From 712c292e26945aa1e90ad1f2e74a21889ad20dfb Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Sun, 6 Apr 2025 16:54:54 -0700 Subject: [PATCH] Remove unnecessary HttpView.currentView() casts in JSPs --- elisa/src/org/labkey/elisa/view/runDetailsView.jsp | 2 +- .../src/org/labkey/elispot/view/plateSummary.jsp | 2 +- .../controllers/executescript/chooseAnalysisName.jsp | 2 +- .../executescript/chooseRunsToAnalyze.jsp | 2 +- .../executescript/confirmRunsToImport.jsp | 2 +- .../org/labkey/flow/controllers/well/chooseGraph.jsp | 2 +- flow/src/org/labkey/flow/view/exportAnalysis.jsp | 2 +- .../src/org/labkey/luminex/view/defaultValues.jsp | 2 +- .../src/org/labkey/luminex/view/exclusionWarning.jsp | 2 +- .../labkey/luminex/view/guideSetConfirmDelete.jsp | 2 +- .../org/labkey/luminex/view/leveyJenningsMenu.jsp | 10 ++-------- .../org/labkey/luminex/view/leveyJenningsReport.jsp | 8 +------- .../org/labkey/luminex/view/titrationWellRoles.jsp | 2 +- .../microarray/view/uploadFeatureAnnotation.jsp | 4 +--- ms2/src/org/labkey/ms2/blastAdmin.jsp | 2 +- .../compare/compareProteinProphetQueryOptions.jsp | 2 +- .../org/labkey/ms2/compare/spectraCountOptions.jsp | 4 ++-- ms2/src/org/labkey/ms2/decoySummary.jsp | 2 +- ms2/src/org/labkey/ms2/editElution.jsp | 2 +- ms2/src/org/labkey/ms2/filterHeader.jsp | 5 +++-- ms2/src/org/labkey/ms2/manageViews.jsp | 2 +- ms2/src/org/labkey/ms2/ms2Admin.jsp | 4 +++- ms2/src/org/labkey/ms2/pickView.jsp | 4 +++- .../org/labkey/ms2/pipeline/ConfigureSequenceDB.jsp | 2 +- .../labkey/ms2/pipeline/comet/setCometDefaults.jsp | 2 +- .../labkey/ms2/pipeline/mascot/setMascotDefaults.jsp | 2 +- .../ms2/pipeline/sequest/setSequestDefaults.jsp | 2 +- .../labkey/ms2/pipeline/tandem/setTandemDefaults.jsp | 2 +- ms2/src/org/labkey/ms2/protein.jsp | 5 +++-- ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp | 3 ++- ms2/src/org/labkey/ms2/proteinDisambiguation.jsp | 2 +- ms2/src/org/labkey/ms2/runSummary.jsp | 2 +- ms2/src/org/labkey/ms2/search/peptidePanel.jsp | 2 +- ms2/src/org/labkey/ms2/showPeptide.jsp | 10 +++++----- ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp | 12 +++++++++--- ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp | 2 +- ms2/src/org/labkey/ms2/showProteinGroup.jsp | 3 ++- ms2/src/org/labkey/ms2/showSensitivityDetails.jsp | 7 ++++--- ms2/src/org/labkey/ms2/testMascot.jsp | 9 +++++---- nab/src/org/labkey/nab/view/nabQC.jsp | 8 +++----- .../org/labkey/protein/view/proteinCoverageMap.jsp | 3 ++- 41 files changed, 75 insertions(+), 74 deletions(-) diff --git a/elisa/src/org/labkey/elisa/view/runDetailsView.jsp b/elisa/src/org/labkey/elisa/view/runDetailsView.jsp index 7d68cf1429..114950bcdd 100644 --- a/elisa/src/org/labkey/elisa/view/runDetailsView.jsp +++ b/elisa/src/org/labkey/elisa/view/runDetailsView.jsp @@ -30,7 +30,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ElisaController.RunDetailsForm form = me.getModelBean(); String appId = "run-details-" + getRequestScopedUID(); %> diff --git a/elispotassay/src/org/labkey/elispot/view/plateSummary.jsp b/elispotassay/src/org/labkey/elispot/view/plateSummary.jsp index e171887632..f935c873f8 100644 --- a/elispotassay/src/org/labkey/elispot/view/plateSummary.jsp +++ b/elispotassay/src/org/labkey/elispot/view/plateSummary.jsp @@ -30,7 +30,7 @@ } %> <% - JspView me = (JspView)HttpView.currentView(); + JspView me = HttpView.currentView(); ElispotController.PlateSummaryBean bean = me.getModelBean(); String renderId = "plate-summary-div-" + 1; // getRequestScopedUID(); // TODO ElispotAssayTest test expects 1 diff --git a/flow/src/org/labkey/flow/controllers/executescript/chooseAnalysisName.jsp b/flow/src/org/labkey/flow/controllers/executescript/chooseAnalysisName.jsp