Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
-[//]: # Copyright (C) The Arvados Authors. All rights reserved.
-[//]: #
-[//]: # SPDX-License-Identifier: CC-BY-SA-3.0
+[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
[Arvados](https://arvados.org) is a free software distributed computing platform
for bioinformatics, data science, and high throughput analysis of massive data
## Community
-The [#arvados](irc://irc.oftc.net:6667/#arvados IRC) (Internet Relay Chat)
+The [#arvados](irc://irc.oftc.net:6667/#arvados) IRC (Internet Relay Chat)
channel at the
[Open and Free Technology Community (irc.oftc.net)](http://www.oftc.net/oftc/)
is available for live discussion and support. You can use a traditional IRC
development. The
[Arvados developer mailing list](http://lists.arvados.org/mailman/listinfo/arvados-dev)
is a forum for more technical discussion, intended for developers and
-contributers to Arvados.
+contributors to Arvados.
## Development
components can be found on the
["Hacking Arvados" page of the Arvados wiki](https://dev.arvados.org/projects/arvados/wiki/Hacking).
+## Contributing
+
+When making a pull request, please ensure *every git commit message* includes a one-line [Developer Certificate of Origin](https://dev.arvados.org/projects/arvados/wiki/Developer_Certificate_Of_Origin). If you have already made commits without it, fix them with `git commit --amend` or `git rebase`.
+
## Licensing
Arvados is Free Software. See COPYING for information about Arvados Free
IFS=$'\n' read -a ignores -r -d $'\000' <.licenseignore || true
result=0
-git ls-files -z ${@} | \
- while read -rd $'\000' fnm
+
+coproc git ls-files -z ${@} </dev/null
+while read -rd $'\000' fnm
+do
+ grepAfter=2
+ grepBefore=0
+ cs=
+ cc=
+ ce=
+ fixer=
+ if [[ ! -f ${fnm} ]] || [[ -L ${fnm} ]] || [[ ! -s ${fnm} ]]
+ then
+ continue
+ fi
+
+ ignore=
+ for pattern in "${ignores[@]}"
do
- grepAfter=2
- grepBefore=0
- cs=
- cc=
- ce=
- fixer=
- if [[ ! -f ${fnm} ]] || [[ -L ${fnm} ]] || [[ ! -s ${fnm} ]]
+ if [[ ${fnm} == ${pattern} ]]
then
- continue
+ ignore=1
fi
+ done
+ if [[ ${ignore} = 1 ]]; then continue; fi
- ignore=
- for pattern in "${ignores[@]}"
- do
- if [[ ${fnm} == ${pattern} ]]
+ case ${fnm} in
+ Makefile | */Makefile \
+ | *.dockerfile | */Dockerfile.* | */Dockerfile | *.dockerignore \
+ | */MANIFEST.in | */fuse.conf | */gitolite.rc \
+ | *.pl | *.pm | *.PL \
+ | *.rb | *.rb.example | *.rake | *.ru \
+ | *.gemspec | */Gemfile | */Rakefile \
+ | services/login-sync/bin/* \
+ | sdk/cli/bin/* \
+ | *.py \
+ | sdk/python/bin/arv-* \
+ | sdk/cwl/bin/* \
+ | services/nodemanager/bin/* \
+ | services/fuse/bin/* \
+ | tools/crunchstat-summary/bin/* \
+ | crunch_scripts/* \
+ | *.yaml | *.yml | *.yml.example | *.cwl \
+ | *.sh | *.service \
+ | */run | */run-service | */restart-dns-server \
+ | */nodemanager/doc/*.cfg \
+ | */nodemanager/tests/fake*.cfg.template \
+ | */nginx.conf \
+ | build/build.list)
+ fixer=fixer
+ cc="#"
+ ;;
+ *.md)
+ fixer=fixer
+ cc="[//]: #"
+ ;;
+ *.rst)
+ fixer=fixer
+ cc=".."
+ ;;
+ *.erb)
+ fixer=fixer
+ cs="<%# "
+ cc=""
+ ce=" %>"
+ ;;
+ *.liquid)
+ fixer=fixer
+ cs=$'{% comment %}\n'
+ cc=""
+ ce=$'\n{% endcomment %}'
+ grepAfter=3
+ grepBefore=1
+ ;;
+ *.textile)
+ fixer=fixer
+ cs="###. "
+ cc="...."
