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Genesys PGR
Genesys Backend
Commits
94d43f60
Commit
94d43f60
authored
Jul 27, 2017
by
Maxym Borodenko
Committed by
Matija Obreza
Aug 03, 2017
Browse files
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Add DOI field
parent
0d4e4e7c
Changes
15
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15 changed files
with
130 additions
and
1 deletion
+130
-1
src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java
...a/org/genesys2/server/model/elastic/AccessionDetails.java
+11
-0
src/main/java/org/genesys2/server/model/genesys/Accession.java
...ain/java/org/genesys2/server/model/genesys/Accession.java
+1
-1
src/main/java/org/genesys2/server/model/genesys/AccessionData.java
...java/org/genesys2/server/model/genesys/AccessionData.java
+11
-0
src/main/java/org/genesys2/server/model/json/AccessionJson.java
...in/java/org/genesys2/server/model/json/AccessionJson.java
+10
-0
src/main/java/org/genesys2/server/model/json/Api1Constants.java
...in/java/org/genesys2/server/model/json/Api1Constants.java
+5
-0
src/main/java/org/genesys2/server/service/FilterConstants.java
...ain/java/org/genesys2/server/service/FilterConstants.java
+2
-0
src/main/java/org/genesys2/server/service/impl/DirectMysqlQuery.java
...va/org/genesys2/server/service/impl/DirectMysqlQuery.java
+1
-0
src/main/java/org/genesys2/server/service/impl/FilterHandler.java
.../java/org/genesys2/server/service/impl/FilterHandler.java
+1
-0
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
.../org/genesys2/server/service/impl/GenesysServiceImpl.java
+1
-0
src/main/resources/content/language.properties
src/main/resources/content/language.properties
+2
-0
src/main/resources/liquibase/liquibase-changeLog.yml
src/main/resources/liquibase/liquibase-changeLog.yml
+35
-0
src/main/webapp/WEB-INF/jsp/accession/details.jsp
src/main/webapp/WEB-INF/jsp/accession/details.jsp
+14
-0
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
+21
-0
src/main/webapp/WEB-INF/tags/filters/filter-list.tag
src/main/webapp/WEB-INF/tags/filters/filter-list.tag
+5
-0
src/main/webapp/WEB-INF/tags/filters/filter.tag
src/main/webapp/WEB-INF/tags/filters/filter.tag
+10
-0
No files found.
src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java
View file @
94d43f60
...
...
@@ -60,6 +60,8 @@ public class AccessionDetails {
private
Boolean
art15
;
private
Integer
sampStat
;
private
List
<
Integer
>
storage
;
@Field
(
type
=
FieldType
.
String
)
private
String
doi
;
@Field
(
type
=
FieldType
.
Object
)
private
Institute
institute
;
...
...
@@ -132,6 +134,7 @@ public class AccessionDetails {
ad
.
cropName
=
accession
.
getCropName
();
ad
.
inSgsv
=
accession
.
getInSvalbard
()
!=
null
&&
accession
.
getInSvalbard
()
==
true
?
true
:
false
;
ad
.
cropName
=
accession
.
getCropName
();
ad
.
doi
=
accession
.
getDoi
();
if
(
accession
.
getAccessionId
().
getPdci
()
!=
null
)
{
ad
.
pdciScore
=
accession
.
getAccessionId
().
getPdci
().
getScore
();
...
...
@@ -538,4 +541,12 @@ public class AccessionDetails {
public
void
setAcceName
(
String
acceName
)
{
this
.
acceName
=
acceName
;
}
public
String
getDoi
()
{
return
doi
;
}
public
void
setDoi
(
String
doi
)
{
this
.
doi
=
doi
;
}
}
src/main/java/org/genesys2/server/model/genesys/Accession.java
View file @
94d43f60
...
...
@@ -40,7 +40,7 @@ import javax.persistence.UniqueConstraint;
@Entity
@Table
(
name
=
"accession"
,
// Unique constraints
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UQ_accession_genus_inst"
,
columnNames
=
{
"instituteId"
,
"taxGenus"
,
"acceNumb"
})
},
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UQ_accession_genus_inst"
,
columnNames
=
{
"instituteId"
,
"taxGenus"
,
"acceNumb"
})
,
@UniqueConstraint
(
name
=
"UQ_accession_doi"
,
columnNames
=
{
"doi"
})
},
// Indexes
indexes
=
{
@Index
(
name
=
"IX_seqNo"
,
columnList
=
"seqNo"
),
@Index
(
name
=
"IX_accession_lastModifiedDate"
,
columnList
=
"lastModifiedDate"
)
})
public
class
Accession
extends
AccessionData
{
...
...
src/main/java/org/genesys2/server/model/genesys/AccessionData.java
View file @
94d43f60
...
...
@@ -81,6 +81,9 @@ public abstract class AccessionData implements IdUUID, Serializable {
@JoinColumn
(
name
=
"id"
)
private
AccessionId
accessionId
;
@Column
(
name
=
"doi"
)
private
String
doi
;
@Column
(
name
=
"instCode"
,
length
=
10
,
nullable
=
false
)
private
String
instituteCode
;
...
