mirror of
https://github.com/pcvolkmer/mv64e-onkostar-data.git
synced 2025-09-13 07:52:52 +00:00
feat: add project model consent
This commit is contained in:
@@ -42,6 +42,7 @@ Um Mithilfe wird gebeten.
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| DNPM-Datenmodell 2.1 - Bereich | Status | Anmerkung |
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|----------------------------------|--------|---------------------------------------------------------------------------------------|
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| MV Metadaten | ⛅ | MV Consent anhand DNPM-Formular. Kein Broad Consent
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| Patient | ✅ | Verwendet Patienten-ID, nicht 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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@@ -0,0 +1,46 @@
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/*
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* This file is part of mv64e-onkostar-data
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*
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* Copyright (C) 2025 Paul-Christian Volkmer
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*
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||||
* This program is free software: you can redistribute it and/or modify
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||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
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||||
*
|
||||
* 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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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_consentmv'
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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 ConsentMvCatalogue extends AbstractDataCatalogue {
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private ConsentMvCatalogue(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_consentmv";
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}
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public static ConsentMvCatalogue create(JdbcTemplate jdbcTemplate) {
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return new ConsentMvCatalogue(jdbcTemplate);
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}
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}
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@@ -0,0 +1,46 @@
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/*
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* This file is part of mv64e-onkostar-data
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*
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* Copyright (C) 2025 Paul-Christian Volkmer
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||||
*
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||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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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_consentmvverlauf'
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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 ConsentMvVerlaufCatalogue extends AbstractSubformDataCatalogue {
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private ConsentMvVerlaufCatalogue(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_consentmvverlauf";
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}
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public static ConsentMvVerlaufCatalogue create(JdbcTemplate jdbcTemplate) {
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return new ConsentMvVerlaufCatalogue(jdbcTemplate);
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}
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}
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@@ -0,0 +1,138 @@
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/*
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* This file is part of mv64e-onkostar-data
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*
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* Copyright (C) 2025 Paul-Christian Volkmer
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||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*
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*/
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package dev.pcvolkmer.onco.datamapper.mapper;
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import dev.pcvolkmer.mv64e.mtb.ConsentProvision;
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import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent;
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import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose;
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import dev.pcvolkmer.mv64e.mtb.Provision;
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import dev.pcvolkmer.onco.datamapper.ResultSet;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.ConsentMvCatalogue;
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import dev.pcvolkmer.onco.datamapper.datacatalogues.ConsentMvVerlaufCatalogue;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.List;
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import java.util.stream.Collectors;
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/**
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* Mapper class to load and map diagnosis data from database table 'dk_dnpm_consentmv'
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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 ConsentMvDataMapper implements DataMapper<ModelProjectConsent> {
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private final ConsentMvCatalogue catalogue;
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private final ConsentMvVerlaufCatalogue consentMvVerlaufCatalogue;
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public ConsentMvDataMapper(
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final ConsentMvCatalogue catalogue,
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final ConsentMvVerlaufCatalogue consentMvVerlaufCatalogue
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) {
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this.catalogue = catalogue;
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this.consentMvVerlaufCatalogue = consentMvVerlaufCatalogue;
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}
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/**
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* Loads and maps consent data using the consent form database id
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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 Consent data
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*/
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@Override
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public ModelProjectConsent getById(int id) {
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var data = catalogue.getById(id);
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var builder = ModelProjectConsent.builder();
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builder
