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INB
ELIXIR
tools-platform
biotools-git-populous
Commits
39d571fe
Commit
39d571fe
authored
Feb 05, 2020
by
redmitry@list.ru
Browse files
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parent
55790a3a
Changes
3
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pom.xml
View file @
39d571fe
...
...
@@ -60,8 +60,8 @@
<dependencies>
<dependency>
<groupId>
es.bsc.inb.elixir
</groupId>
<artifactId>
openebench
-schema-model
</artifactId>
<version>
1.1.0
</version>
<artifactId>
biotools
-schema-model
</artifactId>
<version>
3.2.0-ext
</version>
</dependency>
<dependency>
<groupId>
org.eclipse
</groupId>
...
...
@@ -93,13 +93,8 @@
<repositories>
<repository>
<id>
biotools-schema-model
</id>
<url>
https://gitlab.bsc.es/inb/elixir/tools-platform/biotools-schema-model/raw/maven
</url>
</repository>
<repository>
<id>
org.eclipse.jgit
</id>
<url>
https://gitlab.bsc.es/inb/maven/jgit-nio/raw/master/
</url>
<id>
inb-bsc-maven
</id>
<url>
https://gitlab.bsc.es/inb/maven/raw/master
</url>
</repository>
</repositories>
...
...
src/main/java/es/bsc/inb/elixir/biotools/git/populous/BiotoolsConverter.java
View file @
39d571fe
...
...
@@ -25,39 +25,39 @@
package
es.bsc.inb.elixir.biotools.git.populous
;
import
es.bsc.inb.elixir.
openebench
.model.AccessibilityType
;
import
es.bsc.inb.elixir.
openebench
.model.CostType
;
import
es.bsc.inb.elixir.
openebench
.model.Credit
;
import
es.bsc.inb.elixir.
openebench
.model.DataType
;
import
es.bsc.inb.elixir.
openebench
.model.Documentation
;
import
es.bsc.inb.elixir.
openebench
.model.DocumentationType
;
import
es.bsc.inb.elixir.
openebench
.model.Download
;
import
es.bsc.inb.elixir.
openebench
.model.DownloadType
;
import
es.bsc.inb.elixir.
openebench
.model.EDAMdata
;
import
es.bsc.inb.elixir.
openebench
.model.EDAMformat
;
import
es.bsc.inb.elixir.
openebench
.model.ElixirNode
;
import
es.bsc.inb.elixir.
openebench
.model.ElixirPlatform
;
import
es.bsc.inb.elixir.
openebench
.model.EntityType
;
import
es.bsc.inb.elixir.
openebench
.model.ExternalId
;
import
es.bsc.inb.elixir.
openebench
.model.ExternalIdType
;
import
es.bsc.inb.elixir.
openebench
.model.Function
;
import
es.bsc.inb.elixir.
openebench
.model.Input
;
import
es.bsc.inb.elixir.
openebench
.model.Labels
;
import
es.bsc.inb.elixir.
openebench
.model.LanguageType
;
import
es.bsc.inb.elixir.
openebench
.model.LicenseType
;
import
es.bsc.inb.elixir.
openebench
.model.Link
;
import
es.bsc.inb.elixir.
openebench
.model.MaturityType
;
import
es.bsc.inb.elixir.
openebench
.model.OperatingSystemType
;
import
es.bsc.inb.elixir.
openebench
.model.Operation
;
import
es.bsc.inb.elixir.
openebench
.model.Output
;
import
es.bsc.inb.elixir.
openebench
.model.Publication
;
import
es.bsc.inb.elixir.
openebench
.model.PublicationType
;
import
es.bsc.inb.elixir.
openebench
.model.RoleType
;
import
es.bsc.inb.elixir.
openebench
.model.Summary
;
import
es.bsc.inb.elixir.
openebench
.model.Tool
;
import
es.bsc.inb.elixir.
openebench
.model.ToolLinkType
;
import
es.bsc.inb.elixir.
openebench
.model.ToolType
;
import
es.bsc.inb.elixir.
openebench
.model.Topic
;
import
es.bsc.inb.elixir.
biotools
.model.AccessibilityType
;
import
es.bsc.inb.elixir.
biotools
.model.CostType
;
import
es.bsc.inb.elixir.
biotools
.model.Credit
;
import
es.bsc.inb.elixir.
biotools
.model.DataType
;
import
es.bsc.inb.elixir.
biotools
.model.Documentation
;
import
es.bsc.inb.elixir.
biotools
.model.DocumentationType
;
import
es.bsc.inb.elixir.
