Skip to content

lk-region-form -> data-region-form #243

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
labkey-adam merged 3 commits into from
Mar 18, 2025
Merged

lk-region-form -> data-region-form #243

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
46db24c
lk-region-form -> data-region-form
labkey-adam Mar 12, 2025
f1c7970
Migrate renderGridCellContents() and renderDetailsCellContents()
labkey-adam Mar 13, 2025
2c27a82
Finish renderGridCellContents migration (#244)
bbimber Mar 16, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 8 additions & 6 deletions mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +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 @@ -34,7 +35,7 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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 @@ -45,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
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 @@ -57,8 +58,9 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
text = parts[0];
}

out.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
16 changes: 9 additions & 7 deletions mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +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 @@ -49,7 +50,7 @@ public Object getExcelCompatibleValue(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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 @@ -60,20 +61,21 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
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)
{
out.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
{
out.write(delim + "<a>" + elements[0] + "</a>");
out.write(PageFlowUtil.link(elements[0]).clearClasses());
}

delim = "<br>";
delim = HtmlString.BR;
}
}
};
Expand Down
14 changes: 8 additions & 6 deletions mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +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 @@ -34,7 +35,7 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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 @@ -45,7 +46,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
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 @@ -64,8 +65,9 @@ else if (geneName.startsWith("ENSMMUE"))
url = "http://ensembl.org/Macaca_mulatta/Gene/Summary?db=core;g=" + geneName;
}

out.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
8 changes: 4 additions & 4 deletions mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +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 @@ -44,15 +44,15 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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));
out.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
15 changes: 11 additions & 4 deletions mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +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 @@ -31,7 +31,7 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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 @@ -60,7 +60,14 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
}
}

out.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
8 changes: 3 additions & 5 deletions mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.util.PageFlowUtil;

import java.io.IOException;
import java.io.Writer;
import org.labkey.api.writer.HtmlWriter;

/**
* Created by bimber on 5/17/2017.
Expand All @@ -21,7 +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 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 @@ -30,7 +28,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
if (jbrowseId != null && trackName != null)
{
DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName, ContainerManager.getForId(containerId));
out.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
25 changes: 13 additions & 12 deletions mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +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 @@ -52,34 +53,34 @@ private FieldKey getBoundKey(String colName)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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));
out.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)
{
out.write(delim);
DetailsURL url = DetailsURL.fromString("/jbrowse/genotypeTable.view?trackId=" + primaryTrack + "&chr=" + contig + "&start=" + position + "&stop=" + position, ContainerManager.getForId(containerId));
out.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 @@ -97,8 +98,8 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
{
String url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
out.write(delim);
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View in ClinVar</a>");
delim = "<br>";
out.write(PageFlowUtil.link("View in ClinVar").href(url));
delim = HtmlString.BR;
}
}
}
Expand All @@ -110,7 +111,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
contigE = contigE.replaceAll("^0", "");
String url = "https://ensembl.org/Macaca_mulatta/Location/View?db=core;r=" + contigE + ":" + start +"-" + stop;
out.write(delim);
out.write("<a class=\"labkey-text-link\" href=\"" + url + "\");\">View Region in Ensembl</a>");
out.write(PageFlowUtil.link("View Region in Ensembl").href(url));
}
};
}
Expand Down
19 changes: 11 additions & 8 deletions mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +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 @@ -48,12 +48,15 @@ private FieldKey getBoundKey(String colName)
private boolean _clickHandlerRegistered = false;

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Integer rowId = ctx.get(getBoundKey("rowid"), Integer.class);
if (rowId != null)
{
out.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 @@ -69,20 +72,20 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
{
if (rowId != null)
{
out.write("<br>");
out.write(HtmlString.BR);
}

DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
out.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)
{
out.write("<br>");
out.write(HtmlString.BR);

DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + rowId, ContainerManager.getForId(containerId));
out.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
7 changes: 3 additions & 4 deletions mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,8 @@
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.Set;

/**
Expand Down Expand Up @@ -67,14 +66,14 @@ protected FieldKey getBoundKey(String... colNames)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer 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));
out.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
Loading