldung = Meldung {
-            raw_value:
-                "  <Test>\n  <Test2/>\n  <Content>Test</Content>\n  <Test3/>\n  <Test2/>\n</Test>\n"
-                    .into(),
-        };
-
-        assert_eq!(
-            meldung.sanitized_xml_string(),
-            "<Test><Test2></Test2><Content>Test</Content><Test3></Test3><Test2></Test2></Test>"
-                .to_string()
-        );
-    }
-}

src/main.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -18,23 +18,21 @@
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
 
-use std::collections::HashMap;
 use std::error::Error;
+use std::path::Path;
 
 use clap::Parser;
 use console::{style, Term};
-use csv::WriterBuilder;
+use csv::Writer;
 use itertools::Itertools;
 
 use crate::cli::{Cli, SubCommand};
 use crate::common::{Check, DiffRecord, Icd10GroupSize};
 use crate::database::DatabaseSource;
-use crate::lkrexport::{to_database_id, LkrExportProtocolFile, Meldung};
 
 mod cli;
 mod common;
 mod database;
-mod lkrexport;
 mod opal;
 mod resources;
 
@@ -51,9 +49,9 @@ fn request_password_if_none(password: Option<String>) -> String {
     }
 }
 
-fn sanitize_year(year: &str) -> String {
+fn sanitize_year(year: String) -> String {
     if year.len() == 4 {
-        year.to_string()
+        year
     } else {
         format!("2{:0>3}", year)
     }
@@ -67,48 +65,26 @@ fn print_items(items: &[Icd10GroupSize]) {
             .to_string(),
     );
     items.iter().for_each(|item| {
-        let _ = term.write_line(&format!(
+        let _ = term.write_line(&format!("{:<20}={:>6}", item.name, item.size));
-            "{:<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(35)).dim().to_string());
+    let _ = term.write_line(&style("─".repeat(27)).dim().to_string());
     let _ = term.write_line(
-        &style(format!(
+        &style(format!("{:<20}={:>6}", "Summe (C**.*/D**.*)", sum))
-            "{:<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} ={:>6}", "Gesamtsumme", "", sum))
             .dim()
             .to_string(),
     );
-    let _ = term.write_line(&style("─".repeat(35)).dim().to_string());
+    let sum: usize = items.iter().map(|item| item.size).sum();
-}
+    let _ = term.write_line(
-
+        &style(format!("{:<20}={:>6}", "Gesamtsumme", sum))
-fn print_extern_notice(include_extern: bool) {
+            .dim()
-    let _ = Term::stdout().write_line(
+            .to_string(),
-        format!(
-            "{} Die Datenbankanfrage schließt Meldungen mit externer Diagnose {}.",
-            style("Hinweis:").bold().underlined(),
-            match include_extern {
-                true => style("ein").yellow(),
-                false => style("nicht ein (Standard)").green(),
-            }
-        )
-        .as_str(),
     );
+    let _ = term.write_line(&style("─".repeat(27)).dim().to_string());
 }
 
 fn main() -> Result<(), Box<dyn Error>> {
@@ -116,8 +92,8 @@ fn main() -> Result<(), Box<dyn Error>> {
 
     match Cli::parse().cmd {
         SubCommand::OpalFile { file } => {
-            let items =
+            let items = opal::OpalCsvFile::check(Path::new(&file))
-                opal::OpalCsvFile::check(file.as_path()).map_err(|_e| "Kann Datei nicht lesen")?;
+                .map_err(|_e| "Kann Datei nicht lesen")?;
 
             print_items(&items);
         }
@@ -129,36 +105,23 @@ fn main() -> Result<(), Box<dyn Error>> {
             user,
             year,
             ignore_exports_since,
-            ignore_non_obds_2,
-            include_extern,
-            include_histo_zyto,
-            schema_versions,
         } => {
             let password = request_password_if_none(password);
-            let year = sanitize_year(&year);
+            let year = sanitize_year(year);
 
             let _ = term.write_line(
                 &style(format!("Warte auf Daten für das Diagnosejahr {}...", year))
                     .blue()
-                    .bright()
                     .to_string(),
             );
 
             let db = DatabaseSource::new(&database, &host, &password, port, &user);
             let items = db
-                .check(
+                .check(&year, &ignore_exports_since.unwrap_or("9999-12-31".into()))
-                    &year,
-                    &ignore_exports_since.unwrap_or("9999-12-31".into()),
-                    ignore_non_obds_2,
-                    include_extern,
-                    include_histo_zyto,
-                    schema_versions,
-                )
                 .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
 
             let _ = term.clear_last_lines(1);
 