biotools
.model.Download
;
import
es.bsc.inb.elixir.
biotools
.model.DownloadType
;
import
es.bsc.inb.elixir.
biotools
.model.EDAMdata
;
import
es.bsc.inb.elixir.
biotools
.model.EDAMformat
;
import
es.bsc.inb.elixir.
biotools
.model.ElixirNode
;
import
es.bsc.inb.elixir.
biotools
.model.ElixirPlatform
;
import
es.bsc.inb.elixir.
biotools
.model.EntityType
;
import
es.bsc.inb.elixir.
biotools
.model.ExternalId
;
import
es.bsc.inb.elixir.
biotools
.model.ExternalIdType
;
import
es.bsc.inb.elixir.
biotools
.model.Function
;
import
es.bsc.inb.elixir.
biotools
.model.Input
;
import
es.bsc.inb.elixir.
biotools
.model.Labels
;
import
es.bsc.inb.elixir.
biotools
.model.LanguageType
;
import
es.bsc.inb.elixir.
biotools
.model.LicenseType
;
import
es.bsc.inb.elixir.
biotools
.model.Link
;
import
es.bsc.inb.elixir.
biotools
.model.MaturityType
;
import
es.bsc.inb.elixir.
biotools
.model.OperatingSystemType
;
import
es.bsc.inb.elixir.
biotools
.model.Operation
;
import
es.bsc.inb.elixir.
biotools
.model.Output
;
import
es.bsc.inb.elixir.
biotools
.model.Publication
;
import
es.bsc.inb.elixir.
biotools
.model.PublicationType
;
import
es.bsc.inb.elixir.
biotools
.model.RoleType
;
import
es.bsc.inb.elixir.
biotools
.model.Summary
;
import
es.bsc.inb.elixir.
biotools
.model.Tool
;
import
es.bsc.inb.elixir.
biotools
.model.ToolLinkType
;
import
es.bsc.inb.elixir.
biotools
.model.ToolType
;
import
es.bsc.inb.elixir.
biotools
.model.Topic
;
import
java.time.ZonedDateTime
;
import
java.time.format.DateTimeParseException
;
import
java.util.ArrayList
;
...
...
src/main/java/es/bsc/inb/elixir/biotools/git/populous/Main.java
View file @
39d571fe
...
...
@@ -27,7 +27,7 @@ package es.bsc.inb.elixir.biotools.git.populous;
import
com.google.common.jimfs.Configuration
;
import
com.google.common.jimfs.Jimfs
;
import
es.bsc.inb.elixir.
openebench
.model.Tool
;
import
es.bsc.inb.elixir.
biotools
.model.Tool
;
import
java.io.IOException
;
import
java.io.Writer
;
import
java.nio.file.FileSystem
;
...
...
@@ -43,6 +43,8 @@ import java.util.logging.Logger;
import
javax.json.JsonObject
;
import
javax.json.bind.Jsonb
;
import
javax.json.bind.JsonbBuilder
;
import
javax.json.bind.JsonbConfig
;
import
javax.json.bind.config.PropertyOrderStrategy
;
import
org.eclipse.jgit.api.Git
;
import
org.eclipse.jgit.api.errors.GitAPIException
;
import
org.eclipse.jgit.transport.UsernamePasswordCredentialsProvider
;
...
...
@@ -85,7 +87,7 @@ public class Main {
final
List
<
String
>
path
=
params
.
get
(
"--path"
);
final
List
<
String
>
suffix
=
params
.
get
(
"--suffix"
);
final
String
sfx
=
suffix
==
null
||
suffix
.
isEmpty
()
?
".o
p
eb.json"
:
suffix
.
get
(
0
);
final
String
sfx
=
suffix
==
null
||
suffix
.
isEmpty
()
?
".oeb.json"
:
suffix
.
get
(
0
);
List
<
String
>
user
=
params
.
get
(
"-u"
);
if
(
user
==
null
)
{
...
...
@@ -140,7 +142,9 @@ public class Main {
.
setCredentialsProvider
(
new
UsernamePasswordCredentialsProvider
(
user
,
password
))
.
call
())
{
final
Jsonb
jsonb
=
JsonbBuilder
.
create
();
final
Jsonb
jsonb
=
JsonbBuilder
.
create
(
new
JsonbConfig
().
withPropertyOrderStrategy
(
PropertyOrderStrategy
.
LEXICOGRAPHICAL
)
.
withFormatting
(
true
));
final
BiotoolsRepositoryIterator
iter
=
new
BiotoolsRepositoryIterator
();
while
(
iter
.
hasNext
())
{
...
...
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