Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
@@ -1,12 +1,15 @@
<%@ page import="org.apache.commons.lang3.StringUtils" %>
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page import="org.labkey.api.security.permissions.DeletePermission" %>
<%@ page import="org.labkey.api.security.permissions.InsertPermission" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.util.DOM" %>
<%@ page import="org.labkey.api.util.HtmlString" %>
<%@ page import="org.labkey.api.util.SafeToRender" %>
<%@ 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.api.view.template.ClientDependencies" %>
<%@ page import="org.labkey.skylinetoolsstore.RatingManager" %>
<%@ page import="org.labkey.skylinetoolsstore.SkylineToolsStoreController" %>
<%@ page import="org.labkey.skylinetoolsstore.SkylineToolsStoreManager" %>
Expand All @@ -17,19 +20,14 @@
<%@ page import="java.text.DateFormat" %>
<%@ page import="java.text.SimpleDateFormat" %>
<%@ page import="java.util.ArrayList" %>
<%@ page import="java.util.Arrays" %>
<%@ page import="java.util.HashMap" %>
<%@ page import="java.util.Iterator" %>
<%@ page import="java.util.List" %>
<%@ page import="java.util.Map" %>
<%@ page import="java.util.Arrays" %>
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.util.DOM" %>
<%@ page import="static org.labkey.api.util.DOM.IMG" %>
<%@ page import="static org.labkey.api.util.DOM.Attribute.src" %>
<%@ page import="static org.labkey.api.util.DOM.Attribute.alt" %>
<%@ page import="org.labkey.api.util.PageFlowUtil" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>

<%!
Expand All @@ -46,7 +44,7 @@
<link rel="stylesheet" href="https://code.jquery.com/ui/1.13.2/themes/smoothness/jquery-ui.min.css">

<%
JspView<?> me = (JspView<?>) HttpView.currentView();
JspView<?> me = HttpView.currentView();
final SkylineTool tool = (SkylineTool)me.getModelBean();
final boolean admin = getUser().hasSiteAdminPermission();

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
<link rel="stylesheet" href="https://code.jquery.com/ui/1.13.2/themes/smoothness/jquery-ui.min.css">

<%
JspView<?> me = (JspView<?>)HttpView.currentView();
JspView<?> me = HttpView.currentView();
List<SkylineTool> tools = (List<SkylineTool>)me.getModelBean();

final boolean admin = getUser().hasSiteAdminPermission();
Expand Down
5 changes: 3 additions & 2 deletions lincs/src/org/labkey/lincs/view/customGCTForm.jsp
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
<%@ page import="org.labkey.lincs.LincsController" %>
<%@ page import="org.labkey.lincs.LincsController.CustomGCTBean" %>
<%@ page import="java.util.List" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
Expand All @@ -32,8 +33,8 @@
}
%>
<%
JspView<LincsController.CustomGCTBean> jspView = (JspView<LincsController.CustomGCTBean>) HttpView.currentView();
LincsController.CustomGCTBean bean = jspView.getModelBean();
JspView<CustomGCTBean> jspView = HttpView.currentView();
CustomGCTBean bean = jspView.getModelBean();
LincsController.CustomGCTForm form = bean.getForm();
List<LincsController.SelectedAnnotation> annotations = bean.getAnnotations();
%>
Expand Down
2 changes: 1 addition & 1 deletion lincs/src/org/labkey/lincs/view/downloadCustomGCT.jsp
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
}
%>
<%
JspView<CustomGCTForm> jspView = (JspView<CustomGCTForm>) HttpView.currentView();
JspView<CustomGCTForm> jspView = HttpView.currentView();
CustomGCTForm form = jspView.getModelBean();
List<SelectedAnnotation> annotations = form.getSelectedAnnotationValues();
GctBean gctBean = form.getCustomGctBean();
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
<%@ 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.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
<%@ page import="org.labkey.api.view.ActionURL" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.UnimodModification" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.ChemElement" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.Formula" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.UnimodModification" %>
<%@ page import="java.util.Map" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
Expand All @@ -18,7 +18,7 @@
}
%>
<%
JspView<PanoramaPublicController.CombinationModificationBean> view = (JspView<PanoramaPublicController.CombinationModificationBean>) HttpView.currentView();
JspView<PanoramaPublicController.CombinationModificationBean> view = HttpView.currentView();
var bean = view.getModelBean();
var form = bean.getForm();
var modification = bean.getModification();
Expand Down
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.api.util.StringUtilsLabKey" %>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.MessageExampleBean" %>
<%@ page import="org.labkey.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.api.util.StringUtilsLabKey" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%
JspView<PanoramaPublicController.MessageExampleBean> view = (JspView<PanoramaPublicController.MessageExampleBean>) HttpView.currentView();
JspView<MessageExampleBean> view = HttpView.currentView();
var messageExample = view.getModelBean();
var exampleExpAnnot = messageExample.getExperimentAnnotations();
var exampleShortUrl = exampleExpAnnot.getShortUrl().renderShortURL();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,10 @@
*/
%>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.PanoramaPublicMessageForm" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicNotification" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>