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.date(data.getDate("date"))
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.version(getLatestVersion(id))
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.provisions(getProvisions(data))
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;
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return builder.build();
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}
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private String getLatestVersion(int id) {
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return consentMvVerlaufCatalogue.getAllByParentId(id).stream()
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.sorted((rs1, rs2) -> rs2.getDate("date").compareTo(rs1.getDate("date")))
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.map(resultSet -> resultSet.getString("version"))
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.findFirst()
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.orElse("");
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}
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private List<Provision> getProvisions(final ResultSet resultSet) {
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var result = new ArrayList<Provision>();
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var date = resultSet.getDate("date");
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if (ConsentProvision.PERMIT.toValue().equals(resultSet.getString("sequencing"))) {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.SEQUENCING).type(ConsentProvision.PERMIT)
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.build()
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);
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} else {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.SEQUENCING).type(ConsentProvision.DENY)
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.build()
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);
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}
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if (ConsentProvision.PERMIT.toValue().equals(resultSet.getString("caseidentification"))) {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION).type(ConsentProvision.PERMIT)
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.build()
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);
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} else {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION).type(ConsentProvision.DENY)
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.build()
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);
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}
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if (ConsentProvision.PERMIT.toValue().equals(resultSet.getString("reidentification"))) {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.REIDENTIFICATION).type(ConsentProvision.PERMIT)
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.build()
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);
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} else {
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result.add(
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Provision.builder()
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.date(date)
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.purpose(ModelProjectConsentPurpose.REIDENTIFICATION).type(ConsentProvision.DENY)
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.build()
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);
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}
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return result;
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}
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}
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@@ -0,0 +1,67 @@
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/*
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* This file is part of mv64e-onkostar-data
|
||||
*
|
||||
* Copyright (C) 2025 Paul-Christian Volkmer
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
*
|
||||
*/
|
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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;
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@ExtendWith(MockitoExtension.class)
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class ConsentMvCatalogueTest {
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JdbcTemplate jdbcTemplate;
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ConsentMvCatalogue catalogue;
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@BeforeEach
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void setUp(@Mock JdbcTemplate jdbcTemplate) {
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this.jdbcTemplate = jdbcTemplate;
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this.catalogue = ConsentMvCatalogue.create(jdbcTemplate);
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}
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@Test
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void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
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doAnswer(invocationOnMock -> List.of(resultSet))
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.when(jdbcTemplate)
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.queryForList(anyString(), anyInt());
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this.catalogue.getById(1);
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var captor = ArgumentCaptor.forClass(String.class);
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verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
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assertThat(captor.getValue())
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.isEqualTo("SELECT patient.patienten_id, dk_dnpm_consentmv.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_consentmv JOIN prozedur ON (prozedur.id = dk_dnpm_consentmv.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
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}
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}
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@@ -0,0 +1,83 @@
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/*
|
||||
* This file is part of mv64e-onkostar-data
|
||||
*
|
||||
* Copyright (C) 2025 Paul-Christian Volkmer
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
*
|
||||
*/
|
||||
|
||||
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;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.ArgumentCaptor;
|
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import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
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import org.springframework.jdbc.core.JdbcTemplate;
|
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|
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import java.util.ArrayList;
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import java.util.HashMap;
|
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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;
|
||||
import static org.mockito.ArgumentMatchers.anyInt;
