docs: zeros be gone - add information on how to sanitize Patient_ID (#…

…189)

* docs: add information on how sanitize Patient_ID

closes #188

* docs: add sql syntax highlighting

docker-compose/README.md

@@ -66,7 +66,40 @@ SELECT * FROM (
   SELECT YEAR(STR_TO_DATE(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), '%d.%c.%Y')) AS YEAR, versionsnummer AS VERSIONSNUMMER, lme.id AS ID, CONVERT(lme.xml_daten using utf8) AS XML_DATEN
     FROM lkr_meldung_export lme
     WHERE lme.typ != '-1' AND lme.versionsnummer IS NOT NULL AND lme.XML_DATEN LIKE '%ICD_Version%'
-) o;
+) o
+```
+
+To remove leading zeros from `Patient_ID` (see: https://github.com/bzkf/onco-analytics-on-fhir/issues/188), you could use the following query.
+It will update `XML_DATEN` by replacing the attribute `Patient_ID` by using an `INT` if the value found can be casted into an integer but keeps the original value
+if any other (e.g. alphanumeric value) is used and the cast will result in `0` value.
+
+```sql
+SELECT * FROM (
+    SELECT
+        YEAR(STR_TO_DATE(EXTRACTVALUE(lme.xml_daten, '//Diagnosedatum'), '%d.%c.%Y')) AS YEAR,
+        versionsnummer AS VERSIONSNUMMER,
+        lme.id AS ID,
+        CASE
+        # Patient_ID can be casted into number
+            WHEN CAST(EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID') AS INT) > 0
+            THEN CONVERT(
+                UPDATEXML(
+                    lme.xml_daten,
+                    '//Patienten_Stammdaten/@Patient_ID',
+                    CONCAT('Patient_ID="', EXTRACTVALUE(lme.xml_daten, '//Patienten_Stammdaten/@Patient_ID'),'"')
+                ) USING utf8
+            )
+        ELSE
+        # else fallback - do not touch Patient_ID
+            CONVERT(lme.xml_daten USING UTF8)
+        END AS XML_DATEN
+    FROM lkr_meldung_export lme
+    WHERE
+        typ != '-1'
+        AND versionsnummer IS NOT NULL
+        AND lme.XML_DATEN LIKE '%ICD_Version%'
+        AND EXTRACTVALUE(lme.xml_daten, '//ADT_GEKID/@Schema_Version') LIKE '2.%'
+) o
 ```
 
 If you are not using direct access to Onkostar MySQL/MariaDB database, you should use the following query that will fetch
@@ -81,7 +114,7 @@ SELECT * FROM (
     JOIN lkr_meldung lm ON lme.lkr_meldung = lm.id
     JOIN erkrankung e ON lm.erkrankung_id = e.id
     WHERE lme.typ != '-1' AND lme.versionsnummer IS NOT NULL AND lme.XML_DATEN LIKE '%ICD_Version%'
-) o;
+) o
 ```
 
 ```sh