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Genesys PGR
Genesys Backend
Commits
4c797cbd
Commit
4c797cbd
authored
May 25, 2020
by
Matija Obreza
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Fix: `newAcceNumb` should not be ignored
parent
41dd7269
Changes
2
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2 changed files
with
54 additions
and
14 deletions
+54
-14
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
...org/genesys2/server/service/worker/AccessionUploader.java
+8
-5
src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java
...g/genesys/test/server/services/AccessionUploaderTest.java
+46
-9
No files found.
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
View file @
4c797cbd
...
...
@@ -382,7 +382,7 @@ public class AccessionUploader implements InitializingBean {
private
void
updateAccessionNumber
(
JsonNode
nodeAcceNumb
,
JsonNode
nodeNewNumb
,
Accession
accession
)
{
String
accessionNumber
=
nodeAcceNumb
.
textValue
();
String
newAcceNumb
=
nodeNewNumb
==
null
?
null
:
nodeNewNumb
.
textValue
();
String
newAcceNumb
=
nodeNewNumb
==
null
?
null
:
nodeNewNumb
.
textValue
()
.
trim
()
;
if
(!
accession
.
isPersisted
())
{
if
(
newAcceNumb
!=
null
)
{
...
...
@@ -392,10 +392,13 @@ public class AccessionUploader implements InitializingBean {
accession
.
setAccessionNumber
(
accessionNumber
);
}
else
if
(
accession
.
getDoi
()
!=
null
)
{
// When accession has a DOI, override accession number
accession
.
setAccessionNumber
(
accessionNumber
);
}
else
if
(
newAcceNumb
!=
null
)
{
// DO NOT IMPLICITLY UPDATE ACCESSION NUMBERS
if
(!
accession
.
getAccessionNumber
().
equalsIgnoreCase
(
accessionNumber
))
{
throw
new
InvalidApiUsageException
(
"ACCENUMB for doi="
+
accession
.
getDoi
()
+
" does not match current "
+
accession
.
getAccessionNumber
());
}
}
if
(
StringUtils
.
isNotBlank
(
newAcceNumb
))
{
if
(!
StringUtils
.
equals
(
newAcceNumb
,
accession
.
getAccessionNumber
()))
{
LOG
.
warn
(
"Renaming accession {}: {} to {}"
,
accession
.
getInstitute
().
getCode
(),
accession
.
getAccessionNumber
(),
newAcceNumb
);
accession
.
setAccessionNumber
(
newAcceNumb
);
...
...
src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java
View file @
4c797cbd
...
...
@@ -17,11 +17,7 @@ package org.genesys.test.server.services;
import
static
org
.
hamcrest
.
CoreMatchers
.*;
import
static
org
.
hamcrest
.
MatcherAssert
.
assertThat
;
import
static
org
.
junit
.
Assert
.
assertNull
;
import
static
org
.
junit
.
Assert
.
assertNotNull
;
import
static
org
.
junit
.
Assert
.
assertEquals
;
import
static
org
.
junit
.
Assert
.
assertTrue
;
import
static
org
.
junit
.
Assert
.
fail
;
import
static
org
.
junit
.
Assert
.*;
import
java.util.List
;
...
...
@@ -37,8 +33,8 @@ import org.genesys2.server.persistence.FaoInstituteRepository;
import
org.genesys2.server.persistence.Taxonomy2Repository
;
import
org.genesys2.server.service.InstituteService
;
import
org.genesys2.server.service.worker.AccessionOpResponse
;
import
org.genesys2.server.service.worker.AccessionUploader
;
import
org.genesys2.server.service.worker.AccessionOpResponse.UpsertResult
;
import
org.genesys2.server.service.worker.AccessionUploader
;
import
org.junit.Before
;
import
org.junit.Test
;
import
org.springframework.beans.factory.annotation.Autowired
;
...
...
