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Merged
bbimber merged 1 commit into from
Mar 16, 2025
Merged

Finish HtmlWriter migration #244

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13 changes: 7 additions & 6 deletions mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
Expand All @@ -35,7 +35,7 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim"), String.class));
if (rawValue == null)
Expand All @@ -46,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
List<String> tokens = Arrays.asList(rawValue.split(";"));
Collections.sort(tokens);

String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
for (String entry : tokens)
{
String id = entry;
Expand All @@ -58,8 +58,9 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
text = parts[0];
}

oldWriter.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + id + "\">" + text + "</a>");
delim = "<br>";
out.write(delim);
out.write(PageFlowUtil.link(text).href("https://www.omim.org/entry/" + id).target("_blank").clearClasses());
delim = HtmlString.BR;
}
}
};
Expand Down
15 changes: 8 additions & 7 deletions mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
Expand Down Expand Up @@ -50,7 +50,7 @@ public Object getExcelCompatibleValue(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim_phenotype"), String.class));
if (rawValue == null)
Expand All @@ -61,20 +61,21 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
List<String> tokens = Arrays.asList(rawValue.split(";"));
Collections.sort(tokens);

String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
for (String entry : tokens)
{
String[] elements = entry.split("<>");
out.write(delim);
if (elements.length > 1)
{
oldWriter.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + elements[1] + "\">" + elements[0] + "</a>");
out.write(PageFlowUtil.link(elements[0]).target("_blank").href("https://www.omim.org/entry/" + elements[1]).clearClasses());
}
else
{
oldWriter.write(delim + "<a>" + elements[0] + "</a>");
out.write(PageFlowUtil.link(elements[0]).clearClasses());
}

delim = "<br>";
delim = HtmlString.BR;
}
}
};
Expand Down
13 changes: 7 additions & 6 deletions mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
Expand All @@ -35,7 +35,7 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("overlappingGenes"), String.class));
if (rawValue == null)
Expand All @@ -46,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
List<String> tokens = Arrays.asList(rawValue.split(";"));
Collections.sort(tokens);

String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
for (String geneName : tokens)
{
String url = null;
Expand All @@ -65,8 +65,9 @@ else if (geneName.startsWith("ENSMMUE"))
url = "http://ensembl.org/Macaca_mulatta/Gene/Summary?db=core;g=" + geneName;
}

oldWriter.write(delim + "<a target=\"_blank\" href=\"" + url + "\">" + geneName + "</a>");
delim = "<br>";
out.write(delim);
out.write(PageFlowUtil.link(geneName).href(url).target("_blank").clearClasses());
delim = HtmlString.BR;
}
}
};
Expand Down
7 changes: 3 additions & 4 deletions mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,9 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.List;
import java.util.Set;

Expand Down Expand Up @@ -45,15 +44,15 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String containerId = ctx.get(getBoundKey("container"), String.class);
String omim = ctx.get(getBoundKey("omim_entry"), String.class);
Integer releaseId = ctx.get(getBoundKey("releaseId/rowId"), Integer.class);
if (releaseId != null && omim != null)
{
DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + releaseId + "&query.omim_phenotype~contains=" + omim, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Variants</a>");
out.write(PageFlowUtil.link("View Variants").href(url.getActionURL()).addClass("labkey-text-link"));
}
}
};
Expand Down
14 changes: 10 additions & 4 deletions mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,9 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

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

public class SourceDisplayColumnFactory implements DisplayColumnFactory
Expand All @@ -32,7 +31,7 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String val = ctx.get(getBoundKey("source"), String.class);
if (val == null)
Expand Down Expand Up @@ -61,7 +60,14 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
}
}

oldWriter.write(url == null ? val : "<a href=\"" + url + "\">" + val + "</a>");
if (url == null)
{
out.write(val);
}
else
{
out.write(PageFlowUtil.link(val).href(url).clearClasses());
}
}

private FieldKey getBoundKey(String colName)
Expand Down
7 changes: 2 additions & 5 deletions mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,6 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;

/**
* Created by bimber on 5/17/2017.
*/
Expand All @@ -22,7 +19,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
return new VariantReleaseGenomeBrowserDisplayColumnFactory.BrowserDataColumn(colInfo, PageFlowUtil.set("releaseId/jbrowseId", "releaseId/container", "trackName"))
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String jbrowseId = ctx.get(getBoundKey("releaseId", "jbrowseId"), String.class);
String containerId = ctx.get(getBoundKey("releaseId", "container"), String.class);
Expand All @@ -31,7 +28,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
if (jbrowseId != null && trackName != null)
{
DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
out.write(PageFlowUtil.link("View In Genome Browser").addClass("labkey-text-link").href(url.getActionURL()));
}
}
};
Expand Down
30 changes: 15 additions & 15 deletions mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.io.IOException;
import java.io.Writer;
import java.util.List;
import java.util.Set;

