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sven1103sven1103
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First refactor part
1 parent a8414c2 commit 419a12a

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Lines changed: 1196 additions & 10 deletions

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user-interface/src/main/java/life/qbic/datamanager/files/export/FileNameFormatter.java renamed to application-commons/src/main/java/life/qbic/application/commons/FileNameFormatter.java

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package life.qbic.datamanager.files.export;
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package life.qbic.application.commons;
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import java.time.LocalDate;
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import java.time.format.DateTimeFormatter;

‎project-management-infrastructure/pom.xml‎

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<artifactId>jakarta.xml.bind-api</artifactId>
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<version>4.0.2</version>
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</dependency>
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<!-- Needed for xlsx support !-->
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<dependency>
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<groupId>org.apache.poi</groupId>
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<artifactId>poi</artifactId>
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<version>5.4.0</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
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<dependency>
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<groupId>org.apache.poi</groupId>
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<artifactId>poi-ooxml</artifactId>
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<version>5.4.0</version>
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</dependency>
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</dependencies>
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</project>

‎project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/template/Column.java‎

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package life.qbic.projectmanagement.infrastructure.api.template;
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import java.util.Optional;
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import life.qbic.projectmanagement.infrastructure.api.template.ExampleProvider.Helper;
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/**
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* A column in a file (for example xlsx files or TSV files)
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*
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* @since 1.8.0
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*/
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public interface Column {
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/**
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* The index of the column 0-based
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*
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* @return the index of this column
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*/
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int index();
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/**
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* The name of the column as it can be used in a header cell for the column
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*
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* @return the name of the column
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*/
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String headerName();
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/**
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* @return true if filling out this column is mandatory; false otherwise
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*/
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boolean isMandatory();
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/**
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* @return true if the content of this column is only provided and not considered relevant for
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* parsing; false otherwise
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*/
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boolean isReadOnly();
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/**
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* Information on how to fill this column
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*
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* @return a helper with information on how to fill this column. Can be {@link Optional#empty()}
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* if no help is provided.
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*/
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Optional<Helper> getFillHelp();
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}

‎project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/template/ConfoundingVariableColumn.java‎

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package life.qbic.projectmanagement.infrastructure.api.template;
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import java.util.Optional;
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import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.VariableReference;
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import life.qbic.projectmanagement.infrastructure.api.template.ExampleProvider.Helper;
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public record ConfoundingVariableColumn(VariableReference variableReference, int index,
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String headerName) implements Column {
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@Override
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public boolean isMandatory() {
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return false;
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}
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@Override
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public boolean isReadOnly() {
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return false;
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}
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@Override
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public Optional<Helper> getFillHelp() {
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return Optional.empty();
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}
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}

‎project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/template/ExampleProvider.java‎

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package life.qbic.projectmanagement.infrastructure.api.template;
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/**
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* TODO!
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* <b>short description</b>
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*
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* <p>detailed description</p>
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*
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* @since <version tag>
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*/
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public interface ExampleProvider {
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record Helper(String exampleValue, String description) {
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}
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Helper getHelper(Column column);
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}

‎project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/template/RegisterColumn.java‎

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package life.qbic.projectmanagement.infrastructure.api.template;
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import java.util.Arrays;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import life.qbic.projectmanagement.infrastructure.api.template.ExampleProvider.Helper;
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/**
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* <b>Sample Register Columns</b>
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*
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* <p>Enumeration of the columns shown in the file used for sample registration
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* in the context of sample batch file based upload. Provides the name of the header column, the
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* column index and if the column should be set to readOnly in the generated sheet
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* </p>
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*/
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public enum RegisterColumn implements Column {
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SAMPLE_NAME("Sample Name", 0, false, true),
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ANALYSIS("Analysis to be performed", 1, false, true),
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BIOLOGICAL_REPLICATE("Biological Replicate", 2, false, false),
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CONDITION("Condition", 3, false, true),
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SPECIES("Species", 4, false, true),
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SPECIMEN("Specimen", 5, false, true),
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ANALYTE("Analyte", 6, false, true),
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COMMENT("Comment", 7, false, false);
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private static final ExampleProvider exampleProvider = column -> {
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if (column instanceof RegisterColumn registerColumn) {
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return switch (registerColumn) {
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case SAMPLE_NAME -> new Helper("Free text, e.g. RNA Sample 1, RNA Sample 2",
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"A visual aid to simplify navigation for the person managing the metadata.");
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case ANALYSIS -> new Helper("Enumeration, Select a value from the dropdown",
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"The test performed on samples for the purpose of finding and measuring chemical substances.");
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case BIOLOGICAL_REPLICATE -> new Helper("Free text, e.g. patient1, patient2, Mouse1", """
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Different samples measured accross multiple conditions.
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Tip: You can use this column to identifiy whether the samples belong to the same source.""");
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case CONDITION -> new Helper("Enumeration, Select a value from the dropdown", """
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A distinct value or condition of the independent variable at which the dependent variable is measured in order to carry out statistical analysis.
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Note: The values in the dropdown are the predefined values from the experimental design.""");
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case SPECIES -> new Helper("Enumeration, Select a value from the dropdown", """
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Scientific name of the organism(s) from which the biological material is derived. E.g. Homo sapiens, Mus musculus.
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Note: The values in the dropdown are the predefined values from the experimental design.""");
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case ANALYTE -> new Helper("Enumeration, Select a value from the dropdown", """
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The chemical substance extracted from the biological material that is identified and measured.
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Note: The values in the dropdown are the predefined values from the experimental design.""");
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case SPECIMEN -> new Helper("Enumeration, Select a value from the dropdown", """
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Name of the biological material from which the analytes would be extracted.
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Note: The values in the dropdown are the predefined values from the experimental design.""");
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case COMMENT -> new Helper("Free text", "Notes about the sample. (Max 500 characters)");
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};
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}
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throw new IllegalArgumentException(
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"Column not of class " + RegisterColumn.class.getName() + " but is "
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+ column.getClass().getName());
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};
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private final String headerName;
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private final int columnIndex;
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private final boolean readOnly;
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private final boolean mandatory;
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public static int maxColumnIndex() {
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return Arrays.stream(values())
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.mapToInt(RegisterColumn::index)
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.max().orElse(0);
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}
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public static Set<String> headerNames() {
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return Arrays.stream(values()).map(RegisterColumn::headerName).collect(Collectors.toSet());
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}
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/**
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* @param headerName the name in the header
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* @param columnIndex the index of the column this property is in
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* @param readOnly is the property read only
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* @param mandatory
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*/
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RegisterColumn(String headerName, int columnIndex, boolean readOnly, boolean mandatory) {
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this.headerName = headerName;
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this.columnIndex = columnIndex;
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this.readOnly = readOnly;
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this.mandatory = mandatory;
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}
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@Override
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public String headerName() {
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return headerName;
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}
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@Override
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public int index() {
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return columnIndex;
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}
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@Override
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public boolean isReadOnly() {
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return readOnly;
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}
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@Override
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public boolean isMandatory() {
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return mandatory;
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}
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@Override
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public Optional<Helper> getFillHelp() {
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return Optional.of(exampleProvider.getHelper(this));
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}
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}

