[med-svn] [Git][med-team/nextflow][master] 7 commits: routine-update: New upstream version
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Wed Jun 2 17:17:49 BST 2021
Steffen Möller pushed to branch master at Debian Med / nextflow
Commits:
2cbb03ba by Steffen Moeller at 2021-06-02T17:23:29+02:00
routine-update: New upstream version
- - - - -
d43fd20f by Steffen Moeller at 2021-06-02T17:23:37+02:00
New upstream version 21.04.1+dfsg
- - - - -
71e77a29 by Steffen Moeller at 2021-06-02T17:23:47+02:00
Update upstream source from tag 'upstream/21.04.1+dfsg'
Update to upstream version '21.04.1+dfsg'
with Debian dir 698c44a032a0a96b264ff1c51017e11c30eca1bd
- - - - -
242e3ebe by Steffen Moeller at 2021-06-02T17:23:50+02:00
routine-update: Standards-Version: 4.5.1
- - - - -
16851505 by Steffen Moeller at 2021-06-02T17:23:57+02:00
routine-update: Rules-Requires-Root: no
- - - - -
ced6c240 by Steffen Moeller at 2021-06-02T17:24:19+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
9b1e91bb by Steffen Moeller at 2021-06-02T18:16:18+02:00
Added Pierre as uploader, routine-update, extra clean
- - - - -
16 changed files:
- VERSION
- changelog.txt
- debian/changelog
- debian/control
- debian/rules
- debian/upstream/metadata
- docs/conf.py
- modules/nextflow/src/main/groovy/nextflow/Session.groovy
- modules/nextflow/src/main/groovy/nextflow/trace/TraceFileObserver.groovy
- modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
- modules/nf-commons/src/main/nextflow/Const.groovy
- modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
- nextflow
- nextflow.md5
- nextflow.sha1
- nextflow.sha256
Changes:
=====================================
VERSION
=====================================
@@ -1 +1 @@
-21.04.0
+21.04.1
=====================================
changelog.txt
=====================================
@@ -1,5 +1,10 @@
NEXTFLOW CHANGE-LOG
===================
+21.04.1 [stable] - 14 May 2021
+- Fix nested params file parse #2091
+- Fix Malformed config error reporting #2105
+- Fix Use default opts for trace file creation [09e6c6ac]
+
21.04.0 [stable] - 2 May 2021
- Fix NPE when AWS Batch job container is not returned [412b6fde]
- Fix execution hang when native task fail to submit #2060 [1253485d]
=====================================
debian/changelog
=====================================
@@ -1,5 +1,13 @@
-nextflow (21.04.0+dfsg-1) UNRELEASED; urgency=medium
+nextflow (21.04.1+dfsg-1) UNRELEASED; urgency=medium
+ [ Pierre Gruet ]
* Initial release (Closes: #<bug>)
- -- Pierre Gruet <pgt at debian.org> Mon, 03 May 2021 17:54:42 +0200
+ [ routine-update ]
+ * New upstream version
+ * Standards-Version: 4.5.1
+ * Rules-Requires-Root: no
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+
+ -- Pierre Gruet <pgt at debian.org> Wed, 02 Jun 2021 17:24:27 +0200
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: nextflow
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Steffen Moeller <moeller at debian.org>
+ Steffen Moeller <moeller at debian.org>,
+ Pierre Gruet <pgt at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -26,10 +27,11 @@ Build-Depends: debhelper-compat (= 13),
libswagger-core-java,
libyaml-snake-java,
junit4 <!nocheck>
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/nextflow
Vcs-Git: https://salsa.debian.org/med-team/nextflow.git
Homepage: https://github.com/nextflow-io/nextflow
+Rules-Requires-Root: no
Package: nextflow
Architecture: all
=====================================
debian/rules
=====================================
@@ -23,6 +23,7 @@ include /usr/share/dpkg/default.mk
override_dh_auto_clean:
dh_auto_clean
if [ -e hiddenBuildSrc ]; then mv hiddenBuildSrc buildSrc; fi
+ rm -rf modules/nextflow/build/ modules/nf-httpfs/build/ plugins/nf-console/build/ plugins/nf-ga4gh/build/ plugins/nf-tower/build/
override_dh_auto_configure:
dh_auto_configure
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/nextflow-io/nextflow/issues
+Bug-Submit: https://github.com/nextflow-io/nextflow/issues/new
Reference:
Author: >
Paolo Di Tommaso and Maria Chatzou and Evan W Floden and Pablo Prieto Barja
@@ -12,3 +14,5 @@ Reference:
PMID: 28398311
URL: https://www.nature.com/articles/nbt.3820
eprint: https://www.nature.com/articles/nbt.3820.pdf
+Repository: https://github.com/nextflow-io/nextflow.git
+Repository-Browse: https://github.com/nextflow-io/nextflow
=====================================
docs/conf.py
=====================================
@@ -50,7 +50,7 @@ copyright = u'2020, Seqera Labs. 2013-2019, Centre for Genomic Regulation (CRG).
