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Genesys PGR
Genesys Backend
Commits
b2c817e3
Commit
b2c817e3
authored
Oct 08, 2018
by
Viacheslav Pavlov
Committed by
Matija Obreza
Oct 10, 2018
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API endpoint for listing accessions by set of UUIDs
- with Unit test
parent
eff6e8d6
Changes
4
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4 changed files
with
78 additions
and
3 deletions
+78
-3
src/main/java/org/genesys2/server/api/v1/AccessionController.java
.../java/org/genesys2/server/api/v1/AccessionController.java
+12
-1
src/main/java/org/genesys2/server/service/AccessionService.java
...in/java/org/genesys2/server/service/AccessionService.java
+1
-0
src/main/java/org/genesys2/server/service/impl/AccessionServiceImpl.java
...rg/genesys2/server/service/impl/AccessionServiceImpl.java
+16
-1
src/test/java/org/genesys/test/server/api/v1/AccessionControllerTest.java
...g/genesys/test/server/api/v1/AccessionControllerTest.java
+49
-1
No files found.
src/main/java/org/genesys2/server/api/v1/AccessionController.java
View file @
b2c817e3
...
...
@@ -202,8 +202,19 @@ public class AccessionController {
}
/**
*
Converts AccessionIdentifiers to UUID
*
Gets accessions by list of uuid-s
*
* @param uuids accession identifi`ers to lookup in DB
* @return list of Accessions
*/
@PostMapping
(
value
=
"/for-uuid"
,
produces
=
{
MediaType
.
APPLICATION_JSON_VALUE
})
public
List
<
Accession
>
forUuids
(
@RequestBody
Set
<
UUID
>
uuids
)
{
return
accessionService
.
forUuids
(
uuids
);
}
/**
* Converts AccessionIdentifiers to UUID
*
* @param identifiers accession identifiers to lookup in DB
* @return map with UUIDs and related AccessionIdentifiers
*/
...
...
src/main/java/org/genesys2/server/service/AccessionService.java
View file @
b2c817e3
...
...
@@ -87,6 +87,7 @@ public interface AccessionService {
*/
Map
<
UUID
,
AccessionIdentifier3
>
toUUID
(
List
<?
extends
AccessionIdentifier3
>
identifiers
);
List
<
Accession
>
forUuids
(
Set
<
UUID
>
uuids
);
/**
* Loads {@link Accession} by IDs and executes the action on each accession in a
* Spring transaction. Spring security context not supported.
...
...
src/main/java/org/genesys2/server/service/impl/AccessionServiceImpl.java
View file @
b2c817e3
...
...
@@ -130,7 +130,22 @@ public class AccessionServiceImpl implements AccessionService {
return
res
;
}
@Override
@Override
public
List
<
Accession
>
forUuids
(
Set
<
UUID
>
uuids
)
{
final
int
chunkSize
=
100
;
List
<
UUID
>
uuidList
=
new
ArrayList
<>(
uuids
);
List
<
Accession
>
accessions
=
new
ArrayList
<>(
uuidList
.
size
());
for
(
int
i
=
0
;
i
<
uuidList
.
size
();
i
+=
chunkSize
){
List
<
UUID
>
chunk
=
uuidList
.
subList
(
i
,
i
+
chunkSize
);
accessions
.
addAll
((
List
<
Accession
>)
accessionRepository
.
findAll
(
QAccession
.
accession
.
accessionId
.
uuid
.
in
(
chunk
)));
}
return
accessions
;
}
@Override
public
long
countAccessions
(
AccessionFilter
filter
)
{
long
total
=
elasticsearchService
.
count
(
Accession
.
class
,
filter
);
...
...
src/test/java/org/genesys/test/server/api/v1/AccessionControllerTest.java
View file @
b2c817e3
...
...
@@ -22,12 +22,15 @@ import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.docu
import
static
org
.
springframework
.
test
.
web
.
servlet
.
request
.
MockMvcRequestBuilders
.*;
import
static
org
.
springframework
.
test
.
web
.
servlet
.
result
.
