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Migrate renderGridCellContents() and renderDetailsCellContents()
1 parent 46db24c commit f1c7970

12 files changed

+51
-41
lines changed

‎mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import org.labkey.api.data.DisplayColumnFactory;
88
import org.labkey.api.data.RenderContext;
99
import org.labkey.api.query.FieldKey;
10+
import org.labkey.api.writer.HtmlWriter;
1011

1112
import java.io.IOException;
1213
import java.io.Writer;
@@ -34,7 +35,7 @@ private FieldKey getBoundKey(String colName)
3435
}
3536

3637
@Override
37-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
38+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
3839
{
3940
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim"), String.class));
4041
if (rawValue == null)
@@ -57,7 +58,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
5758
text = parts[0];
5859
}
5960

60-
out.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + id + "\">" + text + "</a>");
61+
oldWriter.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + id + "\">" + text + "</a>");
6162
delim = "<br>";
6263
}
6364
}

‎mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import org.labkey.api.data.DisplayColumnFactory;
88
import org.labkey.api.data.RenderContext;
99
import org.labkey.api.query.FieldKey;
10+
import org.labkey.api.writer.HtmlWriter;
1011

1112
import java.io.IOException;
1213
import java.io.Writer;
@@ -49,7 +50,7 @@ public Object getExcelCompatibleValue(RenderContext ctx)
4950
}
5051

5152
@Override
52-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
53+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
5354
{
5455
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim_phenotype"), String.class));
5556
if (rawValue == null)
@@ -66,11 +67,11 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6667
String[] elements = entry.split("<>");
6768
if (elements.length > 1)
6869
{
69-
out.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + elements[1] + "\">" + elements[0] + "</a>");
70+
oldWriter.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + elements[1] + "\">" + elements[0] + "</a>");
7071
}
7172
else
7273
{
73-
out.write(delim + "<a>" + elements[0] + "</a>");
74+
oldWriter.write(delim + "<a>" + elements[0] + "</a>");
7475
}
7576

7677
delim = "<br>";

‎mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import org.labkey.api.data.DisplayColumnFactory;
88
import org.labkey.api.data.RenderContext;
99
import org.labkey.api.query.FieldKey;
10+
import org.labkey.api.writer.HtmlWriter;
1011

1112
import java.io.IOException;
1213
import java.io.Writer;
@@ -34,7 +35,7 @@ private FieldKey getBoundKey(String colName)
3435
}
3536

3637
@Override
37-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
38+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
3839
{
3940
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("overlappingGenes"), String.class));
4041
if (rawValue == null)
@@ -64,7 +65,7 @@ else if (geneName.startsWith("ENSMMUE"))
6465
url = "http://ensembl.org/Macaca_mulatta/Gene/Summary?db=core;g=" + geneName;
6566
}
6667

67-
out.write(delim + "<a target=\"_blank\" href=\"" + url + "\">" + geneName + "</a>");
68+
oldWriter.write(delim + "<a target=\"_blank\" href=\"" + url + "\">" + geneName + "</a>");
6869
delim = "<br>";
6970
}
7071
}

‎mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88
import org.labkey.api.data.RenderContext;
99
import org.labkey.api.query.DetailsURL;
1010
import org.labkey.api.query.FieldKey;
11+
import org.labkey.api.writer.HtmlWriter;
1112

1213
import java.io.IOException;
1314
import java.io.Writer;
@@ -44,15 +45,15 @@ private FieldKey getBoundKey(String colName)
4445
}
4546

4647
@Override
47-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
48+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
4849
{
4950
String containerId = ctx.get(getBoundKey("container"), String.class);
5051
String omim = ctx.get(getBoundKey("omim_entry"), String.class);
5152
Integer releaseId = ctx.get(getBoundKey("releaseId/rowId"), Integer.class);
5253
if (releaseId != null && omim != null)
5354
{
5455
DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + releaseId + "&query.omim_phenotype~contains=" + omim, ContainerManager.getForId(containerId));
55-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Variants</a>");
56+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Variants</a>");
5657
}
5758
}
5859
};

