Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Genesys PGR
Genesys Backend
Commits
95952753
Commit
95952753
authored
Sep 10, 2018
by
Alexander Prendetskiy
Committed by
Matija Obreza
Sep 11, 2018
Browse files
New methods to AccessionController v1 to return details
parent
548b5799
Changes
3
Hide whitespace changes
Inline
Side-by-side
src/main/java/org/genesys2/server/api/v1/AccessionController.java
View file @
95952753
...
...
@@ -26,29 +26,28 @@ import javax.servlet.http.HttpServletRequest;
import
org.genesys.blocks.model.JsonViews
;
import
org.genesys.catalog.api.FilteredPage
;
import
org.genesys.catalog.model.dataset.Dataset
;
import
org.genesys.catalog.service.DatasetService
;
import
org.genesys.catalog.service.ShortFilterService
;
import
org.genesys2.server.api.ApiBaseController
;
import
org.genesys2.server.api.model.AccessionHeaderJson
;
import
org.genesys2.server.model.genesys.Accession
;
import
org.genesys2.server.model.genesys.PDCI
;
import
org.genesys2.server.model.impl.AccessionIdentifier3
;
import
org.genesys2.server.model.impl.Subset
;
import
org.genesys2.server.service.AccessionService
;
import
org.genesys2.server.service.ElasticsearchService
;
import
org.genesys2.server.service.ElasticsearchService.TermResult
;
import
org.genesys2.server.service.SubsetService
;
import
org.genesys2.server.service.filter.AccessionFilter
;
import
org.genesys2.server.service.impl.SearchException
;
import
org.genesys2.spring.ResourceNotFoundException
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.data.domain.PageRequest
;
import
org.springframework.data.domain.Sort
;
import
org.springframework.http.MediaType
;
import
org.springframework.security.access.prepost.PreAuthorize
;
import
org.springframework.web.bind.annotation.GetMapping
;
import
org.springframework.web.bind.annotation.PathVariable
;
import
org.springframework.web.bind.annotation.PostMapping
;
import
org.springframework.web.bind.annotation.RequestBody
;
import
org.springframework.web.bind.annotation.RequestMapping
;
import
org.springframework.web.bind.annotation.RequestMethod
;
import
org.springframework.web.bind.annotation.RequestParam
;
import
org.springframework.web.bind.annotation.RestController
;
import
org.springframework.web.bind.annotation.*
;
import
org.springframework.web.servlet.HandlerMapping
;
import
com.fasterxml.jackson.annotation.JsonView
;
...
...
@@ -83,6 +82,12 @@ public class AccessionController {
@Autowired
private
ElasticsearchService
elasticsearchService
;
@Autowired
private
DatasetService
datasetService
;
@Autowired
private
SubsetService
subsetService
;
private
final
Set
<
String
>
terms
=
Sets
.
newHashSet
(
"institute.code"
,
"institute.country.code3"
,
"cropName"
,
"crop.shortName"
,
"taxonomy.genus"
,
"taxonomy.species"
,
"taxonomy.genusSpecies"
,
"countryOfOrigin.code3"
,
"sampStat"
,
"available"
,
"mlsStatus"
,
"donorCode"
,
"sgsv"
,
"storage"
,
"duplSite"
,
"breederCode"
);
...
...
@@ -175,6 +180,40 @@ public class AccessionController {
return
accessionService
.
toUUID
(
identifiers
);
}
@RequestMapping
(
value
=
"/details/10.{dummy:[0-9]+}/**}"
,
method
=
RequestMethod
.
GET
,
produces
=
{
MediaType
.
APPLICATION_JSON_VALUE
})
@JsonView
(
JsonViews
.
Minimal
.
class
)
public
AccessionDetailsJson
getAccessionDetailsByDoi
(
HttpServletRequest
request
)
{
final
String
fullPath
=
(
String
)
request
.
getAttribute
(
HandlerMapping
.
PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE
);
final
String
doi
=
fullPath
.
substring
(
API_BASE
.
length
()
+
1
);
Accession
accession
=
accessionService
.
getByDoi
(
doi
);
return
getAccessionDetails
(
accession
);
}
@GetMapping
(
value
=
"/details/{UUID}"
,
consumes
=
MediaType
.
APPLICATION_JSON_VALUE
)
@JsonView
(
JsonViews
.
Minimal
.
class
)
public
AccessionDetailsJson
getAccessionDetailsByUUID
(
@PathVariable
(
"UUID"
)
final
UUID
uuid
)
{
Accession
accession
=
accessionService
.
getByUuid
(
uuid
);
return
getAccessionDetails
(
accession
);
}
private
AccessionDetailsJson
getAccessionDetails
(
Accession
accession
)
{
if
(
accession
==
null
)
{
throw
new
ResourceNotFoundException
();
}
List
<
Dataset
>
datasets
=
datasetService
.
listByAccession
(
accession
.
getAccessionId
());
List
<
Subset
>
subsets
=
subsetService
.
listByAccession
(
accession
.
getAccessionId
());
AccessionDetailsJson
accessionDetails
=
new
AccessionDetailsJson
();
accessionDetails
.
details
=
accession
;
accessionDetails
.
pdci
=
accession
.
getAccessionId
().
getPdci
();
accessionDetails
.
datasets
=
datasets
;
accessionDetails
.
subsets
=
subsets
;
return
accessionDetails
;
}
/**
* Get term overview for filters
...
...
@@ -238,4 +277,11 @@ public class AccessionController {
return
objectMapper
.
readValue
(
objectMapper
.
writeValueAsString
(
filter
),
AccessionFilter
.
class
);
}
public
static
class
AccessionDetailsJson
{
public
Accession
details
;
public
PDCI
pdci
;
public
List
<
Dataset
>
datasets
;
public
List
<
Subset
>
subsets
;
}
}
src/main/java/org/genesys2/server/service/SubsetService.java
View file @
95952753
...
...
@@ -16,9 +16,11 @@
package
org.genesys2.server.service
;
import
java.util.List
;
import
java.util.Set
;
import
java.util.UUID
;
import
org.genesys2.server.model.genesys.AccessionId
;
import
org.genesys2.server.model.impl.Subset
;
import
org.genesys2.server.service.filter.SubsetFilter
;
import
org.springframework.data.domain.Page
;
...
...
@@ -131,4 +133,6 @@ public interface SubsetService {
*/
Subset
approveSubset
(
Subset
subset
);
List
<
Subset
>
listByAccession
(
AccessionId
accessionId
);
}
src/main/java/org/genesys2/server/service/impl/SubsetServiceImpl.java
View file @
95952753
...
...
@@ -333,4 +333,9 @@ public class SubsetServiceImpl implements SubsetService {
return
deepLoad
(
subsetRepository
.
save
(
loaded
));
}
@Override
public
List
<
Subset
>
listByAccession
(
AccessionId
accessionId
)
{
return
(
List
<
Subset
>)
subsetRepository
.
findAll
(
QSubset
.
subset
.
accessions
.
contains
(
accessionId
));
}
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment