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Replace Organisation Id with Organisation URL
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Co-authored-by: Shraddha Pawar <[email protected]>
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@KochTobi @Shraddha0903
KochTobi and Shraddha0903 committed Oct 25, 2024
1 parent 9883159 commit a09ed29
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Showing 9 changed files with 22 additions and 22 deletions.
8 changes: 4 additions & 4 deletions user-interface/src/main/java/life/qbic/datamanager/parser/MetadataConverter.java
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Expand Up @@ -132,7 +132,7 @@ private List<MeasurementMetadata> convertNewProteomicsMeasurement(ParsingResult
var technicalReplicateName = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.TECHNICAL_REPLICATE_NAME.headerName(), "");
var organisationId = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.ORGANISATION_ID.headerName(), "");
ProteomicsMeasurementRegisterColumn.ORGANISATION_URL.headerName(), "");
var msDevice = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.MS_DEVICE.headerName(), "");
var samplePoolGroup = parsingResult.getValueOrDefault(i,
Expand Down Expand Up @@ -192,7 +192,7 @@ private List<MeasurementMetadata> convertExistingProteomicsMeasurement(
var technicalReplicateName = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementEditColumn.TECHNICAL_REPLICATE_NAME.headerName(), "");
var organisationId = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementEditColumn.ORGANISATION_ID.headerName(), "");
ProteomicsMeasurementEditColumn.ORGANISATION_URL.headerName(), "");
var msDevice = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementEditColumn.MS_DEVICE.headerName(), "");
var samplePoolGroup = parsingResult.getValueOrDefault(i,
Expand Down Expand Up @@ -252,7 +252,7 @@ private List<MeasurementMetadata> convertExistingNGSMeasurement(ParsingResult pa
""))
);
var organisationId = parsingResult.getValueOrDefault(i,
NGSMeasurementEditColumn.ORGANISATION_ID.headerName(), "");
NGSMeasurementEditColumn.ORGANISATION_URL.headerName(), "");
var instrument = parsingResult.getValueOrDefault(i,
NGSMeasurementEditColumn.INSTRUMENT.headerName(), "");
var facility = parsingResult.getValueOrDefault(i,
Expand Down Expand Up @@ -304,7 +304,7 @@ private List<MeasurementMetadata> convertNewNGSMeasurement(ParsingResult parsing
""))
);
var organisationId = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.ORGANISATION_ID.headerName(), "");
NGSMeasurementRegisterColumn.ORGANISATION_URL.headerName(), "");
var instrument = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.INSTRUMENT.headerName(), "");
var facility = parsingResult.getValueOrDefault(i,
Expand Down
6 changes: 3 additions & 3 deletions ...face/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementEditColumn.java
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Expand Up @@ -20,7 +20,7 @@ public enum NGSMeasurementEditColumn implements Column {
SAMPLE_ID("QBiC Sample Id", 1, true, true),
SAMPLE_NAME("Sample Name", 2, true, false),
POOL_GROUP("Sample Pool Group", 3, true, false),
ORGANISATION_ID("Organisation ID", 4, false, true),
ORGANISATION_URL("Organisation URL", 4, false, true),
ORGANISATION_NAME("Organisation Name", 5, true, false),
FACILITY("Facility", 6, false, true),
INSTRUMENT("Instrument", 7, false, true),
Expand All @@ -46,10 +46,10 @@ public enum NGSMeasurementEditColumn implements Column {
"A visual aid to simplify sample navigation for the person managing the metadata.");
case POOL_GROUP -> new Helper("Free text, e.g. pool group 1",
"A group of samples that are pooled together for a measurement. All samples in a pool group should have the same label.");
case ORGANISATION_ID -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
case ORGANISATION_URL -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
A unique identifier of the organisation where the measurement has been conducted.
Tip: You can click on the column header (%s) to go to the ROR registry website where you can search your organisation and find its ROR URL.
""".formatted(ORGANISATION_ID.headerName()));
""".formatted(ORGANISATION_URL.headerName()));
case ORGANISATION_NAME -> new Helper("Free text, e.g. University of Tübingen",
"The name of the organisation where the measurement has been conducted.");
case FACILITY -> new Helper("Free text, e.g. Quantitative Biology Centre",
Expand Down
6 changes: 3 additions & 3 deletions .../src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementRegisterColumn.java
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Expand Up @@ -19,7 +19,7 @@ public enum NGSMeasurementRegisterColumn implements Column {
SAMPLE_ID("QBiC Sample Id", 0, false, true),
SAMPLE_NAME("Sample Name", 1, true, false),
POOL_GROUP("Sample Pool Group", 2, false, false),
ORGANISATION_ID("Organisation ID", 3, false, true),
ORGANISATION_URL("Organisation URL", 3, false, true),
FACILITY("Facility", 4, false, true),
INSTRUMENT("Instrument", 5, false, true),
SEQUENCING_READ_TYPE("Sequencing Read Type", 6, false, true),
Expand All @@ -45,10 +45,10 @@ public enum NGSMeasurementRegisterColumn implements Column {
"A visual aid to simplify sample navigation for the person managing the metadata. Is ignored after upload.");
case POOL_GROUP -> new Helper("Free text, e.g. pool group 1",
"A group of samples that are pooled together for a measurement. All samples in a pool group should have the same label.");
case ORGANISATION_ID -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
case ORGANISATION_URL -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
A unique identifier of the organisation where the measurement has been conducted.