# The short X.Y version.
version = '21.04'
# The full version, including alpha/beta/rc tags.
-release = '21.04.0'
+release = '21.04.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
=====================================
modules/nextflow/src/main/groovy/nextflow/Session.groovy
=====================================
@@ -1121,10 +1121,13 @@ class Session implements ISession {
private void getContainerConfig0(String engine, List<Map> drivers) {
- def config = this.config?.get(engine) as Map
- if( config ) {
+ def config = this.config?.get(engine)
+ if( config instanceof Map ) {
config.engine = engine
- drivers << config
+ drivers.add((Map)config)
+ }
+ else if( config!=null ) {
+ log.warn "Malformed configuration for container engine '$engine' -- One or more attributes should be provided"
}
}
=====================================
modules/nextflow/src/main/groovy/nextflow/trace/TraceFileObserver.groovy
=====================================
@@ -16,10 +16,10 @@
*/
package nextflow.trace
+
import java.nio.charset.Charset
import java.nio.file.Files
import java.nio.file.Path
-import java.nio.file.StandardOpenOption
import java.util.concurrent.ConcurrentHashMap
import groovy.transform.CompileStatic
@@ -210,7 +210,7 @@ class TraceFileObserver implements TraceObserver {
tracePath.rollFile()
// create a new trace file
- traceFile = new PrintWriter(Files.newBufferedWriter(tracePath, Charset.defaultCharset(), StandardOpenOption.APPEND, StandardOpenOption.CREATE))
+ traceFile = new PrintWriter(Files.newBufferedWriter(tracePath, Charset.defaultCharset()))
// launch the agent
writer = new Agent<PrintWriter>(traceFile)
=====================================
modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
=====================================
@@ -1905,6 +1905,70 @@ class ConfigBuilderTest extends Specification {
then:
cfg2.params.test.foo == "CLI_FOO"
cfg2.params.test.bar == "bar_def"
+
+ cleanup:
+ folder?.deleteDir()
+ }
+
+ def 'parse nested json' () {
+ given:
+ def folder = Files.createTempDirectory('test')
+ and:
+ def config = folder.resolve('nf.json')
+ config.text = '''\
+ {
+ "title": "something",
+ "nested": {
+ "name": "Mike",
+ "and": {
+ "more": "nesting",
+ "still": {
+ "another": "layer"
+ }
+ }
+ }
+ }
+ '''.stripIndent()
+
+ when:
+ def cfg1 = new ConfigBuilder().setCmdRun(new CmdRun(paramsFile: config.toString())).build()
+
+ then:
+ cfg1.params.title == "something"
+ cfg1.params.nested.name == 'Mike'
+ cfg1.params.nested.and.more == 'nesting'
+ cfg1.params.nested.and.still.another == 'layer'
+
+ cleanup:
+ folder?.deleteDir()
+ }
+
+ def 'parse nested yaml' () {
+ given:
+ def folder = Files.createTempDirectory('test')
+ and:
+ def config = folder.resolve('nf.yaml')
+ config.text = '''\
+ title: "something"
+ nested:
+ name: "Mike"
+ and:
+ more: nesting
+ still:
+ another: layer
+ '''.stripIndent()
+
+ when:
+ def cfg1 = new ConfigBuilder().setCmdRun(new CmdRun(paramsFile: config.toString())).build()
+
+ then:
+ cfg1.params.title == "something"
+ cfg1.params.nested.name == 'Mike'
+ cfg1.params.nested.and.more == 'nesting'