-            print_extern_notice(include_extern);
             print_items(&items);
         }
         SubCommand::Export {
@@ -171,18 +134,13 @@ fn main() -> Result<(), Box<dyn Error>> {
             output,
             year,
             ignore_exports_since,
-            ignore_non_obds_2,
-            xls_csv,
-            include_extern,
-            include_histo_zyto,
         } => {
             let password = request_password_if_none(password);
-            let year = sanitize_year(&year);
+            let year = sanitize_year(year);
 
             let _ = term.write_line(
                 &style(format!("Warte auf Daten für das Diagnosejahr {}...", year))
                     .blue()
-                    .bright()
                     .to_string(),
             );
 
@@ -191,23 +149,13 @@ fn main() -> Result<(), Box<dyn Error>> {
                 .export(
                     &year,
                     &ignore_exports_since.unwrap_or("9999-12-31".into()),
-                    ignore_non_obds_2,
                     pat_id,
-                    include_extern,
-                    include_histo_zyto,
                 )
                 .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
 
             let _ = term.clear_last_lines(1);
 
-            let writer_builder = &mut WriterBuilder::new();
+            let mut writer = Writer::from_path(Path::new(&output)).expect("writeable file");
-            let mut writer_builder = writer_builder.has_headers(true);
-            if xls_csv {
-                writer_builder = writer_builder.delimiter(b';');
-            }
-            let mut writer = writer_builder
-                .from_path(output.as_path())
-                .expect("writeable file");
 
             items
                 .iter()
@@ -218,13 +166,11 @@ fn main() -> Result<(), Box<dyn Error>> {
                     "{} Conditions für das Jahr {} in Datei '{}' exportiert",
                     items.len(),
                     year,
-                    output.to_str().unwrap_or_default()
+                    output
                 ))
                 .green()
                 .to_string(),
             );
-
-            print_extern_notice(include_extern);
         }
         SubCommand::Compare {
             pat_id,
@@ -236,17 +182,13 @@ fn main() -> Result<(), Box<dyn Error>> {
             file,
             year,
             ignore_exports_since,
-            ignore_non_obds_2,
-            include_extern,
-            include_histo_zyto,
         } => {
             let password = request_password_if_none(password);
-            let year = sanitize_year(&year);
+            let year = sanitize_year(year);
 
             let _ = term.write_line(
                 &style(format!("Warte auf Daten für das Diagnosejahr {}...", year))
                     .blue()
-                    .bright()
                     .to_string(),
             );
 
@@ -255,21 +197,18 @@ fn main() -> Result<(), Box<dyn Error>> {
                 .export(
                     &year,
                     &ignore_exports_since.unwrap_or("9999-12-31".into()),
-                    ignore_non_obds_2,
                     pat_id,
-                    include_extern,
-                    include_histo_zyto,
                 )
                 .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
 
             let _ = term.clear_last_lines(1);
 
-            let csv_items =
+            let csv_items = opal::OpalCsvFile::export(Path::new(&file))
-                opal::OpalCsvFile::export(file.as_path()).map_err(|_e| "Kann Datei nicht lesen")?;
+                .map_err(|_e| "Kann Datei nicht lesen")?;
 
             let mut not_in_csv = db_items
                 .iter()
-                .filter(|&db_item| {
+                .filter(|db_item| {
                     !csv_items
                         .iter()
                         .map(|csv_item| &csv_item.condition_id)
@@ -277,14 +216,12 @@ fn main() -> Result<(), Box<dyn Error>> {
                 })
                 .collect::<Vec<_>>();
 