‎mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@
99
import org.labkey.api.data.DisplayColumnFactory;
1010
import org.labkey.api.data.RenderContext;
1111
import org.labkey.api.query.FieldKey;
12+
import org.labkey.api.writer.HtmlWriter;
1213

1314
import java.io.IOException;
1415
import java.io.Writer;
@@ -31,7 +32,7 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
3132
}
3233

3334
@Override
34-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
35+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
3536
{
3637
String val = ctx.get(getBoundKey("source"), String.class);
3738
if (val == null)
@@ -60,7 +61,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6061
}
6162
}
6263

63-
out.write(url == null ? val : "<a href=\"" + url + "\">" + val + "</a>");
64+
oldWriter.write(url == null ? val : "<a href=\"" + url + "\">" + val + "</a>");
6465
}
6566

6667
private FieldKey getBoundKey(String colName)

‎mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
import org.labkey.api.data.RenderContext;
77
import org.labkey.api.query.DetailsURL;
88
import org.labkey.api.util.PageFlowUtil;
9+
import org.labkey.api.writer.HtmlWriter;
910

1011
import java.io.IOException;
1112
import java.io.Writer;
@@ -21,7 +22,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
2122
return new VariantReleaseGenomeBrowserDisplayColumnFactory.BrowserDataColumn(colInfo, PageFlowUtil.set("releaseId/jbrowseId", "releaseId/container", "trackName"))
2223
{
2324
@Override
24-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
25+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
2526
{
2627
String jbrowseId = ctx.get(getBoundKey("releaseId", "jbrowseId"), String.class);
2728
String containerId = ctx.get(getBoundKey("releaseId", "container"), String.class);
@@ -30,7 +31,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
3031
if (jbrowseId != null && trackName != null)
3132
{
3233
DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName, ContainerManager.getForId(containerId));
33-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
34+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
3435
}
3536
}
3637
};

‎mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java‎

Lines changed: 9 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
1111
import org.labkey.api.data.RenderContext;
1212
import org.labkey.api.query.DetailsURL;
1313
import org.labkey.api.query.FieldKey;
14+
import org.labkey.api.writer.HtmlWriter;
1415

1516
import java.io.IOException;
1617
import java.io.Writer;
@@ -52,7 +53,7 @@ private FieldKey getBoundKey(String colName)
5253
}
5354

5455
@Override
55-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
56+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
5657
{
5758
String jbrowseId = StringUtils.trimToNull(ctx.get(getBoundKey("releaseId/jbrowseId"), String.class));
5859
String primaryTrack = ctx.get(getBoundKey("releaseId/primaryTrack"), String.class);
@@ -67,15 +68,15 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6768
if (jbrowseId != null)
6869
{
6970
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId + "&location=" + contig + ":" + start + ".." + stop + "&highlight=" + contig + ":" + position + ".." + (position + length - 1), ContainerManager.getForId(containerId));
70-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
71+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
7172
delim = "<br>";
7273
}
7374

7475
if (primaryTrack != null)
7576
{
76-
out.write(delim);
77+
oldWriter.write(delim);
7778
DetailsURL url = DetailsURL.fromString("/jbrowse/genotypeTable.view?trackId=" + primaryTrack + "&chr=" + contig + "&start=" + position + "&stop=" + position, ContainerManager.getForId(containerId));
78-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Genotypes At Position</a>");
79+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View Genotypes At Position</a>");
7980
delim = "<br>";
8081
}
8182

@@ -96,8 +97,8 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
9697
if (!StringUtils.isEmpty(parts[1]))
9798
{
9899
String url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
99-
out.write(delim);
100-
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View in ClinVar</a>");
100+
oldWriter.write(delim);
101+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View in ClinVar</a>");
101102
delim = "<br>";
102103
}
103104
}
@@ -109,8 +110,8 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
109110
String contigE = contig.replaceAll("chr", "");
110111
contigE = contigE.replaceAll("^0", "");
111112
String url = "https://ensembl.org/Macaca_mulatta/Location/View?db=core;r=" + contigE + ":" + start +"-" + stop;
112-
out.write(delim);
113-
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View Region in Ensembl</a>");
113+
oldWriter.write(delim);
114+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View Region in Ensembl</a>");
114115
}
115116
};
116117
}

