From fcfb656f513c1ce4ca2e2ebc2a3a795d1c4ddef2 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Mon, 14 Apr 2025 07:46:14 -0700 Subject: [PATCH 1/2] Simplify and expand use of LinkBuilder factory methods --- .../mgap/query/OMIMDisplayColumnFactory.java | 3 ++- .../query/OMIMPhenotypeDisplayColumnFactory.java | 5 +++-- .../OverlappingGenesDisplayColumnFactory.java | 3 ++- .../PhenotypeVariantLinkDisplayColumnFactory.java | 3 ++- .../mgap/query/SourceDisplayColumnFactory.java | 3 ++- ...erReleaseGenomeBrowserDisplayColumnFactory.java | 3 ++- .../VariantListJBrowseDisplayColumnFactory.java | 9 +++++---- .../query/VariantReleaseDisplayColumnFactory.java | 7 ++++--- ...ntReleaseGenomeBrowserDisplayColumnFactory.java | 3 ++- .../AnimalRequestActionsDisplayColumnFactory.java | 3 ++- .../RequestReviewActionsDisplayColumnFactory.java | 3 ++- .../RequestScoreActionsDisplayColumnFactory.java | 14 ++++++++------ 12 files changed, 36 insertions(+), 23 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java index 0befb04b..e48267fe 100644 --- a/mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/OMIMDisplayColumnFactory.java @@ -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; @@ -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; } } diff --git a/mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java index ed07c8ec..04528de7 100644 --- a/mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/OMIMPhenotypeDisplayColumnFactory.java @@ -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; @@ -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; diff --git a/mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java index f6664ea7..d1b357ec 100644 --- a/mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/OverlappingGenesDisplayColumnFactory.java @@ -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; @@ -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; } } diff --git a/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java index 929f9933..3fb42b80 100644 --- a/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java @@ -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; @@ -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")); } } }; diff --git a/mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java index 1d7b5721..c5adfc56 100644 --- a/mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/SourceDisplayColumnFactory.java @@ -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; @@ -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)); } } diff --git a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java index 57aec2e5..66856e6b 100644 --- a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java @@ -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; @@ -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")); } } }; diff --git a/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java index 82f2f001..ef0496d0 100644 --- a/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java @@ -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; @@ -68,7 +69,7 @@ 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; } @@ -76,7 +77,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { 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; } @@ -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; } } @@ -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)); } }; } diff --git a/mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java index 8b05a0ca..b1c304a0 100644 --- a/mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java @@ -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; @@ -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())) ); @@ -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); @@ -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())); } } diff --git a/mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java index e3803216..dab0b13d 100644 --- a/mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/VariantReleaseGenomeBrowserDisplayColumnFactory.java @@ -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; @@ -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())); } } diff --git a/mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java index 696920b4..a74c3b3c 100644 --- a/mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java +++ b/mcc/src/org/labkey/mcc/query/AnimalRequestActionsDisplayColumnFactory.java @@ -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; @@ -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 diff --git a/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java index e1287613..3b6dd161 100644 --- a/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java +++ b/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java @@ -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; @@ -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")); } @Override diff --git a/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java index b95d4312..2d09bb3e 100644 --- a/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java +++ b/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java @@ -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; @@ -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); @@ -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")); } } else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString("pendingRabReviews"), Integer.class) == 0) @@ -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) @@ -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) { From 497f4a63c33096b0763b187acb6f5e87be4689ba Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Mon, 14 Apr 2025 08:26:12 -0700 Subject: [PATCH 2/2] Remove redundant addClass() calls --- .../query/PhenotypeVariantLinkDisplayColumnFactory.java | 3 +-- ...TracksPerReleaseGenomeBrowserDisplayColumnFactory.java | 2 +- .../query/VariantListJBrowseDisplayColumnFactory.java | 5 ++--- .../query/RequestReviewActionsDisplayColumnFactory.java | 3 +-- .../query/RequestScoreActionsDisplayColumnFactory.java | 8 ++++---- 5 files changed, 9 insertions(+), 12 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java index 3fb42b80..f6bf277e 100644 --- a/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/PhenotypeVariantLinkDisplayColumnFactory.java @@ -9,7 +9,6 @@ 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; import java.util.List; @@ -53,7 +52,7 @@ 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(LinkBuilder.labkeyLink("View Variants", url.getActionURL()).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("View Variants", url.getActionURL())); } } }; diff --git a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java index 66856e6b..7e73046d 100644 --- a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java @@ -29,7 +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(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL()).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL())); } } }; diff --git a/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java index ef0496d0..d81d23ea 100644 --- a/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/VariantListJBrowseDisplayColumnFactory.java @@ -13,7 +13,6 @@ 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; import java.util.List; @@ -69,7 +68,7 @@ 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(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL()).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL())); delim = HtmlString.BR; } @@ -77,7 +76,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { out.write(delim); DetailsURL url = DetailsURL.fromString("/jbrowse/genotypeTable.view?trackId=" + primaryTrack + "&chr=" + contig + "&start=" + position + "&stop=" + position, ContainerManager.getForId(containerId)); - out.write(LinkBuilder.labkeyLink("View Genotypes At Position", url.getActionURL()).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("View Genotypes At Position", url.getActionURL())); delim = HtmlString.BR; } diff --git a/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java index 3b6dd161..868f18ab 100644 --- a/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java +++ b/mcc/src/org/labkey/mcc/query/RequestReviewActionsDisplayColumnFactory.java @@ -12,7 +12,6 @@ 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; @@ -45,7 +44,7 @@ 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(LinkBuilder.labkeyLink("Enter Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("Enter Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL()))); } @Override diff --git a/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java index 2d09bb3e..59b27c49 100644 --- a/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java +++ b/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java @@ -50,7 +50,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out) return; } - out.write(LinkBuilder.labkeyLink("Contact Investigator", "mailto:" + u.getEmail() + "?subject=MCC Request #" + requestRowId).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("Contact Investigator", "mailto:" + u.getEmail() + "?subject=MCC Request #" + requestRowId)); } String status = ctx.get(getBoundKey("requestId", "status"), String.class); @@ -78,7 +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(LinkBuilder.labkeyLink("Enter MCC Internal Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("Enter MCC Internal Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL()))); } } else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString("pendingRabReviews"), Integer.class) == 0) @@ -87,7 +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(LinkBuilder.labkeyLink("Enter Resource Availability Assessment", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("Enter Resource Availability Assessment", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL()))); } } else if (st == MccManager.RequestStatus.PendingDecision) @@ -96,7 +96,7 @@ else if (st == MccManager.RequestStatus.PendingDecision) { DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=finalReview", requestContainer); out.write(HtmlString.BR); - out.write(LinkBuilder.labkeyLink("Enter Final Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL())).addClass("labkey-text-link")); + out.write(LinkBuilder.labkeyLink("Enter Final Review", url.getActionURL().addReturnUrl(ctx.getViewContext().getActionURL()))); } } else if (st == MccManager.RequestStatus.Approved)