diff --git a/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java b/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java index 21565e607..838a64f68 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java +++ b/flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java @@ -44,10 +44,10 @@ import org.labkey.api.security.User; import org.labkey.api.settings.AppProps; import org.labkey.api.util.HtmlString; +import org.labkey.api.util.InputBuilder; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.SimpleNamedObject; import org.labkey.api.util.StringExpression; -import org.labkey.api.util.InputBuilder; import org.labkey.api.view.GridView; import org.labkey.api.writer.HtmlWriter; import org.labkey.flow.analysis.model.ISampleInfo; @@ -58,8 +58,6 @@ import org.labkey.flow.util.KeywordUtil; import org.springframework.validation.Errors; -import java.io.IOException; -import java.io.Writer; import java.sql.ResultSet; import java.util.ArrayList; import java.util.Collection; @@ -72,6 +70,10 @@ import java.util.Set; import java.util.stream.Collectors; +import static org.labkey.api.util.DOM.Attribute.src; +import static org.labkey.api.util.DOM.IMG; +import static org.labkey.api.util.DOM.at; + public class SamplesConfirmGridView extends GridView { public static final Logger LOG = LogManager.getLogger(SamplesConfirmGridView.class); @@ -368,23 +370,23 @@ public MatchedFlagDisplayColumn() } @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { Boolean match = ctx.get(MATCHED_FLAG_FIELD_KEY, Boolean.class); if (match != null) { - oldWriter.write(""); String fileName = ctx.get(SAMPLE_NAME_FIELD_KEY, String.class); - PageFlowUtil.popupHelp(HtmlString.of("Matched the previously imported FCS file '" + fileName + "'"), "Matched").appendTo(oldWriter); + out.write(PageFlowUtil.popupHelp(HtmlString.of("Matched the previously imported FCS file '" + fileName + "'"), "Matched")); } else { - oldWriter.write("/_images/cancel.png\" />"); - PageFlowUtil.popupHelp(HtmlString.of("Failed to match a previously imported FCS file. Please manually select a matching FCS file or skip importing this row."), "Not matched").appendTo(oldWriter); + out.write(PageFlowUtil.popupHelp(HtmlString.of("Failed to match a previously imported FCS file. Please manually select a matching FCS file or skip importing this row."), "Not matched")); } } } diff --git a/flow/src/org/labkey/flow/query/FlowSchema.java b/flow/src/org/labkey/flow/query/FlowSchema.java index 4bc6a0dfa..3f3444942 100644 --- a/flow/src/org/labkey/flow/query/FlowSchema.java +++ b/flow/src/org/labkey/flow/query/FlowSchema.java @@ -16,6 +16,7 @@ package org.labkey.flow.query; +import jakarta.servlet.http.HttpServletRequest; import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -25,7 +26,28 @@ import org.labkey.api.assay.AssayService; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheManager; -import org.labkey.api.data.*; +import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.FilterInfo; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MaterializedQueryHelper; +import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.NullColumnInfo; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.WrappedColumnInfo; import org.labkey.api.exp.PropertyColumn; import org.labkey.api.exp.PropertyDescriptor; import org.labkey.api.exp.api.DataType; @@ -70,6 +92,8 @@ import org.labkey.api.study.assay.SpecimenForeignKey; import org.labkey.api.study.publish.StudyPublishService; import org.labkey.api.util.ContainerContext; +import org.labkey.api.util.HtmlString; +import org.labkey.api.util.LinkBuilder; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.StringExpressionFactory; import org.labkey.api.view.ActionURL; @@ -100,10 +124,7 @@ import org.labkey.flow.view.FlowQueryView; import org.springframework.validation.BindException; -import jakarta.servlet.http.HttpServletRequest; import java.beans.PropertyChangeEvent; -import java.io.IOException; -import java.io.Writer; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -447,37 +468,26 @@ public TableInfo getLookupTableInfo() return ret; } - private static final DisplayColumnFactory _targetStudyDisplayColumnFactory = new DisplayColumnFactory() + private static final DisplayColumnFactory _targetStudyDisplayColumnFactory = colInfo -> new DataColumn(colInfo) { @Override - public DisplayColumn createRenderer(ColumnInfo