feat: export data from database into OPAL-like CSV file

README.md

@@ -57,3 +57,23 @@ Options:
   -u, --user <USER>          Benutzername
   -y, --year <YEAR>          Jahr der Diagnose
 ```
+
+## Export aus der Onkostar-Datenbank
+
+Die Anwendung ist in der Lage, die Spalten
+
+* `pat_id`: Patienten-ID (optional über Parameter `--pat-id`)
+* `cond_id`: Condition-ID
+* `conditiondate`: Datum der Diagnose
+* `condcodingcode`: Der ICD-10-Code der Diagnose
+
+in eine CSV-Datei zum Abgleich mit der OPAL-CSV-Datei zu exportieren.
+
+Hierbei gelten die gleichen Datenbank-Parameter wie unter [Kennzahlen aus der Onkostar-Datenbank](#kennzahlen-aus-der-onkostar-datenbank),
+zusätzlich gibt es noch die folgenden Parameter:
+
+```
+Options:
+      --pat-id               Export mit Klartext-Patienten-OD
+  -o, --output <OUTPUT>      Ausgabedatei
+```

src/cli.rs

@@ -59,4 +59,34 @@ pub enum SubCommand {
         #[arg(short = 'y', long, help = "Jahr der Diagnose")]
         year: String,
     },
+    #[command(
+        about = "Erstellt eine (reduzierte) CSV-Datei zum direkten Vergleich mit der OPAL-CSV-Datei"
+    )]
+    Export {
+        #[arg(long, help = "Export mit Klartext-Patienten-ID")]
+        pat_id: bool,
+        #[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 = 'o', long, help = "Ausgabedatei")]
+        output: String,
+        #[arg(short = 'y', long, help = "Jahr der Diagnose")]
+        year: String,
+    },
 }

src/database.rs

@@ -20,12 +20,25 @@
 
 use mysql::prelude::Queryable;
 use mysql::{params, Pool};
+use serde::Serialize;
 
 use crate::common::Icd10GroupSize;
-use crate::resources::SQL_QUERY;
+use crate::resources::{EXPORT_QUERY, SQL_QUERY};
 
 pub struct DatabaseSource(String);
 
+#[derive(Serialize, Debug)]
+pub struct ExportData {
+    #[serde(rename = "pat_id")]
+    pat_id: Option<String>,
+    #[serde(rename = "cond_id")]
+    condition_id: String,
+    #[serde(rename = "condition_date")]
+    diagnosis_date: String,
+    #[serde(rename = "condcodingcode")]
+    icd_10_code: String,
+}
+
 impl DatabaseSource {
     pub fn new(database: &str, host: &str, password: &str, port: u16, user: &str) -> Self {
         let password = urlencoding::encode(password);
@@ -50,8 +63,36 @@ impl DatabaseSource {
                     };
                 }
             }
-            Err(e) => {
-                println!("{}", e);
+            Err(_) => {
+                return Err(());
+            }
+        }
+
+        Err(())
+    }
+
+    pub fn export(&self, year: &str, use_pat_id: bool) -> Result<Vec<ExportData>, ()> {
+        match Pool::new(self.0.as_str()) {
+            Ok(pool) => {
+                if let Ok(mut connection) = pool.get_conn() {
+                    return match connection.exec_map(
+                        EXPORT_QUERY,
+                        params! {"year" => year},
+                        |(condition_id, icd_10_code, diagnosis_date, pat_id)| ExportData {
+                            condition_id,
+                            icd_10_code,
+                            diagnosis_date,
+                            pat_id: if use_pat_id { Some(pat_id) } else { None },
+                        },
+                    ) {
+                        Ok(result) => Ok(result),
+                        Err(_) => {
+                            return Err(());
+                        }
+                    };
+                }
+            }
+            Err(_) => {
                 return Err(());
             }
         }

src/main.rs

@@ -23,6 +23,7 @@ use std::path::Path;
 
 use clap::Parser;
 use console::{style, Term};
+use csv::Writer;
 
 use crate::cli::{Cli, SubCommand};
 use crate::common::Icd10GroupSize;
@@ -96,6 +97,52 @@ fn main() -> Result<(), Box<dyn Error>> {
 
             print_items(&items);
         }
+        SubCommand::Export {
+            pat_id,
+            database,
+            host,
+            password,
+            port,
+            user,
+            output,
+            year,
+        } => {
+            let password = if let Some(password) = password {
+                password
+            } else {
+                let password = dialoguer::Password::new()
+                    .with_prompt("Password")
+                    .interact()
+                    .unwrap_or_default();
+                let _ = term.clear_last_lines(1);
+                password
+            };
+
+            let year = if year.len() == 4 {
+                year
+            } else {
+                format!("2{:0>3}", year)
+            };
+
+            let _ = term.write_line(
+                &style(format!("Warte auf Daten für das Diagnosejahr {}...", year))
+                    .blue()
+                    .to_string(),
+            );
+
+            let db = DatabaseSource::new(&database, &host, &password, port, &user);
+            let items = db
+                .export(&year, pat_id)
+                .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
+
+            let _ = term.clear_last_lines(1);
+
+            let mut writer = Writer::from_path(Path::new(&output)).expect("writeable file");
+
+            items
+                .iter()
+                .for_each(|item| writer.serialize(item).unwrap());
+        }
     }
 
     Ok(())

src/resources/export.sql

@@ -0,0 +1,53 @@
+/*
+ * 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
+    o1.cond_id,
+    o1.condcodingcode,
+    o1.diagnosedatum,
+    o1.pid
+FROM (
+
+    SELECT DISTINCT
+        EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID') AS pid,
+        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(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')
+    WHERE lme.xml_daten LIKE '%ICD_Version%'
+        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>%')
+
+    ) o1
+    LEFT OUTER JOIN (
+
+    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,
+        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
+ON (o1.cond_id = o2.cond_id AND o1.versionsnummer < max_version)
+WHERE diagnosejahr = :year AND o2.cond_id IS NULL;

src/resources/mod.rs

@@ -19,3 +19,5 @@
  */
 
 pub const SQL_QUERY: &str = include_str!("query.sql");
+
+pub const EXPORT_QUERY: &str = include_str!("export.sql");