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Genesys PGR
Genesys Backend
Commits
ab21b45e
Commit
ab21b45e
authored
May 16, 2017
by
Matija Obreza
1
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Display of latin names updated
parent
01f7cfc1
Changes
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10 changed files
with
71 additions
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42 deletions
+71
-42
src/main/java/org/genesys2/server/model/elastic/Taxonomy.java
...main/java/org/genesys2/server/model/elastic/Taxonomy.java
+11
-0
src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java
...ain/java/org/genesys2/server/model/genesys/Taxonomy2.java
+18
-0
src/main/sourceapp/1/styles/genesys.scss
src/main/sourceapp/1/styles/genesys.scss
+0
-2
src/main/webapp/WEB-INF/jsp/accession/details.jsp
src/main/webapp/WEB-INF/jsp/accession/details.jsp
+5
-5
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
+23
-22
src/main/webapp/WEB-INF/jsp/accession/overview.jsp
src/main/webapp/WEB-INF/jsp/accession/overview.jsp
+7
-6
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
+1
-1
src/main/webapp/WEB-INF/jsp/resolver/reverse.jsp
src/main/webapp/WEB-INF/jsp/resolver/reverse.jsp
+1
-1
src/main/webapp/WEB-INF/jsp/wiews/details.jsp
src/main/webapp/WEB-INF/jsp/wiews/details.jsp
+2
-2
src/main/webapp/WEB-INF/tags/term-result.tag
src/main/webapp/WEB-INF/tags/term-result.tag
+3
-3
No files found.
src/main/java/org/genesys2/server/model/elastic/Taxonomy.java
View file @
ab21b45e
...
...
@@ -9,6 +9,8 @@ import org.springframework.data.elasticsearch.annotations.FieldType;
public
class
Taxonomy
{
private
String
sciName
;
private
String
sciNameHtml
;
@Field
(
index
=
FieldIndex
.
not_analyzed
,
type
=
FieldType
.
String
)
private
String
genus
;
@Field
(
index
=
FieldIndex
.
not_analyzed
,
type
=
FieldType
.
String
)
...
...
@@ -29,6 +31,7 @@ public class Taxonomy {
}
Taxonomy
t
=
new
Taxonomy
();
t
.
sciName
=
taxonomy
.
getTaxonName
();
t
.
sciNameHtml
=
taxonomy
.
getTaxonNameHtml
();
t
.
genus
=
taxonomy
.
getGenus
();
t
.
species
=
taxonomy
.
getSpecies
();
t
.
genusSpecies
=
taxonomy
.
getGenus
()
+
" "
+
taxonomy
.
getSpecies
();
...
...
@@ -45,6 +48,14 @@ public class Taxonomy {
public
void
setSciName
(
String
sciName
)
{
this
.
sciName
=
sciName
;
}
public
String
getSciNameHtml
()
{
return
sciNameHtml
;
}
public
void
setSciNameHtml
(
String
sciNameHtml
)
{
this
.
sciNameHtml
=
sciNameHtml
;
}
public
String
getGenus
()
{
return
genus
;
...
...
src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java
View file @
ab21b45e
...
...
@@ -27,6 +27,7 @@ import javax.persistence.Lob;
import
javax.persistence.OneToMany
;
import
javax.persistence.PrePersist
;
import
javax.persistence.Table
;
import
javax.persistence.Transient
;
import
javax.persistence.UniqueConstraint
;
import
org.apache.commons.lang.StringUtils
;
...
...
@@ -122,6 +123,23 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
}
return
sb
.
toString
();
}
@Transient
public
String
getTaxonNameHtml
()
{
final
StringBuilder
sb
=
new
StringBuilder
();
sb
.
append
(
"<i>"
).
append
(
genus
).
append
(
" "
).
append
(
species
).
append
(
"</i>"
);
if
(
StringUtils
.
isNotBlank
(
spAuthor
))
{
sb
.
append
(
" "
).
append
(
spAuthor
);
}
if
(
StringUtils
.
isNotBlank
(
subtaxa
))
{
sb
.
append
(
" <i>"
).
append
(
subtaxa
).
append
(
"</i>"
);
}
if
(
StringUtils
.
isNotBlank
(
subtAuthor
))
{
sb
.
append
(
" "
).
append
(
subtAuthor
);
}
return
sb
.
toString
();
}
public
void
setTaxonName
(
String
taxonName
)
{
// Ignore what they provide
...