Expand All @@ -43,7 +44,7 @@
}
</script>
<%
JspView<PanoramaPublicController.PanoramaPublicMessageForm> view = (JspView<PanoramaPublicController.PanoramaPublicMessageForm>) HttpView.currentView();
JspView<PanoramaPublicMessageForm> view = HttpView.currentView();
var form = view.getModelBean();
%>

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
}
%>
<%
JspView<PanoramaPublicController.SpecLibInfoBean> view = (JspView<PanoramaPublicController.SpecLibInfoBean>) HttpView.currentView();
JspView<PanoramaPublicController.SpecLibInfoBean> view = HttpView.currentView();
var bean = view.getModelBean();
var form = bean.getForm();
var library = bean.getLibrary();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,10 @@
*/
%>
<%@ page import="org.apache.commons.lang3.StringUtils" %>
<%@ page import="org.labkey.api.security.permissions.AdminPermission" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.util.DOM" %>
<%@ page import="org.labkey.api.util.HtmlString" %>
<%@ page import="org.labkey.api.view.ActionURL" %>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
Expand All @@ -24,29 +28,25 @@
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.ExperimentAnnotationsDetails" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.ShowExperimentAnnotationsAction" %>
<%@ page import="org.labkey.panoramapublic.datacite.DataCiteService" %>
<%@ page import="org.labkey.panoramapublic.model.CatalogEntry" %>
<%@ page import="org.labkey.panoramapublic.model.DataLicense" %>
<%@ page import="org.labkey.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.panoramapublic.model.Journal" %>
<%@ page import="org.labkey.panoramapublic.query.JournalManager" %>
<%@ page import="java.text.SimpleDateFormat" %>
<%@ page import="org.labkey.panoramapublic.model.Submission" %>
<%@ page import="org.labkey.panoramapublic.model.JournalSubmission" %>
<%@ page import="org.labkey.api.security.permissions.AdminPermission" %>
<%@ page import="org.labkey.panoramapublic.query.DataValidationManager" %>
<%@ page import="org.labkey.panoramapublic.model.Submission" %>
<%@ page import="org.labkey.panoramapublic.model.validation.DataValidation" %>
<%@ page import="org.labkey.panoramapublic.model.validation.PxStatus" %>
<%@ page import="org.labkey.api.util.HtmlString" %>
<%@ page import="static org.labkey.api.util.DOM.SPAN" %>
<%@ page import="static org.labkey.api.util.DOM.Attribute.style" %>
<%@ page import="org.labkey.api.util.DOM" %>
<%@ page import="org.labkey.panoramapublic.model.validation.PxStatus" %>
<%@ page import="static org.labkey.api.util.DOM.Attribute.title" %>
<%@ page import="static org.labkey.api.util.DOM.Attribute.href" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.ProteomeXchangeService" %>
<%@ page import="org.labkey.panoramapublic.query.CatalogEntryManager" %>
<%@ page import="org.labkey.panoramapublic.query.DataValidationManager" %>
<%@ page import="org.labkey.panoramapublic.query.JournalManager" %>
<%@ page import="org.labkey.panoramapublic.view.publish.CatalogEntryWebPart" %>
<%@ page import="org.labkey.panoramapublic.model.CatalogEntry" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.panoramapublic.proteomexchange.ProteomeXchangeService" %>
<%@ page import="org.labkey.panoramapublic.datacite.DataCiteService" %>
<%@ page import="java.text.SimpleDateFormat" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>

