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https://github.com/pcvolkmer/mv64e-onkostar-data.git
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feat: add Tumor-Proben
This commit is contained in:
42
README.md
42
README.md
@ -36,25 +36,25 @@ var jsonResult = Converter.toJsonString(
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## Status
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| DNPM-Datenmodell 2.1 - Bereich | Status | Anmerkung |
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|----------------------------------|--------|----------------------------------------------------------------|
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| Patient | ✅ | Verwendet Datenbank-ID, keine managing Site |
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| Episoden | ✅ | |
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| Diagnosen | ✅ | Entsprechend Formularaufbau nur Diagnose der aktuellen Episode |
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| Verwandten-Diagnosen | ✅ | |
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| Systemische Leitlinien-Therapien | ✅ | Siehe auch: https://github.com/dnpm-dip/mtb-model/issues/9 |
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| Leitlinien-Prozeduren | ✅ | Siehe auch: https://github.com/dnpm-dip/mtb-model/issues/9 |
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| ECOG-Verlauf | ✅ | |
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| Tumor-Proben | ⌛ | Aktuell in Arbeit |
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| vorherige Molekular-Diagnostik | ⌛ | Aktuell in Arbeit |
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| Histologie-Berichte | ⌛ | Aktuell in Arbeit |
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| IHC-Berichte | | |
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| MSI-Befunde | | |
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| NGS-Berichte | ⌛ | Aktuell in Arbeit |
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| MTB-Beschlüsse | ⌛ | Aktuell in Arbeit |
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| Follow-Up Verlauf | | |
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| Antrag Kostenübernahme | | |
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| Antwort Kostenübernahme | | |
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| Therapien | | |
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| Response Befunde | | |
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| DNPM-Datenmodell 2.1 - Bereich | Status | Anmerkung |
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|----------------------------------|--------|----------------------------------------------------------------------------|
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| Patient | ✅ | Verwendet Datenbank-ID, keine managing Site |
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| Episoden | ✅ | |
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| Diagnosen | ✅ | Entsprechend Formularaufbau nur Diagnose der aktuellen Episode |
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| Verwandten-Diagnosen | ✅ | |
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| Systemische Leitlinien-Therapien | ✅ | Siehe auch: https://github.com/dnpm-dip/mtb-model/issues/9 |
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| Leitlinien-Prozeduren | ✅ | Siehe auch: https://github.com/dnpm-dip/mtb-model/issues/9 |
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| ECOG-Verlauf | ✅ | |
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| Tumor-Proben | ⛅ | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen |
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| vorherige Molekular-Diagnostik | ⌛ | Aktuell in Arbeit |
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| Histologie-Berichte | ⌛ | Aktuell in Arbeit |
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| IHC-Berichte | | |
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| MSI-Befunde | | |
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| NGS-Berichte | ⌛ | Aktuell in Arbeit |
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| MTB-Beschlüsse | ⌛ | Aktuell in Arbeit |
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| Follow-Up Verlauf | | |
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| Antrag Kostenübernahme | | |
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| Antwort Kostenübernahme | | |
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| Therapien | | |
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| Response Befunde | | |
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@ -71,6 +71,12 @@ public class DataCatalogueFactory {
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return TherapieplanCatalogue.create(jdbcTemplate);
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} else if (c == EinzelempfehlungCatalogue.class) {
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return EinzelempfehlungCatalogue.create(jdbcTemplate);
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} else if (c == MolekulargenetikCatalogue.class) {
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return MolekulargenetikCatalogue.create(jdbcTemplate);
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} else if (c == RebiopsieCatalogue.class) {
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return RebiopsieCatalogue.create(jdbcTemplate);
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} else if (c == ReevaluationCatalogue.class) {
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return ReevaluationCatalogue.create(jdbcTemplate);
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}
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throw new DataCatalogueCreationException(clazz);
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});
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@ -0,0 +1,26 @@
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package dev.pcvolkmer.onco.datamapper.datacatalogues;
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import org.springframework.jdbc.core.JdbcTemplate;
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/**
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* Load raw result sets from database table 'dk_molekulargenetik'
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*
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* @author Paul-Christian Volkmer
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* @since 0.1
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*/
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public class MolekulargenetikCatalogue extends AbstractSubformDataCatalogue {
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private MolekulargenetikCatalogue(JdbcTemplate jdbcTemplate) {
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super(jdbcTemplate);
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}
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@Override
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protected String getTableName() {
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return "dk_molekulargenetik";
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}
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public static MolekulargenetikCatalogue create(JdbcTemplate jdbcTemplate) {