...
src/main/sourceapp/1/styles/genesys.scss
View file @
ab21b45e
...
...
@@ -2567,7 +2567,6 @@ table.accessions {
font-family
:
$default-font-family
;
font-size
:
12px
;
.sci-name
{
font-style
:
italic
;
direction
:
ltr
;
}
thead
tr
{
...
...
@@ -2781,7 +2780,6 @@ table.accessions {
span
{
display
:
inline
;
&
.sci-name
{
font-style
:
italic
;
direction
:
ltr
;
}
}
...
...
src/main/webapp/WEB-INF/jsp/accession/details.jsp
View file @
ab21b45e
...
...
@@ -120,7 +120,7 @@
<div
class=
"col-lg-6 col-md-6 col-sm-6 col-xs-12"
property=
"dwc:genus"
>
<p>
<a
href=
"
<c:url
value=
"/acn/t/${accession.taxonomy.genus}"
/>
"
><span
dir=
"ltr"
class=
"sci-name"
>
<
c:out
value=
"
${
accession
.
taxonomy
.
genus
}
"
/
>
<
i><c:out
value=
"
${
accession
.
taxonomy
.
genus
}
"
/></i
>
</span></a>
</p>
</div>
...
...
@@ -134,9 +134,9 @@
<div
class=
"col-lg-6 col-md-6 col-sm-6 col-xs-12"
>
<p>
<a
href=
"
<c:url
value=
"/acn/t/${accession.taxonomy.genus}/${accession.taxonomy.species}"
/>
"
><span
class=
"sci-name"
dir=
"ltr"
>
<
c:out
value=
"
${
accession
.
taxonomy
.
genus
}
${accession.taxonomy.species}"
/
>
</span></a>
—
<a
href=
"
<c:url
value=
"/wiews/${accession.institute.code}/t/${accession.taxonomy.genus}/${accession.taxonomy.species}"
/>
"
><spring:message
code=
"accession.taxonomy-at-institute"
arguments=
"
${
accession
.
taxonomy
.
genus
}
${accession.taxonomy.species}
|||${accession.institute.code}"
argumentSeparator=
"|||"
/></a>
<
i><c:out
value=
"
${
accession
.
taxonomy
.
genus
}
${accession.taxonomy.species}"
/></i
>
</span></a>
—
<a
href=
"
<c:url
value=
"/wiews/${accession.institute.code}/t/${accession.taxonomy.genus}/${accession.taxonomy.species}"
/>
"
><spring:message
code=
"accession.taxonomy-at-institute"
htmlEscape=
"false"
arguments=
"
<i>${accession.taxonomy.genus} ${accession.taxonomy.species}</i>
|||${accession.institute.code}"
argumentSeparator=
"|||"
/></a>
</p>
</div>
</div>
...
...
@@ -150,7 +150,7 @@
<div
class=
"col-lg-6 col-md-6 col-sm-6 col-xs-12"
>
<p>
<span
dir=
"ltr"
class=
"sci-name"
>
<c:out
value=
"
${
accession
.
taxonomy
.
taxonName
}
"
/>
<c:out
escapeXml=
"false"
value=
"
${
accession
.
taxonomy
.
taxonNameHtml
}
"
/>
</span>
</p>
</div>
...
...
src/main/webapp/WEB-INF/jsp/accession/explore2.jsp
View file @
ab21b45e
...
...
