Merge pull request #4 from pcvolkmer/issue_1

feat: show schema versions and change extern detection

README.md

@@ -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

src/cli.rs

@@ -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"

src/common.rs

@@ -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<_>>();

src/database.rs

@@ -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>, ()> {
-        match Pool::new(self.0.as_str()) {
+        let params = params! {
-            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 }
-                        },
+        };
-                        |(icd10_group, count)| Icd10GroupSize {
+
-                            name: icd10_group,
+        match Pool::new(self.0.as_str()) {
-                            size: count,
+            Ok(pool) => {
-                        },
+                if let Ok(mut connection) = pool.try_get_conn(Duration::from_secs(3)) {
+                    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(()),
+                        },
+                        false => match connection.exec_map(SQL_QUERY, params, result_mapper()) {
+                            Ok(result) => Ok(result),
+                            Err(_) => Err(()),
+                        },
                     };
                 }
             }

src/main.rs

@@ -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))
+        &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")?;
 

src/resources/mod.rs

@@ -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");

src/resources/query.sql

@@ -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(EXTRACTVALUE(lme.xml_daten, '//Primaertumor_ICD_Code'), ' ', 1) AS condcodingcode,
-        SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lm.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) AS diagnosejahr
+        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 lme.typ <> -1
-        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 SUBSTRING_INDEX(SUBSTRING_INDEX(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), ' ', 1), '.', -1) = :year
-        AND (lm.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 (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 (
+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;

src/resources/query_with_schema_version.sql

@@ -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;