<%!
Expand All @@ -65,7 +65,7 @@
%>

<%
JspView<ExperimentAnnotationsDetails> me = (JspView<ExperimentAnnotationsDetails>) HttpView.currentView();
JspView<ExperimentAnnotationsDetails> me = HttpView.currentView();
ExperimentAnnotationsDetails annotDetails = me.getModelBean();
ExperimentAnnotations annot = annotDetails.getExperimentAnnotations();
ActionURL editUrl = PanoramaPublicController.getEditExperimentDetailsURL(getContainer(), annot.getId(),
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -17,16 +17,16 @@
%>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
<%@ page import="org.apache.commons.io.FileUtils" %>
<%@ page import="org.labkey.api.data.ContainerManager" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.settings.LookAndFeelProperties" %>
<%@ 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.api.view.template.ClientDependencies" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.panoramapublic.catalog.CatalogEntrySettings" %>
<%@ page import="org.labkey.panoramapublic.query.CatalogEntryManager" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.settings.LookAndFeelProperties" %>
<%@ page import="org.labkey.api.data.ContainerManager" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%!
@Override
Expand All @@ -39,7 +39,7 @@
}
%>
<%
JspView<PanoramaPublicController.CatalogEntryBean> view = (JspView<PanoramaPublicController.CatalogEntryBean>) HttpView.currentView();
JspView<PanoramaPublicController.CatalogEntryBean> view = HttpView.currentView();
var bean = view.getModelBean();
var form = bean.getForm();

Expand Down
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page import="org.labkey.api.util.PageFlowUtil" %>
<%@ 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.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>

Expand All @@ -17,7 +17,7 @@

<labkey:errors/>
<%
JspView<PanoramaPublicController.PublicationDetailsBean> me = (JspView<PanoramaPublicController.PublicationDetailsBean>) HttpView.currentView();
JspView<PanoramaPublicController.PublicationDetailsBean> me = HttpView.currentView();
var bean = me.getModelBean();
var form = bean.getForm();
%>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@

<labkey:errors/>
<%
JspView<PanoramaPublicController.PanoramaPublicRequest> me = (JspView<PanoramaPublicController.PanoramaPublicRequest>) HttpView.currentView();
JspView<PanoramaPublicController.PanoramaPublicRequest> me = HttpView.currentView();
PanoramaPublicController.PanoramaPublicRequest bean = me.getModelBean();
PanoramaPublicController.PublishExperimentForm form = bean.getForm();

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.GetPxActionsAction" %>
<%@ page import="org.labkey.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.panoramapublic.model.Journal" %>
<%@ page import="org.labkey.panoramapublic.query.ExperimentAnnotationsManager" %>
<%@ page import="org.labkey.panoramapublic.model.Submission" %>
<%@ page import="org.labkey.panoramapublic.model.JournalSubmission" %>
<%@ page import="org.labkey.panoramapublic.model.Submission" %>
<%@ page import="org.labkey.panoramapublic.query.ExperimentAnnotationsManager" %>
<%@ page import="static org.labkey.panoramapublic.PanoramaPublicController.*" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
Expand All @@ -47,7 +47,7 @@
%>