index fa8d9a3b52..ac65e584dd 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/chooseAnalysisName.jsp +++ b/flow/src/org/labkey/flow/controllers/executescript/chooseAnalysisName.jsp @@ -30,7 +30,7 @@ <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ChooseRunsToAnalyzeForm form = me.getModelBean(); Container c = getContainer(); %> diff --git a/flow/src/org/labkey/flow/controllers/executescript/chooseRunsToAnalyze.jsp b/flow/src/org/labkey/flow/controllers/executescript/chooseRunsToAnalyze.jsp index c6be4e571b..2a5c715a3a 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/chooseRunsToAnalyze.jsp +++ b/flow/src/org/labkey/flow/controllers/executescript/chooseRunsToAnalyze.jsp @@ -44,7 +44,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ChooseRunsToAnalyzeForm form = me.getModelBean(); ChooseRunsView view = new ChooseRunsView(form); Collection targetExperiments = new ArrayList(form.getAvailableAnalyses()); diff --git a/flow/src/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp b/flow/src/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp index ac63b18561..da9da6f73c 100644 --- a/flow/src/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp +++ b/flow/src/org/labkey/flow/controllers/executescript/confirmRunsToImport.jsp @@ -32,7 +32,7 @@ <%@ page import="java.util.Set" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ImportRunsForm form = me.getModelBean(); Container c = getContainer(); diff --git a/flow/src/org/labkey/flow/controllers/well/chooseGraph.jsp b/flow/src/org/labkey/flow/controllers/well/chooseGraph.jsp index 23cd43aaff..42556ca5f0 100644 --- a/flow/src/org/labkey/flow/controllers/well/chooseGraph.jsp +++ b/flow/src/org/labkey/flow/controllers/well/chooseGraph.jsp @@ -39,7 +39,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - HttpView me = (HttpView) HttpView.currentView(); + HttpView me = HttpView.currentView(); ChooseGraphForm form = me.getModelBean(); boolean hasScripts = false; diff --git a/flow/src/org/labkey/flow/view/exportAnalysis.jsp b/flow/src/org/labkey/flow/view/exportAnalysis.jsp index c7236aa5b7..3847efe142 100644 --- a/flow/src/org/labkey/flow/view/exportAnalysis.jsp +++ b/flow/src/org/labkey/flow/view/exportAnalysis.jsp @@ -28,7 +28,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ExportAnalysisForm bean = me.getModelBean(); Map exportFormats = new EnumMap<>(AnalysisSerializer.Options.class); diff --git a/luminex/src/org/labkey/luminex/view/defaultValues.jsp b/luminex/src/org/labkey/luminex/view/defaultValues.jsp index bc235d3ea4..ce33d80d10 100644 --- a/luminex/src/org/labkey/luminex/view/defaultValues.jsp +++ b/luminex/src/org/labkey/luminex/view/defaultValues.jsp @@ -24,7 +24,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); DefaultValuesForm bean = me.getModelBean(); List analytes = bean.getAnalytes(); List positivityThresholds = bean.getPositivityThresholds(); diff --git a/luminex/src/org/labkey/luminex/view/exclusionWarning.jsp b/luminex/src/org/labkey/luminex/view/exclusionWarning.jsp index 4528fd92bc..947a0feb79 100644 --- a/luminex/src/org/labkey/luminex/view/exclusionWarning.jsp +++ b/luminex/src/org/labkey/luminex/view/exclusionWarning.jsp @@ -25,7 +25,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); LuminexRunUploadForm bean = me.getModelBean(); long exclusionCount = bean.getExclusionCount(); long lostExclusions = bean.getLostExclusions(); diff --git a/luminex/src/org/labkey/luminex/view/guideSetConfirmDelete.jsp b/luminex/src/org/labkey/luminex/view/guideSetConfirmDelete.jsp index 795d7db42a..314674a594 100644 --- a/luminex/src/org/labkey/luminex/view/guideSetConfirmDelete.jsp +++ b/luminex/src/org/labkey/luminex/view/guideSetConfirmDelete.jsp @@ -39,7 +39,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); LuminexController.GuideSetsDeleteBean bean = me.getModelBean(); List guideSets = bean.getGuideSets(); diff --git a/luminex/src/org/labkey/luminex/view/leveyJenningsMenu.jsp b/luminex/src/org/labkey/luminex/view/leveyJenningsMenu.jsp index 33691341a0..fc32b144b4 100644 --- a/luminex/src/org/labkey/luminex/view/leveyJenningsMenu.jsp +++ b/luminex/src/org/labkey/luminex/view/leveyJenningsMenu.jsp @@ -14,22 +14,16 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - -/** -* User: jeckels -* Date: August 27, 2013 -*/ - %> +<%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.luminex.LeveyJenningsForm" %> <%@ page import="org.labkey.luminex.LeveyJenningsMenuView" %> <%@ page import="org.labkey.luminex.LuminexController" %> -<%@ page import="org.labkey.api.view.ActionURL" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - LeveyJenningsMenuView me = (LeveyJenningsMenuView) HttpView.currentView(); + LeveyJenningsMenuView me = HttpView.currentView(); LeveyJenningsMenuView.Bean bean = me.getModelBean(); %> diff --git a/luminex/src/org/labkey/luminex/view/leveyJenningsReport.jsp b/luminex/src/org/labkey/luminex/view/leveyJenningsReport.jsp index cbf2ba080f..2cb079eb5d 100644 --- a/luminex/src/org/labkey/luminex/view/leveyJenningsReport.jsp +++ b/luminex/src/org/labkey/luminex/view/leveyJenningsReport.jsp @@ -14,12 +14,6 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - -/** -* User: cnathe -* Date: Sept 19, 2011 -*/ - %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> @@ -36,7 +30,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); LeveyJenningsForm bean = me.getModelBean(); %> diff --git a/luminex/src/org/labkey/luminex/view/titrationWellRoles.jsp b/luminex/src/org/labkey/luminex/view/titrationWellRoles.jsp index b971f867c3..b86252bfe1 100644 --- a/luminex/src/org/labkey/luminex/view/titrationWellRoles.jsp +++ b/luminex/src/org/labkey/luminex/view/titrationWellRoles.jsp @@ -42,7 +42,7 @@ <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); LuminexRunUploadForm bean = me.getModelBean(); Map titrationsWithTypes = bean.getParser().getTitrationsWithTypes(); diff --git a/microarray/src/org/labkey/microarray/view/uploadFeatureAnnotation.jsp b/microarray/src/org/labkey/microarray/view/uploadFeatureAnnotation.jsp index 073561780a..6276ad120d 100644 --- a/microarray/src/org/labkey/microarray/view/uploadFeatureAnnotation.jsp +++ b/microarray/src/org/labkey/microarray/view/uploadFeatureAnnotation.jsp @@ -18,7 +18,6 @@ <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.data.ContainerManager" %> <%@ page import="org.labkey.api.security.permissions.InsertPermission" %> -<%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> @@ -27,7 +26,6 @@ <%@ page import="org.springframework.validation.Errors" %> <%@ page import="org.springframework.validation.ObjectError" %> <%@ page import="java.util.LinkedHashMap" %> -<%@ page import="java.util.List" %> <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @@ -38,7 +36,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); String vendor = me.getModelBean().getVendor(); String name = me.getModelBean().getName(); String description = me.getModelBean().getDescription(); diff --git a/ms2/src/org/labkey/ms2/blastAdmin.jsp b/ms2/src/org/labkey/ms2/blastAdmin.jsp index 2f6c634bc4..8a315080ad 100644 --- a/ms2/src/org/labkey/ms2/blastAdmin.jsp +++ b/ms2/src/org/labkey/ms2/blastAdmin.jsp @@ -19,7 +19,7 @@ <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - HttpView me = (HttpView) HttpView.currentView(); + HttpView me = HttpView.currentView(); String url = me.getModelBean(); %> diff --git a/ms2/src/org/labkey/ms2/compare/compareProteinProphetQueryOptions.jsp