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return new MolekulargenetikCatalogue(jdbcTemplate);
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}
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}
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@ -0,0 +1,26 @@
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package dev.pcvolkmer.onco.datamapper.datacatalogues;
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import org.springframework.jdbc.core.JdbcTemplate;
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/**
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* Load raw result sets from database table 'dk_dnpm_uf_rebiopsie'
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*
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* @author Paul-Christian Volkmer
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* @since 0.1
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*/
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public class RebiopsieCatalogue extends AbstractSubformDataCatalogue {
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private RebiopsieCatalogue(JdbcTemplate jdbcTemplate) {
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super(jdbcTemplate);
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}
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@Override
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protected String getTableName() {
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return "dk_dnpm_uf_rebiopsie";
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}
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public static RebiopsieCatalogue create(JdbcTemplate jdbcTemplate) {
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return new RebiopsieCatalogue(jdbcTemplate);
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}
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}
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@ -0,0 +1,26 @@
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package dev.pcvolkmer.onco.datamapper.datacatalogues;
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import org.springframework.jdbc.core.JdbcTemplate;
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/**
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* Load raw result sets from database table 'dk_dnpm_uf_reevaluation'
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*
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* @author Paul-Christian Volkmer
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* @since 0.1
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*/
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public class ReevaluationCatalogue extends AbstractSubformDataCatalogue {
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private ReevaluationCatalogue(JdbcTemplate jdbcTemplate) {
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super(jdbcTemplate);
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}
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@Override
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protected String getTableName() {
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return "dk_dnpm_uf_reevaluation";
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}
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public static ReevaluationCatalogue create(JdbcTemplate jdbcTemplate) {
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return new ReevaluationCatalogue(jdbcTemplate);
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}
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}
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@ -0,0 +1,215 @@
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package dev.pcvolkmer.onco.datamapper.mapper;
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import dev.pcvolkmer.mv64e.mtb.*;
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import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
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import dev.pcvolkmer.onco.datamapper.ResultSet;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
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import java.util.List;
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import java.util.stream.Collectors;
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import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
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/**
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* Mapper class to load and map patient data from database table 'dk_molekulargenetik'
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*
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* @author Paul-Christian Volkmer
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* @since 0.1
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*/
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public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpecimen> {
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private final MolekulargenetikCatalogue molekulargenetikCatalogue;
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private final TherapieplanCatalogue therapieplanCatalogue;
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private final RebiopsieCatalogue rebiopsieCatalogue;
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private final ReevaluationCatalogue reevaluationCatalogue;
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private final EinzelempfehlungCatalogue einzelempfehlungCatalogue;
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private final PropertyCatalogue propertyCatalogue;
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public MolekulargenetikToSpecimenDataMapper(
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final MolekulargenetikCatalogue molekulargenetikCatalogue,
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final TherapieplanCatalogue therapieplanCatalogue,
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final RebiopsieCatalogue rebiopsieCatalogue,
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final ReevaluationCatalogue reevaluationCatalogue,
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final EinzelempfehlungCatalogue einzelempfehlungCatalogue,
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final PropertyCatalogue propertyCatalogue
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) {
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this.molekulargenetikCatalogue = molekulargenetikCatalogue;
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this.therapieplanCatalogue = therapieplanCatalogue;
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this.rebiopsieCatalogue = rebiopsieCatalogue;
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this.reevaluationCatalogue = reevaluationCatalogue;
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this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
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this.propertyCatalogue = propertyCatalogue;
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}
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/**
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* Loads and maps a specimen using the database id
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* The result does not include a diagnosis reference!
