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Genesys PGR
Genesys Backend
Commits
7c59eda1
Commit
7c59eda1
authored
Nov 09, 2015
by
Matija Obreza
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Plain Diff
Genesys API /{instCode}/names returns results per accession
parent
fffb1b22
Changes
3
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3 changed files
with
65 additions
and
14 deletions
+65
-14
src/main/java/org/genesys2/server/service/BatchRESTService.java
...in/java/org/genesys2/server/service/BatchRESTService.java
+2
-2
src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java
...rg/genesys2/server/service/impl/BatchRESTServiceImpl.java
+22
-4
src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java
...2/server/servlet/controller/rest/AccessionController.java
+41
-8
No files found.
src/main/java/org/genesys2/server/service/BatchRESTService.java
View file @
7c59eda1
/**
* Copyright 201
4
Global Crop Diversity Trust
* Copyright 201
5
Global Crop Diversity Trust
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
...
...
@@ -30,7 +30,7 @@ public interface BatchRESTService {
List
<
UpsertResponse
>
upsertAccessionData
(
FaoInstitute
institute
,
Map
<
AccessionHeaderJson
,
ObjectNode
>
batch
)
throws
RESTApiException
;
void
upsertAccessionNames
(
FaoInstitute
institute
,
List
<
AccessionNamesJson
>
batch
)
throws
RESTApiException
;
List
<
UpsertResponse
>
upsertAccessionNames
(
FaoInstitute
institute
,
List
<
AccessionNamesJson
>
batch
)
throws
RESTApiException
;
int
deleteAccessions
(
FaoInstitute
institute
,
List
<
AccessionHeaderJson
>
batch
)
throws
RESTApiException
;
...
...
src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java
View file @
7c59eda1
/**
* Copyright 201
4
Global Crop Diversity Trust
* Copyright 201
5
Global Crop Diversity Trust
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
...
...
@@ -109,7 +109,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
if
(
current
.
getGenus
().
contains
(
" "
)
||
current
.
getGenus
().
contains
(
"sp."
))
{
throw
new
RESTApiException
(
"GENUS cannot contain spaces or 'sp.'. Offending genus: "
+
current
.
getGenus
());
}
if
(
LOG
.
isDebugEnabled
())
{
LOG
.
debug
(
"Ensuring "
+
current
);
}
...
...
@@ -932,14 +932,24 @@ public class BatchRESTServiceImpl implements BatchRESTService {
@Override
@Transactional
@PreAuthorize
(
"hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')"
)
public
void
upsertAccessionNames
(
FaoInstitute
institute
,
List
<
AccessionNamesJson
>
batch
)
throws
RESTApiException
{
public
List
<
UpsertResponse
>
upsertAccessionNames
(
FaoInstitute
institute
,
List
<
AccessionNamesJson
>
batch
)
throws
RESTApiException
{
LOG
.
info
(
"Batch processing "
+
batch
.
size
()
+
" entries for "
+
institute
);
final
boolean
useUniqueAcceNumbs
=
institute
.
hasUniqueAcceNumbs
();
final
List
<
UpsertResponse
>
upsertResponses
=
new
ArrayList
<
UpsertResponse
>();
final
List
<
AccessionAlias
>
toSave
=
new
ArrayList
<
AccessionAlias
>();
final
List
<
AccessionAlias
>
toRemove
=
new
ArrayList
<
AccessionAlias
>();
final
boolean
useUniqueAcceNumbs
=
institute
.
hasUniqueAcceNumbs
();
for
(
final
AccessionNamesJson
dataJson
:
batch
)
{
UpsertResponse
upsertResponse
=
new
UpsertResponse
(
dataJson
.
instCode
,
dataJson
.
acceNumb
,
dataJson
.
genus
);
upsertResponses
.
add
(
upsertResponse
);
UpsertResult
upsertResult
=
null
;
if
(!
institute
.
getCode
().
equals
(
dataJson
.
instCode
))
{
throw
new
RESTApiException
(
"Accession does not belong to instCode="
+
institute
.
getCode
()
+
" acn="
+
dataJson
);
}
Accession
accession
=
null
;
try
{
if
(
useUniqueAcceNumbs
)
{
...
...
@@ -954,13 +964,20 @@ public class BatchRESTServiceImpl implements BatchRESTService {
if
(
accession
==
null
)
{
LOG
.
warn
(
"No such accession "
+
dataJson
);
upsertResponse
.
setError
(
"No such asccession "
+
dataJson
);
continue
;
}
else
{
upsertResult
=
new
UpsertResult
(
UpsertResult
.
Type
.
