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Merged
labkey-adam merged 2 commits into from
Apr 14, 2025
Merged

Simplify and expand use of LinkBuilder factory methods #251

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fcfb656
Simplify and expand use of LinkBuilder factory methods
labkey-adam Apr 14, 2025
497f4a6
Remove redundant addClass() calls
labkey-adam Apr 14, 2025
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3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -59,7 +60,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
}

out.write(delim);
out.write(PageFlowUtil.link(text).href("https://www.omim.org/entry/" + id).target("_blank").clearClasses());
out.write(LinkBuilder.simpleLink(text, "https://www.omim.org/entry/" + id).target("_blank"));
delim = HtmlString.BR;
}
}
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5 changes: 3 additions & 2 deletions mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -68,11 +69,11 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
out.write(delim);
if (elements.length > 1)
{
out.write(PageFlowUtil.link(elements[0]).target("_blank").href("https://www.omim.org/entry/" + elements[1]).clearClasses());
out.write(LinkBuilder.simpleLink(elements[0], "https://www.omim.org/entry/" + elements[1]).target("_blank"));
}
else
{
out.write(PageFlowUtil.link(elements[0]).clearClasses());
out.write(LinkBuilder.simpleLink(elements[0]));
}

delim = HtmlString.BR;
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3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -66,7 +67,7 @@ else if (geneName.startsWith("ENSMMUE"))
}

out.write(delim);
out.write(PageFlowUtil.link(geneName).href(url).target("_blank").clearClasses());
out.write(LinkBuilder.simpleLink(geneName, url).target("_blank"));
delim = HtmlString.BR;
}
}
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3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -52,7 +53,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
if (releaseId != null && omim != null)
{
DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + releaseId + "&query.omim_phenotype~contains=" + omim, ContainerManager.getForId(containerId));
out.write(PageFlowUtil.link("View Variants").href(url.getActionURL()).addClass("labkey-text-link"));
out.write(LinkBuilder.labkeyLink("View Variants", url.getActionURL()).addClass("labkey-text-link"));
}
}
};
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3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java
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Expand Up @@ -9,6 +9,7 @@
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -66,7 +67,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
}
else
{
out.write(PageFlowUtil.link(val).href(url).clearClasses());
out.write(LinkBuilder.simpleLink(val, url));
}
}

Expand Down
3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java
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Expand Up @@ -5,6 +5,7 @@
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand All @@ -28,7 +29,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
if (jbrowseId != null && trackName != null)
{
DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName, ContainerManager.getForId(containerId));
out.write(PageFlowUtil.link("View In Genome Browser").addClass("labkey-text-link").href(url.getActionURL()));
out.write(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL()).addClass("labkey-text-link"));
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@bbimber bbimber Apr 14, 2025

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addClass not needed, right (and maybe not needed before either)?

}
}
};
Expand Down
9 changes: 5 additions & 4 deletions mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java
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Expand Up @@ -12,6 +12,7 @@
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -68,15 +69,15 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
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(PageFlowUtil.link("View In Genome Browser").href(url.getActionURL()).addClass("labkey-text-link"));
out.write(LinkBuilder.labkeyLink("View In Genome Browser", 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(PageFlowUtil.link("View Genotypes At Position").href(url.getActionURL()).addClass("labkey-text-link"));
out.write(LinkBuilder.labkeyLink("View Genotypes At Position", url.getActionURL()).addClass("labkey-text-link"));
delim = HtmlString.BR;
}

Expand All @@ -98,7 +99,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
out.write(delim);
out.write(PageFlowUtil.link("View in ClinVar").href(url));
out.write(LinkBuilder.labkeyLink("View in ClinVar", url));
delim = HtmlString.BR;
}
}
Expand All @@ -111,7 +112,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
contigE = contigE.replaceAll("^0", "");
String url = "https://ensembl.org/Macaca_mulatta/Location/View?db=core;r=" + contigE + ":" + start +"-" + stop;
out.write(delim);
out.write(PageFlowUtil.link("View Region in Ensembl").href(url));
out.write(LinkBuilder.labkeyLink("View Region in Ensembl", url));
}
};
}
Expand Down
7 changes: 4 additions & 3 deletions mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java
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Expand Up @@ -10,6 +10,7 @@
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.template.ClientDependency;
Expand Down Expand Up @@ -53,7 +54,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
Integer rowId = ctx.get(getBoundKey("rowid"), Integer.class);
if (rowId != null)
{
out.write(PageFlowUtil.link("Download").
out.write(LinkBuilder.labkeyLink("Download").
addClass("vrdc-row").
attributes(PageFlowUtil.map("data-rowid", rowId.toString()))
);
Expand All @@ -76,7 +77,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
}

DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
out.write(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL()));
}

Boolean showVariantList = ctx.get(getBoundKey("hasSignificantVariants"), Boolean.class);
Expand All @@ -85,7 +86,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
out.write(HtmlString.BR);

