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minerva
core
Commits
6776cd9e
Commit
6776cd9e
authored
Apr 21, 2021
by
Piotr Gawron
Browse files
fetching gene variants returned 500
parent
8ff3c1e0
Changes
6
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CHANGELOG
View file @
6776cd9e
...
...
@@ -11,6 +11,8 @@ minerva (16.0.0~alpha.2) stable; urgency=medium
their
lines
(#
1471
)
*
Bug
fix
:
when
selecting
drug
in
the
alias
window
the
input
text
is
updated
(#
1365
)
*
Bug
fix
:
there
was
no
possibility
to
see
gene
variants
(
regression
16.0.0
~
alpha
.1
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Fri
,
26
Mar
2021
10
:
00
:
00
+
0200
...
...
frontend-js/package-lock.json
View file @
6776cd9e
This diff is collapsed.
Click to expand it.
model/src/main/java/lcsb/mapviewer/model/overlay/GeneVariant.java
View file @
6776cd9e
...
...
@@ -7,6 +7,8 @@ import javax.persistence.*;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
com.fasterxml.jackson.annotation.JsonIgnore
;
import
lcsb.mapviewer.common.exception.NotImplementedException
;
/**
...
...
@@ -72,6 +74,7 @@ public class GeneVariant implements Serializable {
*/
private
String
variantIdentifier
;
@JsonIgnore
@ManyToOne
private
GeneVariantDataOverlayEntry
dataOverlayEntry
;
...
...
rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
View file @
6776cd9e
...
...
@@ -7,6 +7,7 @@ import java.util.stream.Collectors;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
org.hibernate.Hibernate
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.stereotype.Service
;
import
org.springframework.transaction.annotation.Transactional
;
...
...
@@ -431,6 +432,7 @@ public class OverlayRestImpl extends BaseRestImpl {
case
"genevariations"
:
if
(
overlayEntry
instanceof
GeneVariantDataOverlayEntry
)
{
value
=
((
GeneVariantDataOverlayEntry
)
overlayEntry
).
getGeneVariants
();
Hibernate
.
initialize
(((
GeneVariantDataOverlayEntry
)
overlayEntry
).
getGeneVariants
());
}
else
{
value
=
new
Object
[]
{};
}
...
...
web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
View file @
6776cd9e
...
...
@@ -42,6 +42,7 @@ import org.springframework.web.context.WebApplicationContext;
import
lcsb.mapviewer.api.projects.chemicals.ChemicalRestImpl
;
import
lcsb.mapviewer.common.*
;
import
lcsb.mapviewer.converter.zip.ZipEntryFileFactory
;
import
lcsb.mapviewer.model.*
;
import
lcsb.mapviewer.model.cache.UploadedFileEntry
;
import
lcsb.mapviewer.model.graphics.*
;
...
...
@@ -560,6 +561,11 @@ abstract public class ControllerIntegrationTest {
}
protected
DataOverlay
createOverlay
(
Project
project
,
User
admin
,
String
content
)
throws
Exception
{
return
createOverlay
(
project
,
admin
,
content
,
DataOverlayType
.
GENERIC
);
}
protected
DataOverlay
createOverlay
(
Project
project
,
User
admin
,
String
content
,
DataOverlayType
type
)
throws
Exception
{
UploadedFileEntry
file
=
new
UploadedFileEntry
();
file
.
setFileContent
(
content
.
getBytes
());
file
.
setLength
(
content
.
getBytes
().
length
);
...
...
@@ -568,7 +574,7 @@ abstract public class ControllerIntegrationTest {
ColorSchemaReader
reader
=
new
ColorSchemaReader
();
DataOverlay
overlay
=
new
DataOverlay
();
overlay
.
setColorSchemaType
(
DataOverlayType
.
GENERIC
);
overlay
.
setColorSchemaType
(
type
);
overlay
.
setInputData
(
file
);
overlay
.
setProject
(
project
);
overlay
.
setName
(
"test title"
);
...
...
@@ -576,6 +582,7 @@ abstract public class ControllerIntegrationTest {
overlay
.
setCreator
(
admin
);
Map
<
String
,
String
>
headers
=
new
HashMap
<>();
headers
.
put
(
TextFileUtils
.
COLUMN_COUNT_PARAM
,
"2"
);
headers
.
put
(
ZipEntryFileFactory
.
LAYOUT_HEADER_PARAM_TYPE
,
type
.
toString
());
overlay
.
addEntries
(
reader
.
readColorSchema
(
new
ByteArrayInputStream
(
content
.
getBytes
()),
headers
));
dataOverlayDao
.
add
(
overlay
);
return
overlay
;
...
...
web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
View file @
6776cd9e
...
...
@@ -1483,7 +1483,6 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
}
@Test
public
void
testRemoveUserOverlayAsAnonymous
()
throws
Exception
{
DataOverlay
overlay
=
createOverlayInSeparateThread
(
TEST_PROJECT
,
user
);
RequestBuilder
request
=
delete
(
"/projects/"
+
TEST_PROJECT
+
"/overlays/"
+
overlay
.
getId
());
...
...
@@ -1492,4 +1491,37 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
.
andExpect
(
status
().
isForbidden
());
}
@Test
public
void
testFetchGeneticDataOverlayData
()
throws
Exception
{
MockHttpSession
session
=
createSession
(
BUILT_IN_TEST_ADMIN_LOGIN
,
BUILT_IN_TEST_ADMIN_PASSWORD
);
DataOverlay
overlay
=
callInSeparateThread
(()
->
{
try
{
return
createOverlay
(
project
,
user
,
"#TYPE=GENETIC_VARIANT\n"
+
"#GENOME_TYPE=UCSC\n"
+
"#GENOME_VERSION=xenLae2\n"
+
"position\toriginal_dna\talternative_dna\tgene_name\tdescription\tcolor\tcontig\n"
+
"10146\tAC\tA\tGSTA4\tupstream\t#ff0000\tchr1"
,
DataOverlayType
.
GENETIC_VARIANT
);
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
return
null
;
}
});
assertNotNull
(
overlay
);
for
(
Element
element_iterator
:
map
.
getElements
())
{
if
(
element_iterator
.
getName
().
equals
(
"GSTA4"
))
{
element
=
element_iterator
;
}
}
assertEquals
(
element
.
getName
(),
"GSTA4"
);
RequestBuilder
request
=
get
(
"/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/elements/{elementId}/"
,
TEST_PROJECT
,
overlay
.
getId
(),
map
.
getId
(),
element
.
getId
())
.
session
(
session
);
mockMvc
.
perform
(
request
)
.
andExpect
(
status
().
is2xxSuccessful
());
}
}
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