colInfo) + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { - return new DataColumn(colInfo) + String targetStudyId = (String)getBoundColumn().getValue(ctx); + if (targetStudyId != null && !targetStudyId.isEmpty()) { - @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + Container c = ContainerManager.getForId(targetStudyId); + if (c != null) { - String targetStudyId = (String)getBoundColumn().getValue(ctx); - if (targetStudyId != null && targetStudyId.length() > 0) + var ss = StudyService.get(); + Study study = null == ss ? null : ss.getStudy(c); + var urlProvider = PageFlowUtil.urlProvider(ProjectUrls.class); + if (study != null && urlProvider != null) { - Container c = ContainerManager.getForId(targetStudyId); - if (c != null) - { - var ss = StudyService.get(); - Study study = null == ss ? null : ss.getStudy(c); - var urlProvider = PageFlowUtil.urlProvider(ProjectUrls.class); - if (study != null && urlProvider != null) - { - oldWriter.write(""); - oldWriter.write(study.getLabel().replaceAll(" ", " ")); - oldWriter.write(""); - } - } + LinkBuilder.simpleLink(HtmlString.unsafe(PageFlowUtil.filter(study.getLabel()).replaceAll(" ", " ")), urlProvider.getBeginURL(c)).appendTo(out); } } - }; + } } }; @@ -487,6 +497,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit * * basically rejoins what is effectively a vertically partitioned table (ACKK) */ + // TODO: Delete this? Unused! class JoinFlowDataTable extends AbstractTableInfo implements ExpDataTable { final ExpDataTable _expData; @@ -882,12 +893,12 @@ public String renderURL(RenderContext ctx) } @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { String url = renderURL(ctx); if (url != null) { - oldWriter.write(PageFlowUtil.iconLink("fa fa-download", null).href(url).toString()); + out.write(PageFlowUtil.iconLink("fa fa-download", null).href(url)); } } }; diff --git a/flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java b/flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java index 014889c8b..7b5487f1e 100644 --- a/flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java +++ b/flow/src/org/labkey/flow/webparts/AnalysisScriptsWebPart.java @@ -17,7 +17,6 @@ package org.labkey.flow.webparts; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.data.ActionButton; import org.labkey.api.data.ButtonBar; import org.labkey.api.data.ColumnInfo; @@ -28,26 +27,20 @@ import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasedColumn; import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.util.HtmlString; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; import org.labkey.api.view.Portal; import org.labkey.api.view.SimpleWebPartFactory; import org.labkey.api.view.ViewContext; -import org.labkey.api.writer.HtmlWriter; import org.labkey.flow.controllers.editscript.ScriptController; -import org.labkey.flow.controllers.executescript.AnalysisScriptController; -import org.labkey.flow.data.FlowProtocolStep; -import org.labkey.flow.data.FlowScript; import org.labkey.flow.query.FlowQuerySettings; import org.labkey.flow.query.FlowSchema; import org.labkey.flow.query.FlowTableType; import org.labkey.flow.view.FlowQueryView; import org.springframework.web.servlet.mvc.Controller; -import java.io.IOException; -import java.io.Writer; import java.util.ArrayList; import java.util.Collections; import java.util.List; @@ -87,8 +80,6 @@ public List getDisplayColumns() ColumnInfo colRowId = new AliasedColumn("RowId", table.getColumn("RowId")); if (getContainer().hasPermission(getUser(), UpdatePermission.class)) { - // PerformAnalsysisColumn is too expensive - //ret.add(new PerformAnalysisColumn(colRowId)); ret.add(new ScriptActionColumn("Copy", ScriptController.CopyAction.class, colRowId)); ret.add(new ScriptActionColumn("Delete", ScriptController.DeleteAction.class, colRowId)); } @@ -131,54 +122,4 @@ public List getAnalyticsProviders() return Collections.emptyList(); } } - - public class PerformAnalysisColumn extends DataColumn - { - public PerformAnalysisColumn(ColumnInfo col) - { - super(col); - setCaption("Execute Script"); - setNoWrap(true); - setWidth("auto"); - } - - public FlowScript getScript(RenderContext ctx) - { - Object value = getBoundColumn().getValue(ctx); - if (!(value instanceof Number)) - return null; - int id = ((Number) value).intValue(); - return FlowScript.fromScriptId(id); - } - - @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException - { - FlowScript script = getScript(ctx); - if (script != null) - { - String and = ""; - - if (script.hasStep(FlowProtocolStep.calculateCompensation)) - { - ActionURL url = script.urlFor(AnalysisScriptController.ChooseRunsToAnalyzeAction.class, FlowProtocolStep.calculateCompensation); - oldWriter.write("Compensation"); - and = "