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*
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* @param id The database id of the procedure data set
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* @return The loaded Patient data
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*/
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@Override
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public TumorSpecimen getById(int id) {
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var data = molekulargenetikCatalogue.getById(id);
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var builder = TumorSpecimen.builder();
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builder
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.id(data.getString("id"))
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.patient(getPatientReference(data.getString("patient_id")))
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.type(getTumorSpecimenCoding(data.getString("materialfixierung")))
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.collection(getCollection(data))
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// TODO add diagnosis later
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;
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return builder.build();
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}
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/**
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* Loads and maps specimens by using the referencing KPA database id
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*
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* @param kpaId The database id of the referencing KPA procedure data set
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* @param diagnoseReferenz The reference object to the diagnosis
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* @return The loaded Patient data
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*/
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public List<TumorSpecimen> getAllByKpaId(int kpaId, Reference diagnoseReferenz) {
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var therapieplanIds = therapieplanCatalogue.getByKpaId(kpaId);
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var osMolGen = therapieplanIds.stream()
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.map(einzelempfehlungCatalogue::getAllByParentId)
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.flatMap(einzelempfehlungen ->
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einzelempfehlungen
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.stream()
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.map(einzelempfehlung -> einzelempfehlung.getInteger("ref_molekulargenetik"))
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)
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.collect(Collectors.toSet());
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// Addition: Rebiopsie
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osMolGen.addAll(
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therapieplanIds.stream()
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.map(rebiopsieCatalogue::getAllByParentId)
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.flatMap(einzelempfehlungen ->
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einzelempfehlungen
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.stream()
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.map(einzelempfehlung -> einzelempfehlung.getInteger("ref_molekulargenetik"))
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)
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.collect(Collectors.toSet())
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);
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// Addition: Reevaluation
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osMolGen.addAll(
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therapieplanIds.stream()
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.map(reevaluationCatalogue::getAllByParentId)
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.flatMap(einzelempfehlungen ->
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einzelempfehlungen
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.stream()
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.map(einzelempfehlung -> einzelempfehlung.getInteger("ref_molekulargenetik"))
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)
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.collect(Collectors.toSet())
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);
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return osMolGen.stream()
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.map(this::getById)
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.peek(it -> it.setDiagnosis(diagnoseReferenz))
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.collect(Collectors.toList());
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}
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// TODO: Kein genaues Mapping mit Formular OS.Molekulargenetik möglich - best effort
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private TumorSpecimenCoding getTumorSpecimenCoding(String value) {
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if (value == null) {
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return null;
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}
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var resultBuilder = TumorSpecimenCoding.builder()
