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Genesys PGR
Genesys Backend
Commits
da44b81f
Commit
da44b81f
authored
Oct 14, 2018
by
Matija Obreza
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Plain Diff
Added AccessionFilter#alias support
- alias name must contain at least one word character (number or letter)
parent
b4cb5c55
Changes
6
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6 changed files
with
68 additions
and
14 deletions
+68
-14
src/main/java/org/genesys2/server/model/genesys/AccessionAlias.java
...ava/org/genesys2/server/model/genesys/AccessionAlias.java
+15
-9
src/main/java/org/genesys2/server/service/filter/AccessionFilter.java
...a/org/genesys2/server/service/filter/AccessionFilter.java
+6
-0
src/main/java/org/genesys2/server/service/filter/AppliedFiltersConverter.java
...nesys2/server/service/filter/AppliedFiltersConverter.java
+4
-0
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
...org/genesys2/server/service/worker/AccessionUploader.java
+1
-1
src/main/resources/liquibase/liquibase-changeLog.yml
src/main/resources/liquibase/liquibase-changeLog.yml
+14
-4
src/test/java/org/genesys/test/simpletest/NamesTest.java
src/test/java/org/genesys/test/simpletest/NamesTest.java
+28
-0
No files found.
src/main/java/org/genesys2/server/model/genesys/AccessionAlias.java
View file @
da44b81f
...
...
@@ -45,6 +45,8 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
private
static
final
long
serialVersionUID
=
4990299133164025782L
;
private
static
final
Pattern
HAS_WORD_CHARACTER
=
Pattern
.
compile
(
"\\w"
,
Pattern
.
MULTILINE
);
private
static
Pattern
USED_BY_PATTERN
=
Pattern
.
compile
(
"^((\\p{Alnum}+):(.+))?$"
);
public
static
enum
AliasType
{
...
...
@@ -99,15 +101,19 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
public
AccessionAlias
(
AliasType
aliasType
,
String
name
)
{
this
.
aliasType
=
aliasType
;
Matcher
m
=
USED_BY_PATTERN
.
matcher
(
name
);
if
(
m
.
matches
())
{
this
.
usedBy
=
StringUtils
.
trimToNull
(
m
.
group
(
2
));
this
.
name
=
StringUtils
.
trimToNull
(
m
.
group
(
3
));
}
else
{
if
(
name
.
startsWith
(
":"
))
{
name
=
StringUtils
.
trimToNull
(
name
.
substring
(
1
));
if
(
name
!=
null
)
{
Matcher
m
=
USED_BY_PATTERN
.
matcher
(
name
);
if
(
m
.
matches
())
{
this
.
usedBy
=
StringUtils
.
trimToNull
(
m
.
group
(
2
));
this
.
name
=
StringUtils
.
trimToNull
(
m
.
group
(
3
));
}
else
{
if
(
name
.
startsWith
(
":"
))
{
name
=
StringUtils
.
trimToNull
(
name
.
substring
(
1
));
}
this
.
name
=
name
;
}
this
.
name
=
name
;
}
else
{
this
.
name
=
null
;
}
}
...
...
@@ -167,7 +173,7 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
}
public
boolean
isEmpty
()
{
return
StringUtils
.
isBlank
(
name
);
return
StringUtils
.
isBlank
(
name
)
||
!
HAS_WORD_CHARACTER
.
matcher
(
name
).
find
()
;
}
@Override
...
...
src/main/java/org/genesys2/server/service/filter/AccessionFilter.java
View file @
da44b81f
...
...
@@ -91,6 +91,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
/** acce.lists uuid */
public
Set
<
UUID
>
list
;
/** accession aliases */
public
StringFilter
alias
;
/* (non-Javadoc)
* @see org.genesys.blocks.model.filters.BasicModelFilter#buildQuery()
...
...
@@ -169,6 +172,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
if
(
CollectionUtil
.
isNotEmpty
(
uuid
))
{
and
.
and
(
accession
.
accessionId
.
uuid
.
in
(
uuid
));
}
if
(
alias
!=
null
)
{
and
.
and
(
alias
.
buildQuery
(
accession
.
accessionId
.
aliases
.
any
().
name
));
}
// TODO Do we have to change this?
if
(
sgsv
!=
null
)
{
and
.
and
(
accession
.
accessionId
.
duplSite
.
any
().
eq
(
"NOR051"
));
...