-            print_extern_notice(include_extern);
-
             let _ = term.write_line(
                 &style(format!(
                     "{} Conditions aus der Datenbank für das Jahr {} - aber nicht in Datei '{}'",
                     not_in_csv.len(),
                     year,
-                    file.to_str().unwrap_or_default()
+                    file
                 ))
                 .green()
                 .to_string(),
@@ -299,7 +236,7 @@ fn main() -> Result<(), Box<dyn Error>> {
 
             not_in_csv
                 .iter()
-                .for_each(|&item| match Check::is_relevant(&item.icd_10_code) {
+                .for_each(|item| match Check::is_relevant(&item.icd_10_code) {
                     true => {
                         let _ = term.write_line(&format!(
                             "{:<64}   {:<10}   {:<5}   {:<5}   {}",
@@ -330,7 +267,7 @@ fn main() -> Result<(), Box<dyn Error>> {
 
             let mut not_in_db = csv_items
                 .iter()
-                .filter(|&csv_item| {
+                .filter(|csv_item| {
                     !db_items
                         .iter()
                         .map(|db_item| &db_item.condition_id)
@@ -342,7 +279,7 @@ fn main() -> Result<(), Box<dyn Error>> {
                 &style(format!(
                     "{} Conditions aus Datei '{}' - aber nicht in der Datenbank für das Jahr {}",
                     not_in_db.len(),
-                    file.to_str().unwrap_or_default(),
+                    file,
                     year
                 ))
                 .green()
@@ -443,185 +380,6 @@ fn main() -> Result<(), Box<dyn Error>> {
                 ));
             });
         }
-        SubCommand::CheckExport {
-            database,
-            host,
-            password,
-            port,
-            user,
-            file,
-            package,
-        } => {
-            let password = request_password_if_none(password);
-
-            let _ = term.write_line(
-                &style(format!(
-                    "Warte auf Daten für den LKR-Export '{}'...",
-                    package
-                ))
-                .blue()
-                .bright()
-                .to_string(),
-            );
-
-            let db = DatabaseSource::new(&database, &host, &password, port, &user);
-
-            let db_entries = db
-                .exported(package)
-                .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
-
-            let db_meldungen = db_entries
-                .iter()
-                .map(|entry| LkrExportProtocolFile::parse(&entry.1))
-                .filter(|entry| entry.is_ok())
-                .flat_map(|entry| entry.unwrap().meldungen())
-                .filter(|meldung| meldung.id().is_some())
-                .map(|meldung| (meldung.id().unwrap(), meldung))
-                .collect::<HashMap<_, _>>();
-
-            let xml_meldungen = LkrExportProtocolFile::parse_file(file.as_path())
-                .map_err(|_e| "Fehler bei Zugriff auf die Protokolldatei")?
-                .meldungen()
-                .into_iter()
-                .filter(|meldung| meldung.id().is_some())
-                .map(|meldung| (meldung.id().unwrap(), meldung))
-                .collect::<HashMap<_, _>>();
-
-            let missing_xml_ids = db_meldungen
-                .keys()
-                .filter(|&key| !xml_meldungen.contains_key(key))
-                .collect_vec();
-
-            let _ = term.clear_last_lines(1);
-
-            let _ = term.write_line(
-                &style(format!(
-                    "{} Datenbankeinträge mit {} Meldungen abgerufen",
-                    db_entries.len(),
-                    db_meldungen.len()
-                ))
-                .green()
-                .to_string(),
-            );
-
-            fn print_missing_ids(missing_ids: &[&String], term: &Term) {
-                missing_ids.iter().sorted().for_each(|&item| {
-                    let _ = term.write_line(&format!(
-                        "{} ({})",
-                        item,
-                        to_database_id(item).unwrap_or("?".into())
-                    ));
-                });
-            }
-
-            if db_meldungen.len() != xml_meldungen.len() {
-                let _ = term.write_line(
-                    &style("\nNicht übereinstimmende Anzahl an Meldungen:")
-                        .yellow()
-                        .to_string(),
-                );
-                let _ = term.write_line(&format!(
-                    "Datenbank:      {:>10}\nProtokolldatei: {:>10}",
-                    db_meldungen.len(),
-                    xml_meldungen.len()
-                ));
-
-                let missing_db_ids = xml_meldungen
-                    .keys()
