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Genesys PGR
Genesys Backend
Commits
4b2a725e
Commit
4b2a725e
authored
Apr 17, 2015
by
Matija Obreza
Browse files
Generated UUIDs when missing and include in RDF and HTML
parent
f6ca37a6
Changes
10
Hide whitespace changes
Inline
Side-by-side
src/main/java/org/genesys2/server/model/genesys/AccessionId.java
View file @
4b2a725e
...
...
@@ -37,7 +37,7 @@ import org.genesys2.server.model.VersionedAuditedModel;
@Table
(
name
=
"acce"
)
public
class
AccessionId
extends
VersionedAuditedModel
implements
IdUUID
{
@Column
(
columnDefinition
=
"binary(16)"
,
updatable
=
false
)
@Column
(
columnDefinition
=
"binary(16)"
)
protected
UUID
uuid
;
@PrePersist
...
...
src/main/java/org/genesys2/server/persistence/domain/AccessionIdRepository.java
View file @
4b2a725e
...
...
@@ -16,9 +16,16 @@
package
org.genesys2.server.persistence.domain
;
import
java.util.List
;
import
org.genesys2.server.model.genesys.AccessionId
;
import
org.springframework.data.domain.Pageable
;
import
org.springframework.data.jpa.repository.JpaRepository
;
import
org.springframework.data.jpa.repository.Query
;
public
interface
AccessionIdRepository
extends
JpaRepository
<
AccessionId
,
Long
>
{
@Query
(
"select aid from AccessionId aid where aid.uuid is null"
)
List
<
AccessionId
>
findMissingUuid
(
Pageable
pageable
);
}
src/main/java/org/genesys2/server/service/GenesysService.java
View file @
4b2a725e
...
...
@@ -217,5 +217,7 @@ public interface GenesysService {
Set
<
AccessionDetails
>
getAccessionDetails
(
Collection
<
Long
>
accessionIds
);
int
assignMissingUuid
(
int
count
);
}
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
4b2a725e
...
...
@@ -31,6 +31,7 @@ import java.util.HashSet;
import
java.util.List
;
import
java.util.Map
;
import
java.util.Set
;
import
java.util.UUID
;
import
java.util.zip.ZipEntry
;
import
java.util.zip.ZipOutputStream
;
...
...
@@ -102,6 +103,7 @@ import org.springframework.cache.annotation.CacheEvict;
import
org.springframework.dao.IncorrectResultSizeDataAccessException
;
import
org.springframework.data.domain.Page
;
import
org.springframework.data.domain.PageImpl
;
import
org.springframework.data.domain.PageRequest
;
import
org.springframework.data.domain.Pageable
;
import
org.springframework.data.repository.query.Param
;
import
org.springframework.jdbc.core.RowCallbackHandler
;
...
...
@@ -1508,4 +1510,18 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
return
accessionRepository
.
listAccessionsIds
(
taxonomy
);
}
@Override
@Transactional
public
int
assignMissingUuid
(
int
count
)
{
List
<
AccessionId
>
accessionIds
=
accessionIdRepository
.
findMissingUuid
(
new
PageRequest
(
0
,
count
));
for
(
AccessionId
accessionId
:
accessionIds
)
{
if
(
accessionId
.
getUuid
()==
null
)
{
accessionId
.
setUuid
(
UUID
.
randomUUID
());
}
}
accessionIdRepository
.
save
(
accessionIds
);
LOG
.
info
(
"Generated "
+
accessionIds
.
size
()
+
" new UUIDs"
);
return
accessionIds
.
size
();
}
}
src/main/java/org/genesys2/server/servlet/controller/admin/AdminController.java
View file @
4b2a725e
...
...
@@ -354,4 +354,12 @@ public class AdminController {
}
return
"redirect:/admin/"
;
}
@RequestMapping
(
"/assign-uuid"
)
public
String
assignUuid
()
{
while
(
genesysService
.
assignMissingUuid
(
100
)>
0
)
{
}
return
"redirect:/admin/"
;
}
}
src/main/resources/spring/spring.properties
View file @
4b2a725e
...
...
@@ -25,7 +25,7 @@ db.url=jdbc:mysql://localhost/genesys5?useUnicode=true&characterEncoding=UTF-8&u
db.driverClassName
=
com.mysql.jdbc.Driver
db.username
=
root
db.password
=
db.showSql
=
tru
e
db.showSql
=
fals
e
db.hbm2ddl
=
false
hibernate.dialect
=
org.hibernate.dialect.MySQL5InnoDBDialect
...
...
src/main/webapp/WEB-INF/decorator/main.jsp
View file @
4b2a725e
...
...