...
@@ -414,4 +417,12 @@ public abstract class AccessionData implements IdUUID, Serializable {
public
void
setCrop
(
Crop
crop
)
{
this
.
crop
=
crop
;
}
public
String
getDoi
()
{
return
doi
;
}
public
void
setDoi
(
String
doi
)
{
this
.
doi
=
doi
;
}
}
src/main/java/org/genesys2/server/model/json/AccessionJson.java
View file @
94d43f60
...
...
@@ -78,6 +78,8 @@ public class AccessionJson {
private
boolean
historic
;
@JsonProperty
(
value
=
Accession
.
ACCEURL
)
private
String
acceUrl
;
@JsonProperty
(
value
=
Accession
.
DOI
)
private
String
doi
;
public
long
getVersion
()
{
return
version
;
...
...
@@ -302,4 +304,12 @@ public class AccessionJson {
public
void
setAcceUrl
(
String
acceUrl
)
{
this
.
acceUrl
=
acceUrl
;
}
public
String
getDoi
()
{
return
doi
;
}
public
void
setDoi
(
String
doi
)
{
this
.
doi
=
doi
;
}
}
src/main/java/org/genesys2/server/model/json/Api1Constants.java
View file @
94d43f60
...
...
@@ -191,6 +191,11 @@ public interface Api1Constants {
*/
public
static
final
String
CROPNAME
=
"cropName"
;
/**
* Accession DOI (Digital Object Identifier)
*/
public
static
final
String
DOI
=
"doi"
;
}
public
static
interface
Institute
{
...
...
src/main/java/org/genesys2/server/service/FilterConstants.java
View file @
94d43f60
...
...
@@ -91,4 +91,6 @@ public interface FilterConstants {
public
static
final
String
LAST_MODIFIED_DATE
=
"lastModifiedDate"
;
public
static
final
String
DOI
=
"doi"
;
}
src/main/java/org/genesys2/server/service/impl/DirectMysqlQuery.java
View file @
94d43f60
...
...
@@ -208,6 +208,7 @@ public class DirectMysqlQuery {
createQuery
(
whereBuffer
,
"col.collMissId"
,
filters
.
get
(
FilterConstants
.
COLLMISSID
),
params
);
createQuery
(
whereBuffer
,
"storage.storage"
,
filters
.
get
(
FilterConstants
.
STORAGE
),
params
);
createQuery
(
whereBuffer
,
"pdci.score"
,
filters
.
get
(
FilterConstants
.
PDCI
),
params
);
createQuery
(
whereBuffer
,
"doi"
,
filters
.
get
(
FilterConstants
.
DOI
),
params
);
for
(
final
AppliedFilter
methodFilter
:
filters
.
methodFilters
())
{
// Handle Genesys Method!
...
...
src/main/java/org/genesys2/server/service/impl/FilterHandler.java
View file @
94d43f60
...
...
@@ -83,6 +83,7 @@ public class FilterHandler {
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
CROPS
,
DataType
.
STRING
));
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
CROPNAME
,
DataType
.
STRING
));
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
LISTS
,
DataType
.
STRING
));
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
DOI
,
DataType
.
STRING
));
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
REGION_ORIGIN
,
DataType
.
STRING
));
this
.
availableFilters
.
add
(
new
BasicFilter
(
FilterConstants
.
REGION_HOLD_INSTITUTE
,
DataType
.
STRING
));
...
...
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
94d43f60
...
...
@@ -220,6 +220,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
columnList
.
add
(
"geo."
+
Api1Constants
.
Geo
.
LATITUDE_LONGITUDE
);
columnList
.
add
(
"coll."
+
Api1Constants
.
Collecting
.
COLLMISSID
);
columnList
.
add
(
"pdci."
+
Api1Constants
.
Pdci
.
SCORE
);
columnList
.
add
(
Api1Constants
.
Accession
.
DOI
);
availableDisplayColumns
=
Collections
.
unmodifiableList
(
columnList
);
List
<
String
>
displayList
=
new
ArrayList
<
String
>();
...
...
src/main/resources/content/language.properties
View file @
94d43f60
...
...
@@ -431,6 +431,7 @@ filter.lastModifiedDate=Last Modified Date
filter.alias
=
Accession name
filter.crops
=
Crop name
filter.cropName
=
Provided crop name
filter.doi
=
DOI
filter.regionOfOrigin
=
Region of Origin
filter.regionOfHoldingInstitute
=
Region of Holding Institute
filter.orgCty.iso3
=
Country of Origin
...
...
@@ -753,6 +754,7 @@ resolver.resolve=Resolve
resolver.page.reverse.title
=
Resolution results
accession.purl
=
Permanent URL
accession.doi
=
DOI
menu.admin.kpi
=
KPI
admin.kpi.index.page
=
KPI
...