DetailsURL url = DetailsURL.fromString("/mgap/variantList.view?release=" + rowId, ContainerManager.getForId(containerId));
out.write(PageFlowUtil.link("Significant Variant List", url.getActionURL()));
out.write(LinkBuilder.labkeyLink("Significant Variant List", url.getActionURL()));
}
}

Expand Down
3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java
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Expand Up @@ -8,6 +8,7 @@
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

Expand Down Expand Up @@ -73,7 +74,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
if (jbrowseId != null)
{
DetailsURL url = DetailsURL.fromString("/jbrowse/browser.view?database=" + jbrowseId, ContainerManager.getForId(containerId));
out.write(PageFlowUtil.link("View In Genome Browser", url.getActionURL()));
out.write(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL()));
}
}

Expand Down
3 changes: 2 additions & 1 deletion mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java
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Expand Up @@ -5,6 +5,7 @@
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.api.data.RenderContext;
Expand All @@ -26,7 +27,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
int rowId = ctx.get(getBoundKey("rowid"), Integer.class);
out.write(PageFlowUtil.link("Contact MCC").href("mailto:" + MccManager.get().getMccAdminEmail() + "?subject=MCC Request #" + rowId));
out.write(LinkBuilder.labkeyLink("Contact MCC", "mailto:" + MccManager.get().getMccAdminEmail() + "?subject=MCC Request #" + rowId));
}

@Override
Expand Down
3 changes: 2 additions & 1 deletion mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java
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Expand Up @@ -11,6 +11,7 @@
import org.labkey.api.query.FieldKey;
import org.labkey.api.security.User;
import org.labkey.api.security.UserManager;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.mcc.MccManager;
Expand Down Expand Up @@ -44,7 +45,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
String requestId = ctx.get(getBoundKey("requestId"), String.class);
Container requestContainer = MccManager.get().getMCCRequestContainer(ctx.getContainer());
DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=rabReview", requestContainer);
out.write(PageFlowUtil.link("Enter Review").href(url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link"));
out.write(LinkBuilder.labkeyLink("Enter Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link"));
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@bbimber bbimber Apr 14, 2025

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same as above. this was pre-existing your change and doesnt really harm anything either

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@labkey-adam labkey-adam Apr 14, 2025

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Correct... not needed (it's set by default) but harmless. I'll clear these out before merging, just for clarity.

}

@Override
Expand Down
14 changes: 8 additions & 6 deletions mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java
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Expand Up @@ -13,6 +13,7 @@
import org.labkey.api.security.User;
import org.labkey.api.security.UserManager;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.LinkBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.template.ClientDependency;
Expand Down Expand Up @@ -49,7 +50,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
return;
}

out.write(PageFlowUtil.link("Contact Investigator").addClass("labkey-text-link").href("mailto:" + u.getEmail() + "?subject=MCC Request #" + requestRowId));
out.write(LinkBuilder.labkeyLink("Contact Investigator", "mailto:" + u.getEmail() + "?subject=MCC Request #" + requestRowId).addClass("labkey-text-link"));
}

String status = ctx.get(getBoundKey("requestId", "status"), String.class);
Expand Down Expand Up @@ -77,7 +78,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=primaryReview", requestContainer);
out.write(HtmlString.BR);
out.write(PageFlowUtil.link("Enter MCC Internal Review").addClass("labkey-text-link").href(url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())));
out.write(LinkBuilder.labkeyLink("Enter MCC Internal Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link"));
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@bbimber bbimber Apr 14, 2025

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same as above

}
}
else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString("pendingRabReviews"), Integer.class) == 0)
Expand All @@ -86,7 +87,7 @@ else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString
{
DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=resourceAvailability", requestContainer);
out.write(HtmlString.BR);
out.write(PageFlowUtil.link("Enter Resource Availability Assessment").addClass("labkey-text-link").href(url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())));
out.write(LinkBuilder.labkeyLink("Enter Resource Availability Assessment", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link"));
}
}
else if (st == MccManager.RequestStatus.PendingDecision)
Expand All @@ -95,16 +96,17 @@ else if (st == MccManager.RequestStatus.PendingDecision)
{
DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=finalReview", requestContainer);
out.write(HtmlString.BR);
out.write(PageFlowUtil.link("Enter Final Review").addClass("labkey-text-link").href(url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())));
out.write(LinkBuilder.labkeyLink("Enter Final Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link"));
}
}
else if (st == MccManager.RequestStatus.Approved)
{
out.write(HtmlString.BR);
out.write(PageFlowUtil.link("Mark Fulfilled").
out.write(LinkBuilder.labkeyLink("Mark Fulfilled").
addClass("labkey-text-link").
addClass("rsadc-approved").
attributes(PageFlowUtil.map("data-requestrowid", String.valueOf(requestRowId))));
attributes(PageFlowUtil.map("data-requestrowid", String.valueOf(requestRowId)))
);

if (!_hasRegisteredApprovedHandler)
{
Expand Down