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Fix BiologicsReportTest - don't offer files with no content #7250

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Merged
labkey-jeckels merged 1 commit into from
Dec 8, 2025
Merged

Fix BiologicsReportTest - don't offer files with no content #7250

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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/reports/report/r/ParamReplacementSvc.java
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Original file line number Diff line number Diff line change
Expand Up @@ -659,7 +659,7 @@ public void toFile(List<ParamReplacement> outputSubst, FileLike file) throws Exc
}
}

public Collection<ParamReplacement> fromFile(FileLike file) throws Exception
public Collection<ParamReplacement> fromFile(FileLike file) throws IOException
{
Map<String, ParamReplacement> outputSubstMap = new HashMap<>();
if (file.exists())
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException
return;

out.write("<table class=\"labkey-output\">");
renderTitle(model, out);
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td>");
else
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4 changes: 2 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ public HtmlOutputView(ParamReplacement param, String label)
@Override
protected String renderInternalAsString(FileLike file) throws Exception
{
if (file.exists())
if (existsWithContent(file))
return PageFlowUtil.addScriptNonces(PageFlowUtil.getStreamContentsAsString(file.openInputStream()));

return null;
Expand All @@ -113,7 +113,7 @@ protected void renderInternal(Object model, PrintWriter out) throws Exception
if (null != html)
{
out.write("<table class=\"labkey-output\">");
renderTitle(model, out);
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td>");
else
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4 changes: 2 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/ImageOutput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ protected String renderInternalAsString(FileLike file) throws IOException
{
String imgUrl = null;

if (file.exists())
if (existsWithContent(file))
{
FileLike imgFile;
if (!_deleteFile)
Expand Down Expand Up @@ -157,7 +157,7 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException
if (null != imgUrl)
{
out.write("<table class=\"labkey-output\">");
renderTitle(model, out);
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td>");
else
Expand Down
6 changes: 3 additions & 3 deletions api/src/org/labkey/api/reports/report/r/view/JsonOutput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ public JsonOutput()
}

@Override
public HttpView getView(ViewContext context)
public HttpView<?> getView(ViewContext context)
{
return new JsonOutputView(this);
}
Expand Down Expand Up @@ -85,7 +85,7 @@ public JsonOutputView(ParamReplacement param)
@Override
protected String renderInternalAsString(FileLike file) throws IOException
{
if (file.exists())
if (existsWithContent(file))
return PageFlowUtil.getStreamContentsAsString(file.openInputStream());

return null;
Expand All @@ -101,7 +101,7 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException
if (null != rawValue)
{
out.write("<table class=\"labkey-output\">");
renderTitle(model, out);
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td><pre>");
else
Expand Down
25 changes: 7 additions & 18 deletions api/src/org/labkey/api/reports/report/r/view/ROutputView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,8 @@
import org.labkey.vfs.FileLike;

import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
Expand Down Expand Up @@ -128,7 +125,7 @@ protected String renderInternalAsString(FileLike file) throws Exception
return null;
}

protected void renderTitle(Object model, PrintWriter out)
protected void renderTitle(PrintWriter out)
{
StringBuilder sb = new StringBuilder();

Expand Down Expand Up @@ -164,7 +161,7 @@ protected FileLike moveToTemp(FileLike file) throws IOException
return null;
}

protected boolean exists(File file)
protected boolean existsWithContent(FileLike file)
{
long size = 0;

Expand All @@ -181,11 +178,7 @@ protected boolean exists(File file)
if (ALLOW_REMOTE_FILESIZE_BYPASS && _isRemote)
return true;

try
{
size = Files.size(Paths.get(file.getAbsolutePath()));
}
catch(IOException ignore){}
size = file.getSize();
}

return (size > 0);
Expand All @@ -199,16 +192,12 @@ public static void cleanUpTemp(final long cutoff)

if (tempDir.exists())
{
File[] filesToDelete = tempDir.listFiles(new FileFilter(){
@Override
public boolean accept(File file)
File[] filesToDelete = tempDir.listFiles(file -> {
if (!file.isDirectory() && file.getName().startsWith(PREFIX))
{
if (!file.isDirectory() && file.getName().startsWith(PREFIX))
{
return file.lastModified() < cutoff;
}
return false;
return file.lastModified() < cutoff;
}
return false;
});

for (File file : filesToDelete)
Expand Down
4 changes: 2 additions & 2 deletions api/src/org/labkey/api/reports/report/r/view/TextOutput.java
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ public TextOutputView(ParamReplacement param)
@Override
protected String renderInternalAsString(FileLike file) throws IOException
{
if (file.exists())
if (existsWithContent(file))
return PageFlowUtil.getStreamContentsAsString(file.openInputStream());

return null;
Expand All @@ -101,7 +101,7 @@ protected void renderInternal(Object model, PrintWriter out) throws IOException
if (null != rawValue)
{
out.write("<table class=\"labkey-output\">");
renderTitle(model, out);
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td><pre>");
else
Expand Down
169 changes: 88 additions & 81 deletions api/src/org/labkey/api/reports/report/r/view/TsvOutput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ public static class TabReportView extends ROutputView
@Override
protected String renderInternalAsString(FileLike file) throws IOException
{
if (file.exists())
if (existsWithContent(file))
return PageFlowUtil.getStreamContentsAsString(file.openInputStream());

return null;
Expand All @@ -126,104 +126,111 @@ protected void renderInternal(Object model, PrintWriter out) throws Exception
TabLoader tabLoader = createTabLoader(file);
if (tabLoader != null)
{
ColumnDescriptor[] cols = tabLoader.getColumns();
List<Map<String, Object>> data = tabLoader.load();
try
{
ColumnDescriptor[] cols = tabLoader.getColumns();
List<Map<String, Object>> data = tabLoader.load();

List<ColumnDescriptor> display = new ArrayList<>();
HashMap<String, ColumnDescriptor> hrefs = new HashMap<>(tabLoader.getColumns().length * 2);
HashMap<String, ColumnDescriptor> styles = new HashMap<>(tabLoader.getColumns().length * 2);
List<ColumnDescriptor> display = new ArrayList<>();
HashMap<String, ColumnDescriptor> hrefs = new HashMap<>(tabLoader.getColumns().length * 2);
HashMap<String, ColumnDescriptor> styles = new HashMap<>(tabLoader.getColumns().length * 2);

for (ColumnDescriptor col : cols)
hrefs.put(col.name, null);
for (ColumnDescriptor col : cols)
hrefs.put(col.name, null);

for (ColumnDescriptor col : cols)
{
if (col.name.endsWith(".href") || col.name.endsWith("_href"))
for (ColumnDescriptor col : cols)
{
String name = col.name.substring(0,col.name.length()-".href".length());
if (hrefs.containsKey(name))
if (col.name.endsWith(".href") || col.name.endsWith("_href"))
{
hrefs.put(name,col);
continue;
String name = col.name.substring(0, col.name.length() - ".href".length());
if (hrefs.containsKey(name))
{
hrefs.put(name, col);
continue;
}
}
}
if (col.name.endsWith(".style") || col.name.endsWith("_style"))
{
String name = col.name.substring(0,col.name.length()-".style".length());
if (hrefs.containsKey(name))
if (col.name.endsWith(".style") || col.name.endsWith("_style"))
{
styles.put(name,col);
continue;
String name = col.name.substring(0, col.name.length() - ".style".length());
if (hrefs.containsKey(name))
{
styles.put(name, col);
continue;
}
}
display.add(col);
}
display.add(col);
}

int row = 0;
out.write("<table class=\"labkey-data-region-legacy labkey-show-borders\">");
renderTitle(model, out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td><table>");
else
out.write("<tr><td><table class=\"labkey-r-tsvout\">");
out.write("<tr>");
for (ColumnDescriptor col : display)
{
if (Number.class.isAssignableFrom(col.getDataClass()))
out.write("<td class=\"labkey-column-header\" align=\"right\">");
int row = 0;
out.write("<table class=\"labkey-data-region-legacy labkey-show-borders\">");
renderTitle(out);
if (isCollapse())
out.write("<tr style=\"display:none\"><td><table>");
else
out.write("<td class=\"labkey-column-header\">");
out.write(PageFlowUtil.filter(col.name, true, true));
out.write("</td>");
row++;
}
out.write("</tr>");

for (Map<String, Object> m : data)
{
if (row % 2 == 0)
out.write("<tr class=\"labkey-row\">");
else
out.write("<tr class=\"labkey-alternate-row\">");
out.write("<tr><td><table class=\"labkey-r-tsvout\">");
out.write("<tr>");
for (ColumnDescriptor col : display)
{
Object colVal = m.get(col.name);
if ("NA".equals(colVal))
colVal = null;
ColumnDescriptor hrefCol = hrefs.get(col.name);
String href = hrefCol == null ? null : ConvertUtils.convert((m.get(hrefCol.name)));
ColumnDescriptor styleCol = styles.get(col.name);
String style = styleCol == null ? null : ConvertUtils.convert((m.get(styleCol.name)));

out.write("<td");
if (Number.class.isAssignableFrom(col.clazz))
out.write(" align=\"right\"");
if (null != style)
{
out.write(" style=\"");
out.write(PageFlowUtil.filter(style));
out.write("\"");
}
out.write(">");
if (null != href)
{
out.write("<a href=\"");
out.write(PageFlowUtil.filter(href));
out.write("\">");
}
if (null == colVal)
out.write("&nbsp;");
if (Number.class.isAssignableFrom(col.getDataClass()))
out.write("<td class=\"labkey-column-header\" align=\"right\">");
else
out.write(PageFlowUtil.filter(ConvertUtils.convert(colVal), true, true));
if (null != href)
out.write("</a>");
out.write("<td class=\"labkey-column-header\">");
out.write(PageFlowUtil.filter(col.name, true, true));
out.write("</td>");
row++;
}
out.write("</tr>");
row++;

for (Map<String, Object> m : data)
{
if (row % 2 == 0)
out.write("<tr class=\"labkey-row\">");
else
out.write("<tr class=\"labkey-alternate-row\">");
for (ColumnDescriptor col : display)
{
Object colVal = m.get(col.name);
if ("NA".equals(colVal))
colVal = null;
ColumnDescriptor hrefCol = hrefs.get(col.name);
String href = hrefCol == null ? null : ConvertUtils.convert((m.get(hrefCol.name)));
ColumnDescriptor styleCol = styles.get(col.name);
String style = styleCol == null ? null : ConvertUtils.convert((m.get(styleCol.name)));

out.write("<td");
if (Number.class.isAssignableFrom(col.clazz))
out.write(" align=\"right\"");
if (null != style)
{
out.write(" style=\"");
out.write(PageFlowUtil.filter(style));
out.write("\"");
}
out.write(">");
if (null != href)
{
out.write("<a href=\"");
out.write(PageFlowUtil.filter(href));
out.write("\">");
}
if (null == colVal)
out.write("&nbsp;");
else
out.write(PageFlowUtil.filter(ConvertUtils.convert(colVal), true, true));
if (null != href)
out.write("</a>");
out.write("</td>");
}
out.write("</tr>");
row++;
}
out.write("</table></td></tr>");
out.write("</table>");
}
finally
{
tabLoader.close();
}
out.write("</table></td></tr>");
out.write("</table>");
}
}
}
Expand Down