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Merged
merged 3 commits into from
Mar 16, 2025
Merged

Finish migration #342

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4714fbe
Finish renderGridCellContents migration
bbimber Mar 15, 2025
ff5e430
Finish renderGridCellContents migration
bbimber Mar 15, 2025
940a01d
Finish renderGridCellContents migration
bbimber Mar 16, 2025
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10 changes: 4 additions & 6 deletions ...eAnalysis/src/org/labkey/sequenceanalysis/query/DownloadSequenceDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,6 @@
import org.labkey.api.view.template.ClientDependency;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.Collections;
import java.util.LinkedHashSet;
import java.util.Map;
Expand All @@ -39,12 +37,12 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
private boolean _handlerRegistered = false;

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Object val = ctx.get(FieldKey.fromString(getBoundColumn().getFieldKey().getParent(), "rowId"));
oldWriter.write(PageFlowUtil.link("Download Sequence").attributes(Map.of(
Integer val = ctx.get(FieldKey.fromString(getBoundColumn().getFieldKey().getParent(), "rowId"), Integer.class);
out.write(PageFlowUtil.link("Download Sequence").attributes(Map.of(
"data-rowid", val.toString()
)).addClass("sdc-row").toString());
)).addClass("sdc-row"));

if (!_handlerRegistered)
{
Expand Down
13 changes: 6 additions & 7 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/query/GenbankDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,26 +24,25 @@ public GenbankDisplayColumnFactory()
@Override
public DisplayColumn createRenderer(ColumnInfo colInfo)
{
DataColumn ret = new DataColumn(colInfo)
return new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Object val = ctx.get(getBoundColumn().getFieldKey());
String val = ctx.get(getBoundColumn().getFieldKey(), String.class);
if (val != null)
{
String[] vals = String.valueOf(val).replaceAll("\\s+", "").split(";|,");
String[] vals = val.replaceAll("\\s+", "").split("[;,]");
String delim = "";
for (String v : vals)
{
oldWriter.write(delim + "<a href=" + getFormattedURL(v) + ">" + PageFlowUtil.encode(v) + "</a>");
out.write(delim);
out.write(PageFlowUtil.link(v).href(getFormattedURL(v)));
delim = "; ";
}
}
}
};

return ret;
}

protected String getFormattedURL(String v)
Expand Down
24 changes: 17 additions & 7 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,15 +26,15 @@
import org.labkey.api.query.QueryForeignKey;
import org.labkey.api.query.QueryService;
import org.labkey.api.security.User;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.template.ClientDependency;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.sequenceanalysis.SequenceAnalysisSchema;

import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.Collection;
import java.util.Set;

Expand Down Expand Up @@ -259,7 +259,7 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Integer rowId = ctx.get(getBoundKey("rowId"), Integer.class);
if (rowId != null)
Expand All @@ -268,18 +268,28 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
if (value != null)
{
String[] tokens = value.split(",");
String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
for (String token : tokens)
{
ActionURL url = QueryService.get().urlFor(ctx.getViewContext().getUser(), ctx.getContainer(), QueryAction.executeQuery, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_OUTPUTFILES);
url.addParameter("query.fileSets~contains", token);

oldWriter.write(delim + "<a href=\"" + url.getURIString() + "\"" + ">" + token + "</a>");
delim = ",<br>";
out.write(delim);
out.write(PageFlowUtil.link(token).href(url));
delim = HtmlString.join(Arrays.asList(HtmlString.of(","), HtmlString.BR), HtmlString.EMPTY_STRING);
}
}

oldWriter.write("<a class=\"fa fa-pencil lk-dr-action-icon sfs-row\" data-tt=\"tooltip\" data-rowid=\"" + rowId +"\" data-original-title=\"add/edit\"></a>");
out.write(PageFlowUtil.link("").
addClass("fa fa-pencil").
addClass("lk-dr-action-icon").
addClass("sfs-row").
attributes(PageFlowUtil.map(
"data-tt", "tooltip",
"data-rowid", rowId.toString(),
"data-original-title", "add/edit"
))
);

if (!_handlerRegistered)
{
Expand Down
22 changes: 10 additions & 12 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,13 @@
import org.labkey.api.query.SimpleUserSchema;
import org.labkey.api.security.User;
import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl;

import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.LinkedHashSet;

Expand Down Expand Up @@ -260,21 +259,19 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
return new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Object o = getValue(ctx);
if (o != null)
{
ActionURL url = QueryService.get().urlFor(getUser(), ctx.getContainer(), QueryAction.executeQuery, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READ_DATA);
url.addFilter("query", FieldKey.fromString("readset"), CompareType.EQUAL, o);

oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url + "\">");
oldWriter.write("View File(s)");
oldWriter.write("</a>");
out.write(PageFlowUtil.link("View File(s)").href(url).addClass("labkey-text-link"));
}
else
{
oldWriter.write("No Files");
out.write("No Files");
}
}
};
Expand Down Expand Up @@ -449,19 +446,20 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
return new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String result = StringUtils.trimToNull(super.getFormattedHtml(ctx).toString());
String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
if (result != null)
{
String[] tokens = result.split(",");
for (String token : tokens)
{
String url = DetailsURL.fromString(_baseUrl + PageFlowUtil.encode(token), ctx.getContainer()).getActionURL().toString();
ActionURL url = DetailsURL.fromString(_baseUrl + PageFlowUtil.encode(token), ctx.getContainer()).getActionURL();

oldWriter.write(delim + "<a href=\"" + url + "\">" + token + "</a>");
delim = "<br>";
out.write(delim);
out.write(PageFlowUtil.link(token).href(url));
delim = HtmlString.BR;
}
}
}
Expand Down