MockMvcResultMatchers
.*;
import
java.util.ArrayList
;
import
java.util.List
;
import
java.util.UUID
;
import
java.util.concurrent.atomic.AtomicInteger
;
import
java.util.stream.Collectors
;
import
org.genesys.test.base.AbstractApiTest
;
import
org.genesys2.server.api.v0.AccessionController
;
import
org.genesys2.server.model.genesys.
Accession
;
import
org.genesys2.server.model.genesys.
*
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.persistence.AccessionIdRepository
;
...
...
@@ -35,6 +38,7 @@ import org.genesys2.server.persistence.AccessionRepository;
import
org.genesys2.server.persistence.FaoInstituteRepository
;
import
org.genesys2.server.persistence.Taxonomy2Repository
;
import
org.genesys2.server.service.InstituteService
;
import
org.genesys2.server.service.TaxonomyService
;
import
org.junit.After
;
import
org.junit.Before
;
import
org.junit.Rule
;
...
...
@@ -81,6 +85,8 @@ public class AccessionControllerTest extends AbstractApiTest {
private
InstituteService
instituteService
;
@Autowired
private
Taxonomy2Repository
taxonomyRepository
;
@Autowired
private
TaxonomyService
taxonomyService
;
MockMvc
mockMvc
;
...
...
@@ -146,6 +152,28 @@ public class AccessionControllerTest extends AbstractApiTest {
assertThat
(
accessionRepository
.
count
(),
is
(
1L
));
}
@Test
public
void
getAccessionsTest
()
throws
Exception
{
// Also works with 2000, 5000, 10000, 15000
int
amount
=
1000
;
List
<
Accession
>
accessions
=
setUpAccessions
(
amount
);
assertThat
(
accessionRepository
.
count
(),
is
((
long
)(
amount
)));
List
<
UUID
>
uuids
=
accessions
.
stream
().
map
(
Accession:
:
getAccessionId
).
map
(
AccessionId:
:
getUuid
).
collect
(
Collectors
.
toList
());
final
String
s
=
objectMapper
.
writeValueAsString
(
uuids
);
mockMvc
.
perform
(
post
(
org
.
genesys2
.
server
.
api
.
v1
.
AccessionController
.
API_BASE
+
"/for-uuid"
)
.
contentType
(
MediaType
.
APPLICATION_JSON
)
.
content
(
s
))
.
andExpect
(
status
().
isOk
())
.
andExpect
(
jsonPath
(
"$"
,
hasSize
(
amount
)));
}
@Test
public
void
updateAccessionNoChange
()
throws
Exception
{
ObjectNode
accessionJson
=
setUpAccession
();
...
...
@@ -367,6 +395,26 @@ public class AccessionControllerTest extends AbstractApiTest {
return
objectMapper
.
readValue
(
responseBody
,
Accession
.
class
);
}
private
List
<
Accession
>
setUpAccessions
(
int
amount
)
{
final
List
<
Accession
>
accessions
=
new
ArrayList
<>(
amount
);
for
(
int
i
=
0
;
i
<
amount
;
i
++)
{
accessions
.
add
(
addAccessionInDB
());
}
return
accessionRepository
.
save
(
accessions
);
}
private
Accession
addAccessionInDB
()
{
Accession
a
=
new
Accession
();
a
.
setAccessionId
(
new
AccessionId
());
a
.
setInstitute
(
institute
);
a
.
setAccessionNumber
(
"ACC"
+
System
.
currentTimeMillis
()
+
"-"
+
acceNumb
.
incrementAndGet
());
Taxonomy2
taxon
=
new
Taxonomy2
();
taxon
.
setGenus
(
"Hordeum"
);
a
.
setTaxonomy
(
taxonomyService
.
ensureTaxonomy
(
taxon
));
return
a
;
}
private
ObjectNode
setUpAccession
()
{
ObjectNode
accession
=
objectMapper
.
createObjectNode
();
accession
.
put
(
"instCode"
,
institute
.
getCode
());
...
...
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