@@ -5,6 +5,7 @@
<html
lang=
"${pageContext.response.locale.language}"
dir=
"${pageContext.response.locale.language=='fa' || pageContext.response.locale.language=='ar' ? 'rtl' : 'ltr'}"
xmlns:rdf=
"http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:schema=
"http://schema.org/"
xmlns:dc=
"http://purl.org/dc/elements/1.1/"
xmlns:dwc=
"http://rs.tdwg.org/dwc/terms/"
xmlns:germplasm=
"http://purl.org/germplasm/germplasmTerm#"
xmlns:germplasmType=
"http://purl.org/germplasm/germplasmType#"
...
...
src/main/webapp/WEB-INF/jsp/accession/details-turtle.jsp
View file @
4b2a725e
...
...
@@ -3,6 +3,7 @@
@prefix rdf:
<http:
//www.w3.org/1999/02/22-rdf-syntax-ns#
>
.
@prefix wgs84_pos:
<http:
//www.w3.org/2003/01/geo/wgs84_pos#
>
.
@prefix dc:
<http:
//purl.org/dc/elements/1.1
/>
.
# using DarwinCore
@prefix dwc:
<http:
//rs.tdwg.org/dwc/terms
/>
.
# using https://code.google.com/p/darwincore-germplasm/
...
...
@@ -13,6 +14,7 @@
<http:
//www.genesys-pgr.org/acn/id/${accession.id}
>
a germplasm:GermplasmAccession;
germplasm:germplasmID "
<c:out
value=
"
${
accession
.
id
}
"
/>
";
dc:identifier "urn:uuid:
<c:out
value=
"
${
accession
.
uuid
}
"
/>
";
dwc:catalogNumber "
<c:out
value=
"
${
accession
.
accessionName
}
"
/>
";
dwc:institutionCode "
<c:out
value=
"
${
accession
.
instituteCode
}
"
/>
";
dwc:instituteId "
<c:out
value=
"
${
accession
.
institute
.
id
}
"
/>
";
...
...
src/main/webapp/WEB-INF/jsp/accession/details.jsp
View file @
4b2a725e
...
...
@@ -103,16 +103,6 @@
</div>
<div
class=
"crop-details"
>
<c:if
test=
"
${
accession
.
uuid
ne
null
}
"
>
<div
class=
"row text-muted"
>
<div
class=
"col-xs-4"
><spring:message
code=
"accession.uuid"
/></div>
<div
class=
"col-xs-8"
><c:out
value=
"
${
accession
.
uuid
}
"
/></div>
</div>
<div
class=
"row"
>
<div
class=
"col-xs-4"
><spring:message
code=
"accession.purl"
/></div>
<div
class=
"col-xs-8"
><a
href=
"https://purl.org/germplasm/id/${accession.uuid}"
><c:out
value=
"https://purl.org/germplasm/id/${accession.uuid}"
/></a></div>
</div>
</c:if>
<div
class=
"row"
>
<div
class=
"col-xs-4"
><spring:message
code=
"accession.holdingInstitute"
/></div>
<div
class=
"col-xs-8"
><a
property=
"dwc:institutionCode"
href=
"
<c:url
value=
"/wiews/${accession.instituteCode}"
/>
"
>
<c:out
value=
"
${
accession
.
institute
.
fullName
}
"
/>
...
...
@@ -224,6 +214,17 @@
<div
class=
"col-xs-4"
><spring:message
code=
"accession.donor.accessionNumber"
/></div>
<div
class=
"col-xs-8"
>
${accessionExchange.accNumbDonor}
</div>
</div>
<c:if
test=
"
${
accession
.
uuid
ne
null
}
"
>
<div
class=
"row text-muted"
>
<div
class=
"col-xs-4"
><spring:message
code=
"accession.uuid"
/></div>
<div
class=
"col-xs-8"
><span
property=
"dc:identifier"
>
urn:uuid:
<c:out
value=
"
${
accession
.
uuid
}
"
/></span></div>
</div>
<div
class=
"row"
>
<div
class=
"col-xs-4"
><spring:message
code=
"accession.purl"
/></div>
<div
class=
"col-xs-8"
><span
property=
"dc:identifier"
><a
href=
"https://purl.org/germplasm/id/${accession.uuid}"
><c:out
value=
"https://purl.org/germplasm/id/${accession.uuid}"
/></a></span></div>
</div>
</c:if>
</c:if>
<c:if
test=
"
${
accessionCollect
ne
null
}
"
>
...
...
src/main/webapp/WEB-INF/jsp/admin/index.jsp
View file @
4b2a725e
...
...