+ ce=
+ ;;
+ *.css)
+ fixer=fixer
+ cs="/* "
+ cc=""
+ ce=" */"
+ ;;
+ *.coffee)
+ fixer=fixer
+ cs="### "
+ cc=""
+ ce=" ###"
+ ;;
+ *.go | *.scss | *.java | *.js)
+ fixer=fixer
+ cc="//"
+ ;;
+ *.sql)
+ fixer=fixer
+ cc="--"
+ ;;
+ *.html | *.svg)
+ fixer=fixer
+ cs="<!-- "
+ cc=""
+ ce=" -->"
+ ;;
+ *)
+ cc="#"
+ hashbang=$(head -n1 ${fnm})
+ if [[ ${hashbang} = "#!/bin/sh" ]] || [[ ${hashbang} = "#!/bin/bash" ]]
then
- ignore=1
- fi
- done
- if [[ ${ignore} = 1 ]]; then continue; fi
-
- case ${fnm} in
- Makefile | */Makefile \
- | *.dockerfile | */Dockerfile.* | */Dockerfile | *.dockerignore \
- | */MANIFEST.in | */fuse.conf | */gitolite.rc \
- | *.pl | *.pm | *.PL \
- | *.rb | *.rb.example | *.rake | *.ru \
- | *.gemspec | */Gemfile | */Rakefile \
- | services/login-sync/bin/* \
- | sdk/cli/bin/* \
- | *.py \
- | sdk/python/bin/arv-* \
- | sdk/cwl/bin/* \
- | services/nodemanager/bin/* \
- | services/fuse/bin/* \
- | tools/crunchstat-summary/bin/* \
- | crunch_scripts/* \
- | *.yaml | *.yml | *.yml.example | *.cwl \
- | *.sh | *.service \
- | */run | */run-service | */restart-dns-server \
- | */nodemanager/doc/*.cfg \
- | */nodemanager/tests/fake*.cfg.template \
- | */nginx.conf \
- | build/build.list)
- fixer=fixer
- cc="#"
- ;;
- *.md)
- fixer=fixer
- cc="[//]: #"
- ;;
- *.rst)
- fixer=fixer
- cc=".."
- ;;
- *.erb)
- fixer=fixer
- cs="<%# "
- cc=""
- ce=" %>"
- ;;
- *.liquid)
- fixer=fixer
- cs=$'{% comment %}\n'
- cc=""
- ce=$'\n{% endcomment %}'
- grepAfter=3
- grepBefore=1
- ;;
- *.textile)
- fixer=fixer
- cs="###. "
- cc="...."
- ce=
- ;;
- *.css)
- fixer=fixer
- cs="/* "
- cc=""
- ce=" */"
- ;;
- *.coffee)
fixer=fixer
- cs="### "
- cc=""
- ce=" ###"
- ;;
- *.go | *.scss | *.java | *.js)
- fixer=fixer
- cc="//"
- ;;
- *.sql)
- fixer=fixer
- cc="--"
- ;;
- *.html | *.svg)
- fixer=fixer
- cs="<!-- "
- cc=""
- ce=" -->"
- ;;
- *)
- cc="#"
- hashbang=$(head -n1 ${fnm})
- if [[ ${hashbang} = "#!/bin/sh" ]] || [[ ${hashbang} = "#!/bin/bash" ]]
- then
- fixer=fixer
- fi
- ;;
- esac
- wantGPL="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
+ fi
+ ;;
+ esac
+ wantGPL="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
${cc}
${cc}${cc:+ }SPDX-License-Identifier: AGPL-3.0${ce}"
- wantApache="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
+ wantApache="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
${cc}
${cc}${cc:+ }SPDX-License-Identifier: Apache-2.0${ce}"
- wantBYSA="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
+ wantBYSA="${cs:-${cc}${cc:+ }}Copyright (C) The Arvados Authors. All rights reserved.