@@ -312,10 +308,28 @@ public class AccessionUploaderTest extends AbstractServicesTest {
assertThat
(
accessionRepository
.
count
(),
is
(
1
l
));
assertThat
(
op
.
size
(),
is
(
1
));
assertThat
(
op
.
get
(
0
).
getError
(),
notNullValue
());
assertThat
(
op
.
get
(
0
).
getError
(),
is
(
"DOI not included for accession with registered DOI=
10.1000/Test"
));
assertThat
(
op
.
get
(
0
).
getError
(),
is
(
"DOI not included for accession with registered DOI=
"
+
DOI_1
));
}
/**
* Updates to accession with existing DOI must always include the DOI
*/
@Test
public
void
testRenameAccession
()
{
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
));
Accession
a1
=
accessionRepository
.
findByDoi
(
DOI_1
);
assertThat
(
a1
.
getDoi
(),
is
(
DOI_1
));
assertThat
(
a1
.
getAccessionNumber
(),
is
(
ACCENUMB_1
));
ArrayNode
withNewAcceNumb
=
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_2
,
DOI_1
);
((
ObjectNode
)
withNewAcceNumb
.
get
(
0
)).
put
(
"newAcceNumb"
,
ACCENUMB_2
);
accessionUploader
.
upsertAccessions
(
institute
,
withNewAcceNumb
);
Accession
a2
=
accessionRepository
.
findByDoi
(
DOI_1
);
assertThat
(
a2
.
getAccessionNumber
(),
is
(
ACCENUMB_2
));
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_1
));
}
/**
* Updating accession number and taxonomy must work with DOI only.
*/
...
...
@@ -324,14 +338,37 @@ public class AccessionUploaderTest extends AbstractServicesTest {
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
));
Accession
a1
=
accessionRepository
.
findOne
(
institute
,
null
,
ACCENUMB_1
,
GENUS_1
);
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_
2
,
GENUS_2
,
DOI_1
));
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_
1
,
GENUS_2
,
DOI_1
));
assertThat
(
accessionRepository
.
count
(),
is
(
1
l
));
Accession
a2
=
accessionRepository
.
findByDoi
(
DOI_1
);
assertThat
(
a2
.
getId
(),
equalTo
(
a1
.
getId
()));
assertThat
(
a2
.
getUuid
(),
equalTo
(
a1
.
getUuid
()));
// Genus not updated, missing species
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_1
));
assertThat
(
a2
.
getAccessionNumber
(),
is
(
ACCENUMB_2
));
assertThat
(
a2
.
getAccessionNumber
(),
is
(
ACCENUMB_1
));
ArrayNode
withSpecies
=
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_2
,
DOI_1
);
ObjectNode
taxa
=
(
ObjectNode
)
withSpecies
.
get
(
0
).
get
(
"taxonomy"
);
taxa
.
put
(
"species"
,
"hello"
);
accessionUploader
.
upsertAccessions
(
institute
,
withSpecies
);
a2
=
accessionRepository
.
findByDoi
(
DOI_1
);
// Genus updated!
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_2
));
assertThat
(
a2
.
getTaxonomy
().
getSpecies
(),
is
(
"hello"
));
}
/**
* Updating accession number must NOT work with DOI only.
*/
@Test
public
void
testComplainWrongAccenumbWithDOI
()
{
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
));
Accession
a1
=
accessionRepository
.
findOne
(
institute
,
null
,
ACCENUMB_1
,
GENUS_1
);
assertThat
(
a1
,
notNullValue
());
List
<
AccessionOpResponse
>
res
=
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccessions
(
institute
.
getCode
(),
ACCENUMB_2
,
GENUS_2
,
DOI_1
));
assertThat
(
res
.
get
(
0
).
getResult
().
getAction
(),
is
(
UpsertResult
.
Type
.
ERROR
));
assertThat
(
res
.
get
(
0
).
getError
(),
is
(
"ACCENUMB for doi="
+
DOI_1
+
" does not match current "
+
ACCENUMB_1
));
}
/**
...
...
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