@@ -8,119 +8,124 @@
<title><spring:message
code=
"admin.page.title"
/></title>
</head>
<body>
<h1>
<spring:message
code=
"admin.page.title"
/>
</h1>
<%@ include
file=
"/WEB-INF/jsp/admin/menu.jsp"
%>
<h3>
Full-text Search
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindex-elastic"
/>
"
>
<input
type=
"text"
name=
"startAt"
disabled=
"true"
/>
<input
type=
"text"
name=
"filter"
/>
<label>
<input
type=
"checkbox"
name=
"slow"
value=
"false"
/>
No sleep
</label>
<input
type=
"submit"
class=
"btn btn-default"
value=
"ES reindex"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/clear-queues"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Clear ES update queues"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Country data
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshCountries"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Refresh country data"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAlternateNames"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update alternate GEO names"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateITPGRFA"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update country ITPGRFA status"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
WIEWS
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshWiews"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Refresh WIEWS data"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Svalbard Global Seed Vault
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateSGSV"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update SGSV"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Accession
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAccessionCountryRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update accession country info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateInstituteCountryRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update WIEWS country info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAccessionInstituteRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update accession institute info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/convertNames"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Convert old names to aliases"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
C
&
E
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshMetadataMethods"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Recalculate metadata methods"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Content
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/sanitize"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Sanitize HTML content"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Full-text Search
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindexEverything"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Reindex search indexes"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindexEntity"
/>
"
>
<select
name=
"entity"
>
<option
value=
"org.genesys2.server.model.impl.Country"
>
Countries
</option>
<option
value=
"org.genesys2.server.model.impl.FaoInstitute"
>
WIEWS Institutes
</option>
<option
value=
"org.genesys2.server.model.impl.ActivityPost"
>
Posts
</option>
<option
value=
"org.genesys2.server.model.impl.Article"
>
Articles
</option>
<option
value=
"org.genesys2.server.model.impl.Organization"
>
Organizations
</option>
<option
value=
"org.genesys2.server.model.genesys.Accession"
>
Accessions
</option>
<option
value=
"org.genesys2.server.model.genesys.AccessionAlias"
>
Accession alias
</option>
<option
value=
"org.genesys2.server.model.genesys.Taxonomy2"
>
Taxonomy2
</option>
</select>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Reindex search indexes"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h1>
<spring:message
code=
"admin.page.title"
/>
</h1>
<%@ include
file=
"/WEB-INF/jsp/admin/menu.jsp"
%>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/assign-uuid"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Assign missing UUIDs"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Full-text Search
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindex-elastic"
/>
"
>
<input
type=
"text"
name=
"startAt"
disabled=
"disabled"
/>
<input
type=
"text"
name=
"filter"
/>
<label>
<input
type=
"checkbox"
name=
"slow"
value=
"false"
/>
No sleep
</label>
<input
type=
"submit"
class=
"btn btn-default"
value=
"ES reindex"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/clear-queues"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Clear ES update queues"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Country data
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshCountries"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Refresh country data"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAlternateNames"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update alternate GEO names"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateITPGRFA"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update country ITPGRFA status"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
WIEWS
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshWiews"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Refresh WIEWS data"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Svalbard Global Seed Vault
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateSGSV"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update SGSV"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Accession
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAccessionCountryRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update accession country info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateInstituteCountryRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Update WIEWS country info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/updateAccessionInstituteRefs"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Update accession institute info"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/convertNames"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Convert old names to aliases"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
C
&
E
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/refreshMetadataMethods"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Recalculate metadata methods"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Content
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/sanitize"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Sanitize HTML content"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<h3>
Full-text Search
</h3>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindexEverything"
/>
"
>
<input
type=
"submit"
class=
"btn btn-default"
class=
"btn btn-default"
value=
"Reindex search indexes"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
<form
method=
"post"
action=
"
<c:url
value=
"/admin/reindexEntity"
/>
"
>
<select
name=
"entity"
>
<option
value=
"org.genesys2.server.model.impl.Country"
>
Countries
</option>
<option
value=
"org.genesys2.server.model.impl.FaoInstitute"
>
WIEWS Institutes
</option>
<option
value=
"org.genesys2.server.model.impl.ActivityPost"
>
Posts
</option>
<option
value=
"org.genesys2.server.model.impl.Article"
>
Articles
</option>
<option
value=
"org.genesys2.server.model.impl.Organization"
>
Organizations
</option>
<option
value=
"org.genesys2.server.model.genesys.Accession"
>
Accessions
</option>
<option
value=
"org.genesys2.server.model.genesys.AccessionAlias"
>
Accession alias
</option>
<option
value=
"org.genesys2.server.model.genesys.Taxonomy2"
>
Taxonomy2
</option>
</select>
<input
type=
"submit"
class=
"btn btn-default"
value=
"Reindex search indexes"
/>
<!-- CSRF protection -->
<input
type=
"hidden"
name=
"${_csrf.parameterName}"
value=
"${_csrf.token}"
/>
</form>
</body>
</html>
\ No newline at end of file
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