"; - } - - if (script.hasStep(FlowProtocolStep.analysis)) - { - ActionURL url = script.urlFor(AnalysisScriptController.ChooseRunsToAnalyzeAction.class, FlowProtocolStep.analysis); - oldWriter.write(and); - oldWriter.write("Statistics and Graphs"); - } - - } - else - { - oldWriter.write(" "); - } - } - } - } diff --git a/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java b/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java index 8aa1f9bbb..b5d7a1fcf 100644 --- a/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java +++ b/luminex/src/org/labkey/luminex/query/AnalyteSinglePointControlTable.java @@ -121,7 +121,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo) return new JavaScriptDisplayColumn(colInfo, List.of("clientapi/ext3", "vis/vis", "luminex/LeveyJenningsPlotHelpers.js", "luminex/LeveyJenningsReport.css")) { @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { int protocolId = schema.getProtocol().getRowId(); int analyte = (int)ctx.get("analyte"); @@ -131,7 +131,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit HtmlString html = HtmlString.unsafe(String.format("", AppProps.getInstance().getContextPath() + "/luminex/ljPlotIcon.png")); - renderLink(oldWriter, html, onClick, null); + renderLink(out, html, onClick, null); } @Override diff --git a/luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java b/luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java index e76cb9f2d..0064e99d4 100644 --- a/luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java +++ b/luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java @@ -54,17 +54,11 @@ import org.labkey.luminex.model.GuideSet; import org.labkey.luminex.model.Titration; -import java.io.IOException; -import java.io.Writer; import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.Objects; -/** - * User: jeckels - * Date: 7/8/11 - */ public class AnalyteTitrationTable extends AbstractCurveFitPivotTable { public AnalyteTitrationTable(final LuminexProtocolSchema schema, ContainerFilter cf, boolean filter) @@ -126,7 +120,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo) return new JavaScriptDisplayColumn(colInfo, List.of("clientapi/ext3", "vis/vis", "luminex/LeveyJenningsPlotHelpers.js", "luminex/LeveyJenningsReport.css")) { @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { int protocolId = schema.getProtocol().getRowId(); int analyte = (int)ctx.get("analyte"); diff --git a/luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java b/luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java index 4d79f8d53..71d347dec 100644 --- a/luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java +++ b/luminex/src/org/labkey/luminex/query/ExclusionUIDisplayColumn.java @@ -89,7 +89,7 @@ public HtmlString getTitle(RenderContext ctx) } @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { String type = (String)ctx.get(_typeFieldKey); String description = (String)ctx.get(_descriptionFieldKey); @@ -112,11 +112,11 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit // add onclick handler to call the well exclusion window creation function String onClick = "openExclusionsWellWindow(" + _protocolId + ", " + runId + ", " + dataId + ", " + jsString(wellID) + ", " + (description == null ? null : jsString(description)) + ", " + jsString(type) + ");"; - LinkBuilder.simpleLink(img).href("#").onClick(onClick).appendTo(oldWriter); + LinkBuilder.simpleLink(img).href("#").onClick(onClick).appendTo(out); } else { - oldWriter.write(img.toString()); + out.write(img); } } diff --git a/luminex/src/org/labkey/luminex/query/GuideSetTable.java b/luminex/src/org/labkey/luminex/query/GuideSetTable.java index 325188a24..a43376589 100644 --- a/luminex/src/org/labkey/luminex/query/GuideSetTable.java +++ b/luminex/src/org/labkey/luminex/query/GuideSetTable.java @@ -16,6 +16,8 @@ package org.labkey.luminex.query; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssaySchema; +import org.labkey.api.assay.AssayService; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; @@ -48,8 +50,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.UserPrincipal; import org.labkey.api.security.permissions.Permission; -import org.labkey.api.assay.AssaySchema; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.HtmlString; import org.labkey.api.writer.HtmlWriter; import org.labkey.luminex.LuminexDataHandler; @@ -57,8 +57,6 @@ import org.labkey.luminex.model.AnalyteTitration; import org.labkey.luminex.model.GuideSet; -import java.io.IOException; -import java.io.Writer; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -150,12 +148,12 @@ public DisplayColumn createRenderer(ColumnInfo colInfo) { return new DataColumn(colInfo){ @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { if ( (Boolean)ctx.get(this.getColumnInfo().getFieldKey()) ) - oldWriter.write("Value-based"); + out.write("Value-based"); else - oldWriter.write("Run-based"); + out.write("Run-based"); } }; } diff --git a/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java b/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java index 95afc5e3d..7f5e410fd 100644 --- a/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java +++ b/luminex/src/org/labkey/luminex/query/LuminexProtocolSchema.java @@ -85,6 +85,10 @@ import java.util.Map; import java.util.Set; +import static org.labkey.api.util.DOM.Attribute.src; +import static org.labkey.api.util.DOM.IMG; +import static org.labkey.api.util.DOM.at; + /** * Maps to a single assay design for schema tables/queries (batch, run, data, analyte, titration, curve fit, etc.) */ @@ -624,7 +628,7 @@ public void addQueryFieldKeys(Set keys) } @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { Map pdfs = new HashMap<>(); for (Map.Entry entry : _pdfColumns.entrySet()) @@ -642,9 +646,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit { ActionURL url = PageFlowUtil.urlProvider(ExperimentUrls.class).getShowFileURL(getContainer()); url.addParameter("rowId", entry.getKey().toString()); - oldWriter.write(""); - oldWriter.write(""); - oldWriter.write(""); + LinkBuilder.simpleLink(IMG(at(src, AppProps.getInstance().getContextPath() + "/_images/sigmoidal_curve.png")), url).appendTo(out); } } else if (pdfs.size() > 1) @@ -664,7 +666,7 @@ else if (pdfs.size() > 1) HtmlString image = HtmlString.unsafe(""); LinkBuilder.simpleLink(image) .onMouseOver("return showHelpDiv(this, 'Titration Curves', " + PageFlowUtil.jsString(PageFlowUtil.filter(sb.toString())) + ");") - .appendTo(oldWriter); + .appendTo(out); } } }; diff --git a/ms2/src/org/labkey/ms2/MS2Controller.java b/ms2/src/org/labkey/ms2/MS2Controller.java index 038bcf7e1..f2ac864c7 100644 --- a/ms2/src/org/labkey/ms2/MS2Controller.java +++ b/ms2/src/org/labkey/ms2/MS2Controller.java @@ -648,17 +648,16 @@ private LinkBuilder modificationHref(MS2Run run) fixed.put(mod.getAminoAcid(), Formats.f3.format(mod.getMassDiff())); } - StringBuilder onClick = new StringBuilder("showHelpDiv(this, 'Modifications', "); - onClick.append(PageFlowUtil.jsString( - DOM.createHtml(TABLE( - var.isEmpty() && fixed.isEmpty() ? TR(TD(at(DOM.Attribute.colspan, 2), STRONG("None"))) : null, - appendMods(fixed, "Fixed"), - !var.isEmpty() && !fixed.isEmpty() ? TR(TD(HtmlString.NBSP)) : null, - appendMods(var, "Variable"))))); - - onClick.append(", 100); return false;"); - - return LinkBuilder.labkeyLink("Show Modifications").onClick(onClick.toString()).id("modificationsLink"); + String onClick = "showHelpDiv(this, 'Modifications', " + PageFlowUtil.jsString( + DOM.createHtml(TABLE( + var.isEmpty() && fixed.isEmpty() ? TR(TD(at(DOM.Attribute.colspan, 2), STRONG("None"))) : null, + appendMods(fixed, "Fixed"), + !var.isEmpty() && !fixed.isEmpty() ? TR(TD(HtmlString.NBSP)) : null, + appendMods(var, "Variable")) + )) + + ", 100); return false;"; + + return LinkBuilder.labkeyLink("Show Modifications").onClick(onClick).id("modificationsLink"); } private DOM.Renderable appendMods(Map mods, String heading) diff --git a/ms2/src/org/labkey/ms2/ProteinListDisplayColumn.java b/ms2/src/org/labkey/ms2/ProteinListDisplayColumn.java index 0d54e2b59..a68231e17 100644 --- a/ms2/src/org/labkey/ms2/ProteinListDisplayColumn.java +++ b/ms2/src/org/labkey/ms2/ProteinListDisplayColumn.java @@ -16,24 +16,23 @@ package org.labkey.ms2; -import org.labkey.api.data.SimpleDisplayColumn; -import org.labkey.api.data.RenderContext; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.view.ActionURL; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.collections.CaseInsensitiveHashMap; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.query.FieldKey; +import org.labkey.api.util.HtmlString; +import org.labkey.api.util.LinkBuilder; +import org.labkey.api.view.ActionURL; import org.labkey.api.writer.HtmlWriter; -import java.io.Writer; -import java.io.IOException; -import java.util.