<%
JspView<CopyExperimentBean> me = (JspView<CopyExperimentBean>) HttpView.currentView();
JspView<CopyExperimentBean> me = HttpView.currentView();
var bean = me.getModelBean();
CopyExperimentForm form = bean.getForm();
ExperimentAnnotations expAnnot = form.lookupExperiment();
Expand Down
Original file line number Diff line number Diff line change
@@ -1,6 +1,3 @@
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%
/*
* Copyright (c) 2014-2019 LabKey Corporation
Expand All @@ -18,10 +15,13 @@
* limitations under the License.
*/
%>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.CreateJournalGroupForm" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%
JspView<PanoramaPublicController.CreateJournalGroupForm> view = (JspView<PanoramaPublicController.CreateJournalGroupForm>) HttpView.currentView();
PanoramaPublicController.CreateJournalGroupForm form = view.getModelBean();
JspView<CreateJournalGroupForm> view = HttpView.currentView();
CreateJournalGroupForm form = view.getModelBean();
%>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>

Expand Down
Original file line number Diff line number Diff line change
@@ -1,16 +1,15 @@
<%@ page import="org.labkey.panoramapublic.query.JournalManager" %>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.api.util.PageFlowUtil" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.files.FileContentService" %>
<%@ page import="org.labkey.api.settings.AppProps" %>
<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
<%@ page import="org.labkey.api.view.HttpView" %>
<%@ page import="org.labkey.api.view.JspView" %>
<%@ page import="org.labkey.api.webdav.WebdavService" %>
<%@ page import="org.labkey.panoramapublic.query.JournalManager" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
<labkey:errors/>
<%
JspView<JournalManager.PublicDataUser> me = (JspView<JournalManager.PublicDataUser>) HttpView.currentView();
JspView<JournalManager.PublicDataUser> me = HttpView.currentView();
var publicDataUser = me.getModelBean();
// NOTE: This is a link to the data download documentation page on PanoramaWeb. It will not work on any other server.
var downloadDataDocHref = "/home/wiki-page.view?name=download_public_data";
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@
<%@ 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.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.panoramapublic.query.DataValidationManager" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
Expand All @@ -34,7 +34,7 @@

<labkey:errors/>
<%
JspView<PanoramaPublicController.MissingMetadataBean> me = (JspView<PanoramaPublicController.MissingMetadataBean>) HttpView.currentView();
JspView<PanoramaPublicController.MissingMetadataBean> me = HttpView.currentView();
PanoramaPublicController.MissingMetadataBean bean = me.getModelBean();
DataValidationManager.MissingMetadata missingMetadata = bean.getMissingMetadata();

Expand Down
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page import="org.labkey.api.util.PageFlowUtil" %>
<%@ 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.panoramapublic.PanoramaPublicController" %>
<%@ page import="org.labkey.api.portal.ProjectUrls" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>

Expand All @@ -17,7 +17,7 @@

<labkey:errors/>
<%
JspView<PanoramaPublicController.PublicationDetailsBean> me = (JspView<PanoramaPublicController.PublicationDetailsBean>) HttpView.currentView();
JspView<PanoramaPublicController.PublicationDetailsBean> me = HttpView.currentView();
var bean = me.getModelBean();
var form = bean.getForm();
%>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,12 @@
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.PublishExperimentForm" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.PublishExperimentFormBean" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.ResubmitExperimentAction" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.UpdateSubmissionAction" %>
<%@ page import="org.labkey.panoramapublic.model.DataLicense" %>
<%@ page import="org.labkey.panoramapublic.model.ExperimentAnnotations" %>
<%@ page import="org.labkey.panoramapublic.model.Journal" %>
<%@ page import="org.labkey.panoramapublic.query.ExperimentAnnotationsManager" %>
<%@ page import="java.util.Set" %>
<%@ page import="org.labkey.panoramapublic.PanoramaPublicController.UpdateSubmissionAction" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>

Expand All @@ -48,7 +48,7 @@

<labkey:errors/>
<%
JspView<PublishExperimentFormBean> me = (JspView<PublishExperimentFormBean>) HttpView.currentView();
JspView<PublishExperimentFormBean> me = HttpView.currentView();
PublishExperimentFormBean bean = me.getModelBean();
PublishExperimentForm form = bean.getForm();

Expand Down
Loading