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.system("dnpm-dip/mtb/tumor-specimen/type");
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switch (value) {
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case "2":
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resultBuilder
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.code(TumorSpecimenCodingCode.CRYO_FROZEN)
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.display("Cryo-frozen");
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break;
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case "3":
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resultBuilder
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.code(TumorSpecimenCodingCode.FFPE)
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.display("FFPE");
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break;
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default:
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resultBuilder
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.code(TumorSpecimenCodingCode.UNKNOWN)
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.display("Unbekannt");
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break;
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}
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return resultBuilder.build();
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}
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private Collection getCollection(ResultSet data) {
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if (data == null || data.getString("entnahmemethode") == null || data.getString("probenmaterial") == null) {
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return null;
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}
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var methodBuilder = TumorSpecimenCollectionMethodCoding.builder()
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.system("dnpm-dip/mtb/tumor-specimen/collection/method");
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switch (data.getString("entnahmemethode")) {
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case "B":
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methodBuilder
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.code(TumorSpecimenCollectionMethodCodingCode.BIOPSY)
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.display("Biopsie");
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break;
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case "R":
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methodBuilder
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.code(TumorSpecimenCollectionMethodCodingCode.RESECTION)
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.display("Resektat");
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break;
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case "LB":
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methodBuilder
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.code(TumorSpecimenCollectionMethodCodingCode.LIQUID_BIOPSY)
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.display("Liquid Biopsy");
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break;
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case "Z":
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methodBuilder
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.code(TumorSpecimenCollectionMethodCodingCode.CYTOLOGY)
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.display("Zytologie");
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break;
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case "U":
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default:
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methodBuilder
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.code(TumorSpecimenCollectionMethodCodingCode.UNKNOWN)
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.display("Unbekannt");
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break;
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}
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// TODO: Kein genaues Mapping mit Formular OS.Molekulargenetik möglich - best effort
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var localizationBuilder = TumorSpecimenCollectionLocalizationCoding.builder()
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.system("dnpm-dip/mtb/tumor-specimen/collection/localization");
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switch (data.getString("probenmaterial")) {
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case "T":
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localizationBuilder
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.code(TumorSpecimenCollectionLocalizationCodingCode.PRIMARY_TUMOR)
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.display("Primärtumor");
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break;
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case "LK":
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case "M":
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case "ITM":
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case "SM":
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localizationBuilder
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.code(TumorSpecimenCollectionLocalizationCodingCode.METASTASIS)
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.display("Metastase");
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break;
