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lk-region-form -> data-region-form (#243)
1 parent f686599 commit 775c549

13 files changed

+94
-76
lines changed

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

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,10 @@
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.util.HtmlString;
11+
import org.labkey.api.util.PageFlowUtil;
12+
import org.labkey.api.writer.HtmlWriter;
1013

11-
import java.io.IOException;
12-
import java.io.Writer;
1314
import java.util.Arrays;
1415
import java.util.Collections;
1516
import java.util.List;
@@ -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, HtmlWriter out)
3839
{
3940
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim"), String.class));
4041
if (rawValue == null)
@@ -45,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
4546
List<String> tokens = Arrays.asList(rawValue.split(";"));
4647
Collections.sort(tokens);
4748

48-
String delim = "";
49+
HtmlString delim = HtmlString.EMPTY_STRING;
4950
for (String entry : tokens)
5051
{
5152
String id = entry;
@@ -57,8 +58,9 @@ 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-
delim = "<br>";
61+
out.write(delim);
62+
out.write(PageFlowUtil.link(text).href("https://www.omim.org/entry/" + id).target("_blank").clearClasses());
63+
delim = HtmlString.BR;
6264
}
6365
}
6466
};

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

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,10 @@
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.util.HtmlString;
11+
import org.labkey.api.util.PageFlowUtil;
12+
import org.labkey.api.writer.HtmlWriter;
1013

11-
import java.io.IOException;
12-
import java.io.Writer;
1314
import java.util.Arrays;
1415
import java.util.Collections;
1516
import java.util.List;
@@ -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, HtmlWriter out)
5354
{
5455
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("omim_phenotype"), String.class));
5556
if (rawValue == null)
@@ -60,20 +61,21 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6061
List<String> tokens = Arrays.asList(rawValue.split(";"));
6162
Collections.sort(tokens);
6263

63-
String delim = "";
64+
HtmlString delim = HtmlString.EMPTY_STRING;
6465
for (String entry : tokens)
6566
{
6667
String[] elements = entry.split("<>");
68+
out.write(delim);
6769
if (elements.length > 1)
6870
{
69-
out.write(delim + "<a target=\"_blank\" href=\"https://www.omim.org/entry/" + elements[1] + "\">" + elements[0] + "</a>");
71+
out.write(PageFlowUtil.link(elements[0]).target("_blank").href("https://www.omim.org/entry/" + elements[1]).clearClasses());
7072
}
7173
else
7274
{
73-
out.write(delim + "<a>" + elements[0] + "</a>");
75+
out.write(PageFlowUtil.link(elements[0]).clearClasses());
7476
}
7577

76-
delim = "<br>";
78+
delim = HtmlString.BR;
7779
}
7880
}
7981
};

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

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,10 @@
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.util.HtmlString;
11+
import org.labkey.api.util.PageFlowUtil;
12+
import org.labkey.api.writer.HtmlWriter;
1013

11-
import java.io.IOException;
12-
import java.io.Writer;
1314
import java.util.Arrays;
1415
import java.util.Collections;
1516
import java.util.List;
@@ -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, HtmlWriter out)
3839
{
3940
String rawValue = StringUtils.trimToNull(ctx.get(getBoundKey("overlappingGenes"), String.class));
4041
if (rawValue == null)
@@ -45,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
4546
List<String> tokens = Arrays.asList(rawValue.split(";"));
4647
Collections.sort(tokens);
4748

48-
String delim = "";
49+
HtmlString delim = HtmlString.EMPTY_STRING;
4950
for (String geneName : tokens)
5051
{
5152
String url = null;
@@ -64,8 +65,9 @@ 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-
delim = "<br>";
68+
out.write(delim);
69+
out.write(PageFlowUtil.link(geneName).href(url).target("_blank").clearClasses());
70+
delim = HtmlString.BR;
6971
}
7072
}
7173
};

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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,9 +8,9 @@
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.util.PageFlowUtil;
12+
import org.labkey.api.writer.HtmlWriter;
1113

12-
import java.io.IOException;
13-
import java.io.Writer;
1414
import java.util.List;
1515
import java.util.Set;
1616