Expand Down Expand Up @@ -53,34 +53,34 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String jbrowseId = StringUtils.trimToNull(ctx.get(getBoundKey("releaseId/jbrowseId"), String.class));
String primaryTrack = ctx.get(getBoundKey("releaseId/primaryTrack"), String.class);
String containerId = ctx.get(getBoundKey("container"), String.class);
String contig = StringUtils.trimToNull(ctx.get(getBoundKey("contig"), String.class));
String ref = ctx.get(getBoundKey("reference"), String.class);
Integer position = ctx.get(getBoundKey("position"), Integer.class);
String delim = "";
HtmlString delim = HtmlString.EMPTY_STRING;
int start = position - 200;
int stop = position + 200;
int length = ref.length();
if (jbrowseId != null)
{
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId + "&location=" + contig + ":" + start + ".." + stop + "&highlight=" + contig + ":" + position + ".." + (position + length - 1), ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
delim = "<br>";
out.write(PageFlowUtil.link("View In Genome Browser").href(url.getActionURL()).addClass("labkey-text-link"));
delim = HtmlString.BR;
}

if (primaryTrack != null)
{
oldWriter.write(delim);
out.write(delim);
DetailsURL url = DetailsURL.fromString("/jbrowse/genotypeTable.view?trackId=" + primaryTrack + "&chr=" + contig + "&start=" + position + "&stop=" + position, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Genotypes At Position</a>");
delim = "<br>";
out.write(PageFlowUtil.link("View Genotypes At Position").href(url.getActionURL()).addClass("labkey-text-link"));
delim = HtmlString.BR;
}

if (ctx.get(FieldKey.fromString("identifier")) != null)
if (ctx.get(FieldKey.fromString("identifier"), String.class) != null)
{
String identifier = StringUtils.trimToNull(ctx.get(getBoundKey("identifier"), String.class));
if (identifier != null && identifier.contains(":"))
Expand All @@ -97,9 +97,9 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
if (!StringUtils.isEmpty(parts[1]))
{
String url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
oldWriter.write(delim);
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View in ClinVar</a>");
delim = "<br>";
out.write(delim);
out.write(PageFlowUtil.link("View in ClinVar").href(url));
delim = HtmlString.BR;
}
}
}
Expand All @@ -110,8 +110,8 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
String contigE = contig.replaceAll("chr", "");
contigE = contigE.replaceAll("^0", "");
String url = "https://ensembl.org/Macaca_mulatta/Location/View?db=core;r=" + contigE + ":" + start +"-" + stop;
oldWriter.write(delim);
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View Region in Ensembl</a>");
out.write(delim);
out.write(PageFlowUtil.link("View Region in Ensembl").href(url));
}
};
}
Expand Down
18 changes: 10 additions & 8 deletions mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,12 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.template.ClientDependency;
import org.labkey.api.writer.HtmlWriter;

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

/**
Expand Down Expand Up @@ -49,12 +48,15 @@ private FieldKey getBoundKey(String colName)
private boolean _clickHandlerRegistered = false;

@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)
{
oldWriter.write("<a class=\"labkey-text-link vrdc-row\" data-rowid=" + PageFlowUtil.jsString(rowId.toString()) + ">Download</a>");
out.write(PageFlowUtil.link("Download").
addClass("vrdc-row").
attributes(PageFlowUtil.map("data-rowid", rowId.toString()))
);

if (!_clickHandlerRegistered)
{
Expand All @@ -70,20 +72,20 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit
{
if (rowId != null)
{
oldWriter.write("<br>");
out.write(HtmlString.BR);
}

DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
}

Boolean showVariantList = ctx.get(getBoundKey("hasSignificantVariants"), Boolean.class);
if (showVariantList)
{
oldWriter.write("<br>");
out.write(HtmlString.BR);

DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + rowId, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">Significant Variant List</a>");
out.write(PageFlowUtil.link("Significant Variant List", url.getActionURL()));
}
}

Expand Down
6 changes: 2 additions & 4 deletions mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,6 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

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

/**
Expand Down Expand Up @@ -68,14 +66,14 @@ protected FieldKey getBoundKey(String... colNames)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String jbrowseId = ctx.get(getBoundKey("jbrowseId"), String.class);
String containerId = ctx.get(getBoundKey("container"), String.class);
if (jbrowseId != null)
{
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
}
}

Expand Down
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