diff --git a/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java b/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java
index a1a388a1416555569e367effa0aeb0c955a55fc1..e83e673f3b1db489a50fea60e52ef8cd948385f0 100644
--- a/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java
+++ b/src/main/java/nl/fairbydesign/backend/parsers/ExcelValidator.java
@@ -604,24 +604,29 @@ public class ExcelValidator {
for (observation_unit observation_unit : study.getAllHasPart()) {
for (Sample sample : observation_unit.getAllHasPart()) {
for (Assay assay : sample.getAllHasPart()) {
- if (assay.getClassTypeIri().endsWith("AmpliconLibraryAssay")) {
- AmpliconLibraryAssay assay1 = (AmpliconLibraryAssay) assay;
- for (Data_sample data_sample : assay1.getAllHasPart()) {
- data_sample.getName();
- }
- } else if (assay.getClassTypeIri().endsWith("AmpliconAssay")) {
- AmpliconAssay assay1 = (AmpliconAssay) assay;
- for (Data_sample data_sample : assay1.getAllHasPart()) {
- data_sample.getName();
- }
- } else if (assay.getClassTypeIri().endsWith("RNASeqAssay")) {
- RNASeqAssay assay1 = (RNASeqAssay) assay;
- for (Data_sample data_sample : assay1.getAllHasPart()) {
- data_sample.getName();
- }
- } else if (assay.getClassTypeIri().endsWith("DNASeqAssay")) {
- DNASeqAssay assay1 = (DNASeqAssay) assay;
- for (Data_sample data_sample : assay1.getAllHasPart()) {
+// if (assay.getClassTypeIri().endsWith("AmpliconLibraryAssay")) {
+// AmpliconLibraryAssay assay1 = (AmpliconLibraryAssay) assay;
+// for (Data_sample data_sample : assay1.getAllHasPart()) {
+// data_sample.getName();
+// }
+// } else if (assay.getClassTypeIri().endsWith("AmpliconAssay")) {
+// AmpliconAssay assay1 = (AmpliconAssay) assay;
+// for (Data_sample data_sample : assay1.getAllHasPart()) {
+// data_sample.getName();
+// }
+// } else if (assay.getClassTypeIri().endsWith("RNASeqAssay")) {
+// RNASeqAssay assay1 = (RNASeqAssay) assay;
+// for (Data_sample data_sample : assay1.getAllHasPart()) {
+// data_sample.getName();
+// }
+// } else if (assay.getClassTypeIri().endsWith("DNASeqAssay")) {
+// DNASeqAssay assay1 = (DNASeqAssay) assay;
+// for (Data_sample data_sample : assay1.getAllHasPart()) {
+// data_sample.getName();
+// }
+// } else
+ if (assay.getClassTypeIri().endsWith("Assay")) {
+ for (Data_sample data_sample : assay.getAllHasPart()) {
data_sample.getName();
}
} else {
@@ -752,24 +757,30 @@ public class ExcelValidator {
logger.info("Parsing " + sheet.getSheetName());
ArrayList<String> header = new ArrayList<>();
- // Assay type
- AssayType assayType;
- if (sheet.getSheetName().endsWith("AmpliconAssay")) {
- assayType = AssayType.Amplicon;
- } else if (sheet.getSheetName().endsWith("AmpliconLibrary")) {
- assayType = AssayType.AmpliconLibrary;
- } else if (sheet.getSheetName().endsWith("RNA")) {
- assayType = AssayType.Transcriptomics;
- } else if (sheet.getSheetName().toLowerCase().endsWith("illumina")) {
- assayType = AssayType.Genomics;
- } else if (sheet.getSheetName().toLowerCase().endsWith("nanopore")) {
- assayType = AssayType.Genomics;
- } else if (sheet.getSheetName().endsWith("Proteomics")) {
- assayType = AssayType.Proteomics;
- } else if (sheet.getSheetName().endsWith("Metabolomics")) {
- assayType = AssayType.Metabolomics;
+ // Assay type after " - " split, strip, camel case it and then remove spaces and turn into a URI
+ String assayTypeIRI;
+ if (sheet.getSheetName().contains(" - ")) {
+ String[] name = sheet.getSheetName().split(" - ");
+ String assayName = name[name.length-1];
+ boolean validAssayName = false;
+ // Check if it is part of the excel package
+ for (Metadata metadata : metadataArrayList) {
+ if (metadata.getPackage().toLowerCase(Locale.ROOT).contains(assayName.toLowerCase(Locale.ROOT))) {
+ validAssayName = true;
+ break;
+ }
+ }
+ if (!validAssayName) {
+ throw new Exception("This assay name is not supported: " + assayName);
+ }
+
+ // Create IRI
+ assayName = StringUtils.capitalize(assayName).replaceAll(" +", "");
+ assayTypeIRI = "http://m-unlock.nl/ontology/" + assayName;
+
} else {
- throw new Exception("The sheet " + sheet.getSheetName() + " is of an unsupported assay type");
+ // some kind of exception
+ throw new Exception("Assay sheet formatting is not correct should be according to: Assay - type");
}
// Header capture
@@ -803,8 +814,6 @@ public class ExcelValidator {
fileCell = row.getCell(header.indexOf(FORWARD_FILENAME), Row.MissingCellPolicy.CREATE_NULL_AS_BLANK);
} else if (header.indexOf(FILE_NAME) != -1) {
fileCell = row.getCell(header.indexOf(FILE_NAME), Row.MissingCellPolicy.CREATE_NULL_AS_BLANK);
- } else {
- // No file given yet...