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default:
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localizationBuilder
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.code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN)
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.display("Unbekannt");
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break;
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}
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return Collection.builder()
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.method(methodBuilder.build())
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.localization(localizationBuilder.build())
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.build();
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}
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}
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@ -1,6 +1,7 @@
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package dev.pcvolkmer.onco.datamapper.mapper;
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import dev.pcvolkmer.mv64e.mtb.Mtb;
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import dev.pcvolkmer.mv64e.mtb.Reference;
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import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
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import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
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@ -80,15 +81,26 @@ public class MtbDataMapper implements DataMapper<Mtb> {
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catalogueFactory.catalogue(EcogCatalogue.class)
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);
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var einzelempfehlungCatalogue = catalogueFactory.catalogue(EinzelempfehlungCatalogue.class);
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var therapieplanCatalogue = catalogueFactory.catalogue(TherapieplanCatalogue.class);
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var therapieplanDataMapper = new TherapieplanDataMapper(
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therapieplanCatalogue,
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catalogueFactory.catalogue(EinzelempfehlungCatalogue.class),
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einzelempfehlungCatalogue,
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propertyCatalogue
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);
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var verwandteDataMapper = new KpaVerwandteDataMapper(catalogueFactory.catalogue(VerwandteCatalogue.class));
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var molekulargenetikCatalogue = catalogueFactory.catalogue(MolekulargenetikCatalogue.class);
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var molekulargenetikToSpecimenDataMapper = new MolekulargenetikToSpecimenDataMapper(
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molekulargenetikCatalogue,
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therapieplanCatalogue,
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catalogueFactory.catalogue(RebiopsieCatalogue.class),
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catalogueFactory.catalogue(ReevaluationCatalogue.class),
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einzelempfehlungCatalogue,
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propertyCatalogue
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);
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var resultBuilder = Mtb.builder();
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try {
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@ -96,11 +108,13 @@ public class MtbDataMapper implements DataMapper<Mtb> {
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var patient = patientDataMapper.getById(Integer.parseInt(kpaPatient.getId()));
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kpaPatient.setAddress(patient.getAddress());
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var diagnosis = diagnosisDataMapper.getById(kpaId);
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resultBuilder
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.patient(kpaPatient)
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.episodesOfCare(List.of(mtbEpisodeDataMapper.getById(kpaId)))
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// DNPM Klinik/Anamnese
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.diagnoses(List.of(diagnosisDataMapper.getById(kpaId)))
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.diagnoses(List.of(diagnosis))
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.guidelineProcedures(prozedurMapper.getByParentId(kpaId))
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.guidelineTherapies(therapielinieMapper.getByParentId(kpaId))
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.performanceStatus(ecogMapper.getByParentId(kpaId))
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@ -112,6 +126,13 @@ public class MtbDataMapper implements DataMapper<Mtb> {
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.map(therapieplanDataMapper::getById)
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.collect(Collectors.toList())
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)
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// Tumorproben
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.specimens(
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molekulargenetikToSpecimenDataMapper.getAllByKpaId(