-                    .filter(|&key| !db_meldungen.contains_key(key))
-                    .collect_vec();
-
-                if !missing_db_ids.is_empty() {
-                    let _ = term.write_line(
-                        &style("\nIn der Datenbank fehlende Meldungen:")
-                            .yellow()
-                            .to_string(),
-                    );
-
-                    print_missing_ids(&missing_db_ids, &term);
-                }
-
-                if !missing_xml_ids.is_empty() {
-                    let _ = term.write_line(
-                        &style("\nIn der Protokolldatei fehlende Meldungen:")
-                            .yellow()
-                            .to_string(),
-                    );
-
-                    print_missing_ids(&missing_xml_ids, &term);
-                }
-            }
-
-            let multiple_meldung_entries = db_entries
-                .iter()
-                .map(|(lkr_meldung, meldung)| (lkr_meldung, LkrExportProtocolFile::parse(meldung)))
-                .filter_map(|(lkr_meldung, meldung)| {
-                    if meldung.unwrap().meldungen().len() > 1 {
-                        Some(lkr_meldung)
-                    } else {
-                        None
-                    }
-                })
-                .sorted()
-                .collect_vec();
-
-            if !multiple_meldung_entries.is_empty() {
-                let _ = term.write_line(
-                    &style("\nFolgende Einträge in `lkr_meldung_export` haben mehrere Meldungsinhalte in `xml_daten`:")
-                        .yellow()
-                        .to_string(),
-                );
-
-                multiple_meldung_entries.iter().for_each(|&item| {
-                    let _ = term.write_line(&item.to_string());
-                });
-            }
-
-            let different_content = db_meldungen
-                .iter()
-                .filter(|(id, _)| !missing_xml_ids.contains(id))
-                .filter(|(id, meldung)| {
-                    xml_meldungen
-                        .get(&id.to_string())
-                        .unwrap_or(&Meldung {
-                            raw_value: String::new(),
-                        })
-                        .sanitized_xml_string()
-                        != meldung.sanitized_xml_string()
-                })
-                .map(|(_, meldung)| meldung.id().unwrap_or("?".into()))
-                .collect_vec();
-
-            if !different_content.is_empty() {
-                let _ = term.write_line(
-                    &style(&format!(
-                        "\nFolgende {} Meldungen unterscheiden sich in der Datenbank und der Protokolldatei:",
-                        different_content.len()
-                    ))
-                    .yellow()
-                    .to_string(),
-                );
-
-                let _ = term.write_line(
-                    "Dies kann auch aufgrund der verwendeten XML-Encodierung auftreten und bedeutet nicht immer eine inhaltliche Abweichung."
-                );
-
-                different_content
-                    .iter()
-                    .sorted_by(|&id1, &id2| {
-                        to_database_id(id1)
-                            .unwrap_or_default()
-                            .cmp(&to_database_id(id2).unwrap_or_default())
-                    })
-                    .for_each(|id| {
-                        let _ = term.write_line(&format!(
-                            "{} ({})",
-                            id,
-                            to_database_id(id).unwrap_or("?".into())
-                        ));
-                    });
-            }
-        }
     }
 
     Ok(())

src/opal.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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

src/resources/export.sql

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -33,21 +33,19 @@ FROM (
         SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1) AS diagnosedatum,
         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')
+    JOIN lkr_export le ON (le.id = lme.lkr_export)
     WHERE lme.xml_daten LIKE '%ICD_Version%'
-        AND lme.typ <> -1
-        AND lme.xml_daten NOT LIKE '%<Menge_Tumorkonferenz%'
         AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
-        AND (lme.xml_daten NOT LIKE '%histologie_zytologie%' OR 1 = :include_histo_zyto)
+        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 (EXTRACTVALUE(lme.xml_daten, '//Meldende_Stelle') NOT LIKE '%9999%' OR 1 <= :include_extern)
+        AND le.exportiert_am < :ignore_exports_since
-        AND (EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') LIKE '2.%' OR 1 = :ignore_non_obds_2)
     ) o1
     LEFT OUTER JOIN (
 
