feat: add sub command to request values from database

Cargo.toml

@@ -9,6 +9,10 @@ edition = "2021"
 clap = { version = "4.4", features = ["std", "help", "usage", "derive", "error-context"], default-features = false }
 console = "0.15"
 csv = "1.3"
+dialoguer = "0.11"
 itertools = "0.12"
+mysql = "24.0"
 serde = { version = "1.0", features = ["derive"] }
+urlencoding = "2.1"
+
 

README.md

@@ -27,3 +27,26 @@ bzkf-rwdp-check opal-file --file <Opal-CSV-Datei>.csv
 ```
 
 Die Anwendung gibt nun eine Liste der ICD-10-Gruppen mit Anzahl der _Conditions_ aus.
+
+## Prüfung der Daten in der Onkostar-Datenbank
+
+Die Anzahl der _Conditions_, gruppiert nach ICD-10-Gruppe, kann auch mit dem Befehl `database` aus der Onkostar-Datenbank
+abgerufen werden.
+
+```
+bzkf-rwdp-check database --user me --year 2024
+```
+
+Die Anwendung gibt auch hier eine Liste der ICD-10-Gruppen mit Anzahl der _Conditions_ aus.
+
+Dieser Befehl hat noch weitere Parameter:
+
+```
+Options:
+  -D, --database <DATABASE>  Datenbank-Name [default: onkostar]
+  -h, --host <HOST>          Datenbank-Host [default: localhost]
+  -P, --port <PORT>          Datenbank-Host [default: 3306]
+  -p, --password <PASSWORD>  Passwort. Wenn nicht angegeben, wird danach gefragt
+  -u, --user <USER>          Benutzername
+  -y, --year <YEAR>          Jahr der Diagnose
+```

src/cli.rs

@@ -22,7 +22,7 @@ use clap::{Parser, Subcommand};
 
 #[derive(Parser)]
 #[command(author, version, about)]
-#[command(arg_required_else_help(true))]
+#[command(arg_required_else_help(true), disable_help_flag(true))]
 pub struct Cli {
     #[command(subcommand)]
     pub cmd: SubCommand,
@@ -30,20 +30,33 @@ pub struct Cli {
 
 #[derive(Subcommand)]
 pub enum SubCommand {
-    #[command(
+    #[command(about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL")]
-    about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL"
-    )]
     OpalFile {
-        #[arg(short, long, help = "CSV-File für Opal")] file: String
+        #[arg(short, long, help = "CSV-File für Opal")]
+        file: String,
     },
-    #[command(
+    #[command(about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL")]
-    about = "Ermittelt die Prüfwerte aus einem CSV-File für OPAL"
-    )]
     Database {
-        #[arg(long, help = "Datenbank-Host", default_value="localhost")] host: String,
+        #[arg(short = 'D', long, help = "Datenbank-Name", default_value = "onkostar")]
-        #[arg(long, help = "Datenbank-Host", default_value="3306")] port: u16,
+        database: String,
-        #[arg(long, help = "Benutzername")] user: 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 = 'y', long, help = "Jahr der Diagnose")]
+        year: String,
+    },
 }

src/database.rs

@@ -0,0 +1,61 @@
+/*
+ * 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.
+ */
+
+use mysql::prelude::Queryable;
+use mysql::{params, Pool};
+
+use crate::common::Icd10GroupSize;
+use crate::resources::SQL_QUERY;
+
+pub struct DatabaseSource(String);
+
+impl DatabaseSource {
+    pub fn new(database: &str, host: &str, password: &str, port: u16, user: &str) -> Self {
+        let password = urlencoding::encode(password);
+        let url = format!("mysql://{user}:{password}@{host}:{port}/{database}");
+        DatabaseSource(url)
+    }
+
+    pub fn check(&self, year: &str) -> Result<Vec<Icd10GroupSize>, ()> {
+        match Pool::new(self.0.as_str()) {
+            Ok(pool) => {
+                if let Ok(mut connection) = pool.get_conn() {
+                    return match connection.exec_map(
+                        SQL_QUERY,
+                        params! {"year" => year},
+                        |(icd10_group, count)| Icd10GroupSize {
+                            name: icd10_group,
+                            size: count,
+                        },
+                    ) {
+                        Ok(result) => Ok(result),
+                        Err(_) => Err(()),
+                    };
+                }
+            }
+            Err(e) => {
+                println!("{}", e);
+                return Err(());
+            }
+        }
+
+        Err(())
+    }
+}

src/main.rs

@@ -25,10 +25,26 @@ use clap::Parser;
 use console::{style, Term};
 
 use crate::cli::{Cli, SubCommand};
+use crate::common::Icd10GroupSize;
+use crate::database::DatabaseSource;
 
-mod opal;
-mod common;
 mod cli;
+mod common;
+mod database;
+mod opal;
+mod resources;
+
+fn print_items(items: &[Icd10GroupSize]) {
+    let term = Term::stdout();
+    let _ = term.write_line(
+        &style("Anzahl der Conditions nach ICD-10-Gruppe")
+            .yellow()
+            .to_string(),
+    );
+    items.iter().for_each(|item| {
+        let _ = term.write_line(&format!("{:<20}={:>6}", item.name, item.size));
+    });
+}
 
 fn main() -> Result<(), Box<dyn Error>> {
     let term = Term::stdout();
@@ -38,13 +54,47 @@ fn main() -> Result<(), Box<dyn Error>> {
             let items = opal::OpalCsvFile::check(Path::new(&file))
                 .map_err(|_e| "Kann Datei nicht lesen")?;
 
-            let _ = term.write_line(&style("Anzahl der Conditions nach ICD-Gruppe").yellow().to_string());
+            print_items(&items);
-            items.iter().for_each(|item| {
+        }
-                let _ = term.write_line(&format!("{:<20}={:>6}", item.name, item.size));
+        SubCommand::Database {
-            });
+            database,
-        },
+            host,
-        SubCommand::Database { .. } => {
+            password,
-            todo!("Not implemented yet")
+            port,
+            user,
+            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
+                .check(&year)
+                .map_err(|_e| "Fehler bei Zugriff auf die Datenbank")?;
+
+            let _ = term.clear_last_lines(1);
+
+            print_items(&items);
         }
     }
 

src/resources/mod.rs

@@ -0,0 +1,21 @@
+/*
+ * 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.
+ */
+
+pub const SQL_QUERY: &str = include_str!("query.sql");

src/resources/query.sql

@@ -0,0 +1,133 @@
+/*
+ * 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,
+
+       COUNT(*) as COUNT
+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(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 (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
+GROUP BY ICD10_GROUP;