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kpaId,
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Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
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)
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)
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;
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} catch (DataAccessException e) {
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logger.error("Error while getting Mtb.", e);
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@ -0,0 +1,62 @@
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package dev.pcvolkmer.onco.datamapper.datacatalogues;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.ArgumentCaptor;
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import org.mockito.Mock;
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import org.mockito.junit.jupiter.MockitoExtension;
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import org.springframework.jdbc.core.JdbcTemplate;
|
||||
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import java.util.List;
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import java.util.Map;
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import static org.assertj.core.api.Assertions.assertThat;
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import static org.mockito.ArgumentMatchers.anyInt;
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||||
import static org.mockito.ArgumentMatchers.anyString;
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||||
import static org.mockito.Mockito.doAnswer;
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||||
import static org.mockito.Mockito.verify;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class MolekulargenetikCatalogueTest {
|
||||
|
||||
JdbcTemplate jdbcTemplate;
|
||||
MolekulargenetikCatalogue catalogue;
|
||||
|
||||
@BeforeEach
|
||||
void setUp(@Mock JdbcTemplate jdbcTemplate) {
|
||||
this.jdbcTemplate = jdbcTemplate;
|
||||
this.catalogue = MolekulargenetikCatalogue.create(jdbcTemplate);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getById(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.id) WHERE geloescht = 0 AND prozedur.id = ?");
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getAllByParentId(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,62 @@
|
||||
package dev.pcvolkmer.onco.datamapper.datacatalogues;
|
||||
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.ArgumentCaptor;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.jdbc.core.JdbcTemplate;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.mockito.ArgumentMatchers.anyInt;
|
||||
import static org.mockito.ArgumentMatchers.anyString;
|
||||
import static org.mockito.Mockito.doAnswer;
|
||||
import static org.mockito.Mockito.verify;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class RebiopsieCatalogueTest {
|
||||
|
||||
JdbcTemplate jdbcTemplate;
|
||||
RebiopsieCatalogue catalogue;
|
||||
|
||||
@BeforeEach
|
||||
void setUp(@Mock JdbcTemplate jdbcTemplate) {
|
||||
this.jdbcTemplate = jdbcTemplate;
|
||||
this.catalogue = RebiopsieCatalogue.create(jdbcTemplate);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getById(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) WHERE geloescht = 0 AND prozedur.id = ?");
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getAllByParentId(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,62 @@
|
||||
package dev.pcvolkmer.onco.datamapper.datacatalogues;
|
||||
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.ArgumentCaptor;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.jdbc.core.JdbcTemplate;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.mockito.ArgumentMatchers.anyInt;
|
||||
import static org.mockito.ArgumentMatchers.anyString;
|
||||
import static org.mockito.Mockito.doAnswer;
|
||||
import static org.mockito.Mockito.verify;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class ReevaluationCatalogueTest {
|
||||
|
||||
JdbcTemplate jdbcTemplate;
|
||||
ReevaluationCatalogue catalogue;
|
||||
|
||||
@BeforeEach
|
||||
void setUp(@Mock JdbcTemplate jdbcTemplate) {
|
||||
this.jdbcTemplate = jdbcTemplate;
|
||||
this.catalogue = ReevaluationCatalogue.create(jdbcTemplate);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getById(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) WHERE geloescht = 0 AND prozedur.id = ?");
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
|
||||
doAnswer(invocationOnMock -> List.of(resultSet))
|
||||
.when(jdbcTemplate)
|
||||
.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getAllByParentId(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
|
||||
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT * FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,435 @@
|
||||
package dev.pcvolkmer.onco.datamapper.mapper;
|
||||
|
||||
import dev.pcvolkmer.mv64e.mtb.*;
|
||||
import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
|
||||
import dev.pcvolkmer.onco.datamapper.ResultSet;
|
||||
import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.Arguments;
|
||||
import org.junit.jupiter.params.provider.MethodSource;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.mockito.ArgumentMatchers.anyInt;
|
||||
import static org.mockito.Mockito.doAnswer;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class MolekulargenetikToSpecimenDataMapperTest {
|
||||
|
||||
MolekulargenetikCatalogue molekulargenetikCatalogue;
|
||||
TherapieplanCatalogue therapieplanCatalogue;
|