*; import java.text.DecimalFormat; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.Set; -/** - * User: jeckels - * Date: Feb 15, 2006 - */ public class ProteinListDisplayColumn extends SimpleDisplayColumn { private final SequenceColumnType _sequenceColumn; @@ -70,15 +69,11 @@ public Object getValue(ProteinSummary summary) } @Override - public void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + public void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { url.replaceParameter("proteinGroupId", groupId); url.replaceParameter("seqId", summary.getSeqId()); - out.write(""); - out.write(PageFlowUtil.filter(summary.getName())); - out.write(""); + out.write(LinkBuilder.simpleLink(summary.getName(), url).target("prot")); } }, Description @@ -90,9 +85,9 @@ public Object getValue(ProteinSummary summary) } @Override - public void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + public void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { - out.write(PageFlowUtil.filter(summary.getDescription())); + out.write(summary.getDescription()); } }, BestName @@ -104,9 +99,9 @@ public Object getValue(ProteinSummary summary) } @Override - public void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + public void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { - out.write(PageFlowUtil.filter(summary.getBestName())); + out.write(summary.getBestName()); } }, BestGeneName @@ -118,12 +113,12 @@ public Object getValue(ProteinSummary summary) } @Override - public void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + public void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { String geneName = summary.getBestGeneName(); if (geneName != null) { - out.write(PageFlowUtil.filter(geneName)); + out.write(geneName); } } }, @@ -136,9 +131,9 @@ public Object getValue(ProteinSummary summary) } @Override - public void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + public void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { - out.write(PageFlowUtil.filter(MASS_FORMAT.format(summary.getSequenceMass()))); + out.write(MASS_FORMAT.format(summary.getSequenceMass())); } @Override @@ -150,7 +145,7 @@ public String getTextAlign() public abstract Object getValue(ProteinSummary summary); - public abstract void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException; + public abstract void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId); public String getTextAlign() { @@ -222,13 +217,13 @@ public Object getValue(RenderContext ctx) } @Override - public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWriter out) throws IOException + public void renderGridCellContents(RenderContext ctx, HtmlWriter out) { - Map row = ctx.getRow(); + Map row = ctx.getRow(); if (!row.containsKey(_columnName)) { - oldWriter.write("ProteinGroupId not present in ResultSet"); + out.write("ProteinGroupId not present in ResultSet"); return; } Object groupIdObject = row.get(_columnName); @@ -238,7 +233,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit } if (!(groupIdObject instanceof Number)) { - oldWriter.write("ProteinGroupId is of unexpected type: " + groupIdObject.getClass()); + out.write("ProteinGroupId is of unexpected type: " + groupIdObject.getClass()); return; } int groupId = ((Number) groupIdObject).intValue(); @@ -251,7 +246,7 @@ public void renderGridCellContents(RenderContext ctx, Writer oldWriter, HtmlWrit { for (ProteinSummary summary : summaryList) { - writeInfo(summary, oldWriter, url, groupId); + writeInfo(summary, out, url, groupId); } } } @@ -263,10 +258,10 @@ public void addQueryColumns(Set set) set.add(_columnInfo); } - private void writeInfo(ProteinSummary summary, Writer out, ActionURL url, int groupId) throws IOException + private void writeInfo(ProteinSummary summary, HtmlWriter out, ActionURL url, int groupId) { _sequenceColumn.writeInfo(summary, out, url, groupId); - out.write("
"); + out.write(HtmlString.BR); } public void setColumnInfo(ColumnInfo colInfo)