+ cfg1.params.nested.and.still.another == 'layer'
+
+ cleanup:
+ folder?.deleteDir()
}
}
=====================================
modules/nf-commons/src/main/nextflow/Const.groovy
=====================================
@@ -53,17 +53,17 @@ class Const {
/**
* The application version
*/
- static public final String APP_VER = "21.04.0"
+ static public final String APP_VER = "21.04.1"
/**
* The app build time as linux/unix timestamp
*/
- static public final long APP_TIMESTAMP = 1619972527591
+ static public final long APP_TIMESTAMP = 1621005654076
/**
* The app build number
*/
- static public final int APP_BUILDNUM = 5552
+ static public final int APP_BUILDNUM = 5556
/**
=====================================
modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
=====================================
@@ -40,7 +40,6 @@ import nextflow.util.RateUnit
import org.apache.commons.lang.StringUtils
import org.codehaus.groovy.runtime.DefaultGroovyMethods
import org.codehaus.groovy.runtime.GStringImpl
-import org.codehaus.groovy.runtime.InvokerHelper
import org.codehaus.groovy.runtime.ResourceGroovyMethods
import org.codehaus.groovy.runtime.StringGroovyMethods
import org.slf4j.Logger
@@ -924,11 +923,13 @@ class Bolts {
}
static <T extends Map> T deepClone(T map) {
- final result = InvokerHelper.invokeMethod(map, 'clone', null)
+ if( map == null)
+ return null
+ final result = map instanceof LinkedHashMap ? new LinkedHashMap<>(map) : new HashMap<>(map)
for( def key : map.keySet() ) {
def value = map.get(key)
if( value instanceof Map ) {
- map.put(key, deepClone(value))
+ result.put(key, deepClone(value))
}
}
return (T)result
=====================================
nextflow
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/env bash
#
-# Copyright 2020, Seqera Labs
+# Copyright 2020-2021, Seqera Labs
# Copyright 2013-2019, Centre for Genomic Regulation (CRG)
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,7 @@
# limitations under the License.
[[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'21.04.0'}
+NXF_VER=${NXF_VER:-'21.04.1'}
NXF_ORG=${NXF_ORG:-'nextflow-io'}
NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
NXF_PROT=${NXF_PROT:-'https'}
=====================================
nextflow.md5
=====================================
@@ -1 +1 @@
-ee93085ad75d912a8a2faaf6ef9e0074
+9a93980292546fea270692a8ad4356aa
=====================================
nextflow.sha1
=====================================
@@ -1 +1 @@
-5b38c1b90c92de074bb81c83baedc1179fd8af9d
+9d530c612699209fb6766a1319cfe4a89268616b
=====================================
nextflow.sha256
=====================================
@@ -1 +1 @@
-9b7d117a108a5340ac4f2571c83382b18ced9d2789a8216825c9ad20b60ca02b
+840ca394237e0f4d9f34642ff77c0ac92361319bcc9d9441f3d99f7b6d48ae7d
View it on GitLab: https://salsa.debian.org/med-team/nextflow/-/compare/f458308efd5a81562af6645116322db77c96620e...9b1e91bbd116e70ef9def8794f351a89cc59bc98
--
View it on GitLab: https://salsa.debian.org/med-team/nextflow/-/compare/f458308efd5a81562af6645116322db77c96620e...9b1e91bbd116e70ef9def8794f351a89cc59bc98
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