From 03dcdf996b269c3a0d39a41db2078ddf175b8d5c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 18 Oct 2017 12:40:22 +0200
Subject: [PATCH] small fixes for pdb annotator - class types modified
---
.../annotation/services/annotators/PdbAnnotator.java | 9 +++++----
.../mapviewer/model/map/species/field/UniprotRecord.java | 5 +++++
persist/src/db/{11.0.1 => 11.1.0}/fix_db_20170713.sql | 4 ++--
3 files changed, 12 insertions(+), 6 deletions(-)
rename persist/src/db/{11.0.1 => 11.1.0}/fix_db_20170713.sql (57%)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index 4d69f2e648..f2dca91d0d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
@@ -136,7 +137,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
for (MiriamData md : mds) {
try {
- Set<Structure> structures = (Set<Structure>)uniProtToPdb(md);
+ Collection<Structure> structures = uniProtToPdb(md);
if (structures.size() == 0) {
logger.warn(elementUtils.getElementTag(bioEntity) + " No PDB mapping for UniProt ID: " + md.getResource());
} else {
@@ -159,7 +160,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
for (Structure s : structures) {
s.setUniprot(ur);
}
- ur.setStructures(structures);
+ ur.addStructures(structures);
((Species)bioEntity).getUniprots().add(ur);
}
} catch (WrongResponseCodeIOException exception) {
@@ -259,7 +260,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
*/
public Collection<Structure> uniProtToPdb(MiriamData uniprot) throws IOException {
if (uniprot == null) {
- return null;
+ return new ArrayList<>();
}
if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
@@ -269,7 +270,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
String accessUrl = getPdbMappingUrl(uniprot.getResource());
String json = getWebPageContent(accessUrl);
- return isJson(json) ? processMappingData(json) : null;
+ return isJson(json) ? processMappingData(json) : new ArrayList<>();
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
index 92346cb4f2..ceba7173db 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
+import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
@@ -178,4 +179,8 @@ public class UniprotRecord implements Serializable {
public Set<Structure> getStructures() {
return structures;
}
+
+ public void addStructures(Collection<Structure> structures) {
+ this.structures.addAll(structures);
+ }
}
diff --git a/persist/src/db/11.0.1/fix_db_20170713.sql b/persist/src/db/11.1.0/fix_db_20170713.sql
similarity index 57%
rename from persist/src/db/11.0.1/fix_db_20170713.sql
rename to persist/src/db/11.1.0/fix_db_20170713.sql
index c0f3e49c8e..9bac775133 100644
--- a/persist/src/db/11.0.1/fix_db_20170713.sql
+++ b/persist/src/db/11.1.0/fix_db_20170713.sql
@@ -1,2 +1,2 @@
-DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator'
-INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator')
\ No newline at end of file
+DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator';
+INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator');
\ No newline at end of file
--
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