}
// TODO Reduce list to the core elements
@@ -853,65 +862,68 @@ public class ExcelValidator {
}
// Setting the assay URL based on the type and identifier
- String ASSAYIRI = PREFIX + assayType.getIRI().replaceAll(".*/", "") + "/ASY_" + row.getCell(index).getStringCellValue().trim() + "";
+ String ASSAYIRI = PREFIX + assayTypeIRI.replaceAll(".*/", "") + "/ASY_" + row.getCell(index).getStringCellValue().trim() + "";
// Generic place holders
- Assay assay;
-
- // Section for amplicon / library data
- if (assayType.equals(AssayType.Amplicon)) {
- AmpliconAssay ampliconAssay = domain.make(AmpliconAssay.class, ASSAYIRI);
- assay = ampliconAssay;
- } else if (assayType.equals(AssayType.AmpliconLibrary)) {
- // Create amplicon library object
- if (header.indexOf(LIBRARY_NAME) == -1) {
- logging("Missing LibraryName for AmpliconLibraryAssay");
- }
- String assayLibraryIRI = PREFIX + AssayType.AmpliconLibrary.getIRI().replaceAll(".*/", "") + "/" + getStringValueCell(row.getCell(header.indexOf(LIBRARY_NAME))).trim();
- String assayIRI = PREFIX + AssayType.Amplicon.getIRI().replaceAll(".*/", "") + "/" + getStringValueCell(row.getCell(header.indexOf(ASSAY_IDENTIFIER))).trim();
-
- // logger.debug("Library " + assayLibraryIRI);
-
- AmpliconLibraryAssay ampliconLibraryAssay = domain.make(AmpliconLibraryAssay.class, assayLibraryIRI);
- String ampliconLibraryAssayIdentifier = getStringValueCell(row.getCell(header.indexOf(LIBRARY_NAME))).trim();
- ampliconLibraryAssay.setIdentifier(ampliconLibraryAssayIdentifier);
- ampliconLibraryAssay.setDescription("Amplicon library " + ampliconLibraryAssayIdentifier);
- ampliconLibraryAssay.setLogicalPath("null");
-
- // Cell can be numeric
-// Sample sample = getSample(iriCorrector(getStringValueCell(row.getCell(header.indexOf("SampleIdentifier")))));
- // TODO check if we should do this? Amplicon assay should be a library and attached to assay of type amplicon
- // sample.addAssay(ampliconLibraryAssay);
- // ampliconLibraryAssay.setSample(sample);
- // parsedHeaders.add(LIBRARY_NAME);
- // Skip identifier addition due to amplicon assays having many different identifiers for the same library
- parsedHeaders.add(ASSAY_IDENTIFIER);
- parsedHeaders.add(ASSAY_DESCRIPTION);
- // Prevent adding file objects as strings
- parsedHeaders.add(FORWARD_FILENAME);
- parsedHeaders.add(REVERSE_FILENAME);
-
- otherColumns(header, parsedHeaders, row, ampliconLibraryAssay.getResource().getURI(), metadataArrayList);
- // Remove this for further processing of the assay
- parsedHeaders.removeAll(List.of(new String[]{ASSAY_IDENTIFIER, ASSAY_DESCRIPTION}));
-
- // Create amplicon object even though its not demultiplexed yet?...
