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Merged
labkey-adam merged 5 commits into from
Mar 18, 2025
Merged

lk-region-form -> data-region-form #520

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3f5c599
lk-region-form -> data-region-form
labkey-adam Mar 12, 2025
1c49650
renderInputHtml(), renderDetailsCaptionCell(), and renderHiddenFormIn…
labkey-adam Mar 13, 2025
b1a5649
Migrate renderGridCellContents() and renderDetailsCellContents()
labkey-adam Mar 13, 2025
14c6945
Fewer StackOverflowExceptions, please
labkey-adam Mar 13, 2025
2afd19f
Migrate remaining DisplayColumn methods
labkey-adam Mar 17, 2025
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17 changes: 10 additions & 7 deletions lincs/src/org/labkey/lincs/LincsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartView;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.lincs.cromwell.CromwellConfig;
import org.labkey.lincs.cromwell.CromwellException;
import org.labkey.lincs.psp.LincsPspException;
Expand All @@ -95,7 +96,6 @@
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.Writer;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
Expand All @@ -114,6 +114,7 @@

import static org.labkey.api.util.DOM.BR;
import static org.labkey.api.util.DOM.DIV;
import static org.labkey.api.util.DOM.PRE;

public class LincsController extends SpringActionController
{
Expand Down Expand Up @@ -161,11 +162,11 @@ public boolean accept(File dir, String name)
// Copy both to the GCT folder
for(File file: reportDirFiles)
{
if(file.getName().toLowerCase().equals("lincs.gct"))
if(file.getName().equalsIgnoreCase("lincs.gct"))
{
Files.copy(file.toPath(), gct, StandardCopyOption.REPLACE_EXISTING);
}
else if(file.getName().toLowerCase().equals("console.txt"))
else if(file.getName().equalsIgnoreCase("console.txt"))
{
Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);
}
Expand Down Expand Up @@ -1280,13 +1281,15 @@ private static DataRegion getPspJobDetailsDataRegion()
SimpleDisplayColumn jsonCol = new SimpleDisplayColumn(){

@Override
public void renderDetailsCellContents(RenderContext ctx, Writer out) throws IOException
public void renderDetailsCellContents(RenderContext ctx, HtmlWriter out)
{
String json = ctx.get(FieldKey.fromParts("Json"), String.class);
if(!StringUtils.isBlank(json))
if (!StringUtils.isBlank(json))
{
JSONObject jsonObj = new JSONObject(json);
out.write("<pre>" + PageFlowUtil.filter(jsonObj.toString(2)) + "</pre>");
PRE(
jsonObj.toString(2)
).appendTo(out);
}
else
{
Expand Down Expand Up @@ -1379,7 +1382,7 @@ public ModelAndView getView(LincsPspJobForm form, BindException errors)
DOM.P("Status for job: " + pspJob.getId() +", PSP job Id: " + pspJob.getPspJobId() + ", Run Id: " + pspJob.getRunId()),
"JSON Output:",
DOM.BR(),
DOM.P(DOM.PRE(jsonStatus)))));
DOM.P(PRE(jsonStatus)))));
view.setTitle("PSP job status");
view.setFrame(WebPartView.FrameType.PORTAL);
return view;
Expand Down
68 changes: 40 additions & 28 deletions lincs/src/org/labkey/lincs/LincsDataTable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.analytics.AnalyticsService;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.DataColumn;
Expand All @@ -33,10 +34,9 @@
import org.labkey.api.util.Link;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.lincs.psp.LincsPspJob;

import java.io.IOException;
import java.io.Writer;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
Expand All @@ -45,6 +45,10 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static org.labkey.api.util.DOM.Attribute.style;
import static org.labkey.api.util.DOM.SPAN;
import static org.labkey.api.util.DOM.at;

/**
* Created by vsharma on 8/21/2017.
*/
Expand Down Expand Up @@ -72,17 +76,21 @@ public LincsDataTable(@NotNull TableInfo table, @NotNull UserSchema userSchema)
addColumn(level1Col);
level1Col.setDisplayColumnFactory(colInfo -> new DataColumn(colInfo){
@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
ActionURL downloadUrl = new ActionURL("targetedms", "DownloadDocument", getContainer());
Integer runId = ctx.get(FieldKey.fromParts("Id"), Integer.class);
downloadUrl.addParameter("id", runId);
out.write("<nobr>");
out.write(new Link.LinkBuilder("Download").iconCls("fa fa-download").href(downloadUrl).toString());
ActionURL docDetailsUrl = new ActionURL("targetedms", "ShowPrecursorList", getContainer());
docDetailsUrl.addParameter("id", runId);
out.write("&nbsp;" + new Link.LinkBuilder("Skyline").href(docDetailsUrl).clearClasses().toString());
out.write("</nobr>");

// <span style="white-space: nowrap;"> is recommended instead of deprecated <nobr></nobr>
SPAN(
at(style, "white-space: nowrap;"),
new Link.LinkBuilder("Download").iconCls("fa fa-download").href(downloadUrl),
HtmlString.NBSP,
new Link.LinkBuilder("Skyline").href(docDetailsUrl).clearClasses()
).appendTo(out);
}

@Override
Expand Down Expand Up @@ -133,7 +141,7 @@ public boolean isFilterable()
pspJobCol.setDisplayColumnFactory(colInfo -> new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Integer runId = ctx.get(FieldKey.fromParts("Id"), Integer.class);
if(runId == null)
Expand All @@ -150,7 +158,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
ActionURL url = new ActionURL(LincsController.SubmitPspJobAction.class, getContainer());
url.addParameter("runId", runId);

out.write(new Link.LinkBuilder(" [Submit Job]").href(url).usePost().toString());
out.write(new Link.LinkBuilder(" [Submit Job]").href(url).usePost());
}
return;
}
Expand All @@ -168,7 +176,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
}
ActionURL url = new ActionURL(LincsController.LincsPspJobDetailsAction.class, getContainer());
url.addParameter("runId", pspJob.getRunId());
out.write(PageFlowUtil.link(text).href(url).toString());
out.write(PageFlowUtil.link(text).href(url));
}

@Override
Expand Down Expand Up @@ -290,7 +298,7 @@ private String getAnalyticsScript(String eventAction, String fileName, boolean a
return null;
}

private String externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
private HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
{
String gctFileUrl = davUrl + "GCT/" + PageFlowUtil.encodePath(fileName);
String morpheusUrl = getMorpheusUrl(gctFileUrl, assayType);
Expand All @@ -299,7 +307,9 @@ private String externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay
String onclickEvt = StringUtils.isBlank(analyticsScript) ? "" : "onclick=\"" + analyticsScript + "\"";

String imgUrl = AppProps.getInstance().getContextPath() + "/lincs/GENE-E_icon.png";
return "[&nbsp;<a target=\"_blank\" " + onclickEvt + " href=\"" + morpheusUrl + "\">View in Morpheus</a> <img src=" + imgUrl + " width=\"13\", height=\"13\"/>&nbsp;]";

// TODO: Should use a LinkBuilder, etc.
return HtmlString.unsafe("[&nbsp;<a target=\"_blank\" " + onclickEvt + " href=\"" + morpheusUrl + "\">View in Morpheus</a> <img src=" + imgUrl + " width=\"13\", height=\"13\"/>&nbsp;]");
}

private String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayType)
Expand All @@ -323,7 +333,7 @@ private String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayTyp
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
if(getAssayType() == null)
{
Expand All @@ -333,7 +343,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
String fileName = ctx.get(getDisplayColumn().getFieldKey(), String.class);
if(fileName == null)
{
out.write("&nbsp");
out.write(HtmlString.NBSP);
return;
}

Expand All @@ -355,23 +365,25 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep

String actionName = (getLevel() == LincsModule.LincsLevel.Config) ? "DownloadConfig" : "DownloadGCT";
String analyticsScript = getAnalyticsScript(actionName, downloadFileName, true);
String morpheusUrl = externalHeatmapViewerLink(downloadFileName, getAssayType(), getLevel());
HtmlString morpheusUrl = externalHeatmapViewerLink(downloadFileName, getAssayType(), getLevel());
String downloadText = (getLevel() == LincsModule.LincsLevel.Config) ? "CFG" : "GCT";
renderGridCell(out, analyticsScript, getGctDavUrlUnencoded(downloadFileName), getGctDavUrl(downloadFileName), downloadText, morpheusUrl);
renderGridCell(out, analyticsScript, getGctDavUrlUnencoded(downloadFileName), downloadText, morpheusUrl);
}

private void renderGridCell(Writer out, String analyticsScript, String downloadUrl, String downloadUrlEncoded, String downloadText, String morpheusUrl) throws IOException
private void renderGridCell(HtmlWriter out, String analyticsScript, String downloadUrl, String downloadText, HtmlString morpheusUrl)
{
out.write("<nobr>&nbsp;");
out.write(new Link.LinkBuilder("Download").iconCls("fa fa-download").href(downloadUrl).onClick(analyticsScript).toString());
out.write("&nbsp;");
out.write(new Link.LinkBuilder(downloadText).href(downloadUrl).onClick(analyticsScript).clearClasses().toString());
out.write("&nbsp;");
if(morpheusUrl != null)
{
out.write("&nbsp;" + morpheusUrl + "&nbsp;");
}
out.write("</nobr>");
// <span style="white-space: nowrap;"> is recommended instead of deprecated <nobr></nobr>
SPAN(
at(style, "white-space: nowrap;"),
HtmlString.NBSP,
new Link.LinkBuilder("Download").iconCls("fa fa-download").href(downloadUrl).onClick(analyticsScript),
HtmlString.NBSP,
new Link.LinkBuilder(downloadText).href(downloadUrl).onClick(analyticsScript).clearClasses(),
HtmlString.NBSP,
morpheusUrl != null ? HtmlString.NBSP : null,
morpheusUrl,
morpheusUrl != null ? HtmlString.NBSP : null
).appendTo(out);
}

private boolean fileAvailable(Integer runId, String downloadFileName)
Expand All @@ -396,7 +408,7 @@ private boolean fileAvailable(Integer runId, String downloadFileName)
}
}

String externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, LincsModule.LincsLevel level)
@Nullable HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, LincsModule.LincsLevel level)
{
if(level == LincsModule.LincsLevel.Config)
{
Expand Down
27 changes: 11 additions & 16 deletions lincs/src/org/labkey/lincs/LincsSchema.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,15 +20,13 @@
import org.jetbrains.annotations.Nullable;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.ContainerForeignKey;
import org.labkey.api.data.DataColumn;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.DbSchemaType;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.dialect.SqlDialect;
Expand All @@ -48,13 +46,14 @@
import org.labkey.api.security.UserPrincipal;
import org.labkey.api.security.permissions.Permission;
import org.labkey.api.view.ViewContext;
import org.labkey.api.writer.HtmlWriter;
import org.springframework.validation.BindException;

import java.io.IOException;
import java.io.Writer;
import java.util.List;
import java.util.Set;

import static org.labkey.api.util.DOM.PRE;

public class LincsSchema extends UserSchema
{
public static final String SCHEMA_NAME = "lincs";
Expand Down Expand Up @@ -102,20 +101,16 @@ public TableInfo createTable(String name, ContainerFilter cf)
ContainerForeignKey.initColumn(containerCol, this);

