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Merge from wnprc18.3 svn r.64261 to r.65647 #1370

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Merged
labkey-jeckels merged 3 commits into from
Sep 1, 2020
Merged

Merge from wnprc18.3 svn r.64261 to r.65647 #1370

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aff1896
Merge from wnprc18.3 svn r.64261-64312
labkey-bpatel Jul 6, 2020
cabe162
Merge from wnprc18.3 svn r.64600 to 64828
labkey-bpatel Jul 7, 2020
979485a
Fix ViralLoadAssayTest - restore WNPRC test code, updated to new DOM …
labkey-jeckels Aug 28, 2020
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/assay/AssayProtocolSchema.java
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Original file line number Diff line number Diff line change
Expand Up @@ -318,7 +318,7 @@ protected void overlayMetadata(TableInfo table, String name)

errors = new ArrayList<>();
Path dir = new Path(AssayService.ASSAY_DIR_NAME, getProvider().getResourceName(), QueryService.MODULE_QUERIES_DIRECTORY);
Collection<TableType> metadata = QueryService.get().findMetadataOverride(this, name, false, true, errors, dir);
Collection<TableType> metadata = QueryService.get().findMetadataOverride(this, name, false, false, errors, dir);
if (errors.isEmpty())
table.overlayMetadata(metadata, this, errors);
}
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/data/DisplayColumn.java
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Expand Up @@ -1013,7 +1013,7 @@ public String getCssStyle(RenderContext ctx)

// 34871: Support for column display width
if (!StringUtils.isBlank(getWidth()))
style += "word-break:break-all;";
style += "word-break:break-word;";

return style;
}
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50 changes: 50 additions & 0 deletions api/src/org/labkey/api/reader/ExcelFactory.java
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Expand Up @@ -22,13 +22,18 @@
import org.apache.poi.ss.formula.FormulaParseException;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.ClientAnchor;
import org.apache.poi.ss.usermodel.Comment;
import org.apache.poi.ss.usermodel.CreationHelper;
import org.apache.poi.ss.usermodel.CellType;
import org.apache.poi.ss.usermodel.DataFormat;
import org.apache.poi.ss.usermodel.DataFormatter;
import org.apache.poi.ss.usermodel.DateUtil;
import org.apache.poi.ss.usermodel.Drawing;
import org.apache.poi.ss.usermodel.FormulaError;
import org.apache.poi.ss.usermodel.FormulaEvaluator;
import org.apache.poi.ss.usermodel.IndexedColors;
import org.apache.poi.ss.usermodel.RichTextString;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
import org.apache.poi.ss.usermodel.Sheet;
Expand Down Expand Up @@ -133,6 +138,7 @@ public static Workbook create(InputStream is) throws IOException, InvalidFormatE
public static Workbook createFromArray(JSONArray sheetsArray, ExcelWriter.ExcelDocumentType docType)
{
Workbook workbook = docType.createWorkbook();
CreationHelper factory = workbook.getCreationHelper();

Map<String, CellStyle> customStyles = new HashMap<>();

Expand Down Expand Up @@ -175,6 +181,11 @@ public static Workbook createFromArray(JSONArray sheetsArray, ExcelWriter.ExcelD

boolean forceString = metadataObject != null && metadataObject.has("forceString") && Boolean.TRUE.equals(metadataObject.get("forceString"));

String cellComment = null;
if ( metadataObject != null && metadataObject.has("cellComment")){
cellComment = metadataObject.getString("cellComment");
}

Cell cell = row.createCell(colIndex);
if (value instanceof java.lang.Number)
{
Expand Down Expand Up @@ -229,6 +240,45 @@ else if (value != null)
{
cell.setCellStyle(cellStyle);
}
if (cell != null && cellComment != null)
{
//Determine the size of the comment box based on the length of the comment
int commentBoxWidth = 3;
int commentBoxHeight = 4;

if (cellComment.length() > 30 )
{
commentBoxHeight= 5;
}
if (cellComment.length() > 45 && cellComment.length() < 60)
{
commentBoxWidth= 4;
commentBoxHeight= 4;
}
if (cellComment.length() >= 60)
{
commentBoxHeight = 5;
}
if (cellComment.length() > 70)
{
commentBoxHeight = 6;
commentBoxWidth = 4;
}
ClientAnchor anchor = factory.createClientAnchor();
Drawing drawing = sheet.createDrawingPatriarch();

anchor.setCol1(cell.getColumnIndex()+1);
anchor.setCol2(cell.getColumnIndex()+commentBoxWidth);
anchor.setRow1(row.getRowNum()+1);
anchor.setRow2(row.getRowNum()+commentBoxHeight);

Comment comment = drawing.createCellComment(anchor);
RichTextString str = factory.createRichTextString(cellComment);
comment.setString(str);
comment.setAuthor("LabKey Server");

cell.setCellComment(comment);
}
}
}
}
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4 changes: 3 additions & 1 deletion study/src/org/labkey/study/StudyModule.java
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Expand Up @@ -76,6 +76,7 @@
import org.labkey.api.study.assay.AssayPublishService;
import org.labkey.api.study.reports.CrosstabReport;
import org.labkey.api.study.reports.CrosstabReportDescriptor;
import org.labkey.api.study.security.StudySecurityEscalationAuditProvider;
import org.labkey.api.usageMetrics.UsageMetricsService;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.SystemMaintenance;
Expand Down Expand Up @@ -270,7 +271,7 @@ protected void init()
StudySerializationRegistry.setInstance(StudySerializationRegistryImpl.get());

ExperimentService.get().addExperimentListener(new ExperimentListenerImpl());

DataViewService.get().registerProvider(DatasetViewProvider.TYPE, new DatasetViewProvider());
DataViewService.get().registerProvider(ReportViewProvider.TYPE, new ReportViewProvider());

Expand Down Expand Up @@ -354,6 +355,7 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
AuditLogService.get().registerAuditType(new DatasetAuditProvider());
AuditLogService.get().registerAuditType(new StudyAuditProvider());
AuditLogService.get().registerAuditType(new SpecimenCommentAuditProvider());
AuditLogService.get().registerAuditType(new StudySecurityEscalationAuditProvider());

ReportService.get().registerReport(new StudyController.StudyChartReport());
ReportService.get().registerReport(new StudyQueryReport());
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12 changes: 12 additions & 0 deletions study/src/org/labkey/study/query/DatasetUpdateService.java
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Expand Up @@ -32,7 +32,9 @@
import org.labkey.api.query.SimpleValidationError;
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.Permission;
import org.labkey.api.study.Dataset;
import org.labkey.api.study.security.StudySecurityEscalator;
import org.labkey.study.StudyServiceImpl;
import org.labkey.study.model.DatasetDefinition;
import org.labkey.api.qc.QCState;
Expand Down Expand Up @@ -83,6 +85,16 @@ public DatasetUpdateService(DatasetTableImpl table)
_columnMapping = createMVMapping(domain);
}

protected boolean hasPermission(User user, Class<? extends Permission> acl)
{
if (StudySecurityEscalator.isEscalated()) {
return true;
}
else {
return super.hasPermission(user, acl);
}
}

@Override
protected Map<String, Object> getRow(User user, Container container, Map<String, Object> keys)
throws InvalidKeyException
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