- AmpliconAssay ampliconAssay = domain.make(AmpliconAssay.class, assayIRI);
- // Make link to the amplicon library
- ampliconAssay.setLibrary(ampliconLibraryAssay);
- assay = ampliconAssay;
-
- // Section for RNA sequencing data
- } else if (assayType.equals(AssayType.Transcriptomics)) {
- RNASeqAssay rnaSeqAssay = domain.make(RNASeqAssay.class, ASSAYIRI);
- assay = rnaSeqAssay;
- // Section for DNA sequencing data
- } else if (assayType.equals(AssayType.Genomics)) {
- DNASeqAssay dnaSeqAssay = domain.make(DNASeqAssay.class, ASSAYIRI);
- assay = dnaSeqAssay;
- } else {
- throw new Exception(assayType.getIRI() + " not ready at the moment");
- }
+ Assay assay = domain.make(Assay.class, ASSAYIRI);
+ assay.addAdditionalType(assayTypeIRI);
+
+// // Section for amplicon / library data
+// if (assayType.equals(AssayType.Amplicon)) {
+// AmpliconAssay ampliconAssay = domain.make(AmpliconAssay.class, ASSAYIRI);
+// assay = ampliconAssay;
+// } else if (assayType.equals(AssayType.AmpliconLibrary)) {
+// // Create amplicon library object
+// if (header.indexOf(LIBRARY_NAME) == -1) {
+// logging("Missing LibraryName for AmpliconLibraryAssay");
+// }
+// String assayLibraryIRI = PREFIX + AssayType.AmpliconLibrary.getIRI().replaceAll(".*/", "") + "/" + getStringValueCell(row.getCell(header.indexOf(LIBRARY_NAME))).trim();
+// String assayIRI = PREFIX + AssayType.Amplicon.getIRI().replaceAll(".*/", "") + "/" + getStringValueCell(row.getCell(header.indexOf(ASSAY_IDENTIFIER))).trim();
+//
+// // logger.debug("Library " + assayLibraryIRI);
+//
+// AmpliconLibraryAssay ampliconLibraryAssay = domain.make(AmpliconLibraryAssay.class, assayLibraryIRI);
+// String ampliconLibraryAssayIdentifier = getStringValueCell(row.getCell(header.indexOf(LIBRARY_NAME))).trim();
+// ampliconLibraryAssay.setIdentifier(ampliconLibraryAssayIdentifier);
+// ampliconLibraryAssay.setDescription("Amplicon library " + ampliconLibraryAssayIdentifier);
+// ampliconLibraryAssay.setLogicalPath("null");
+//
+// // Cell can be numeric
+//// Sample sample = getSample(iriCorrector(getStringValueCell(row.getCell(header.indexOf("SampleIdentifier")))));
+// // TODO check if we should do this? Amplicon assay should be a library and attached to assay of type amplicon
+// // sample.addAssay(ampliconLibraryAssay);
+// // ampliconLibraryAssay.setSample(sample);
+// // parsedHeaders.add(LIBRARY_NAME);
+// // Skip identifier addition due to amplicon assays having many different identifiers for the same library
+// parsedHeaders.add(ASSAY_IDENTIFIER);
+// parsedHeaders.add(ASSAY_DESCRIPTION);
+// // Prevent adding file objects as strings
+// parsedHeaders.add(FORWARD_FILENAME);
+// parsedHeaders.add(REVERSE_FILENAME);
+//
+// otherColumns(header, parsedHeaders, row, ampliconLibraryAssay.getResource().getURI(), metadataArrayList);
+// // Remove this for further processing of the assay
+// parsedHeaders.removeAll(List.of(new String[]{ASSAY_IDENTIFIER, ASSAY_DESCRIPTION}));
+//
+// // Create amplicon object even though its not demultiplexed yet?...
