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biopet.biopet
Commits
2b1e8173
Commit
2b1e8173
authored
Nov 02, 2016
by
Peter van 't Hof
Browse files
Removed tool
parent
fa92e13a
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-tools/pom.xml
View file @
2b1e8173
...
...
@@ -29,11 +29,6 @@
<artifactId>
BiopetTools
</artifactId>
<dependencies>
<dependency>
<groupId>
com.typesafe.play
</groupId>
<artifactId>
play-ws_2.10
</artifactId>
<version>
2.4.8
</version>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GitlabIssueToJira.scala
deleted
100644 → 0
View file @
fa92e13a
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
play.api.libs.ws.WSRequest
import
play.api.libs.ws.ning.NingWSClient
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration._
import
scala.concurrent.
{
Await
,
Future
}
import
scala.io.Source
/**
* Created by pjvan_thof on 10-10-16.
*/
object
GitlabIssueToJira
extends
ToolCommand
{
case
class
Args
(
gitlabUrl
:
String
=
null
,
gitlabProject
:
String
=
null
,
gitlabToken
:
String
=
null
,
outputFile
:
File
=
null
,
userMappings
:
Option
[
File
]
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
String
](
"gitlabUrl"
)
required
()
maxOccurs
1
valueName
"<url>"
action
{
(
x
,
c
)
=>
c
.
copy
(
gitlabUrl
=
x
)
}
opt
[
String
](
"gitlabProject"
)
required
()
maxOccurs
1
valueName
"<string>"
action
{
(
x
,
c
)
=>
c
.
copy
(
gitlabProject
=
x
)
}
opt
[
String
](
"gitlabToken"
)
required
()
maxOccurs
1
valueName
"<string>"
action
{
(
x
,
c
)
=>
c
.
copy
(
gitlabToken
=
x
)
}
opt
[
File
](
"outputFile"
)
required
()
maxOccurs
1
valueName
"<string>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
opt
[
File
](
"userMappings"
)
required
()
maxOccurs
1
valueName
"<string>"
action
{
(
x
,
c
)
=>
c
.
copy
(
userMappings
=
Some
(
x
))
}
text
"tsv to say which user belong to eachother, 1e column gitlab user, 2e column jira user"
}
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
// Instantiation of the client
// In a real-life application, you would instantiate one, share it everywhere,
// and call wsClient.close() when you're done
val
wsClient
=
NingWSClient
()
val
gitlabIssuesFuture
=
getGitlabIssues
(
cmdArgs
.
gitlabUrl
,
cmdArgs
.
gitlabProject
,
cmdArgs
.
gitlabToken
,
wsClient
)
gitlabIssuesFuture
.
onFailure
{
case
e
=>
throw
e
}
val
gitlabIssues
=
Await
.
result
(
gitlabIssuesFuture
,
Duration
.
Inf
)
println
(
gitlabIssues
.
size
)
println
(
gitlabIssues
.
head
.
issue
(
"author"
))
println
(
gitlabIssues
.
head
.
comments
.
map
(
_
.
keys
))
val
userMappings
=
cmdArgs
.
userMappings
.
map
(
file
=>
Source
.
fromFile
(
file
).
getLines
().
filter
(
_
.
nonEmpty
).
map
(
_
.
split
(
"\t"
,
2
)).
map
(
x
=>
(
x
(
0
),
x
(
1
))).
toMap
).
getOrElse
(
Map
())
val
gitlabUsers
=
(
gitlabIssues
.
map
(
_
.
issue
(
"author"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"username"
).
toString
)
:::
gitlabIssues
.
flatMap
{
x
=>
if
(!
x
.
isInstanceOf
[
Map
[
String
,
Any
]])
None
else
Some
(
x
.
issue
(
"assignee"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"username"
).
toString
)
}).
distinct
gitlabUsers
.
foreach
(
user
=>
require
(
userMappings
.
contains
(
user
),
s
"User $user can't be found"
))
val
issueValues
=
gitlabIssues
.
reverse
.
map
{
gitlabIssue
=>
val
reporter
=
userMappings
(
gitlabIssue
.
