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Genesys PGR
Genesys Backend
Commits
42c401dd
Commit
42c401dd
authored
Nov 14, 2018
by
Matija Obreza
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Fix: Taxonomy should not be updated when only "genus" is provided
parent
f100a059
Changes
3
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3 changed files
with
84 additions
and
4 deletions
+84
-4
src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java
...ain/java/org/genesys2/server/model/genesys/Taxonomy2.java
+7
-0
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
...org/genesys2/server/service/worker/AccessionUploader.java
+31
-3
src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java
...g/genesys/test/server/services/AccessionUploaderTest.java
+46
-1
No files found.
src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java
View file @
42c401dd
...
...
@@ -33,6 +33,7 @@ import javax.persistence.UniqueConstraint;
import
org.apache.commons.lang3.StringUtils
;
import
org.genesys2.server.model.GlobalVersionedAuditedModel
;
import
org.genesys2.server.model.impl.CropTaxonomy
;
import
org.genesys2.server.model.json.Api1Constants
;
import
org.hibernate.annotations.Type
;
import
org.springframework.data.elasticsearch.annotations.Field
;
import
org.springframework.data.elasticsearch.annotations.FieldIndex
;
...
...
@@ -40,6 +41,7 @@ import org.springframework.data.elasticsearch.annotations.FieldIndex;
import
com.fasterxml.jackson.annotation.JsonIgnore
;
import
com.fasterxml.jackson.annotation.JsonIgnoreProperties
;
import
com.fasterxml.jackson.annotation.JsonInclude
;
import
com.fasterxml.jackson.annotation.JsonProperty
;
@Cacheable
@Entity
...
...
@@ -51,18 +53,23 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
private
static
final
long
serialVersionUID
=
8881324404490162933L
;
@Column
(
nullable
=
false
,
length
=
100
)
@JsonProperty
(
value
=
Api1Constants
.
Accession
.
GENUS
)
private
String
genus
;
@Column
(
nullable
=
false
,
length
=
100
)
@JsonProperty
(
value
=
Api1Constants
.
Accession
.
SPECIES
)
private
String
species
;
@Column
(
nullable
=
false
,
length
=
100
)
@JsonProperty
(
value
=
Api1Constants
.
Accession
.
SPAUTHOR
)
private
String
spAuthor
;
@Column
(
nullable
=
false
,
length
=
100
)
@JsonProperty
(
value
=
Api1Constants
.
Accession
.
SUBTAXA
)
private
String
subtaxa
;
@Column
(
nullable
=
false
,
length
=
100
)
@JsonProperty
(
value
=
Api1Constants
.
Accession
.
SUBTAUTHOR
)
private
String
subtAuthor
;
@Column
(
nullable
=
false
)
...
...
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
View file @
42c401dd
...
...
@@ -44,6 +44,7 @@ import org.genesys2.server.model.genesys.PDCI;
import
org.genesys2.server.model.genesys.Taxonomy2
;
import
org.genesys2.server.model.impl.Country
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.model.json.Api1Constants
;
import
org.genesys2.server.persistence.AccessionRepository
;
import
org.genesys2.server.persistence.FaoInstituteRepository
;
import
org.genesys2.server.service.CropService
;
...
...
@@ -429,9 +430,36 @@ public class AccessionUploader implements InitializingBean {
}
else
if
(
taxonomy
.
equalTo
(
source
))
{
// NOOP
}
else
{
LOG
.
trace
(
"Ensuring taxonomy {}"
,
jsonNode
);
taxonomy
=
taxonomyService
.
ensureTaxonomy
(
source
);
accession
.
setTaxonomy
(
taxonomy
);
LOG
.
trace
(
"Updating taxonomy of {} with {}"
,
accession
.
getAccessionNumber
(),
jsonNode
);
if
(
jsonNode
.
has
(
Api1Constants
.
Accession
.
GENUS
)
&&
jsonNode
.
has
(
Api1Constants
.
Accession
.
SPECIES
))
{
Taxonomy2
updated
=
new
Taxonomy2
(
taxonomy
);
updated
.
setGenus
(
source
.
getGenus
());
updated
.
setSpecies
(
source
.
getSpecies
());
if
(
jsonNode
.
has
(
Api1Constants
.
Accession
.
SPAUTHOR
))
{
updated
.
setSpAuthor
(
source
.
getSpAuthor
());
}
else
{
updated
.
setSpAuthor
(
null
);
}
if
(
jsonNode
.
has
(
Api1Constants
.
Accession
.
SUBTAXA
))
{
updated
.
setSubtaxa
(
source
.
getSubtaxa
());
if
(
jsonNode
.
has
(
Api1Constants
.