@@ -196,7 +196,7 @@
<c:forEach
items=
"
${
selectedColumns
}
"
var=
"col"
varStatus=
"i"
>
<c:choose>
<c:when
test=
"
${
col
eq
'taxonomy.sciName'
}
"
>
<td
class=
"
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
><p><span
dir=
"ltr"
class=
"sci-name"
><c:out
value=
"
${
accession
.
taxonomy
.
sciName
}
"
/></span></p></td>
<td
class=
"
<c:if
test=
'
${
i
.
count
ge
2
}
'
>
hidden-xs
</c:if>
<c:if
test=
'
${
i
.
count
gt
2
}
'
>
hidden-sm
</c:if>
"
><p><span
dir=
"ltr"
class=
"sci-name"
><c:out
escapeXml=
"false"
value=
"
${
accession
.
taxonomy
.
sciNameHtml
}
"
/></span></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'orgCty'
}
"
>
<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><c:out
value=
"
${
jspHelper
.
getCountry
(
accession
.
orgCty
.
iso3
).
getName
(
pageContext
.
response
.
locale
)
}
"
/></p></td>
...
...
@@ -218,13 +218,13 @@
value=
"
${
accession
.
institute
.
code
}
"
/></a></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.genus'
}
"
>
<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><span
dir=
"ltr"
class=
"sci-name"
><
c:out
value=
"
${
accession
.
taxonomy
.
genus
}
"
/
></span></p></td>
<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><span
dir=
"ltr"
class=
"sci-name"
><
i><c:out
value=
"
${
accession
.
taxonomy
.
genus
}
"
/></i
></span></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.species'
}
"
>
<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><span
dir=
"ltr"
class=
"sci-name"
><
c:out
value=
"
${
accession
.
taxonomy
.
species
}
"
/
></span></p></td>
<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><span
dir=
"ltr"
class=
"sci-name"
><
i><c:out
value=
"
${
accession
.
taxonomy
.
species
}
"
/></i
></span></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.subtaxa'
}
"
>
<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><span
dir=
"ltr"
class=
"sci-name"
><
c:out
value=
"
${
accession
.
taxonomy
.
subtaxa
}
"
/
></span></p></td>
<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><span
dir=
"ltr"
class=
"sci-name"
><
i><c:out
value=
"
${
accession
.
taxonomy
.
subtaxa
}
"
/></i
></span></p></td>
</c:when>
<c:when
test=
"
${
col
eq
'crops'
}
"
>
<c:if
test=
"
${
fn:
length
(
accession
.
crops
)
==
0
}
"
>
...
...
@@ -762,8 +762,9 @@
$
(
"
<span/>
"
,
{
dir
:
'
ltr
'
,
'
class
'
:
'
sci-name
'
,
text
:
pagedData
.
content
[
i
].
taxonomy
.
sciName
}).
appendTo
(
$
(
"
<p></p>
"
).
appendTo
(
$
(
"
<td class='
<c:if
test=
"
${
i
.
count
ge
2
}
"
>
hidden-xs
</c:if>
<c:if
test=
"
${
i
.
count
gt
2
}
"
>
hidden-sm
</c:if>
'></td>
"
).
appendTo
(
row
)));
html
:
pagedData
.
content
[
i
].
taxonomy
.
sciNameHtml
}).
appendTo
(
$
(
"
<p></p>
"
).
appendTo
(
$
(
"
<td class='
<c:if
test=
"
${
i
.
count
ge
2
}
"
>
hidden-xs
</c:if>
<c:if
test=
"
${
i
.
count
gt
2
}
"
>
hidden-sm
</c:if>
'></td>
"
)
.
appendTo
(
row
)));
</c:when>
<c:when
test=
"
${
col
eq
'orgCty'
}
"
>
$
(
"
<p/>
"
,
{
...
...
@@ -802,31 +803,31 @@
}).
appendTo
(
row
)));
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.genus'
}
"
>
$
(
"
<span/>
"
,
{
$
(
"
<i/>
"
,
{
text
:
pagedData
.
content
[
i
].
taxonomy
.
genus
})
.
appendTo
(
$
(
"
<span/>
"
,
{
dir
:
"
ltr
"
,
'
class
'
:
"
sci-name
"
,
text
:
pagedData
.
content
[
i
].
taxonomy
.
genus
'
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
)));
}).
appendTo
(
row
)))
)
;
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.species'
}
"
>
$
(
"
<span/>
"
,
{
dir
:
"
ltr
"
,
'
class
'
:
"
sci-name
"
,
text
:
pagedData
.
content
[
i
].
taxonomy
.
species
}).
appendTo
(
$
(
"
<p></p>
"
).
appendTo
(
$
(
"
<td/>
"
,
{
$
(
"
<i/>
"
,
{
text
:
pagedData
.
content
[
i
].
taxonomy
.
species
})
.
