From 32c23e83b2121b1cecafc743b5cda0022952aa91 Mon Sep 17 00:00:00 2001 From: Yusra Haider Date: Thu, 30 Apr 2020 13:25:00 +0100 Subject: [PATCH 1/2] fixed the bug by adding conditions for OtherEntity and GenomeEncodedEntity --- .../panels/DatabaseIdentifierPanel.java | 18 ++++++++++++++++++ .../widgets/panels/PhysicalEntityPanel.java | 4 ++-- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java index 348ce1ce..5976b06c 100644 --- a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java +++ b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java @@ -3,6 +3,7 @@ import com.google.gwt.user.client.ui.HTMLPanel; import com.google.gwt.user.client.ui.Label; import com.google.gwt.user.client.ui.TreeItem; +import org.reactome.web.pwp.client.common.utils.Console; import org.reactome.web.pwp.model.client.classes.*; /** @@ -62,6 +63,22 @@ public DatabaseIdentifierPanel(DetailsPanel parentPanel, PhysicalEntity pe) { initialize(); break; } + } else if (pe instanceof OtherEntity) { + for (DatabaseIdentifier identifier : pe.getCrossReference()) { + this.reference = identifier.getDatabaseName(); + this.id = identifier.getIdentifier(); + this.url = identifier.getUrl(); + initialize(); + break; + } + } else if (pe instanceof GenomeEncodedEntity) { + for (DatabaseIdentifier identifier : pe.getCrossReference()) { + this.reference = identifier.getDatabaseName(); + this.id = identifier.getIdentifier(); + this.url = identifier.getUrl(); + initialize(); + break; + } } else { initWidget(new Label("No reference entity")); } @@ -92,6 +109,7 @@ public DatabaseObject getDatabaseObject() { } public TreeItem asTreeItem() { + Console.info("tree item: " + this.treeItem); return this.treeItem; } diff --git a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/PhysicalEntityPanel.java b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/PhysicalEntityPanel.java index 15f47236..2d4097ac 100644 --- a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/PhysicalEntityPanel.java +++ b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/PhysicalEntityPanel.java @@ -134,7 +134,6 @@ public void onClick(ClickEvent event) { Widget getCrossReferenceTree(){ TreeItem references = new TreeItem(SafeHtmlUtils.fromString("External cross-references")); - DatabaseIdentifierPanel dbIdPanel = new DatabaseIdentifierPanel(physicalEntity); TreeItem reference = dbIdPanel.asTreeItem(); reference.setState(true, false); @@ -142,7 +141,8 @@ Widget getCrossReferenceTree(){ //Links to the complex portal have been added as cross references for Complexes but they //do not have reference entity. The first condition is a hack to accommodate this case - if(!(this.physicalEntity instanceof Complex) && !this.physicalEntity.getCrossReference().isEmpty()){ + if(!(this.physicalEntity instanceof Complex) && !(this.physicalEntity instanceof GenomeEncodedEntity) && + !(this.physicalEntity instanceof OtherEntity) && !this.physicalEntity.getCrossReference().isEmpty()){ Collections.sort(physicalEntity.getCrossReference()); for (DatabaseIdentifier databaseIdentifier : this.physicalEntity.getCrossReference()) { dbIdPanel = new DatabaseIdentifierPanel(databaseIdentifier); From 73baf22c176d6c186d396407625cebbdb85edea9 Mon Sep 17 00:00:00 2001 From: Yusra Haider Date: Thu, 30 Apr 2020 13:30:14 +0100 Subject: [PATCH 2/2] removed unneccessary code --- .../details/common/widgets/panels/DatabaseIdentifierPanel.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java index 5976b06c..4a788b29 100644 --- a/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java +++ b/src/main/java/org/reactome/web/pwp/client/details/common/widgets/panels/DatabaseIdentifierPanel.java @@ -3,7 +3,6 @@ import com.google.gwt.user.client.ui.HTMLPanel; import com.google.gwt.user.client.ui.Label; import com.google.gwt.user.client.ui.TreeItem; -import org.reactome.web.pwp.client.common.utils.Console; import org.reactome.web.pwp.model.client.classes.*; /** @@ -109,7 +108,6 @@ public DatabaseObject getDatabaseObject() { } public TreeItem asTreeItem() { - Console.info("tree item: " + this.treeItem); return this.treeItem; }