${cc}
${cc}${cc:+ }SPDX-License-Identifier: CC-BY-SA-3.0${ce}"
- found=$(head -n20 "$fnm" | egrep -A${grepAfter} -B${grepBefore} 'Copyright.*Arvados' || true)
- case ${fnm} in
- Makefile | build/* | lib/* | tools/* | apps/* | services/* | sdk/cli/bin/crunch-job)
- want=${wantGPL}
- ;;
- crunch_scripts/* | backports/* | docker/* | sdk/*)
- want=${wantApache}
- ;;
- README.md | doc/*)
- want=${wantBYSA}
- ;;
- *)
- want=
- ;;
- esac
- case "$found" in
- "$wantGPL")
- ;;
- "$wantApache")
- ;;
- "$wantBYSA")
- ;;
- "")
- if [[ -z ${found} ]] && [[ -n ${want} ]] && [[ $fix = true ]] && [[ $fixer != "" ]]
- then
- ${fixer} ${fnm}
- else
- echo "missing copyright notice: $fnm"
- result=1
- fi
- ;;
- *)
- echo "nonstandard copyright notice: $fnm '${found}'"
+ wantBYSAmd="[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)"
+ found=$(head -n20 "$fnm" | egrep -A${grepAfter} -B${grepBefore} 'Copyright.*Arvados' || true)
+ case ${fnm} in
+ Makefile | build/* | lib/* | tools/* | apps/* | services/* | sdk/cli/bin/crunch-job)
+ want=${wantGPL}
+ ;;
+ crunch_scripts/* | backports/* | docker/* | sdk/*)
+ want=${wantApache}
+ ;;
+ doc/*)
+ want=${wantBYSA}
+ ;;
+ README.md)
+ want=${wantBYSAmd}
+ ;;
+ *)
+ want=
+ ;;
+ esac
+ case "$found" in
+ "$wantGPL")
+ ;;
+ "$wantApache")
+ ;;
+ "$wantBYSA")
+ ;;
+ "$wantBYSAmd")
+ ;;
+ "")
+ if [[ -z ${found} ]] && [[ -n ${want} ]] && [[ $fix = true ]] && [[ $fixer != "" ]]
+ then
+ ${fixer} ${fnm}
+ else
+ echo "missing copyright notice: $fnm"
result=1
- ;;
- esac
- done
+ fi
+ ;;
+ *)
+ echo "nonstandard copyright notice: $fnm '${found}'"
+ result=1
+ ;;
+ esac
+done <&${COPROC[0]}
exit $result
hints:
DockerRequirement:
- dockerPull: biodckr/bwa
+ dockerPull: lh3lh3/bwa
-baseCommand: [bwa, mem]
+baseCommand: [mem]
arguments:
- {prefix: "-t", valueFrom: $(runtime.cores)}
if !ok {
return os.ErrNotExist
}
+ if locked[oldinode] {
+ // oldinode cannot become a descendant of itself.
+ return ErrInvalidArgument
+ }
if existing, ok := newdn.inodes[newname]; ok {
// overwriting an existing file or dir
if dn, ok := existing.(*dirnode); ok {
c.Check(err, check.IsNil)
}
+func (s *CollectionFSSuite) TestRenameError(c *check.C) {
+ fs, err := (&Collection{}).FileSystem(s.client, s.kc)
+ c.Assert(err, check.IsNil)
+ err = fs.Mkdir("first", 0755)
+ c.Assert(err, check.IsNil)
+ err = fs.Mkdir("first/second", 0755)
+ c.Assert(err, check.IsNil)
+ f, err := fs.OpenFile("first/second/file", os.O_CREATE|os.O_WRONLY, 0755)
+ c.Assert(err, check.IsNil)
+ f.Write([]byte{1, 2, 3, 4, 5})
+ f.Close()
+ err = fs.Rename("first", "first/second/third")
+ c.Check(err, check.Equals, ErrInvalidArgument)
+ err = fs.Rename("first", "first/third")
+ c.Check(err, check.Equals, ErrInvalidArgument)
+ err = fs.Rename("first/second", "second")
+ c.Check(err, check.IsNil)
+ f, err = fs.OpenFile("second/file", 0, 0)
+ c.Assert(err, check.IsNil)
+ data, err := ioutil.ReadAll(f)
+ c.Check(err, check.IsNil)
+ c.Check(data, check.DeepEquals, []byte{1, 2, 3, 4, 5})
+}
+
func (s *CollectionFSSuite) TestRename(c *check.C) {
fs, err := (&Collection{}).FileSystem(s.client, s.kc)
c.Assert(err, check.IsNil)
cmd: "move newdir0/testfile newdir1/\n",
match: `(?ms).*Moving .* succeeded.*`,
},
+ {
+ path: writePath,
+ cmd: "move newdir1 newdir1/\n",
+ match: `(?ms).*Moving .* failed.*`,
+ },
+ {
+ path: writePath,
+ cmd: "get newdir1/testfile '" + checkfile.Name() + "'\n",
+ match: `(?ms).*succeeded.*`,
+ data: testdata,
+ },
{
path: writePath,
cmd: "put '" + localfile.Name() + "' newdir1/testfile1\n",
projects / arvados.git / commitdiff