@@ -44,15 +44,15 @@ private FieldKey getBoundKey(String colName)
4444
}
4545

4646
@Override
47-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
47+
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
4848
{
4949
String containerId = ctx.get(getBoundKey("container"), String.class);
5050
String omim = ctx.get(getBoundKey("omim_entry"), String.class);
5151
Integer releaseId = ctx.get(getBoundKey("releaseId/rowId"), Integer.class);
5252
if (releaseId != null && omim != null)
5353
{
5454
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>");
55+
out.write(PageFlowUtil.link("View Variants").href(url.getActionURL()).addClass("labkey-text-link"));
5656
}
5757
}
5858
};

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

Lines changed: 11 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,9 @@
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.util.PageFlowUtil;
13+
import org.labkey.api.writer.HtmlWriter;
1214

13-
import java.io.IOException;
14-
import java.io.Writer;
1515
import java.util.Set;
1616

1717
public class SourceDisplayColumnFactory implements DisplayColumnFactory
@@ -31,7 +31,7 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
3131
}
3232

3333
@Override
34-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
34+
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
3535
{
3636
String val = ctx.get(getBoundKey("source"), String.class);
3737
if (val == null)
@@ -60,7 +60,14 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6060
}
6161
}
6262

63-
out.write(url == null ? val : "<a href=\"" + url + "\">" + val + "</a>");
63+
if (url == null)
64+
{
65+
out.write(val);
66+
}
67+
else
68+
{
69+
out.write(PageFlowUtil.link(val).href(url).clearClasses());
70+
}
6471
}
6572

6673
private FieldKey getBoundKey(String colName)

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

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -6,9 +6,7 @@
66
import org.labkey.api.data.RenderContext;
77
import org.labkey.api.query.DetailsURL;
88
import org.labkey.api.util.PageFlowUtil;
9-
10-
import java.io.IOException;
11-
import java.io.Writer;
9+
import org.labkey.api.writer.HtmlWriter;
1210

1311
/**
1412
* Created by bimber on 5/17/2017.
@@ -21,7 +19,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
2119
return new VariantReleaseGenomeBrowserDisplayColumnFactory.BrowserDataColumn(colInfo, PageFlowUtil.set("releaseId/jbrowseId", "releaseId/container", "trackName"))
2220
{
2321
@Override
24-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
22+
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
2523
{
2624
String jbrowseId = ctx.get(getBoundKey("releaseId", "jbrowseId"), String.class);
2725
String containerId = ctx.get(getBoundKey("releaseId", "container"), String.class);
@@ -30,7 +28,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
3028
if (jbrowseId != null && trackName != null)
3129
{
3230
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>");
31+
out.write(PageFlowUtil.link("View In Genome Browser").addClass("labkey-text-link").href(url.getActionURL()));
3432
}
3533
}
3634
};

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

Lines changed: 13 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -11,9 +11,10 @@
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.util.HtmlString;
15+
import org.labkey.api.util.PageFlowUtil;
16+
import org.labkey.api.writer.HtmlWriter;
1417

15-
import java.io.IOException;
16-
import java.io.Writer;
1718
import java.util.List;
1819
import java.util.Set;
1920

@@ -52,34 +53,34 @@ 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, HtmlWriter out)
5657
{
5758
String jbrowseId = StringUtils.trimToNull(ctx.get(getBoundKey("releaseId/jbrowseId"), String.class));
5859
String primaryTrack = ctx.get(getBoundKey("releaseId/primaryTrack"), String.class);
5960
String containerId = ctx.get(getBoundKey("container"), String.class);
6061
String contig = StringUtils.trimToNull(ctx.get(getBoundKey("contig"), String.class));
6162
String ref = ctx.get(getBoundKey("reference"), String.class);
6263
Integer position = ctx.get(getBoundKey("position"), Integer.class);
63-
String delim = "";
64+
HtmlString delim = HtmlString.EMPTY_STRING;
6465
int start = position - 200;
6566
int stop = position + 200;
6667
int length = ref.length();
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-
delim = "<br>";
71+
out.write(PageFlowUtil.link("View In Genome Browser").href(url.getActionURL()).addClass("labkey-text-link"));
72+
delim = HtmlString.BR;
7273
}
7374

