From af66cb76fff27c25c793a5c0fd1542085deb5e54 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Fri, 25 Aug 2017 11:19:28 +0200
Subject: [PATCH] chain_id in structure_table changed to VARCHAR(255) + minor
related changes in the code.
---
.../mapviewer/annotation/services/ModelAnnotator.java | 2 +-
.../annotation/services/annotators/PdbAnnotator.java | 2 +-
persist/src/db/11.0.1/fix_db_20170720.sql | 2 +-
persist/src/db/11.0.1/fix_db_20171307.sql | 2 --
.../bioEntities/elements/ElementRestImplTest.java | 10 +++++++---
5 files changed, 10 insertions(+), 8 deletions(-)
delete mode 100644 persist/src/db/11.0.1/fix_db_20171307.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index b82f08768c..a446e1a9bc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -289,7 +289,7 @@ public class ModelAnnotator {
try {
elementAnnotator.annotateElement(element);
} catch (AnnotatorException e) {
- logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName() + " annotation problem");
+ logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName() + " annotation problem: " + e.getMessage());
}
}
counter++;
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 bdfd3764ec..4d69f2e648 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
@@ -157,7 +157,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
ur.setUniprotId(md.getResource());
ur.setSpecies((Species)bioEntity);
for (Structure s : structures) {
- s.setUniprot(ur);
+ s.setUniprot(ur);
}
ur.setStructures(structures);
((Species)bioEntity).getUniprots().add(ur);
diff --git a/persist/src/db/11.0.1/fix_db_20170720.sql b/persist/src/db/11.0.1/fix_db_20170720.sql
index 71cf63626c..396aaa49fa 100644
--- a/persist/src/db/11.0.1/fix_db_20170720.sql
+++ b/persist/src/db/11.0.1/fix_db_20170720.sql
@@ -44,7 +44,7 @@ CREATE TABLE structure_table
iddb integer NOT NULL DEFAULT nextval('structure_table_iddb_seq'::regclass),
uniprot_id integer NOT NULL,
pdb_id character varying(255) NOT NULL, --should be character(4), but to be on the safe side...
- chain_id character varying(1)NOT NULL,
+ chain_id character varying(255) NOT NULL, --should be char(1), but for example 5T0C has has chains AK and BK
struct_start integer,
struct_end integer,
unp_start integer,
diff --git a/persist/src/db/11.0.1/fix_db_20171307.sql b/persist/src/db/11.0.1/fix_db_20171307.sql
deleted file mode 100644
index 94523a2c4d..0000000000
--- a/persist/src/db/11.0.1/fix_db_20171307.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-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
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 b240a8c272..5e9ac8b9f8 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
@@ -60,7 +60,7 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsProcessAllColumns() throws Exception {
try {
ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", true);
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "");
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
for (Map<String, Object> element : result) {
for (String paramName : element.keySet()) {
Object val = element.get(paramName);
@@ -85,7 +85,7 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String proteinType = new GenericProtein("1").getStringType();
ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", false);
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType);
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType, "", "");
assertEquals(12, result.size());
} catch (Exception e) {
@@ -98,7 +98,7 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsVisibility() throws Exception {
try {
ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "");
+ List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
for (Map<String, Object> map : result) {
assertTrue(map.get("hierarchyVisibilityLevel") instanceof String);
}
@@ -174,6 +174,10 @@ public class ElementRestImplTest extends RestTestFunctions {
throw e;
}
}
+
+ private ElementsRestImpl createMockElementRest(String string) throws Exception {
+ return createMockElementRest(string, false);
+ }
private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
Model model = super.getModelForFile(string, true);
--
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