Tip: You can click on the column header (%s) to go to the ROR registry website where you can search your organisation and find its ROR URL.
""".formatted(ORGANISATION_ID.headerName()));
""".formatted(ORGANISATION_URL.headerName()));
case FACILITY -> new Helper("Free text, e.g. Quantitative Biology Centre",
"The facilities name within the organisation (group name, etc.)");
case INSTRUMENT -> new Helper("CURIE (ontology), e.g. EFO:0008637", """
Expand Down
6 changes: 3 additions & 3 deletions ...c/main/java/life/qbic/datamanager/parser/measurement/ProteomicsMeasurementEditColumn.java
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Expand Up @@ -21,7 +21,7 @@ public enum ProteomicsMeasurementEditColumn implements Column {
"Sample Name", 2, true, false),
POOL_GROUP("Sample Pool Group", 3, true, false),
TECHNICAL_REPLICATE_NAME("Technical Replicate", 4, false, false),
ORGANISATION_ID("Organisation ID", 5, false, true),
ORGANISATION_URL("Organisation URL", 5, false, true),
ORGANISATION_NAME("Organisation Name", 6, true, false),
FACILITY("Facility", 7, false, true),
MS_DEVICE("MS Device", 8, false, true),
Expand Down Expand Up @@ -54,10 +54,10 @@ public enum ProteomicsMeasurementEditColumn implements Column {
"A group of samples that are pooled together for a measurement. All samples in a pool group should have the same label.");
case TECHNICAL_REPLICATE_NAME -> new Helper("Free text, e.g. Sample 1A, Sample 1B",
"Repeated measurements of the same sample that represent independent measures of the random noise associated with protocols or equipment.");
case ORGANISATION_ID -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
case ORGANISATION_URL -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
A unique identifier of the organisation where the measurement has been conducted.
Tip: You can click on the column header (%s) to go to the ROR registry website where you can search your organisation and find its ROR URL.
""".formatted(ORGANISATION_ID.headerName()));
""".formatted(ORGANISATION_URL.headerName()));
case ORGANISATION_NAME -> new Helper("Free text, e.g. University of Tübingen",
"The name of the organisation where the measurement has been conducted.");
case FACILITY -> new Helper("Free text, e.g. Quantitative Biology Center",
Expand Down
6 changes: 3 additions & 3 deletions ...in/java/life/qbic/datamanager/parser/measurement/ProteomicsMeasurementRegisterColumn.java
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Expand Up @@ -22,7 +22,7 @@ public enum ProteomicsMeasurementRegisterColumn implements Column {
POOL_GROUP("Sample Pool Group", 2, false, false),
TECHNICAL_REPLICATE_NAME("Technical Replicate", 3, false, false),
CYCLE_FRACTION_NAME("Cycle/Fraction Name", 4, false, false),
ORGANISATION_ID("Organisation ID", 5, false, true),
ORGANISATION_URL("Organisation URL", 5, false, true),
FACILITY("Facility", 6, false, true),
LC_COLUMN("LC Column", 7, false, true),
MS_DEVICE("MS Device", 8, false, true),
Expand Down Expand Up @@ -50,10 +50,10 @@ public enum ProteomicsMeasurementRegisterColumn implements Column {
"A group of samples that are pooled together for a measurement. All samples in a pool group should have the same label.");
case TECHNICAL_REPLICATE_NAME -> new Helper("Free text, e.g. Sample 1A, Sample 1B",
"Repeated measurements of the same sample that represent independent measures of the random noise associated with protocols or equipment.");
case ORGANISATION_ID -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
case ORGANISATION_URL -> new Helper("ROR URL, e.g. https://ror.org/03a1kwz48", """
A unique identifier of the organisation where the measurement has been conducted.
Tip: You can click on the column header (%s) to go to the ROR registry website where you can search your organisation and find its ROR URL.