issue
(
"author"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"username"
).
toString
)
val
assignee
=
if
(!
gitlabIssue
.
issue
(
"author"
).
isInstanceOf
[
Map
[
String
,
Any
]])
None
else
Some
(
userMappings
(
gitlabIssue
.
issue
(
"author"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"username"
).
toString
))
val
milestone
=
if
(!
gitlabIssue
.
issue
(
"milestone"
).
isInstanceOf
[
Map
[
String
,
Any
]])
None
else
Some
(
gitlabIssue
.
issue
(
"milestone"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"title"
).
toString
)
val
comments
=
gitlabIssue
.
comments
.
map
{
comment
=>
Map
(
"body"
->
comment
(
"body"
),
"author"
->
userMappings
(
comment
(
"author"
).
asInstanceOf
[
Map
[
String
,
Any
]](
"username"
).
toString
),
"created_at"
->
comment
(
"created_at"
)
)
}
val
closedDate
:
Option
[
String
]
=
gitlabIssue
.
issue
(
"state"
)
match
{
case
"closed"
=>
Some
(
comments
.
filter
(
c
=>
c
(
"body"
).
toString
.
contains
(
"Status changed to closed"
)).
last
(
"created_at"
).
toString
)
case
_
=>
None
}
val
commentFields
=
comments
.
zipWithIndex
.
map
{
case
(
comment
,
key
)
=>
s
"comment-$key"
->
s
"${comment("
created_at
")};${comment("
author
")};${comment("
body
")}"
}
toMap
val
fields
=
Map
(
"summary"
->
gitlabIssue
.
issue
(
"title"
),
"description"
->
gitlabIssue
.
issue
(
"description"
),
"reporter"
->
reporter
,
"gitlab_iid"
->
gitlabIssue
.
issue
(
"iid"
),
"gitlab_id"
->
gitlabIssue
.
issue
(
"id"
),
"state"
->
gitlabIssue
.
issue
(
"state"
),
"labels"
->
gitlabIssue
.
issue
(
"labels"
).
asInstanceOf
[
List
[
String
]].
mkString
(
" "
),
"weburl"
->
gitlabIssue
.
issue
(
"web_url"
),
"created"
->
gitlabIssue
.
issue
(
"created_at"
),
"updated_at"
->
gitlabIssue
.
issue
(
"updated_at"
)
)
++
assignee
.
map
(
"assignee"
->
_
)
++
milestone
.
map
(
"milestone"
->
_
)
++
closedDate
.
map
(
"resolution_date"
->
_
)
++
closedDate
.
map
(
x
=>
"resolution"
->
"Done"
)
fields
++
commentFields
}
val
keys
=
issueValues
.
flatMap
(
_
.
keys
).
distinct
val
writer
=
new
PrintWriter
(
cmdArgs
.
outputFile
)
writer
.
println
(
keys
.
mkString
(
","
))
issueValues
.
foreach
{
issue
=>
writer
.
print
(
"\""
+
issue
.
get
(
keys
.
head
).
getOrElse
(
""
).
toString
.
replaceAll
(
"\""
,
"\"\""
)
+
"\""
)
keys
.
tail
.
foreach
{
key
=>
val
value
=
issue
.
get
(
key
).
getOrElse
(
""
).
toString
.
replaceAll
(
"\""
,
"\"\""
)
writer
.
print
(
","
+
(
if
(
value
.
nonEmpty
)
"\""
+
value
+
" \""
else
""
))
}
writer
.
println
}
writer
.
close
()
logger
.
info
(
"Done2"
)
wsClient
.
close
()
logger
.
info
(
"Done3"
)
}
def
getWsrequestJsonToMap
(
request
:
WSRequest
,
body
:
Option
[
String
]
=
None
,
method
:
String
=
"GET"
)
=
{
val
f
=
(
method
,
body
)
match
{
case
(
"POST"
,
Some
(
body
))
=>
request
.
withHeaders
(
"Content-Type"
->
"application/json"
).
post
(
body
)
case
(
"PUT"
,
Some
(
body
))
=>
request
.
withHeaders
(
"Content-Type"
->
"application/json"
).
