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Genesys PGR
Genesys Backend
Commits
3beff0cc
Commit
3beff0cc
authored
Sep 07, 2013
by
Matija Obreza
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Wide format for dataset observations
parent
5a0aa586
Changes
6
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6 changed files
with
87 additions
and
9 deletions
+87
-9
src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepository.java
.../rest/common/persistence/domain/TraitValueRepository.java
+5
-0
src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepositoryImpl.java
...t/common/persistence/domain/TraitValueRepositoryImpl.java
+40
-0
src/main/java/org/crophub/rest/common/service/GenesysService.java
.../java/org/crophub/rest/common/service/GenesysService.java
+2
-0
src/main/java/org/crophub/rest/common/service/impl/GenesysServiceImpl.java
.../crophub/rest/common/service/impl/GenesysServiceImpl.java
+6
-0
src/main/java/org/crophub/rest/servlet/controller/DatasetController.java
...rg/crophub/rest/servlet/controller/DatasetController.java
+8
-1
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
+26
-8
No files found.
src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepository.java
View file @
3beff0cc
...
...
@@ -19,8 +19,11 @@ package org.crophub.rest.common.persistence.domain;
import
java.util.List
;
import
java.util.Map
;
import
org.crophub.rest.common.model.genesys.Accession
;
import
org.crophub.rest.common.model.genesys.AccessionTrait
;
import
org.crophub.rest.common.model.genesys.ExperimentTrait
;
import
org.crophub.rest.common.model.genesys.Metadata
;
import
org.crophub.rest.common.model.genesys.Method
;
public
interface
TraitValueRepository
{
...
...
@@ -30,4 +33,6 @@ public interface TraitValueRepository {
Map
<
Long
,
List
<
ExperimentTrait
>>
getValues
(
List
<
AccessionTrait
>
accessionTraits
);
Map
<
Long
,
Map
<
Long
,
Object
>>
getValues
(
Metadata
metadata
,
List
<
Method
>
methods
,
List
<
Accession
>
accessions
);
}
\ No newline at end of file
src/main/java/org/crophub/rest/common/persistence/domain/TraitValueRepositoryImpl.java
View file @
3beff0cc
...
...
@@ -25,8 +25,10 @@ import javax.sql.DataSource;
import
org.apache.commons.logging.Log
;
import
org.apache.commons.logging.LogFactory
;
import
org.crophub.rest.common.model.genesys.Accession
;
import
org.crophub.rest.common.model.genesys.AccessionTrait
;
import
org.crophub.rest.common.model.genesys.ExperimentTrait
;
import
org.crophub.rest.common.model.genesys.Metadata
;
import
org.crophub.rest.common.model.genesys.Method
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.jdbc.core.JdbcTemplate
;
...
...
@@ -108,4 +110,42 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
LOG
.
warn
(
"Done! "
+
methodValues
);
return
methodValues
;
}
@Override
public
Map
<
Long
,
Map
<
Long
,
Object
>>
getValues
(
Metadata
metadata
,
List
<
Method
>
methods
,
List
<
Accession
>
accessions
)
{
Map
<
Long
,
Map
<
Long
,
Object
>>
accessionMetadataValues
=
new
HashMap
<
Long
,
Map
<
Long
,
Object
>>();
for
(
Accession
accession
:
accessions
)
{
// create lists
accessionMetadataValues
.
put
(
accession
.
getId
(),
new
HashMap
<
Long
,
Object
>());
}
for
(
Method
method
:
methods
)
{
// FIXME We're loading all entries for metadata, should limit only to the accessions in the list!
final
List
<
Map
<
String
,
Object
>>
rows
=
this
.
jdbcTemplate
.
queryForList
(
"select `ALIS_Id` as accessionId, `"
+
method
.
getFieldName
()
+
"` as traitvalue from `"
+
method
.
getId
()
+
"` where `Meta_Id`=?"
,
new
Object
[]
{
metadata
.
getId
()
});
if
(
rows
==
null
||
rows
.
size
()
==
0
)
{
// Skip
continue
;
}
for
(
final
Map
<
String
,
Object
>
row
:
rows
)
{
long
accessionId
=
(
Integer
)
row
.
get
(
"accessionId"
);
Object
value
=
row
.
get
(
"traitvalue"
);
if
(
value
!=
null
)
{
Map
<
Long
,
Object
>
accessionValues
=
accessionMetadataValues
.
get
(
accessionId
);
if
(
accessionValues
!=
null
)
accessionValues
.
put
(
method
.
getId
(),
value
);
}
}
}
LOG
.
warn
(
"Done! "
);
return
accessionMetadataValues
;
}
}
src/main/java/org/crophub/rest/common/service/GenesysService.java
View file @
3beff0cc
...
...
@@ -55,4 +55,6 @@ public interface GenesysService {
Map
<
Long
,
List
<
ExperimentTrait
>>
getAccessionTraitValues
(
Accession
accession
);
Map
<
Long
,
Map
<
Long
,
Object
>>
getMetadataTraitValues
(
Metadata
metadata
,
List
<
Accession
>
content
);
}
src/main/java/org/crophub/rest/common/service/impl/GenesysServiceImpl.java
View file @
3beff0cc
...