b/ms2/src/org/labkey/ms2/compare/compareProteinProphetQueryOptions.jsp index 5012a6eeca..2d67e54f51 100644 --- a/ms2/src/org/labkey/ms2/compare/compareProteinProphetQueryOptions.jsp +++ b/ms2/src/org/labkey/ms2/compare/compareProteinProphetQueryOptions.jsp @@ -38,7 +38,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase"%> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% -JspView view = (JspView) HttpView.currentView(); +JspView view = HttpView.currentView(); MS2Controller.CompareOptionsBean bean = view.getModelBean(); MS2Controller.PeptideFilteringComparisonForm form = bean.getForm(); String peptideViewName = form.getPeptideCustomViewName(getViewContext()); diff --git a/ms2/src/org/labkey/ms2/compare/spectraCountOptions.jsp b/ms2/src/org/labkey/ms2/compare/spectraCountOptions.jsp index 6f93c5016c..c4fa547a00 100644 --- a/ms2/src/org/labkey/ms2/compare/spectraCountOptions.jsp +++ b/ms2/src/org/labkey/ms2/compare/spectraCountOptions.jsp @@ -15,7 +15,6 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.ms2.MS2Controller.PeptideFilteringFormElements" %> <%@ page import="org.labkey.api.protein.search.ProphetFilterType" %> <%@ page import="org.labkey.api.util.HtmlString" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> @@ -24,6 +23,7 @@ <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.ms2.MS2Controller" %> +<%@ page import="org.labkey.ms2.MS2Controller.PeptideFilteringFormElements" %> <%@ page import="static org.labkey.ms2.MS2Controller.PeptideFilteringFormElements.peptideFilterType" %> <%@ page import="static org.labkey.api.protein.search.ProphetFilterType.probability" %> <%@ page import="static org.labkey.api.protein.search.ProphetFilterType.customView" %> @@ -41,7 +41,7 @@ } %> <% - JspView view = (JspView) HttpView.currentView(); + JspView view = HttpView.currentView(); MS2Controller.CompareOptionsBean bean = view.getModelBean(); MS2Controller.SpectraCountForm form = bean.getForm(); String peptideViewName = form.getPeptideCustomViewName(getViewContext()); diff --git a/ms2/src/org/labkey/ms2/decoySummary.jsp b/ms2/src/org/labkey/ms2/decoySummary.jsp index 7c43ee3d80..ee863ca1e4 100644 --- a/ms2/src/org/labkey/ms2/decoySummary.jsp +++ b/ms2/src/org/labkey/ms2/decoySummary.jsp @@ -27,7 +27,7 @@ <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = ((JspView)HttpView.currentView()); + JspView me = HttpView.currentView(); MS2Manager.DecoySummaryBean bean = me.getModelBean(); NumberFormat defaultFormat = NumberFormat.getPercentInstance(); diff --git a/ms2/src/org/labkey/ms2/editElution.jsp b/ms2/src/org/labkey/ms2/editElution.jsp index f09f314a34..4e1c1b31d1 100644 --- a/ms2/src/org/labkey/ms2/editElution.jsp +++ b/ms2/src/org/labkey/ms2/editElution.jsp @@ -24,7 +24,7 @@ <%@ page import="java.text.DecimalFormat"%> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); EditElutionGraphContext ctx = me.getModelBean(); MS2Peptide p = ctx.getPeptide(); PeptideQuantitation quant = ctx.getQuantitation(); diff --git a/ms2/src/org/labkey/ms2/filterHeader.jsp b/ms2/src/org/labkey/ms2/filterHeader.jsp index fe88f922ab..15fa1a391d 100644 --- a/ms2/src/org/labkey/ms2/filterHeader.jsp +++ b/ms2/src/org/labkey/ms2/filterHeader.jsp @@ -20,13 +20,14 @@ <%@ page import="org.labkey.api.util.HtmlString" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.ms2.MS2Controller" %> +<%@ page import="org.labkey.ms2.MS2Controller.FilterHeaderBean" %> <%@ page import="org.labkey.ms2.peptideview.MS2RunViewType" %> <%@ page import="static org.labkey.api.util.DOM.Attribute.style" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - MS2Controller.FilterHeaderBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + FilterHeaderBean bean = view.getModelBean(); User user = getUser(); String runChargeFilterColumnName = bean.run.getChargeFilterColumnName(); String grouping = getViewContext().cloneActionURL().getParameter("grouping"); diff --git a/ms2/src/org/labkey/ms2/manageViews.jsp b/ms2/src/org/labkey/ms2/manageViews.jsp index 3d31160089..7c3c81c4d4 100644 --- a/ms2/src/org/labkey/ms2/manageViews.jsp +++ b/ms2/src/org/labkey/ms2/manageViews.jsp @@ -21,7 +21,7 @@ <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - HttpView me = (HttpView) HttpView.currentView(); + HttpView me = HttpView.currentView(); MS2Controller.ManageViewsBean bean = me.getModelBean(); %> diff --git a/ms2/src/org/labkey/ms2/ms2Admin.jsp b/ms2/src/org/labkey/ms2/ms2Admin.jsp index 832771ba07..956ff65671 100644 --- a/ms2/src/org/labkey/ms2/ms2Admin.jsp +++ b/ms2/src/org/labkey/ms2/ms2Admin.jsp @@ -20,10 +20,12 @@ <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.ms2.MS2Controller" %> +<%@ page import="org.labkey.ms2.MS2Controller.MS2AdminBean" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - MS2Controller.MS2AdminBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + MS2AdminBean bean = view.getModelBean(); %> diff --git a/ms2/src/org/labkey/ms2/pickView.jsp b/ms2/src/org/labkey/ms2/pickView.jsp index bc35dc30e4..fc2971bd80 100644 --- a/ms2/src/org/labkey/ms2/pickView.jsp +++ b/ms2/src/org/labkey/ms2/pickView.jsp @@ -19,10 +19,12 @@ <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.ms2.MS2Controller" %> +<%@ page import="org.labkey.ms2.MS2Controller.PickViewBean" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - MS2Controller.PickViewBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + PickViewBean bean = view.getModelBean(); %>

<%=h(bean.viewInstructions)%>

diff --git a/ms2/src/org/labkey/ms2/pipeline/ConfigureSequenceDB.jsp b/ms2/src/org/labkey/ms2/pipeline/ConfigureSequenceDB.jsp index 15d6249373..4fca93b02e 100644 --- a/ms2/src/org/labkey/ms2/pipeline/ConfigureSequenceDB.jsp +++ b/ms2/src/org/labkey/ms2/pipeline/ConfigureSequenceDB.jsp @@ -21,7 +21,7 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - HttpView me = (HttpView) HttpView.currentView(); + HttpView me = HttpView.currentView(); String localPathRoot = me.getModelBean(); %> diff --git a/ms2/src/org/labkey/ms2/pipeline/comet/setCometDefaults.jsp b/ms2/src/org/labkey/ms2/pipeline/comet/setCometDefaults.jsp index 0e2a4e3ea7..8ea523b120 100644 --- a/ms2/src/org/labkey/ms2/pipeline/comet/setCometDefaults.jsp +++ b/ms2/src/org/labkey/ms2/pipeline/comet/setCometDefaults.jsp @@ -31,7 +31,7 @@ } %> <% - JspView view = (JspView) HttpView.currentView(); + JspView view = HttpView.currentView(); PipelineController.SetDefaultsForm form = view.getModelBean(); Container c = getContainer(); %> diff --git a/ms2/src/org/labkey/ms2/pipeline/mascot/setMascotDefaults.jsp b/ms2/src/org/labkey/ms2/pipeline/mascot/setMascotDefaults.jsp index d1aea06696..c5a8cf7a4b 100644 --- a/ms2/src/org/labkey/ms2/pipeline/mascot/setMascotDefaults.jsp +++ b/ms2/src/org/labkey/ms2/pipeline/mascot/setMascotDefaults.jsp @@ -31,7 +31,7 @@ } %> <% - JspView view = (JspView) HttpView.currentView(); + JspView view = HttpView.currentView(); PipelineController.SetDefaultsForm form = view.getModelBean(); Container c = getContainer(); %> diff --git a/ms2/src/org/labkey/ms2/pipeline/sequest/setSequestDefaults.jsp b/ms2/src/org/labkey/ms2/pipeline/sequest/setSequestDefaults.jsp index 5767d8c6c0..29612e8028 100644 --- a/ms2/src/org/labkey/ms2/pipeline/sequest/setSequestDefaults.jsp +++ b/ms2/src/org/labkey/ms2/pipeline/sequest/setSequestDefaults.jsp @@ -31,7 +31,7 @@ } %> <% - JspView view = (JspView) HttpView.currentView(); + JspView view = HttpView.currentView(); PipelineController.SetDefaultsForm form = view.getModelBean(); Container c = getContainer(); %> diff --git a/ms2/src/org/labkey/ms2/pipeline/tandem/setTandemDefaults.jsp b/ms2/src/org/labkey/ms2/pipeline/tandem/setTandemDefaults.jsp index 479912177f..2f42ae57fd 100644 --- a/ms2/src/org/labkey/ms2/pipeline/tandem/setTandemDefaults.jsp +++ b/ms2/src/org/labkey/ms2/pipeline/tandem/setTandemDefaults.jsp @@ -31,7 +31,7 @@ } %> <% - JspView view = (JspView)HttpView.currentView(); + JspView view = HttpView.currentView(); PipelineController.SetDefaultsForm form = view.getModelBean(); Container c = getContainer(); %> diff --git a/ms2/src/org/labkey/ms2/protein.jsp b/ms2/src/org/labkey/ms2/protein.jsp index 102ae91c82..eba6d08487 100644 --- a/ms2/src/org/labkey/ms2/protein.jsp +++ b/ms2/src/org/labkey/ms2/protein.jsp @@ -16,6 +16,7 @@ */ %> <%@ page import="org.labkey.api.util.Formats" %> +<%@ page import="org.labkey.api.util.HtmlString" %> <%@ page import="org.labkey.api.util.Pair" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> @@ -23,11 +24,11 @@ <%@ page import="org.labkey.ms2.PeptideManager" %> <%@ page import="org.labkey.ms2.protein.ProteinViewBean" %> <%@ page import="java.text.Format" %> -<%@ page import="org.labkey.api.util.HtmlString" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - ProteinViewBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + ProteinViewBean bean = view.getModelBean(); Format intFormat = Formats.commaf0; Format percentFormat = Formats.percent; %> diff --git a/ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp b/ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp index 12901090dd..a70f5c121e 100644 --- a/ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp +++ b/ms2/src/org/labkey/ms2/proteinCoverageMapHeader.jsp @@ -22,7 +22,8 @@ <%@ page import="org.labkey.ms2.protein.ProteinViewBean" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - ProteinViewBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + ProteinViewBean bean = view.getModelBean(); if (bean.showPeptides) { diff --git a/ms2/src/org/labkey/ms2/proteinDisambiguation.jsp b/ms2/src/org/labkey/ms2/proteinDisambiguation.jsp index 6d42206e43..9689171998 100644 --- a/ms2/src/org/labkey/ms2/proteinDisambiguation.jsp +++ b/ms2/src/org/labkey/ms2/proteinDisambiguation.jsp @@ -74,7 +74,7 @@ %> <% - JspView>> view = (JspView>>) HttpView.currentView(); + JspView>> view = HttpView.currentView(); Pair> actionWithProteins = view.getModelBean(); List proteins = actionWithProteins.second; ActionURL baseUrl = actionWithProteins.first; diff --git a/ms2/src/org/labkey/ms2/runSummary.jsp b/ms2/src/org/labkey/ms2/runSummary.jsp index a5c08c39e6..adfc0a81d2 100644 --- a/ms2/src/org/labkey/ms2/runSummary.jsp +++ b/ms2/src/org/labkey/ms2/runSummary.jsp @@ -28,7 +28,7 @@ <%@ page import="java.util.List" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - JspView me = ((JspView)HttpView.currentView()); + JspView me = HttpView.currentView(); Container c = getContainer(); MS2Controller.RunSummaryBean bean = me.getModelBean(); MS2Run run = bean.run; diff --git a/ms2/src/org/labkey/ms2/search/peptidePanel.jsp b/ms2/src/org/labkey/ms2/search/peptidePanel.jsp index 1e72589ada..b2b4a817fb 100644 --- a/ms2/src/org/labkey/ms2/search/peptidePanel.jsp +++ b/ms2/src/org/labkey/ms2/search/peptidePanel.jsp @@ -29,7 +29,7 @@ <% // This panel is optionally rendered by proteinPanel.jsp for MS2 deployments only. It requires "MS2/inlineViewDesigner.js", // which is optionally included by searchProteins.jsp. - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ProteinSearchBean bean = me.getModelBean(); ViewContext ctx = getViewContext(); FilterView peptideView = new