-    SELECT DISTINCT
+    SELECT
         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
+        MAX(versionsnummer) 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
 

src/resources/exported-to-lkr.sql

@@ -1,26 +0,0 @@
-/*
- * This file is part of bzkf-rwdp-check
- *
- * Copyright (C) 2024 the original author or authors.
- *
- * 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
-    CONVERT(id,char) AS id,
-    xml_daten
-FROM lkr_meldung_export
-WHERE typ <> -1
-    AND (lkr_export = :export_id OR (0 = :export_id AND lkr_export IN (SELECT MAX(lkr_export) FROM lkr_meldung_export)));

src/resources/mod.rs

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -20,8 +20,4 @@
 
 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");

src/resources/query.sql

@@ -1,7 +1,7 @@
 /*
  * This file is part of bzkf-rwdp-check
  *
- * Copyright (C) 2024 the original author or authors.
+ * 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
@@ -107,35 +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(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')
+    JOIN lkr_export le ON (le.id = lme.lkr_export)
     WHERE lme.xml_daten LIKE '%ICD_Version%'
-        AND lme.typ <> -1
-        AND lme.xml_daten NOT LIKE '%<Menge_Tumorkonferenz%'
         AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
-        AND (lme.xml_daten NOT LIKE '%histologie_zytologie%' OR 1 = :include_histo_zyto)
+        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 (EXTRACTVALUE(lme.xml_daten, '//Meldende_Stelle') NOT LIKE '%9999%' OR 1 <= :include_extern)
+        AND le.exportiert_am < :ignore_exports_since
-        AND (EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') LIKE '2.%' OR 1 = :ignore_non_obds_2)
+    ) o1
- ) o1
+    LEFT OUTER JOIN (
-LEFT OUTER JOIN (
+
-    SELECT DISTINCT
+    SELECT
-        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
+        MAX(versionsnummer) 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
+
+    ) 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;

src/resources/query_with_schema_version.sql

@@ -1,141 +0,0 @@
-/*
- * This file is part of bzkf-rwdp-check
- *
- * Copyright (C) 2024 the original author or authors.
- *
- * 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 lme.xml_daten NOT LIKE '%<Menge_Tumorkonferenz%'
-        AND SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
-        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)
-        AND (EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') LIKE '2.%' OR 1 = :ignore_non_obds_2)
- ) 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;