...
src/main/resources/liquibase/liquibase-changeLog.yml
View file @
94d43f60
...
...
@@ -178,3 +178,38 @@ databaseChangeLog:
-
sql
:
comment
:
accountType#SYSTEM to user#sys==1
sql
:
update user set sys = 1 where accountType = 'SYSTEM';
-
changeSet
:
id
:
1497558768000-2
author
:
maxymborodenko (generated)
changes
:
-
addColumn
:
tableName
:
accession
columns
:
-
column
:
name
:
doi
type
:
varchar(255)
-
changeSet
:
id
:
1497558768000-3
author
:
maxymborodenko (generated)
changes
:
-
addUniqueConstraint
:
columnNames
:
doi
constraintName
:
UQ_accession_doi
deferrable
:
true
disabled
:
true
initiallyDeferred
:
true
tableName
:
accession
tablespace
:
A String
-
changeSet
:
id
:
1497558768000-4
author
:
maxymborodenko (generated)
changes
:
-
addColumn
:
tableName
:
accessionhistoric
columns
:
-
column
:
name
:
doi
type
:
varchar(255)
\ No newline at end of file
src/main/webapp/WEB-INF/jsp/accession/details.jsp
View file @
94d43f60
...
...
@@ -341,6 +341,20 @@
</p>
</div>
</div>
<div
class=
"row"
>
<div
class=
"col-lg-6 col-md-6 col-sm-6 col-xs-12"
>
<p>
<spring:message
code=
"accession.doi"
/>
</p>
</div>
<div
class=
"col-lg-6 col-md-6 col-sm-6 col-xs-12"
>
<p
property=
"dc:identifier"
>
<c:if
test=
"
${
(
accession
.
doi
ne
null
)
&&
(
accession
.
doi
ne
''
)
}
"
>
<a
href=
"
<c:url
value=
"https://www.genesys-pgr.org/${accession.doi}"
/>
"
><c:out
value=
"https://www.genesys-pgr.org/${accession.doi}"
/></a>
</c:if>
</p>
</div>
</div>
</c:if>
...
...
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
View file @
94d43f60
...
...
@@ -239,6 +239,18 @@
<c:when
test=
"
${
col
eq
'pdci.score'
}
"
>
<td
class=
"notimportant
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
><p><fmt:formatNumber
value=
"
${
accession
.
pdciScore
}
"
/></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'doi'
}
"
>
<td
class=
"notimportant
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
>
<c:choose>
<c:when
test=
"
${
accession
.
doi
ne
null
}
"
>
<p>
${accession.doi}
</p>
</c:when>
<c:otherwise>
<p></p>
</c:otherwise>
</c:choose>
</td>
</c:when>
<c:otherwise>
<c:set
var=
"elVal"
value=
"
${
accession
}
"
/>
<c:forTokens
items=
"
${
col
}
"
delims=
"."
var=
"item"
>
...
...
@@ -880,6 +892,15 @@
'
class
'
:
"
notimportant
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
}).
appendTo
(
row
))));
</c:when>
<c:when
test=
"
${
col
eq
'doi'
}
"
>
$
(
"
<i/>
"
,
{
text
:
pagedData
.
content
[
i
].
doi
})
.
appendTo
(
$
(
"
<span/>
"
,
{
dir
:
"
ltr
"
,
'
class
'
:
"
sci-name
"
}).
appendTo
(
$
(
"
<p></p>
"
).
appendTo
(
$
(
"
<td/>
"
,
{
'
class
'
:
"
notimportant
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
}).
appendTo
(
row
))));
</c:when>
<c:when
test=
"
${
col
eq
'crops'
}
"
>
var
cropNamesTd
=
$
(
"
<td/>
"
,
{
'
class
'
:
"
notimportant
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
...
...
src/main/webapp/WEB-INF/tags/filters/filter-list.tag
View file @
94d43f60
...
...
@@ -173,4 +173,9 @@
appliedFilters="${appliedFilters}" type="range"/>
</filters:panel>
<filters:panel id="doi" title="filter.doi">
<filters:filter availableFilters="${availableFilters}" filterMap="${filters}" filterKey="doi"
appliedFilters="${appliedFilters}" type="exact"/>
</filters:panel>
</filters:group>
\ No newline at end of file
src/main/webapp/WEB-INF/tags/filters/filter.tag
View file @
94d43f60
...
...
@@ -123,6 +123,16 @@
</span>
</div>
</c:when>
<c:when test="${type eq 'exact'}">
<div class="input-group">
<input id="<c:out value="${normalizedKey}" />_input" class="span2 form-control string-type" />
<span class="input-group-btn">
<button class="btn btn-secondary notimportant filter-auto" type="button" norm-key="<c:out value="${normalizedKey}" />" i-key="<c:out value="${filter.key}" />">
<span class="glyphicon glyphicon-plus"></span>
</button>
</span>
</div>
</c:when>
<c:when test="${type eq 'range'}">
<c:choose>
<c:when test="${filterKey eq 'geo.latitude'}">
...
...
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