...
src/main/java/org/genesys2/server/service/filter/AppliedFiltersConverter.java
View file @
da44b81f
...
...
@@ -235,6 +235,10 @@ public class AppliedFiltersConverter {
f
.
lastModifiedDate
=
convertDateFilter
(
af
);
break
;
}
case
FilterConstants
.
ALIAS
:
{
f
.
alias
=
convertStringFilter
(
af
);
break
;
}
default
:
throw
new
RuntimeException
(
"Unhandled Accession filter property="
+
filterName
);
}
...
...
src/main/java/org/genesys2/server/service/worker/AccessionUploader.java
View file @
da44b81f
...
...
@@ -409,7 +409,7 @@ public class AccessionUploader implements InitializingBean {
List
<
AccessionRemark
>
toRemove
=
existing
.
stream
().
filter
(
ex
->
ex
==
null
||
ex
.
isEmpty
()
||
remarks
.
stream
().
filter
(
rem
->
ex
.
equalTo
(
rem
)).
count
()
==
0
).
collect
(
Collectors
.
toList
());
if
(!
toRemove
.
isEmpty
()
||
!
toAdd
.
isEmpty
())
{
LOG
.
info
(
"Removing: {} Adding: {}"
,
toRemove
,
toAdd
);
LOG
.
trace
(
"Removing: {} Adding: {}"
,
toRemove
,
toAdd
);
}
existing
.
removeAll
(
toRemove
);
existing
.
addAll
(
toAdd
);
...
...
src/main/resources/liquibase/liquibase-changeLog.yml
View file @
da44b81f
...
...
@@ -4340,12 +4340,22 @@ databaseChangeLog:
join taxonomy2 t2 on a.taxonomyId2 = t2.id;
-
changeSet
:
id
:
1538732843596-5
author
:
vpavlov
comment
:
drop subset_accession
id
:
1538732843596-5
author
:
vpavlov
comment
:
drop subset_accession
changes
:
-
dropTable
:
tableName
:
subset_accession
tableName
:
subset_accession
-
changeSet
:
id
:
1539510451000-1
author
:
mobreza
comment
:
Add index on accession_alias#name
changes
:
-
sql
:
sql
:
>-
CREATE INDEX UK_cus8xep8hi5fv42o3ivu0name ON accession_alias(name(250))
# ENABLE AFTER SOME TIME
# - changeSet:
...
...
src/test/java/org/genesys/test/simpletest/NamesTest.java
View file @
da44b81f
...
...
@@ -16,6 +16,9 @@
package
org.genesys.test.simpletest
;
import
static
org
.
hamcrest
.
CoreMatchers
.*;
import
static
org
.
junit
.
Assert
.
assertThat
;
import
java.util.ArrayList
;
import
java.util.HashSet
;
import
java.util.List
;
...
...
@@ -24,6 +27,8 @@ import java.util.Set;
import
org.apache.commons.lang.ArrayUtils
;
import
org.apache.commons.lang3.StringUtils
;
import
org.genesys.test.base.NoContextTest
;
import
org.genesys2.server.model.genesys.AccessionAlias
;
import
org.genesys2.server.model.genesys.AccessionAlias.AliasType
;
import
org.junit.Test
;
public
class
NamesTest
extends
NoContextTest
{
...
...
@@ -92,4 +97,27 @@ public class NamesTest extends NoContextTest {
}
return
score
;
}
@Test
public
void
testAliasIsBlank
()
{
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
""
).
isEmpty
(),
is
(
true
));
assertThat
(
new
AccessionAlias
(
AliasType
.
OTHERNUMB
,
"-"
).
isEmpty
(),
is
(
true
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
null
).
isEmpty
(),
is
(
true
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"a"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"0"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"Z"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"a0"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"0d"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"Z1"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"aa-"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"00-"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"ZZ-"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"aa-1"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"00-2"
).
isEmpty
(),
is
(
false
));
assertThat
(
new
AccessionAlias
(
AliasType
.
ACCENAME
,
"ZZ-3"
).
isEmpty
(),
is
(
false
));
}
}
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