‎project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/template/SampleRegisterFactory.java‎

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package life.qbic.projectmanagement.infrastructure.api.template;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import java.util.function.BinaryOperator;
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import life.qbic.projectmanagement.application.confounding.ConfoundingVariableService.ConfoundingVariableInformation;
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import org.apache.poi.ss.usermodel.CreationHelper;
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import org.apache.poi.ss.usermodel.Row;
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import org.apache.poi.ss.usermodel.Sheet;
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public class SampleRegisterFactory implements WorkbookFactory {
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private final List<String> analysisMethods;
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private final List<String> conditions;
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private final List<String> analytes;
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private final List<String> species;
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private final List<String> specimen;
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private final List<ConfoundingVariableInformation> confoundingVariables;
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public SampleRegisterFactory(List<String> analysisMethods, List<String> conditions,
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List<String> analytes, List<String> species,
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List<String> specimen, List<ConfoundingVariableInformation> confoundingVariables) {
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this.analysisMethods = analysisMethods;
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this.conditions = conditions;
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this.analytes = analytes;
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this.species = species;
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this.specimen = specimen;
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this.confoundingVariables = confoundingVariables;
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}
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@Override
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public int numberOfRowsToGenerate() {
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return 2_000;
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}
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@Override
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public void enterValuesAsRows(Sheet sheet, CellStyles cellStyles) {
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//nothing to do
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}
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@Override
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public String sheetName() {
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return "Sample Metadata";
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}
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@Override
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public Column[] getColumns() {
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ArrayList<Column> columns = new ArrayList<>(List.of(RegisterColumn.values()));
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var colOffset = RegisterColumn.maxColumnIndex() + 1; //offset + 0 is the next free column
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for (int i = 0; i < confoundingVariables.size(); i++) {
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var confoundingVariable = confoundingVariables.get(i);
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int columnIndex = colOffset + i;
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columns.add(
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new ConfoundingVariableColumn(confoundingVariable.id(), columnIndex,
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confoundingVariable.variableName()));
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}
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return columns.toArray(new Column[0]);
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}
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@Override
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public void customizeValidation(Sheet hiddenSheet, Sheet sheet) {
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WorkbookFactory.addValidation(hiddenSheet,
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sheet,
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1,
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numberOfRowsToGenerate() - 1,
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RegisterColumn.ANALYSIS.index(),
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"Analysis Method",
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analysisMethods);
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WorkbookFactory.addValidation(hiddenSheet,
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sheet,
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1,
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numberOfRowsToGenerate() - 1,
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RegisterColumn.CONDITION.index(),
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"Condition",
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conditions);
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WorkbookFactory.addValidation(hiddenSheet,
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sheet,
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1,
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numberOfRowsToGenerate() - 1,
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RegisterColumn.ANALYTE.index(),
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"Analytes",
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analytes);
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WorkbookFactory.addValidation(hiddenSheet,
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sheet,
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1,
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numberOfRowsToGenerate() - 1,
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RegisterColumn.SPECIES.index(),
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"Species",
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species);
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WorkbookFactory.addValidation(hiddenSheet,
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sheet,
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1,
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numberOfRowsToGenerate() - 1,
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RegisterColumn.SPECIMEN.index(),
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"Specimen",
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specimen);
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}
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@Override
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public Optional<String> longestValueForColumn(int columnIndex) {
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BinaryOperator<String> keepLongerString = (String s1, String s2) -> s1.length() > s2.length()
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? s1 : s2;
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if (columnIndex == RegisterColumn.ANALYSIS.index()) {
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return analysisMethods.stream().reduce(keepLongerString);
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} else if (columnIndex == RegisterColumn.CONDITION.index()) {
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return conditions.stream().reduce(keepLongerString);
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} else if (columnIndex == RegisterColumn.ANALYTE.index()) {
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return analytes.stream().reduce(keepLongerString);
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} else if (columnIndex == RegisterColumn.SPECIES.index()) {
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return species.stream().reduce(keepLongerString);
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} else if (columnIndex == RegisterColumn.SPECIMEN.index()) {
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return specimen.stream().reduce(keepLongerString);
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}
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return Optional.empty();
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}
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@Override
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public void customizeHeaderCells(Row header, CreationHelper creationHelper,
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CellStyles cellStyles) {
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// nothing to do
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}
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}

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