+// AmpliconAssay ampliconAssay = domain.make(AmpliconAssay.class, assayIRI);
+// // Make link to the amplicon library
+// ampliconAssay.setLibrary(ampliconLibraryAssay);
+// assay = ampliconAssay;
+//
+// // Section for RNA sequencing data
+// } else if (assayType.equals(AssayType.Transcriptomics)) {
+// RNASeqAssay rnaSeqAssay = domain.make(RNASeqAssay.class, ASSAYIRI);
+// assay = rnaSeqAssay;
+// // Section for DNA sequencing data
+// } else if (assayType.equals(AssayType.Genomics)) {
+// DNASeqAssay dnaSeqAssay = domain.make(DNASeqAssay.class, ASSAYIRI);
+// assay = dnaSeqAssay;
+// } else {
+// logger.info("Created default Assay");
+// assay = domain.make(Assay.class, ASSAYIRI);
+// // TODO add additional type based on sheet name and default IRI
+// }
/**
* Generic Assay information
@@ -923,7 +935,7 @@ public class ExcelValidator {
// parsedHeaders.addAll(Arrays.asList(ASSAY_DESCRIPTION, ASSAY_TITLE, ASSAY_IDENTIFIER, PLATFORM));
if (fileCell.getCellType().equals(CellType.BLANK)) {
-// logging("No file found for " + assay.getResource().getURI());
+ logger.debug("No file found for " + assay.getResource().getURI());
} else {
String fileName = getStringValueCell(fileCell);
// Check the FileNameForwardPath and FileNameReversePath first
@@ -970,7 +982,8 @@ public class ExcelValidator {
parsedHeaders.addAll(Arrays.asList(FORWARD_FILENAME, REVERSE_FILENAME));
}
- } else if (fileName != null) {
+ // If it is one of the sequence assay types
+ } else if (!assay.getClassTypeIri().endsWith("/Assay")) {
SingleSequenceDataSet singleSequenceDataSet = domain.make(SingleSequenceDataSet.class, PREFIX + fileName);
singleSequenceDataSet.setName(new File(fileName).getName().trim());
singleSequenceDataSet.setContentUrl("null");
@@ -987,6 +1000,15 @@ public class ExcelValidator {
assay.addHasPart(singleSequenceDataSet);
parsedHeaders.addAll(Arrays.asList(FORWARD_FILENAME));
+ } else {
+ Data_sample data_sample = domain.make(Data_sample.class, PREFIX + fileName);
+ data_sample.setName(new File(fileName).getName().trim());
+ data_sample.setContentUrl("null");
+ data_sample.setBase64("null");
+ data_sample.setSha256("null");
+ data_sample.setContentSize(0L);
+ data_sample.setFileFormat(setFileFormat(data_sample.getName()));
+ assay.addHasPart(data_sample);
}
}
@@ -1004,14 +1026,14 @@ public class ExcelValidator {
// parsedHeaders.addAll(Arrays.asList(SAMPLE_IDENTIFIER));
// assay is still an amplicon assay but if it has an amplicon library we should move the files from amplicon assay to amplicon library assay
- if (assayType.equals(AssayType.AmpliconLibrary)) {
- AmpliconAssay ampliconAssay = (AmpliconAssay) assay;
- AmpliconLibraryAssay library = ampliconAssay.getLibrary();
- for (Data_sample data_sample : ampliconAssay.getAllHasPart()) {
- library.addHasPart(data_sample);
- ampliconAssay.remHasPart(data_sample);
- }
- }
+// if (assayType.equals(AssayType.AmpliconLibrary)) {
+// AmpliconAssay ampliconAssay = (AmpliconAssay) assay;
+// AmpliconLibraryAssay library = ampliconAssay.getLibrary();
+// for (Data_sample data_sample : ampliconAssay.getAllHasPart()) {
+// library.addHasPart(data_sample);
+// ampliconAssay.remHasPart(data_sample);
+// }
+// }
// Perform reference incorporation
if (header.indexOf(REFERENCE) != -1) {
diff --git a/src/main/java/nl/fairbydesign/views/template/TemplateView.java b/src/main/java/nl/fairbydesign/views/template/TemplateView.java
index e673ad8464e36629c3a8d39381c10b890a0b7ec8..b09ee5981fb74edcc6a5431227d9228f375086a4 100644
--- a/src/main/java/nl/fairbydesign/views/template/TemplateView.java
+++ b/src/main/java/nl/fairbydesign/views/template/TemplateView.java
@@ -274,7 +274,9 @@ public class TemplateView extends Div {
VerticalLayout placeholder = new VerticalLayout();
createPackageSelectionGrid(placeholder, metadata, help, false);
verticalLayouts.add(placeholder);
- assayLayout.add(addAssayButton, removeAssayButton);
+ HorizontalLayout assayButtons = new HorizontalLayout();
+ assayButtons.add(addAssayButton, removeAssayButton);
+ assayLayout.add(assayButtons);
assayLayout.add(verticalLayouts.get(0));
// Button to add another assay to the assay layout