testdaten/testdaten_1.xml

@@ -1,89 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ADT_GEKID xmlns="http://www.gekid.de/namespace" Schema_Version="2.2.3">
-    <Absender Absender_ID="TEST" Software_ID="ONKOSTAR" Installations_ID="2011">
-        <Absender_Bezeichnung>TEST</Absender_Bezeichnung>
-        <Absender_Anschrift>Musterstraße 1, 012345 Musterhausen</Absender_Anschrift>
-    </Absender>
-    <Menge_Patient>
-        <Patient>
-            <Patienten_Stammdaten Patient_ID="20001234">
-                <KrankenversichertenNr>E123456789</KrankenversichertenNr>
-                <KrankenkassenNr>123456789</KrankenkassenNr>
-                <Patienten_Nachname>Tester</Patienten_Nachname>
-                <Patienten_Titel></Patienten_Titel>
-                <Patienten_Vornamen>Patrick</Patienten_Vornamen>
-                <Patienten_Geburtsname>Tester</Patienten_Geburtsname>
-                <Patienten_Geschlecht>M</Patienten_Geschlecht>
-                <Patienten_Geburtsdatum>01.01.1980</Patienten_Geburtsdatum>
-                <Menge_Adresse>
-                    <Adresse>
-                        <Patienten_Strasse>Testweg</Patienten_Strasse>
-                        <Patienten_Hausnummer>1</Patienten_Hausnummer>
-                        <Patienten_Land>DE</Patienten_Land>
-                        <Patienten_PLZ>01234</Patienten_PLZ>
-                        <Patienten_Ort>Musterhausen</Patienten_Ort>
-                    </Adresse>
-                </Menge_Adresse>
-            </Patienten_Stammdaten>
-            <Menge_Meldung>
-                <Meldung Meldung_ID="TEST1727528" Melder_ID="TEST">
-                    <Meldedatum>11.06.2024</Meldedatum>
-                    <Meldebegruendung>I</Meldebegruendung>
-                    <Meldeanlass>statusaenderung</Meldeanlass>
-                    <Tumorzuordnung Tumor_ID="1">
-                        <Primaertumor_ICD_Code>C17.1</Primaertumor_ICD_Code>
-                        <Primaertumor_ICD_Version>10 2015 GM</Primaertumor_ICD_Version>
-                        <Diagnosedatum>10.06.2024</Diagnosedatum>
-                        <Seitenlokalisation>T</Seitenlokalisation>
-                    </Tumorzuordnung>
-                    <Menge_Tumorkonferenz>
-                        <Tumorkonferenz Tumorkonferenz_ID="1234567">
-                            <Tumorkonferenz_Datum>11.06.2024</Tumorkonferenz_Datum>
-                            <Tumorkonferenz_Typ>praeth</Tumorkonferenz_Typ>
-                        </Tumorkonferenz>
-                    </Menge_Tumorkonferenz>
-                </Meldung>
-            </Menge_Meldung>
-        </Patient>
-        <Patient>
-            <Patienten_Stammdaten Patient_ID="20004321">
-                <KrankenversichertenNr>E123456789</KrankenversichertenNr>
-                <KrankenkassenNr>123456789</KrankenkassenNr>
-                <Patienten_Nachname>Tester</Patienten_Nachname>
-                <Patienten_Titel></Patienten_Titel>
-                <Patienten_Vornamen>Patricia</Patienten_Vornamen>
-                <Patienten_Geburtsname>Tester</Patienten_Geburtsname>
-                <Patienten_Geschlecht>W</Patienten_Geschlecht>
-                <Patienten_Geburtsdatum>01.01.1980</Patienten_Geburtsdatum>
-                <Menge_Adresse>
-                    <Adresse>
-                        <Patienten_Strasse>Testweg</Patienten_Strasse>
-                        <Patienten_Hausnummer>1</Patienten_Hausnummer>
-                        <Patienten_Land>DE</Patienten_Land>
-                        <Patienten_PLZ>01234</Patienten_PLZ>
-                        <Patienten_Ort>Musterhausen</Patienten_Ort>
-                    </Adresse>
-                </Menge_Adresse>
-            </Patienten_Stammdaten>
-            <Menge_Meldung>
-                <Meldung Meldung_ID="001A5D50-TEST" Melder_ID="TEST">
-                    <Meldedatum>11.06.2024</Meldedatum>
-                    <Meldebegruendung>I</Meldebegruendung>
-                    <Meldeanlass>statusaenderung</Meldeanlass>
-                    <Tumorzuordnung Tumor_ID="1">
-                        <Primaertumor_ICD_Code>C17.2</Primaertumor_ICD_Code>
-                        <Primaertumor_ICD_Version>10 2015 GM</Primaertumor_ICD_Version>
-                        <Diagnosedatum>01.01.2024</Diagnosedatum>
-                        <Seitenlokalisation>T</Seitenlokalisation>
-                    </Tumorzuordnung>
-                    <Menge_Tumorkonferenz>
-                        <Tumorkonferenz Tumorkonferenz_ID="1234568">
-                            <Tumorkonferenz_Datum>10.01.2024</Tumorkonferenz_Datum>
-                            <Tumorkonferenz_Typ>praeth</Tumorkonferenz_Typ>
-                        </Tumorkonferenz>
-                    </Menge_Tumorkonferenz>
-                </Meldung>
-            </Menge_Meldung>
-        </Patient>
-    </Menge_Patient>
-</ADT_GEKID>