||||
RebiopsieCatalogue rebiopsieCatalogue;
|
||||
ReevaluationCatalogue reevaluationCatalogue;
|
||||
EinzelempfehlungCatalogue einzelempfehlungCatalogue;
|
||||
PropertyCatalogue propertyCatalogue;
|
||||
|
||||
MolekulargenetikToSpecimenDataMapper mapper;
|
||||
|
||||
@BeforeEach
|
||||
void setUp(
|
||||
@Mock MolekulargenetikCatalogue molekulargenetikCatalogue,
|
||||
@Mock TherapieplanCatalogue therapieplanCatalogue,
|
||||
@Mock RebiopsieCatalogue rebiopsieCatalogue,
|
||||
@Mock ReevaluationCatalogue reevaluationCatalogue,
|
||||
@Mock EinzelempfehlungCatalogue einzelempfehlungCatalogue,
|
||||
@Mock PropertyCatalogue propertyCatalogue
|
||||
) {
|
||||
this.molekulargenetikCatalogue = molekulargenetikCatalogue;
|
||||
this.therapieplanCatalogue = therapieplanCatalogue;
|
||||
this.rebiopsieCatalogue = rebiopsieCatalogue;
|
||||
this.reevaluationCatalogue = reevaluationCatalogue;
|
||||
this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
|
||||
this.propertyCatalogue = propertyCatalogue;
|
||||
|
||||
this.mapper = new MolekulargenetikToSpecimenDataMapper(
|
||||
molekulargenetikCatalogue,
|
||||
therapieplanCatalogue,
|
||||
rebiopsieCatalogue,
|
||||
reevaluationCatalogue,
|
||||
einzelempfehlungCatalogue,
|
||||
propertyCatalogue
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldFetchAllRelatedSpecimens() {
|
||||
|
||||
// Mock Einzelempfehlungen ID
|
||||
when(therapieplanCatalogue.getByKpaId(anyInt()))
|
||||
.thenReturn(List.of(1, 2));
|
||||
|
||||
// Mock Rebiopsien - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 40)));
|
||||
}).when(rebiopsieCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock Reevaluationen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 41)));
|
||||
}).when(reevaluationCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock Einzelempfehlungen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 42)));
|
||||
}).when(einzelempfehlungCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return ResultSet.from(
|
||||
Map.of(
|
||||
"id", id,
|
||||
"patient_id", 4711,
|
||||
"entnahmemethode", "B",
|
||||
"probenmaterial", "T"
|
||||
)
|
||||
);
|
||||
}).when(molekulargenetikCatalogue).getById(anyInt());
|
||||
|
||||
var actual = this.mapper.getAllByKpaId(1, Reference.builder().build());
|
||||
|
||||
assertThat(actual).hasSize(3);
|
||||
|
||||
assertThat(actual.get(0).getId())
|
||||
.isEqualTo("40");
|
||||
assertThat(actual.get(1).getId())
|
||||
.isEqualTo("41");
|
||||
assertThat(actual.get(2).getId())
|
||||
.isEqualTo("42");
|
||||
|
||||
assertThat(actual.get(0).getPatient())
|
||||
.isEqualTo(Reference.builder().id("4711").type("Patient").build());
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldNotFetchRelatedSpecimensTwice() {
|
||||
|
||||
// Mock Einzelempfehlungen ID
|
||||
when(therapieplanCatalogue.getByKpaId(anyInt()))
|
||||
.thenReturn(List.of(1, 2));
|
||||
|
||||
// Mock Rebiopsien - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 40)));
|
||||
}).when(rebiopsieCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock Reevaluationen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 40)));
|
||||
}).when(reevaluationCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock Einzelempfehlungen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 42)));
|
||||
}).when(einzelempfehlungCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return ResultSet.from(
|
||||
Map.of(
|
||||
"id", id,
|
||||
"patient_id", 4711,
|
||||
"entnahmemethode", "B",
|
||||
"probenmaterial", "T"
|
||||
)
|
||||
);
|
||||
}).when(molekulargenetikCatalogue).getById(anyInt());
|
||||
|
||||
var actual = this.mapper.getAllByKpaId(1, Reference.builder().build());
|
||||
|
||||
assertThat(actual).hasSize(2);
|
||||
|
||||
assertThat(actual.get(0).getId())
|
||||
.isEqualTo("40");
|
||||
assertThat(actual.get(1).getId())
|
||||
.isEqualTo("42");
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("specimenTypeTestData")
|
||||
void shouldReturnExpectedSpecimenType(String value, TumorSpecimenCoding coding) {
|
||||
|
||||
// Mock Einzelempfehlungen ID
|
||||
when(therapieplanCatalogue.getByKpaId(anyInt()))
|
||||
.thenReturn(List.of(1, 2));
|
||||
|
||||
// Mock Einzelempfehlungen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 42)));
|
||||
}).when(einzelempfehlungCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return ResultSet.from(
|
||||
Map.of(
|
||||
"id", id,
|
||||
"patient_id", 4711,
|
||||
"materialfixierung", value,
|
||||
"entnahmemethode", "B",
|
||||
"probenmaterial", "T"
|
||||
)
|
||||
);
|
||||
}).when(molekulargenetikCatalogue).getById(anyInt());
|
||||
|
||||
var actual = this.mapper.getAllByKpaId(1, Reference.builder().build());
|
||||
|
||||
assertThat(actual).hasSize(1);
|
||||
assertThat(actual.get(0).getType()).isEqualTo(coding);
|
||||
}
|
||||
|
||||
// Returns all available Onkostar values and - best effort - expected mapping
|
||||
// See property catalogue OS.Material and https://ibmi-ut.atlassian.net/wiki/spaces/DAM/pages/698777783/ line 80
|
||||
static Stream<Arguments> specimenTypeTestData() {
|
||||
return Stream.of(
|
||||
Arguments.of(
|
||||
"0",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"1",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"2",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.CRYO_FROZEN).display("Cryo-frozen")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"3",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.FFPE).display("FFPE")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"4",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"9",