var jsonCol = result.getMutableColumn(FieldKey.fromParts("Json"));
jsonCol.setDisplayColumnFactory(new DisplayColumnFactory()
{
jsonCol.setDisplayColumnFactory(colInfo -> new DataColumn(colInfo){
@Override
public DisplayColumn createRenderer(ColumnInfo colInfo)
public void renderDetailsCellContents(RenderContext ctx, HtmlWriter out)
{
return new DataColumn(colInfo){
@Override
public void renderDetailsCellContents(RenderContext ctx, Writer out) throws IOException
{
String json = ctx.get(colInfo.getFieldKey(), String.class);
JSONObject jsonObj = new JSONObject(json);
out.write("<pre>" + jsonObj.toString(2) + "</pre>");
}
};
String json = ctx.get(colInfo.getFieldKey(), String.class);
JSONObject jsonObj = new JSONObject(json);

PRE(
jsonObj.toString(2)
).appendTo(out);
}
});
return result;
Expand Down
24 changes: 12 additions & 12 deletions panoramapublic/src/org/labkey/panoramapublic/query/CatalogEntryTableInfo.java
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ShortURLRecord;
import org.labkey.api.writer.HtmlWriter;
import org.labkey.panoramapublic.PanoramaPublicController;
import org.labkey.panoramapublic.PanoramaPublicManager;
import org.labkey.panoramapublic.PanoramaPublicSchema;
Expand All @@ -21,8 +22,6 @@
import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;
import org.labkey.panoramapublic.view.publish.ShortUrlDisplayColumnFactory;

import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
Expand Down Expand Up @@ -63,7 +62,7 @@ public Object getDisplayValue(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Object viewCatalogEntryUrl = getValue(ctx);
if (viewCatalogEntryUrl instanceof ActionURL url)
Expand Down Expand Up @@ -108,18 +107,19 @@ public Object getDisplayValue(RenderContext ctx)
}

@Override
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
String fileName = (String) getValue(ctx);
ShortURLRecord shortUrl = ctx.get(_shortUrlFieldKey, ShortURLRecord.class);
ExperimentAnnotations expAnnotations = shortUrl != null ? ExperimentAnnotationsManager.getExperimentForShortUrl(shortUrl) : null;
if (fileName != null && expAnnotations != null)
{
ActionURL downloadLink = PanoramaPublicController.getCatalogImageDownloadUrl(expAnnotations, fileName);
SPAN(at(style, "white-space: nowrap;"),
fileName,
PageFlowUtil.iconLink("fa fa-download", null).href(downloadLink).style("margin-left:10px;").build())
.appendTo(out);
SPAN(
at(style, "white-space: nowrap;"),
fileName,
PageFlowUtil.iconLink("fa fa-download", null).href(downloadLink).style("margin-left:10px;").build()
).appendTo(out);
return;
}
super.renderGridCellContents(ctx, out);
Expand Down Expand Up @@ -157,7 +157,7 @@ public Object getDisplayValue(RenderContext ctx)
reviewCol.setDisplayColumnFactory(colInfo -> new DataColumn(colInfo)
{
@Override
public void renderGridCellContents(RenderContext ctx, Writer out)
public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
{
Integer catalogEntryId = ctx.get(getColumnInfo().getFieldKey(), Integer.class);
if (catalogEntryId != null && ctx.getViewContext().getUser().hasSiteAdminPermission())
Expand All @@ -166,9 +166,9 @@ public void renderGridCellContents(RenderContext ctx, Writer out)
ExperimentAnnotations expAnnotations = ExperimentAnnotationsManager.getExperimentForShortUrl(entry.getShortUrl());
if (expAnnotations != null)
{
DIV(CatalogEntryWebPart.changeStatusButtonBuilder(entry.getApproved(), expAnnotations.getId(), catalogEntryId, expAnnotations.getContainer())
.build())
.appendTo(out);
DIV(
CatalogEntryWebPart.changeStatusButtonBuilder(entry.getApproved(), expAnnotations.getId(), catalogEntryId, expAnnotations.getContainer())
).appendTo(out);
}
}
}
Expand Down
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