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
)));
}).
appendTo
(
row
)))
)
;
</c:when>
<c:when
test=
"
${
col
eq
'taxonomy.subtaxa'
}
"
>
$
(
"
<span/>
"
,
{
dir
:
"
ltr
"
,
'
class
'
:
"
sci-name
"
,
text
:
pagedData
.
content
[
i
].
taxonomy
.
subtaxa
}).
appendTo
(
$
(
"
<p></p>
"
).
appendTo
(
$
(
"
<td/>
"
,
{
$
(
"
<i/>
"
,
{
text
:
pagedData
.
content
[
i
].
taxonomy
.
subtaxa
})
.
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
)));
}).
appendTo
(
row
)))
)
;
</c:when>
<c:when
test=
"
${
col
eq
'crops'
}
"
>
var
cropNamesTd
=
$
(
"
<td/>
"
,
{
...
...
src/main/webapp/WEB-INF/jsp/accession/overview.jsp
View file @
ab21b45e
...
...
@@ -483,22 +483,23 @@
}
case
"
genus
"
:
{
$
(
"
<
a />
"
,
{
href
:
"
/acn/t/
"
+
terms
[
i
].
term
,
text
:
terms
[
i
].
term
}).
appendTo
(
divText
);
$
(
"
<
i />
"
,
{
text
:
terms
[
i
].
term
})
.
appendTo
(
$
(
"
<a />
"
,
{
href
:
"
/acn/t/
"
+
terms
[
i
].
term
})
)
.
appendTo
(
divText
);
break
;
}
case
"
species
"
:
{
span
.
text
(
terms
[
i
].
term
).
appendTo
(
divText
);
$
(
"
<i />
"
,
{
text
:
terms
[
i
].
term
}
).
appendTo
(
divText
);
break
;
}
default
:
{
if
(
type
.
startsWith
(
'
i18n
'
))
{
var
key
=
type
.
substring
(
5
)
+
'
.
'
+
terms
[
i
].
term
;
span
.
addClass
(
"
sci-name
"
).
text
(
messages
[
key
]).
appendTo
(
divText
);
$
(
"
<span />
"
,
{
text
:
messages
[
key
]
})
.
appendTo
(
divText
);
}
else
{
span
.
text
(
terms
[
i
].
term
).
appendTo
(
divText
);
...
...
src/main/webapp/WEB-INF/jsp/metadata/view.jsp
View file @
ab21b45e
...
...
@@ -127,7 +127,7 @@
<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}" />"><c:out value="${accession.countryOfOrigin.getName(pageContext.response.locale)}" /></a></td>
--%>
<td><span
dir=
"ltr"
class=
"sci-name"
><c:out
value=
"
${
accession
.
taxonomy
.
taxonName
}
"
/></span></td>
<td><span
dir=
"ltr"
class=
"sci-name"
><c:out
escapeXml=
"false"
value=
"
${
accession
.
taxonomy
.
taxonNameHtml
}
"
/></span></td>
<%-- <td><a href="<c:url value="/wiews/${accession.institute.code}" />"><c:out value="${accession.institute.code}" /></a></td>
<td><a href="<c:url value="/geo/${accession.institute.country.code3}" />"><c:out value="${accession.institute.country.getName(pageContext.response.locale)}" /></a></td>
--%>
...
...
src/main/webapp/WEB-INF/jsp/resolver/reverse.jsp
View file @
ab21b45e
...
...