FilterView(ctx, true); diff --git a/ms2/src/org/labkey/ms2/showPeptide.jsp b/ms2/src/org/labkey/ms2/showPeptide.jsp index cedf10a8f0..5ef2a11870 100644 --- a/ms2/src/org/labkey/ms2/showPeptide.jsp +++ b/ms2/src/org/labkey/ms2/showPeptide.jsp @@ -15,22 +15,22 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.protein.MassType"%> +<%@ page import="org.labkey.api.protein.PeptideUtils"%> <%@ page import="org.labkey.api.util.Formats"%> <%@ page import="org.labkey.api.util.Pair"%> <%@ page import="org.labkey.api.view.HttpView"%> <%@ page import="org.labkey.api.view.JspView"%> <%@ page import="org.labkey.api.view.template.ClientDependencies"%> <%@ page import="org.labkey.ms2.MS2Fraction"%> -<%@ page import="org.labkey.ms2.MS2GZFileRenderer"%> -<%@ page import="org.labkey.ms2.MS2Manager"%> +<%@ page import="org.labkey.ms2.MS2GZFileRenderer" %> +<%@ page import="org.labkey.ms2.MS2Manager" %> <%@ page import="org.labkey.ms2.MS2Peptide" %> <%@ page import="org.labkey.ms2.MS2RunType" %> -<%@ page import="org.labkey.api.protein.MassType" %> <%@ page import="org.labkey.ms2.ShowPeptideContext" %> <%@ page import="org.labkey.ms2.reader.LibraQuantResult" %> <%@ page import="java.util.ArrayList" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.protein.PeptideUtils" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override @@ -40,7 +40,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); ShowPeptideContext ctx = me.getModelBean(); MS2Peptide p = ctx.peptide; LibraQuantResult libra = p.getLibraQuantResult(); diff --git a/ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp b/ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp index 94990ff00a..3816d744ff 100644 --- a/ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp +++ b/ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp @@ -16,6 +16,7 @@ */ %> <%@ page import="org.labkey.api.view.ViewContext" %> +<%@ page import="org.labkey.ms2.MS2Controller" %> <%@ include file="showSensitivityDetails.jsp" %>

<% @@ -40,10 +41,15 @@ -<% if (bean.run.getNegativeHitCount() > bean.run.getPeptideCount() / 3) { %> +<% + if (bean.run.getNegativeHitCount() > bean.run.getPeptideCount() / 3) + { +%> -<% } %> -<% } %> +<% + } + } +%>
" alt="Charge <%=i%>+ Observed vs. Model"> " alt="Charge <%=i%>+ Cumulative Observed vs. Model">
" alt="Charge <%=i%>+ Observed vs. Prophet">
diff --git a/ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp b/ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp index 5eb1170fa8..94a7f115ba 100644 --- a/ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp +++ b/ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp @@ -27,7 +27,7 @@ <%@ page import="java.text.DecimalFormat" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% -JspView me = (JspView) HttpView.currentView(); +JspView me = HttpView.currentView(); ShowPeptideContext ctx = me.getModelBean(); MS2Peptide p = ctx.peptide; diff --git a/ms2/src/org/labkey/ms2/showProteinGroup.jsp b/ms2/src/org/labkey/ms2/showProteinGroup.jsp index 353cd0e95e..8149ab3103 100644 --- a/ms2/src/org/labkey/ms2/showProteinGroup.jsp +++ b/ms2/src/org/labkey/ms2/showProteinGroup.jsp @@ -25,7 +25,8 @@ <%@ page import="java.util.List" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - ProteinGroupWithQuantitation group = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + ProteinGroupWithQuantitation group = view.getModelBean(); ITraqProteinQuantitation libra = group.getITraqProteinQuantitation(); Format floatFormat = Formats.f2; %> diff --git a/ms2/src/org/labkey/ms2/showSensitivityDetails.jsp b/ms2/src/org/labkey/ms2/showSensitivityDetails.jsp index bc50f5c11c..b7c29d02b5 100644 --- a/ms2/src/org/labkey/ms2/showSensitivityDetails.jsp +++ b/ms2/src/org/labkey/ms2/showSensitivityDetails.jsp @@ -18,11 +18,12 @@ <%@ page import="org.labkey.api.view.ActionURL"%> <%@ page import="org.labkey.api.view.HttpView"%> <%@ page import="org.labkey.api.view.JspView"%> -<%@ page import="org.labkey.ms2.MS2Controller"%> -<%@ page import="java.text.DecimalFormat"%> +<%@ page import="org.labkey.ms2.MS2Controller.PeptideProphetDetailsBean"%> +<%@ page import="java.text.DecimalFormat" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - MS2Controller.PeptideProphetDetailsBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + PeptideProphetDetailsBean bean = view.getModelBean(); DecimalFormat df4 = new DecimalFormat("0.0000"); DecimalFormat df2 = new DecimalFormat("0.00"); ActionURL sensitivityURL = getViewContext().cloneActionURL().setAction(bean.action); diff --git a/ms2/src/org/labkey/ms2/testMascot.jsp b/ms2/src/org/labkey/ms2/testMascot.jsp index 545ef8609c..1428a1e0e6 100644 --- a/ms2/src/org/labkey/ms2/testMascot.jsp +++ b/ms2/src/org/labkey/ms2/testMascot.jsp @@ -15,13 +15,14 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.view.HttpView"%> +<%@ page import="org.apache.commons.lang3.StringUtils"%> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.ms2.MS2Controller" %> -<%@ page import="org.apache.commons.lang3.StringUtils" %> +<%@ page import="org.labkey.ms2.MS2Controller.TestMascotForm" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% - MS2Controller.TestMascotForm form = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + TestMascotForm form = view.getModelBean(); if (!StringUtils.isBlank(form.getMessage())) { diff --git a/nab/src/org/labkey/nab/view/nabQC.jsp b/nab/src/org/labkey/nab/view/nabQC.jsp index a90e85c5b8..ae35f040db 100644 --- a/nab/src/org/labkey/nab/view/nabQC.jsp +++ b/nab/src/org/labkey/nab/view/nabQC.jsp @@ -15,10 +15,11 @@ * limitations under the License. */ %> -<%@ page import="com.fasterxml.jackson.databind.ObjectMapper" %> <%@ page import="org.labkey.api.assay.dilution.DilutionAssayRun" %> <%@ page import="org.labkey.api.assay.nab.Luc5Assay" %> <%@ page import="org.labkey.api.assay.plate.Plate" %> +<%@ page import="org.labkey.api.util.HtmlString" %> +<%@ page import="org.labkey.api.util.JavaScriptFragment" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> @@ -27,12 +28,9 @@ <%@ page import="java.util.ArrayList" %> <%@ page import="java.util.List" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.util.HtmlString" %> <%@ page import="static org.labkey.api.util.DOM.cl" %> <%@ page import="static org.labkey.api.util.DOM.DIV" %> <%@ page import="static org.labkey.api.util.DOM.createHtml" %> -<%@ page import="org.labkey.api.util.JsonUtil" %> -<%@ page import="org.labkey.api.util.JavaScriptFragment" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override @@ -42,7 +40,7 @@ } %> <% - JspView me = (JspView) HttpView.currentView(); + JspView me = HttpView.currentView(); NabAssayController.NabQCForm bean = me.getModelBean(); DilutionAssayRun assay = bean.getAssay(); HtmlString errorMsg = HtmlString.EMPTY_STRING; diff --git a/protein/src/org/labkey/protein/view/proteinCoverageMap.jsp b/protein/src/org/labkey/protein/view/proteinCoverageMap.jsp index b24706733b..c2e171ca74 100644 --- a/protein/src/org/labkey/protein/view/proteinCoverageMap.jsp +++ b/protein/src/org/labkey/protein/view/proteinCoverageMap.jsp @@ -36,7 +36,8 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% - CoverageViewBean bean = ((JspView)HttpView.currentView()).getModelBean(); + JspView view = HttpView.currentView(); + CoverageViewBean bean = view.getModelBean(); var currentURL = getActionURL(); var displayLegend = true; var viewByParam = currentURL.getParameter("viewBy");