7475
if (primaryTrack != null)
7576
{
7677
out.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-
delim = "<br>";
79+
out.write(PageFlowUtil.link("View Genotypes At Position").href(url.getActionURL()).addClass("labkey-text-link"));
80+
delim = HtmlString.BR;
8081
}
8182

82-
if (ctx.get(FieldKey.fromString("identifier")) != null)
83+
if (ctx.get(FieldKey.fromString("identifier"), String.class) != null)
8384
{
8485
String identifier = StringUtils.trimToNull(ctx.get(getBoundKey("identifier"), String.class));
8586
if (identifier != null && identifier.contains(":"))
@@ -97,8 +98,8 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
9798
{
9899
String url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
99100
out.write(delim);
100-
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View in ClinVar</a>");
101-
delim = "<br>";
101+
out.write(PageFlowUtil.link("View in ClinVar").href(url));
102+
delim = HtmlString.BR;
102103
}
103104
}
104105
}
@@ -110,7 +111,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
110111
contigE = contigE.replaceAll("^0", "");
111112
String url = "https://ensembl.org/Macaca_mulatta/Location/View?db=core;r=" + contigE + ":" + start +"-" + stop;
112113
out.write(delim);
113-
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View Region in Ensembl</a>");
114+
out.write(PageFlowUtil.link("View Region in Ensembl").href(url));
114115
}
115116
};
116117
}

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

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -9,12 +9,12 @@
99
import org.labkey.api.data.RenderContext;
1010
import org.labkey.api.query.DetailsURL;
1111
import org.labkey.api.query.FieldKey;
12+
import org.labkey.api.util.HtmlString;
1213
import org.labkey.api.util.PageFlowUtil;
1314
import org.labkey.api.view.HttpView;
1415
import org.labkey.api.view.template.ClientDependency;
16+
import org.labkey.api.writer.HtmlWriter;
1517

16-
import java.io.IOException;
17-
import java.io.Writer;
1818
import java.util.Set;
1919

2020
/**
@@ -48,12 +48,15 @@ private FieldKey getBoundKey(String colName)
4848
private boolean _clickHandlerRegistered = false;
4949

5050
@Override
51-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
51+
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
5252
{
5353
Integer rowId = ctx.get(getBoundKey("rowid"), Integer.class);
5454
if (rowId != null)
5555
{
56-
out.write("<a class=\"labkey-text-link vrdc-row\" data-rowid=" + PageFlowUtil.jsString(rowId.toString()) + ">Download</a>");
56+
out.write(PageFlowUtil.link("Download").
57+
addClass("vrdc-row").
58+
attributes(PageFlowUtil.map("data-rowid", rowId.toString()))
59+
);
5760

5861
if (!_clickHandlerRegistered)
5962
{
@@ -69,20 +72,20 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
6972
{
7073
if (rowId != null)
7174
{
72-
out.write("<br>");
75+
out.write(HtmlString.BR);
7376
}
7477

7578
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>");
79+
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
7780
}
7881

7982
Boolean showVariantList = ctx.get(getBoundKey("hasSignificantVariants"), Boolean.class);
8083
if (showVariantList)
8184
{
82-
out.write("<br>");
85+
out.write(HtmlString.BR);
8386

8487
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>");
88+
out.write(PageFlowUtil.link("Significant Variant List", url.getActionURL()));
8689
}
8790
}
8891

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

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,8 @@
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

13-
import java.io.IOException;
14-
import java.io.Writer;
1514
import java.util.Set;
1615

1716
/**
@@ -67,14 +66,14 @@ protected FieldKey getBoundKey(String... colNames)
6766
}
6867

6968
@Override
70-
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
69+
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
7170
{
7271
String jbrowseId = ctx.get(getBoundKey("jbrowseId"), String.class);
7372
String containerId = ctx.get(getBoundKey("container"), String.class);
7473
if (jbrowseId != null)
7574
{
7675
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>");
76+
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
7877
}
7978
}
8079

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