|
||||
import static org.mockito.ArgumentMatchers.anyString;
|
||||
import static org.mockito.Mockito.*;
|
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|
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@ExtendWith(MockitoExtension.class)
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class ConsentMvVerlaufCatalogueTest {
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JdbcTemplate jdbcTemplate;
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ConsentMvVerlaufCatalogue catalogue;
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@BeforeEach
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void setUp(@Mock JdbcTemplate jdbcTemplate) {
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this.jdbcTemplate = jdbcTemplate;
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this.catalogue = ConsentMvVerlaufCatalogue.create(jdbcTemplate);
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}
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|
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@Test
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void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
|
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doAnswer(invocationOnMock -> List.of(resultSet))
|
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.when(jdbcTemplate)
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.queryForList(anyString(), anyInt());
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|
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this.catalogue.getById(1);
|
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|
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var captor = ArgumentCaptor.forClass(String.class);
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verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
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|
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assertThat(captor.getValue())
|
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.isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_consentmvverlauf.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_consentmvverlauf JOIN prozedur ON (prozedur.id = dk_dnpm_uf_consentmvverlauf.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
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}
|
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|
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@Test
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void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
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doAnswer(invocationOnMock -> List.of(resultSet))
|
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.when(jdbcTemplate)
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.queryForList(anyString(), anyInt());
|
||||
|
||||
this.catalogue.getAllByParentId(1);
|
||||
|
||||
var captor = ArgumentCaptor.forClass(String.class);
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verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
|
||||
|
||||
assertThat(captor.getValue())
|
||||
.isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_consentmvverlauf.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_consentmvverlauf JOIN prozedur ON (prozedur.id = dk_dnpm_uf_consentmvverlauf.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,124 @@
|
||||
/*
|
||||
* This file is part of mv64e-onkostar-data
|
||||
*
|
||||
* Copyright (C) 2025 Paul-Christian Volkmer
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Lesser General Public License as published by
|
||||
* the Free Software Foundation, either version 3 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 Lesser General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Lesser General Public License
|
||||
* along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
*
|
||||
*/
|
||||
|
||||
package dev.pcvolkmer.onco.datamapper.mapper;
|
||||
|
||||
import dev.pcvolkmer.mv64e.mtb.ConsentProvision;
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent;
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose;
|
||||
import dev.pcvolkmer.mv64e.mtb.Provision;
|
||||
import dev.pcvolkmer.onco.datamapper.ResultSet;
|
||||
import dev.pcvolkmer.onco.datamapper.datacatalogues.ConsentMvCatalogue;
|
||||
import dev.pcvolkmer.onco.datamapper.datacatalogues.ConsentMvVerlaufCatalogue;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import javax.sql.DataSource;
|
||||
import java.time.Instant;
|
||||
import java.util.Date;
|
||||
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.Mockito.doAnswer;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class ConsentMvDataMapperTest {
|
||||
|
||||
ConsentMvCatalogue catalogue;
|
||||
ConsentMvVerlaufCatalogue consentMvVerlaufCatalogue;
|
||||
ConsentMvDataMapper dataMapper;
|
||||
|
||||
@BeforeEach
|
||||
void setUp(
|
||||
@Mock ConsentMvCatalogue catalogue,
|
||||
@Mock ConsentMvVerlaufCatalogue consentMvVerlaufCatalogue
|
||||
) {
|
||||
this.catalogue = catalogue;
|
||||
this.consentMvVerlaufCatalogue = consentMvVerlaufCatalogue;
|
||||
this.dataMapper = new ConsentMvDataMapper(catalogue, consentMvVerlaufCatalogue);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldCreateDataMapper(@Mock DataSource dataSource) {
|
||||
assertThat(MtbDataMapper.create(dataSource)).isNotNull();
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldCreateConsent() {
|
||||
doAnswer(invocationOnMock ->
|
||||
ResultSet.from(
|
||||
Map.of(
|
||||
"id", "1",
|
||||
"date", new java.sql.Date(Date.from(Instant.parse("2025-07-12T12:00:00Z")).getTime()),
|
||||
"sequencing", "permit",
|
||||
"caseidentification", "deny",
|
||||
"reidentification", "deny"
|
||||
)
|
||||
)
|
||||
)
|
||||
.when(catalogue)
|
||||
.getById(anyInt());
|
||||
|
||||
doAnswer(invocationOnMock ->
|
||||
List.of(
|
||||
ResultSet.from(
|
||||
Map.of(
|
||||
"id", "1",
|
||||
"date", new java.sql.Date(Date.from(Instant.parse("2025-07-12T12:00:00Z")).getTime()),
|
||||
"version", "01"
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
.when(consentMvVerlaufCatalogue)
|
||||
.getAllByParentId(anyInt());
|
||||
|
||||
var actual = this.dataMapper.getById(1);
|
||||
assertThat(actual).isInstanceOf(ModelProjectConsent.class);
|
||||
assertThat(actual.getDate()).isEqualTo(Date.from(Instant.parse("2025-07-12T00:00:00Z")));
|
||||
assertThat(actual.getVersion()).isEqualTo("01");
|
||||
assertThat(actual.getProvisions()).hasSize(3);
|
||||
assertThat(actual.getProvisions()).containsAll(
|
||||
List.of(
|
||||
Provision.builder()
|
||||
.date(Date.from(Instant.parse("2025-07-12T00:00:00Z")))
|
||||
.purpose(ModelProjectConsentPurpose.SEQUENCING)
|
||||
.type(ConsentProvision.PERMIT)
|
||||
.build(),
|
||||
Provision.builder()
|
||||
.date(Date.from(Instant.parse("2025-07-12T00:00:00Z")))
|
||||
.purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
|
||||
.type(ConsentProvision.DENY)
|
||||
.build(),
|
||||
Provision.builder()
|
||||
.date(Date.from(Instant.parse("2025-07-12T00:00:00Z")))
|
||||
.purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
|
||||
.type(ConsentProvision.DENY)
|
||||
.build()
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user