put
(
body
)
case
(
"GET"
,
None
)
=>
request
.
get
()
case
(
"DELETE"
,
None
)
=>
request
.
delete
()
}
val
r
=
f
.
map
{
wsResponse
=>
if
(
wsResponse
.
status
>=
200
&&
wsResponse
.
status
<=
299
)
ConfigUtils
.
jsonToMap
(
ConfigUtils
.
textToJson
(
wsResponse
.
body
))
else
{
logger
.
error
(
s
"Request gave status ${wsResponse.status}: ${wsResponse.body}"
)
throw
new
IllegalStateException
(
s
"Request gave status ${wsResponse.status}"
)
}
}
r
.
onFailure
{
case
e
=>
throw
new
RuntimeException
(
e
)
}
r
}
case
class
GitlabIssue
(
issue
:
Map
[
String
,
Any
],
comments
:
List
[
Map
[
String
,
Any
]])
def
waitForFuture
[
T
](
future
:
Future
[
T
])
:
T
=
{
Await
.
ready
(
future
,
Duration
.
Inf
)
if
(
future
.
value
.
get
.
isFailure
)
sys
.
exit
(
1
)
Await
.
result
(
future
,
Duration
.
Inf
)
}
def
getGitlabIssues
(
url
:
String
,
project
:
String
,
token
:
String
,
wsClient
:
NingWSClient
,
page
:
Int
=
1
,
perPage
:
Int
=
100
)
:
Future
[
List
[
GitlabIssue
]]
=
{
val
issuesUrl
=
s
"${url}/api/v3/projects/${project.replace("
/
", "
%
2F
")}/issues"
getGitlabPagedOutput
(
issuesUrl
,
token
,
wsClient
,
Map
(
"per_page"
->
"100"
))
.
map
{
issues
=>
issues
.
map
{
issue
=>
//if (issue("user_notes_count") == 0) GitlabIssue(issue, Nil)
GitlabIssue
(
issue
,
waitForFuture
(
getGitlabPagedOutput
(
issuesUrl
+
s
"/${issue("
id
")}/notes"
,
token
,
wsClient
)))
// GitlabIssue(issue, Nil)
}
}
}
def
getGitlabPagedOutput
(
url
:
String
,
token
:
String
,
wsClient
:
NingWSClient
,
queryParams
:
Map
[
String
,
String
]
=
Map
())
:
Future
[
List
[
Map
[
String
,
Any
]]]
=
{
val
f
=
Future
{
val
init
=
wsClient
.
url
(
url
)
.
withHeaders
(
"PRIVATE-TOKEN"
->
token
)
.
withQueryString
(
queryParams
.
toSeq
:
_
*
)
.
get
().
map
{
wsResponse
=>
val
pages
=
wsResponse
.
header
(
"X-Total-Pages"
).
map
(
_
.
toInt
).
getOrElse
(
1
)
val
page1
=
ConfigUtils
.
textToJson
(
wsResponse
.
body
).
array
.
get
.
map
(
ConfigUtils
.
jsonToMap
)
(
page1
,
pages
)
}
val
(
page1
,
pages
)
=
waitForFuture
(
init
)
val
results
=
for
(
i
<-
2
to
pages
)
yield
{
wsClient
.
url
(
url
)
.
withHeaders
(
"PRIVATE-TOKEN"
->
token
)
.
withQueryString
((
queryParams
.
toSeq
:+
(
"page"
->
s
"$i"
))
:
_
*
)
.
get
().
map
{
wsResponse
=>
if
(
wsResponse
.
status
>=
200
&&
wsResponse
.
status
<=
299
)
ConfigUtils
.
textToJson
(
wsResponse
.
body
).
array
.
get
.
map
(
ConfigUtils
.
jsonToMap
)
else
throw
new
IllegalStateException
(
s
"Request gave status ${wsResponse.status}"
)
}
}
results
.
foldLeft
(
page1
)
{
case
(
a
,
b
)
=>
a
++
waitForFuture
(
b
)
}
}
f
.
onFailure
{
case
e
=>
throw
e
}
f
}
}
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