...
@@ -152,4 +152,10 @@ public class GenesysServiceImpl implements GenesysService {
LOG
.
debug
(
"Getting trait values for accession: "
+
accession
);
return
traitValueRepository
.
getValues
(
accessionTraitRepository
.
findByAccession
(
accession
));
}
@Override
public
Map
<
Long
,
Map
<
Long
,
Object
>>
getMetadataTraitValues
(
Metadata
metadata
,
List
<
Accession
>
accessions
)
{
List
<
Method
>
methods
=
metadataMethodRepository
.
listMetadataMethods
(
metadata
);
return
traitValueRepository
.
getValues
(
metadata
,
methods
,
accessions
);
}
}
src/main/java/org/crophub/rest/servlet/controller/DatasetController.java
View file @
3beff0cc
...
...
@@ -16,10 +16,12 @@
package
org.crophub.rest.servlet.controller
;
import
org.crophub.rest.common.model.genesys.Accession
;
import
org.crophub.rest.common.model.genesys.Metadata
;
import
org.crophub.rest.common.service.GenesysService
;
import
org.crophub.spring.ResourceNotFoundException
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.data.domain.Page
;
import
org.springframework.data.domain.PageRequest
;
import
org.springframework.stereotype.Controller
;
import
org.springframework.ui.ModelMap
;
...
...
@@ -56,7 +58,12 @@ public class DatasetController extends BaseController {
}
model
.
addAttribute
(
"metadata"
,
metadata
);
model
.
addAttribute
(
"methods"
,
genesysService
.
listMethods
(
metadata
));
model
.
addAttribute
(
"accessions"
,
genesysService
.
listMetadataAccessions
(
metadata
,
new
PageRequest
(
page
-
1
,
50
)));
Page
<
Accession
>
accessions
=
genesysService
.
listMetadataAccessions
(
metadata
,
new
PageRequest
(
page
-
1
,
50
));
model
.
addAttribute
(
"accessions"
,
accessions
);
// Map[accession.id][method.id]
model
.
addAttribute
(
"accessionMethods"
,
genesysService
.
getMetadataTraitValues
(
metadata
,
accessions
.
getContent
()));
return
"/metadata/view"
;
}
...
...
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
View file @
3beff0cc
...
...
@@ -52,21 +52,39 @@
<thead>
<tr>
<td><spring:message
code=
"accession.accessionName"
/></td>
<td><spring:message
code=
"accession.origin"
/></td>
<td><spring:message
code=
"accession.taxonomy"
/></td>
<td><spring:message
code=
"accession.holdingInstitute"
/></td>
<%--
<td><spring:message code="accession.origin" /></td>
--%>
<td><spring:message
code=
"accession.taxonomy"
/></td>
<%--
<td><spring:message code="accession.holdingInstitute" /></td>
<td><spring:message code="accession.holdingCountry" /></td>
</tr>
--%>
<c:forEach
items=
"
${
methods
}
"
var=
"method"
>
<td>
<c:out
value=
"
${
method
.
fieldName
}
"
/>
<c:if
test=
"
${
method
.
unit
ne
''
}
"
>
[
<c:out
value=
"
${
method
.
unit
}
"
/>
]
</c:if>
</td>
</c:forEach>
</tr>
</thead>
<tbody>
<c:forEach
items=
"
${
accessions
.
content
}
"
var=
"accession"
varStatus=
"status"
>
<tr>
<td><a
href=
"
<c:url
value=
"/acn/id/${accession.id}"
/>
"
><b><c:out
value=
"
${
accession
.
accessionName
}
"
/></b></a></td>
<td><a
href=
"
<c:url
value=
"/geo/${accession.origin.toLowerCase()}"
/>
"
><c:out
value=
"
${
accession
.
countryOfOrigin
.
name
}
"
/></a></td>
<td><c:out
value=
"
${
accession
.
taxonomy
.
taxonName
}
"
/></td>
<td><a
href=
"
<c:url
value=
"/wiews/${accession.institute.code.toLowerCase()}"
/>
"
><c:out
value=
"
${
accession
.
institute
.
code
}
"
/></a></td>
<%--
<td><a href="<c:url value="/geo/${accession.origin.toLowerCase()}" />"><c:out value="${accession.countryOfOrigin.name}" /></a></td>
--%>
<td><c:out
value=
"
${
accession
.
taxonomy
.
taxonName
}
"
/></td>
<%--
<td><a href="<c:url value="/wiews/${accession.institute.code.toLowerCase()}" />"><c:out value="${accession.institute.code}" /></a></td>
<td><a href="<c:url value="/geo/${accession.institute.country.code3.toLowerCase()}" />"><c:out value="${accession.institute.country.name}" /></a></td>
</tr>
--%>
<c:set
value=
"
${
accessionMethods
[
accession
.
id
]
}
"
var=
"methodValues"
/>
<c:forEach
items=
"
${
methods
}
"
var=
"method"
>
<td>
<c:out
value=
"
${
method
.
decode
(
methodValues
[
method
.
id
])
}
"
/>
</td>
</c:forEach>
</tr>
</c:forEach>
</tbody>
</table>
...
...
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