‎mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212
import org.labkey.api.util.PageFlowUtil;
1313
import org.labkey.api.view.HttpView;
1414
import org.labkey.api.view.template.ClientDependency;
15+
import org.labkey.api.writer.HtmlWriter;
1516

1617
import java.io.IOException;
1718
import java.io.Writer;
@@ -48,12 +49,12 @@ private FieldKey getBoundKey(String colName)
4849
private boolean _clickHandlerRegistered = false;
4950

5051
@Override
51-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
52+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
5253
{
5354
Integer rowId = ctx.get(getBoundKey("rowid"), Integer.class);
5455
if (rowId != null)
5556
{
56-
out.write("<a class=\"labkey-text-link vrdc-row\" data-rowid=" + PageFlowUtil.jsString(rowId.toString()) + ">Download</a>");
57+
oldWriter.write("<a class=\"labkey-text-link vrdc-row\" data-rowid=" + PageFlowUtil.jsString(rowId.toString()) + ">Download</a>");
5758

5859
if (!_clickHandlerRegistered)
5960
{
@@ -69,20 +70,20 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6970
{
7071
if (rowId != null)
7172
{
72-
out.write("<br>");
73+
oldWriter.write("<br>");
7374
}
7475

7576
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
76-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
77+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
7778
}
7879

7980
Boolean showVariantList = ctx.get(getBoundKey("hasSignificantVariants"), Boolean.class);
8081
if (showVariantList)
8182
{
82-
out.write("<br>");
83+
oldWriter.write("<br>");
8384

8485
DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + rowId, ContainerManager.getForId(containerId));
85-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">Significant Variant List</a>");
86+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">Significant Variant List</a>");
8687
}
8788
}
8889

‎mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@
99
import org.labkey.api.query.DetailsURL;
1010
import org.labkey.api.query.FieldKey;
1111
import org.labkey.api.util.PageFlowUtil;
12+
import org.labkey.api.writer.HtmlWriter;
1213

1314
import java.io.IOException;
1415
import java.io.Writer;
@@ -67,14 +68,14 @@ protected FieldKey getBoundKey(String... colNames)
6768
}
6869

6970
@Override
70-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
71+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
7172
{
7273
String jbrowseId = ctx.get(getBoundKey("jbrowseId"), String.class);
7374
String containerId = ctx.get(getBoundKey("container"), String.class);
7475
if (jbrowseId != null)
7576
{
7677
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
77-
out.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
78+
oldWriter.write("<a class=\"labkey-text-link\" href=\"" + url.getActionURL().getURIString() + "\");\">View In Genome Browser</a>");
7879
}
7980
}
8081

‎mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,7 @@
77
import org.labkey.api.data.DisplayColumnFactory;
88
import org.labkey.api.data.RenderContext;
99
import org.labkey.api.query.FieldKey;
10-
import org.labkey.api.security.User;
11-
import org.labkey.api.security.UserManager;
10+
import org.labkey.api.writer.HtmlWriter;
1211
import org.labkey.mcc.MccManager;
1312

1413
import java.io.IOException;
@@ -25,10 +24,10 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
2524
return new AbstractMccDisplayColumn(colInfo)
2625
{
2726
@Override
28-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
27+
public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException
2928
{
3029
int rowId = ctx.get(getBoundKey("rowid"), Integer.class);
31-
out.write("<a class=\"labkey-text-link\" href=\"mailto:" + MccManager.get().getMccAdminEmail() + "?subject=MCC Request #" + rowId + "\">Contact MCC</a>");
30+
oldWriter.write("<a class=\"labkey-text-link\" href=\"mailto:" + MccManager.get().getMccAdminEmail() + "?subject=MCC Request #" + rowId + "\">Contact MCC</a>");
3231
}
3332

3433
@Override

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