From 2a99d60a7538502272e1ee259914ee725d3bdd26 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Fri, 21 Jul 2017 13:44:43 +0200
Subject: [PATCH] Working REST API
---
.../model/map/species/field/Structure.java | 23 ++++++++++++++--
.../elements/ElementsRestImpl.java | 27 ++++++++++++++-----
.../elements/ElementRestImplTest.java | 8 +++---
3 files changed, 46 insertions(+), 12 deletions(-)
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
index 5dbe0b9053..5d92fdcce2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java
@@ -1,6 +1,8 @@
package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
+import java.util.Map;
+import java.util.HashMap;
import javax.persistence.Column;
import javax.persistence.Entity;
@@ -12,6 +14,8 @@ import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
+import org.apache.commons.collections.map.HashedMap;
+
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
@@ -23,8 +27,8 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* coverage: the percent coverage of the entire UniProt sequence
* resolution: the resolution of the structure
* start: the structure residue number which maps to the start of the mapped sequence
- * end: the structure residue number which maps to the end of the mapped sequence
* unp_start: the sequence residue number which maps to the structure start
+ * end: the structure residue number which maps to the end of the mapped sequence
* unp_end: the sequence residue number which maps to the structure end
* experimental_method: type of experiment used to determine structure
* tax_id: taxonomic ID of the protein's original organism
@@ -339,6 +343,21 @@ public class Structure implements Serializable {
+ ", unpEnd=" + unpEnd + ", experimentalMethod=" + experimentalMethod + ", taxId=" + taxId + "]";
}
-
+ public Map<String, Object> toMap() {
+ Map<String, Object> result = new HashMap<>();
+
+ result.put("pdbId", this.pdbId);
+ result.put("chainId", this.chainId);
+ result.put("coverage", this.coverage);
+ result.put("resolution", this.resolution);
+ result.put("structStart", this.structStart);
+ result.put("structEnd", this.structEnd);
+ result.put("unpStart", this.unpStart);
+ result.put("unpEnd", this.unpEnd);
+ result.put("experimentalMethod", this.experimentalMethod);
+ result.put("taxId", this.taxId);
+
+ return result;
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 8c664dcdfa..40449080f1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -21,6 +21,8 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ElementModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
+import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@@ -121,11 +123,7 @@ public class ElementsRestImpl extends BaseRestImpl {
value = element.getSubmodel().getSubmodel().getId();
}
} else if (column.equals("bounds")) {
- value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
- } else if (column.equals("others")) {
- if (element instanceof Species) {
- value = ((Species)element).getUniprots();
- }
+ value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
}
else {
value = "Unknown column";
@@ -137,8 +135,9 @@ public class ElementsRestImpl extends BaseRestImpl {
protected Map<String, Object> getOthersForElement(Element element) {
Map<String, Object> result = new HashMap<>();
- List<Map<String, Object>> modifications = new ArrayList<>();
+ List<Map<String, Object>> modifications = new ArrayList<>();
String structuralState = null;
+ Map<String, Object> structures = new HashMap<>();
if (element instanceof Protein) {
Protein protein = ((Protein) element);
modifications = getModifications(protein.getModificationResidues());
@@ -151,9 +150,13 @@ public class ElementsRestImpl extends BaseRestImpl {
AntisenseRna antisenseRna = ((AntisenseRna) element);
modifications = getModifications(((AntisenseRna) element).getRegions());
structuralState = antisenseRna.getState();
+ }
+ if (element instanceof Species) {
+ structures = getStructures(((Species)element).getUniprots());
}
result.put("modifications", modifications);
result.put("structuralState", structuralState);
+ result.put("structures", structures);
return result;
}
@@ -171,6 +174,18 @@ public class ElementsRestImpl extends BaseRestImpl {
}
return result;
}
+
+ private Map<String, Object> getStructures(Set<UniprotRecord> uniprots) {
+ Map<String, Object> result = new HashMap<>();
+ for (UniprotRecord uniprotRec : uniprots) {
+ Set<Object> structs = new HashSet<>();
+ for (Structure struct: uniprotRec.getStructures()) {
+ structs.add(struct.toMap());
+ }
+ result.put(uniprotRec.getUniprotId(), structs);
+ }
+ return result;
+ }
private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
Map<String, Object> result = new HashMap<>();
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 1a51fdfe6a..2cc1b522c5 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -156,20 +156,20 @@ public class ElementRestImplTest extends RestTestFunctions {
}
}
- private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
+ private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
Model model = super.getModelForFile(string, true);
if (annotate) {
- try {
+ try {
Protein protein = new GenericProtein("SNCA");
protein.setElementId("SNCA");
pdbAnnotator.annotateElement(protein);
- model.addElement(protein);
+ model.addElement(protein);
} catch (Exception e) {
}
}
IModelService mockModelService = Mockito.mock(IModelService.class);
Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _elementsRestImpl.setModelService(mockModelService);
+ _elementsRestImpl.setModelService(mockModelService);
return _elementsRestImpl;
}
}
--
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