@@ -39,7 +39,7 @@
</c:choose>
</div>
<div
class=
"col-sm-4"
>
<span
dir=
"ltr"
class=
"sci-name text-clip"
><c:out
value=
"
${
accession
.
taxonomy
.
taxonName
}
"
/></span>
<span
dir=
"ltr"
class=
"sci-name text-clip"
><c:out
escapeXml=
"false"
value=
"
${
accession
.
taxonomy
.
taxonNameHtml
}
"
/></span>
</div>
<div
class=
"col-sm-4"
>
<a
href=
"https://purl.org/germplasm/id/${accession.uuid}"
><c:out
value=
"
${
accession
.
uuid
}
"
/></a>
...
...
src/main/webapp/WEB-INF/jsp/wiews/details.jsp
View file @
ab21b45e
...
...
@@ -387,7 +387,7 @@
<div
class=
"col-lg-8 col-md-6 col-sm-6 col-xs-6 ${status.count % 2 == 0 ? 'even' : 'odd'}"
>
<%-- <span class="index-number">${status.count + pagedData.size * pagedData.number}</span> --%>
<a
title=
"
<spring:message
code=
"faoInstitute.link-species-data"
arguments=
"
${
faoInstitute
.
fullName
}
|${faoInstitute.acronym}|${stat[0]}"
argumentSeparator=
"|"
/>
"
href=
"
<c:url
value=
"/wiews/${faoInstitute.code}/t/${stat[0]}"
/>
"
>
<span
dir=
"ltr"
class=
"sci-name"
><
c:out
value=
"
${
stat
[
0
]
}
"
/
></span>
<span
dir=
"ltr"
class=
"sci-name"
><
i><c:out
value=
"
${
stat
[
0
]
}
"
/></i
></span>
</a>
</div>
<div
class=
"col-lg-4 col-md-6 col-sm-6 col-xs-6 ${status.count % 2 == 0 ? 'even' : 'odd'}"
>
...
...
@@ -416,7 +416,7 @@
<%-- <span class="index-number">${status.count + pagedData.size * pagedData.number}</span> --%>
<a
title=
"
<spring:message
code=
"faoInstitute.link-species-data"
arguments=
"
${
faoInstitute
.
fullName
}
|${faoInstitute.acronym}|${stat[0].genus} ${stat[0].species}"
argumentSeparator=
"|"
/>
"
href=
"
<c:url
value=
"/wiews/${faoInstitute.code}/t/${stat[0].genus}/${stat[0].species}"
/>
"
>
<span
dir=
"ltr"
class=
"sci-name"
>
<c:out
value=
"
${
stat
[
0
].
taxonName
}
"
/>
<c:out
escapeXml=
"false"
value=
"
${
stat
[
0
].
taxonNameHtml
}
"
/>
</span>
</a>
</div>
...
...
src/main/webapp/WEB-INF/tags/term-result.tag
View file @
ab21b45e
...
...
@@ -39,13 +39,13 @@
<spring:message code="boolean.false" />
</c:when>
<c:when test="${type ne null && type.startsWith('i18n')}">
<span
class="sci-name"
><spring:message code="${type.substring(5).concat('.').concat(term.term)}" /></span>
<span><spring:message code="${type.substring(5).concat('.').concat(term.term)}" /></span>
</c:when>
<c:when test="${type=='genus'}">
<a href="<c:url value="/acn/t/${term.term}" />"><span dir="ltr" class="sci-name" ><
c:out value="${term.term}" /
></span></a>
<a href="<c:url value="/acn/t/${term.term}" />"><span dir="ltr" class="sci-name" ><
i><c:out value="${term.term}" /></i
></span></a>
</c:when>
<c:when test="${type=='species'}">
<span dir="ltr" class="sci-name" ><
c:out value="${term.term}" /
></span>
<span dir="ltr" class="sci-name" ><
i><c:out value="${term.term}" /></i
></span>
</c:when>
<c:otherwise><c:out value="${term.term}" /></c:otherwise>
</c:choose>
...
...
Matija Obreza
@mobreza
mentioned in issue
#34 (closed)
·
May 16, 2017
mentioned in issue
#34 (closed)
mentioned in issue #34
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