""".formatted(ORGANISATION_ID.headerName()));
""".formatted(ORGANISATION_URL.headerName()));
case FACILITY -> new Helper("Free text, e.g. Quantitative Biology Center",
"The facility's name within the organisation.");
case MS_DEVICE -> new Helper("CURIE (ontology), e.g. NCIT:C12434", """
Expand Down
4 changes: 2 additions & 2 deletions ...src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java
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Expand Up @@ -65,7 +65,7 @@ private static void writeMeasurementIntoRow(NGSMeasurementEntry ngsMeasurementEn
case SAMPLE_ID -> ngsMeasurementEntry.sampleInformation().sampleId();
case SAMPLE_NAME -> ngsMeasurementEntry.sampleInformation().sampleName();
case POOL_GROUP -> ngsMeasurementEntry.samplePoolGroup();
case ORGANISATION_ID -> ngsMeasurementEntry.organisationId();
case ORGANISATION_URL -> ngsMeasurementEntry.organisationId();
case ORGANISATION_NAME -> ngsMeasurementEntry.organisationName();
case FACILITY -> ngsMeasurementEntry.facility();
case INSTRUMENT -> ngsMeasurementEntry.instrumentCURI();
Expand Down Expand Up @@ -121,7 +121,7 @@ public byte[] getContent() {
cell.setCellStyle(boldStyle);
if (column.isReadOnly()) {
cell.setCellStyle(readOnlyHeaderStyle);
} else if (column.equals(NGSMeasurementEditColumn.ORGANISATION_ID)) {
} else if (column.equals(NGSMeasurementEditColumn.ORGANISATION_URL)) {
CreationHelper creationHelper = workbook.getCreationHelper();
Hyperlink hyperlink = creationHelper.createHyperlink(HyperlinkType.URL);
hyperlink.setAddress("https://ror.org");
Expand Down
2 changes: 1 addition & 1 deletion ...main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java
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Expand Up @@ -78,7 +78,7 @@ public byte[] getContent() {
cell.setCellStyle(boldStyle);
if (column.isReadOnly()) {
cell.setCellStyle(readOnlyHeaderStyle);
} else if (column.equals(NGSMeasurementRegisterColumn.ORGANISATION_ID)) {
} else if (column.equals(NGSMeasurementRegisterColumn.ORGANISATION_URL)) {
CreationHelper creationHelper = workbook.getCreationHelper();
Hyperlink hyperlink = creationHelper.createHyperlink(HyperlinkType.URL);
hyperlink.setAddress("https://ror.org");
Expand Down
4 changes: 2 additions & 2 deletions ...n/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java
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Expand Up @@ -67,7 +67,7 @@ private static void createMeasurementEntry(ProteomicsMeasurementEntry pxpEntry,
case SAMPLE_NAME -> pxpEntry.sampleInformation().sampleName();
case POOL_GROUP -> pxpEntry.samplePoolGroup();
case TECHNICAL_REPLICATE_NAME -> pxpEntry.technicalReplicateName();
case ORGANISATION_ID -> pxpEntry.organisationId();
case ORGANISATION_URL -> pxpEntry.organisationId();
case ORGANISATION_NAME -> pxpEntry.organisationName();
case FACILITY -> pxpEntry.facility();
case MS_DEVICE -> pxpEntry.msDeviceCURIE();
Expand Down Expand Up @@ -123,7 +123,7 @@ public byte[] getContent() {
cell.setCellStyle(boldStyle);
if (measurementColumn.isReadOnly()) {
cell.setCellStyle(readOnlyHeaderStyle);
} else if (measurementColumn.equals(ProteomicsMeasurementEditColumn.ORGANISATION_ID)) {
} else if (measurementColumn.equals(ProteomicsMeasurementEditColumn.ORGANISATION_URL)) {
CreationHelper creationHelper = workbook.getCreationHelper();
Hyperlink hyperlink = creationHelper.createHyperlink(HyperlinkType.URL);
hyperlink.setAddress("https://ror.org");
Expand Down
2 changes: 1 addition & 1 deletion ...va/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java
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Expand Up @@ -76,7 +76,7 @@ public byte[] getContent() {
cell.setCellStyle(boldStyle);
if (measurementColumn.isReadOnly()) {
cell.setCellStyle(readOnlyHeaderStyle);
} else if (measurementColumn.equals(ProteomicsMeasurementRegisterColumn.ORGANISATION_ID)) {
} else if (measurementColumn.equals(ProteomicsMeasurementRegisterColumn.ORGANISATION_URL)) {
CreationHelper creationHelper = workbook.getCreationHelper();
Hyperlink hyperlink = creationHelper.createHyperlink(HyperlinkType.URL);
hyperlink.setAddress("https://ror.org");
Expand Down

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