UPDATE
);
upsertResult
.
setUUID
(
accession
.
getUuid
());
}
// LOG.info("Updating " + dataJson + " with=" + dataJson.aliases);
final
List
<
AccessionAliasJson
>
aliases
=
dataJson
.
aliases
;
final
List
<
AccessionAlias
>
existingAliases
=
genesysService
.
listAccessionAliases
(
accession
.
getAccessionId
());
upsertAccessionAliases
(
accession
.
getAccessionId
(),
aliases
,
null
,
toRemove
,
toSave
,
existingAliases
);
// Set upsert result
upsertResponse
.
setResult
(
upsertResult
);
}
if
(
toSave
.
size
()
>
0
)
{
...
...
@@ -972,6 +989,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
genesysService
.
removeAliases
(
toRemove
);
}
return
upsertResponses
;
}
private
void
upsertAccessionAliases
(
AccessionId
accession
,
List
<
AccessionAliasJson
>
aliases
,
final
AliasType
aliasType
,
List
<
AccessionAlias
>
toRemove
,
...
...
src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java
View file @
7c59eda1
...
...
@@ -261,12 +261,12 @@ public class AccessionController extends RestController {
for
(
AccessionHeaderJson
acceJ
:
batch
.
keySet
())
{
try
{
batchOfOne
.
clear
();
batchOfOne
.
put
(
acceJ
,
batch
.
get
(
acceJ
));
UpsertResponse
accessionResponse
=
batchRESTService
.
upsertAccessionData
(
institute
,
batchOfOne
).
get
(
0
);
response
.
add
(
accessionResponse
);
}
catch
(
RESTApiException
e
)
{
if
(
LOG
.
isInfoEnabled
())
{
LOG
.
info
(
"Error upserting "
+
acceJ
.
instCode
+
": "
+
e
.
getMessage
());
...
...
@@ -290,7 +290,7 @@ public class AccessionController extends RestController {
*/
@RequestMapping
(
value
=
"/{instCode}/names"
,
method
=
{
RequestMethod
.
POST
,
RequestMethod
.
PUT
},
consumes
=
{
MediaType
.
APPLICATION_JSON_VALUE
},
produces
=
{
MediaType
.
APPLICATION_JSON_VALUE
})
public
@ResponseBody
String
upsertAccessionNames
(
@PathVariable
(
"instCode"
)
String
instCode
,
@RequestBody
List
<
AccessionNamesJson
>
batch
)
public
@ResponseBody
List
<
UpsertResponse
>
upsertAccessionNames
(
@PathVariable
(
"instCode"
)
String
instCode
,
@RequestBody
List
<
AccessionNamesJson
>
batch
)
throws
RESTApiException
{
// User's permission to WRITE to this WIEWS institute are checked in
// BatchRESTService.
...
...
@@ -299,14 +299,47 @@ public class AccessionController extends RestController {
throw
new
ResourceNotFoundException
();
}
for
(
final
AccessionNamesJson
aid3
:
batch
)
{
if
(!
instCode
.
equals
(
aid3
.
instCode
))
{
throw
new
RuntimeException
(
"Accession does not belong to instCode="
+
instCode
+
" acn="
+
aid3
);
try
{
List
<
UpsertResponse
>
response
=
null
;
try
{
response
=
batchRESTService
.
upsertAccessionNames
(
institute
,
batch
);
}
catch
(
RESTApiException
e
)
{
LOG
.
info
(
"Retrying upsert names one by one due to "
+
e
.
getMessage
());
response
=
upsertAccessionNames1by1
(
institute
,
batch
);
}
return
response
;
}
catch
(
Throwable
e
)
{
throw
new
RESTApiException
(
"Could not upsert accession names data. "
+
e
.
getMessage
(),
e
);
}
}
private
List
<
UpsertResponse
>
upsertAccessionNames1by1
(
FaoInstitute
institute
,
List
<
AccessionNamesJson
>
batch
)
{
LOG
.
info
(
"Attempting upsert accession names 1 by 1"
);
final
List
<
AccessionNamesJson
>
batchOfOne
=
new
ArrayList
<
AccessionNamesJson
>(
1
);
List
<
UpsertResponse
>
response
=
new
ArrayList
<
UpsertResponse
>();
for
(
AccessionNamesJson
acceJ
:
batch
)
{
batchRESTService
.
upsertAccessionNames
(
institute
,
batch
);
return
JSON_OK
;
try
{
batchOfOne
.
clear
();
batchOfOne
.
add
(
acceJ
);
UpsertResponse
accessionResponse
=
batchRESTService
.
upsertAccessionNames
(
institute
,
batchOfOne
).
get
(
0
);
response
.
add
(
accessionResponse
);
}
catch
(
RESTApiException
e
)
{
if
(
LOG
.
isInfoEnabled
())
{
LOG
.
info
(
"Error upserting "
+
acceJ
.
instCode
+
": "
+
e
.
getMessage
());
}
UpsertResponse
accessionResponse
=
new
UpsertResponse
(
acceJ
.
instCode
,
acceJ
.
acceNumb
,
acceJ
.
genus
);
accessionResponse
.
setError
(
e
.
getMessage
());
response
.
add
(
accessionResponse
);
}
}
return
response
;
}
/**
...
...
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