|
||||
TumorSpecimenCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/type").code(TumorSpecimenCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("specimenMethodTestData")
|
||||
void shouldReturnExpectedSpecimenMethod(String value, TumorSpecimenCollectionMethodCoding coding) {
|
||||
|
||||
// Mock Einzelempfehlungen ID
|
||||
when(therapieplanCatalogue.getByKpaId(anyInt()))
|
||||
.thenReturn(List.of(1, 2));
|
||||
|
||||
// Mock Einzelempfehlungen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 42)));
|
||||
}).when(einzelempfehlungCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return ResultSet.from(
|
||||
Map.of(
|
||||
"id", id,
|
||||
"patient_id", 4711,
|
||||
"entnahmemethode", value,
|
||||
"probenmaterial", "T"
|
||||
)
|
||||
);
|
||||
}).when(molekulargenetikCatalogue).getById(anyInt());
|
||||
|
||||
var actual = this.mapper.getAllByKpaId(1, Reference.builder().build());
|
||||
|
||||
assertThat(actual).hasSize(1);
|
||||
assertThat(actual.get(0).getCollection().getMethod()).isEqualTo(coding);
|
||||
}
|
||||
|
||||
// Returns all available Onkostar values and - best effort - expected mapping
|
||||
// See property catalogue OS.MolDiagEntnahmemethode and https://ibmi-ut.atlassian.net/wiki/spaces/DAM/pages/698777783/ line 84
|
||||
static Stream<Arguments> specimenMethodTestData() {
|
||||
return Stream.of(
|
||||
Arguments.of(
|
||||
"B",
|
||||
TumorSpecimenCollectionMethodCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/method").code(TumorSpecimenCollectionMethodCodingCode.BIOPSY).display("Biopsie")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"R",
|
||||
TumorSpecimenCollectionMethodCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/method").code(TumorSpecimenCollectionMethodCodingCode.RESECTION).display("Resektat")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"LB",
|
||||
TumorSpecimenCollectionMethodCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/method").code(TumorSpecimenCollectionMethodCodingCode.LIQUID_BIOPSY).display("Liquid Biopsy")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"Z",
|
||||
TumorSpecimenCollectionMethodCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/method").code(TumorSpecimenCollectionMethodCodingCode.CYTOLOGY).display("Zytologie")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"U",
|
||||
TumorSpecimenCollectionMethodCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/method").code(TumorSpecimenCollectionMethodCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("specimenLocalizationTestData")
|
||||
void shouldReturnExpectedSpecimenLocalization(String value, TumorSpecimenCollectionLocalizationCoding coding) {
|
||||
|
||||
// Mock Einzelempfehlungen ID
|
||||
when(therapieplanCatalogue.getByKpaId(anyInt()))
|
||||
.thenReturn(List.of(1, 2));
|
||||
|
||||
// Mock Einzelempfehlungen - two referencing the same OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return List.of(ResultSet.from(Map.of("id", id, "ref_molekulargenetik", 42)));
|
||||
}).when(einzelempfehlungCatalogue).getAllByParentId(anyInt());
|
||||
|
||||
// Mock OS.Molekulargenetik
|
||||
doAnswer(invocationOnMock -> {
|
||||
var id = invocationOnMock.getArgument(0, Integer.class);
|
||||
return ResultSet.from(
|
||||
Map.of(
|
||||
"id", id,
|
||||
"patient_id", 4711,
|
||||
"entnahmemethode", "B",
|
||||
"probenmaterial", value
|
||||
)
|
||||
);
|
||||
}).when(molekulargenetikCatalogue).getById(anyInt());
|
||||
|
||||
var actual = this.mapper.getAllByKpaId(1, Reference.builder().build());
|
||||
|
||||
assertThat(actual).hasSize(1);
|
||||
assertThat(actual.get(0).getCollection().getLocalization()).isEqualTo(coding);
|
||||
}
|
||||
|
||||
// Returns all available Onkostar values and - best effort - expected mapping
|
||||
// See property catalogue OS.Probenmaterial and https://ibmi-ut.atlassian.net/wiki/spaces/DAM/pages/698777783/ line 82
|
||||
static Stream<Arguments> specimenLocalizationTestData() {
|
||||
return Stream.of(
|
||||
Arguments.of(
|
||||
"T",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.PRIMARY_TUMOR).display("Primärtumor")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"R",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"LK",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.METASTASIS).display("Metastase")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"M",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.METASTASIS).display("Metastase")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"ITM",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.METASTASIS).display("Metastase")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"SM",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.METASTASIS).display("Metastase")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"KM",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"NG",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"AS",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"PLERG",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"B",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder().
|
||||
system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"L",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"U",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
),
|
||||
Arguments.of(
|
||||
"S",
|
||||
TumorSpecimenCollectionLocalizationCoding.builder()
|
||||
.system("dnpm-dip/mtb/tumor-specimen/collection/localization").code(TumorSpecimenCollectionLocalizationCodingCode.UNKNOWN).display("Unbekannt")
|
||||
.build()
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user