Accession
.
SUBTAUTHOR
))
{
updated
.
setSubtAuthor
(
source
.
getSubtAuthor
());
}
else
{
updated
.
setSubtAuthor
(
null
);
}
}
else
{
updated
.
setSubtaxa
(
null
);
updated
.
setSubtAuthor
(
null
);
}
if
(!
updated
.
equalTo
(
taxonomy
))
{
LOG
.
trace
(
"Ensuring taxonomy {}"
,
updated
);
updated
=
taxonomyService
.
ensureTaxonomy
(
updated
);
accession
.
setTaxonomy
(
updated
);
}
}
}
}
...
...
src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java
View file @
42c401dd
...
...
@@ -22,6 +22,7 @@ import java.util.List;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.model.json.Api1Constants
;
import
org.genesys2.server.persistence.AccessionIdRepository
;
import
org.genesys2.server.persistence.AccessionRepository
;
import
org.genesys2.server.persistence.FaoInstituteRepository
;
...
...
@@ -243,9 +244,33 @@ public class AccessionUploaderTest extends AbstractServicesTest {
Accession
a2
=
accessionRepository
.
findByDoi
(
DOI_1
);
assertThat
(
a2
.
getId
(),
equalTo
(
a1
.
getId
()));
assertThat
(
a2
.
getUuid
(),
equalTo
(
a1
.
getUuid
()));
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_2
));
// Genus not updated, missing species
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_1
));
assertThat
(
a2
.
getAccessionNumber
(),
is
(
ACCENUMB_2
));
}
/**
* Updating accession number and taxonomy must work with DOI only.
*/
@Test
public
void
testUpdateTaxonomysUsingDOI
()
{
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccession
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
));
// update taxonomy
ArrayNode
json
=
upsertAccession
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
);
ObjectNode
taxa
=
(
ObjectNode
)
json
.
get
(
0
).
get
(
"taxonomy"
);
taxa
.
put
(
Api1Constants
.
Accession
.
GENUS
,
GENUS_2
);
taxa
.
put
(
Api1Constants
.
Accession
.
SPECIES
,
"species"
);
taxa
.
put
(
Api1Constants
.
Accession
.
SPAUTHOR
,
"M."
);
accessionUploader
.
upsertAccessions
(
institute
,
json
);
assertThat
(
accessionRepository
.
count
(),
is
(
1
l
));
Accession
a2
=
accessionRepository
.
findByDoi
(
DOI_1
);
assertThat
(
a2
.
getGenus
(),
is
(
GENUS_2
));
assertThat
(
a2
.
getTaxonomy
().
getSpecies
(),
is
(
"species"
));
assertThat
(
a2
.
getTaxonomy
().
getSpAuthor
(),
is
(
"M."
));
assertThat
(
a2
.
getTaxonomy
().
getSubtAuthor
(),
is
(
""
));
}
/**
...
...
@@ -261,6 +286,26 @@ public class AccessionUploaderTest extends AbstractServicesTest {
assertThat
(
op
.
get
(
0
).
getError
(),
is
(
"Accession does not belong to institute "
+
institute2
.
getCode
()));
}
@Test
public
void
testTaxonomyNotModified
()
{
// upload accesion with species
ArrayNode
json
=
upsertAccession
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
);
ObjectNode
taxa
=
(
ObjectNode
)
json
.
get
(
0
).
get
(
"taxonomy"
);
taxa
.
put
(
Api1Constants
.
Accession
.
SPECIES
,
"species"
);
taxa
.
put
(
Api1Constants
.
Accession
.
SPAUTHOR
,
"M."
);
accessionUploader
.
upsertAccessions
(
institute
,
json
);
Accession
a1
=
accessionRepository
.
findOne
(
institute
,
null
,
ACCENUMB_1
,
GENUS_1
);
assertThat
(
a1
.
getTaxonomy
().
getSpecies
(),
equalTo
(
"species"
));
assertThat
(
a1
.
getTaxonomy
().
getSpAuthor
(),
equalTo
(
"M."
));
// Update without providing taxonomy details
accessionUploader
.
upsertAccessions
(
institute
,
upsertAccession
(
institute
.
getCode
(),
ACCENUMB_1
,
GENUS_1
,
DOI_1
));
Accession
a1a
=
accessionRepository
.
findOne
(
institute
,
DOI_1
,
ACCENUMB_1
,
GENUS_1
);
assertThat
(
a1a
.
getTaxonomy
().
getSpecies
(),
equalTo
(
"species"
));
assertThat
(
a1a
.
getTaxonomy
().
getSpAuthor
(),
equalTo
(
"M."
));
}
/**
* Report invalid field in JSON
...
...
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