sdk/R/.Rbuildignore
sdk/R/ArvadosR.Rproj
*.Rd
+*.asc
centos7|psutil|5.0.1|0|python|all
debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|lockfile|0.12.2|2|python|all|--epoch 1
debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|subprocess32|3.5.1|2|python|all
-all|ruamel.yaml|0.15.77|1|python|amd64|--python-setup-py-arguments --single-version-externally-managed --depends "ruamel.ordereddict >=0.4.9"
+all|ruamel.yaml|0.15.77|1|python|amd64|--python-setup-py-arguments --single-version-externally-managed --depends 'python-ruamel.ordereddict >= 0.4.9'
all|cwltest|1.0.20180518074130|4|python|all|--depends 'python-futures >= 3.0.5' --depends 'python-subprocess32 >= 3.5.0'
all|junit-xml|1.8|3|python|all
all|rdflib-jsonld|0.4.0|2|python|all
package_go_binary tools/keep-exercise keep-exercise \
"Performance testing tool for Arvados Keep"
+
+# we need explicit debian_revision values in the dependencies for ruamel.yaml, because we have a package iteration
+# greater than zero. So we parse setup.py, get the ruamel.yaml dependencies, tell fpm not to automatically include
+# them in the package being built, and re-add them manually with an appropriate debian_revision value.
+# See #14552 for the reason for this (nasty) workaround. We use ${ruamel_depends[@]} in a few places further down
+# in this script.
+# Ward, 2018-11-28
+IFS=', ' read -r -a deps <<< `grep ruamel.yaml $WORKSPACE/sdk/python/setup.py |cut -f 3 -dl |sed -e "s/'//g"`
+declare -a ruamel_depends=()
+for i in ${deps[@]}; do
+ i=`echo "$i" | sed -e 's!\([0-9]\)! \1!'`
+ if [[ $i =~ .*\>.* ]]; then
+ ruamel_depends+=(--depends "python-ruamel.yaml $i-1")
+ elif [[ $i =~ .*\<.* ]]; then
+ ruamel_depends+=(--depends "python-ruamel.yaml $i-9")
+ else
+ echo "Encountered ruamel dependency that I can't parse. Aborting..."
+ exit 1
+ fi
+done
+
+
# The Python SDK
# Please resist the temptation to add --no-python-fix-name to the fpm call here
# (which would remove the python- prefix from the package name), because this
arvados_python_client_version=${ARVADOS_BUILDING_VERSION:-$(awk '($1 == "Version:"){print $2}' $WORKSPACE/sdk/python/arvados_python_client.egg-info/PKG-INFO)}
test_package_presence ${PYTHON2_PKG_PREFIX}-arvados-python-client "$arvados_python_client_version" python
if [[ "$?" == "0" ]]; then
- fpm_build $WORKSPACE/sdk/python "${PYTHON2_PKG_PREFIX}-arvados-python-client" 'Curoverse, Inc.' 'python' "$arvados_python_client_version" "--url=https://arvados.org" "--description=The Arvados Python SDK" --depends "${PYTHON2_PKG_PREFIX}-setuptools" --deb-recommends=git
+
+ fpm_build $WORKSPACE/sdk/python "${PYTHON2_PKG_PREFIX}-arvados-python-client" 'Curoverse, Inc.' 'python' "$arvados_python_client_version" "--url=https://arvados.org" "--description=The Arvados Python SDK" --depends "${PYTHON2_PKG_PREFIX}-setuptools" --deb-recommends=git --python-disable-dependency ruamel.yaml "${ruamel_depends[@]}"
fi
# cwl-runner
fi
test_package_presence ${PYTHON2_PKG_PREFIX}-arvados-cwl-runner "$arvados_cwl_runner_version" python "$arvados_cwl_runner_iteration"
if [[ "$?" == "0" ]]; then
- fpm_build $WORKSPACE/sdk/cwl "${PYTHON2_PKG_PREFIX}-arvados-cwl-runner" 'Curoverse, Inc.' 'python' "$arvados_cwl_runner_version" "--url=https://arvados.org" "--description=The Arvados CWL runner" --depends "${PYTHON2_PKG_PREFIX}-setuptools" --depends "${PYTHON2_PKG_PREFIX}-subprocess32 >= 3.5.0" --depends "${PYTHON2_PKG_PREFIX}-pathlib2" --depends "${PYTHON2_PKG_PREFIX}-scandir" "${iterargs[@]}"
+ fpm_build $WORKSPACE/sdk/cwl "${PYTHON2_PKG_PREFIX}-arvados-cwl-runner" 'Curoverse, Inc.' 'python' "$arvados_cwl_runner_version" "--url=https://arvados.org" "--description=The Arvados CWL runner" --depends "${PYTHON2_PKG_PREFIX}-setuptools" --depends "${PYTHON2_PKG_PREFIX}-subprocess32 >= 3.5.0" --depends "${PYTHON2_PKG_PREFIX}-pathlib2" --depends "${PYTHON2_PKG_PREFIX}-scandir" --python-disable-dependency ruamel.yaml "${ruamel_depends[@]}" "${iterargs[@]}"
fi
# schema_salad. This is a python dependency of arvados-cwl-runner,
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
cwltoolversion=$(cat "$WORKSPACE/sdk/cwl/setup.py" | grep cwltool== | sed "s/.*==\(.*\)'.*/\1/")
-test_package_presence python-cwltool "$cwltoolversion" python 2
+test_package_presence python-cwltool "$cwltoolversion" python 3
if [[ "$?" == "0" ]]; then
- fpm_build cwltool "" "" python $cwltoolversion --iteration 2
+ fpm_build cwltool "" "" python $cwltoolversion --iteration 3 --python-disable-dependency ruamel.yaml "${ruamel_depends[@]}"
fi
# The PAM module
fi
declare $(format_last_commit_here "git_ts=%ct git_hash=%h")
- ARVADOS_BUILDING_VERSION="$(git describe --abbrev=0).$(date -ud "@$git_ts" +%Y%m%d%H%M%S)"
+ ARVADOS_BUILDING_VERSION="$(git tag -l |sort -V -r |head -n1).$(date -ud "@$git_ts" +%Y%m%d%H%M%S)"
echo "$ARVADOS_BUILDING_VERSION"
}
- Working with data sets:
- user/tutorials/tutorial-keep.html.textile.liquid
- user/tutorials/tutorial-keep-get.html.textile.liquid
- - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
- - user/tutorials/tutorial-keep-mount.html.textile.liquid
+ - user/tutorials/tutorial-keep-mount-gnu-linux.html.textile.liquid
+ - user/tutorials/tutorial-keep-mount-os-x.html.textile.liquid
+ - user/tutorials/tutorial-keep-mount-windows.html.textile.liquid
- user/topics/keep.html.textile.liquid
+ - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
- user/topics/arv-copy.html.textile.liquid
- user/topics/storage-classes.html.textile.liquid
- user/topics/collection-versioning.html.textile.liquid
TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
{% endcomment %}
+h3. v1.2.1 (2018-11-26)
+
+There are no special upgrade notes for this release.
+
h3. v1.2.0 (2018-09-05)
h4. Regenerate Postgres table statistics
h3. Usage
-Please refer to the "Mounting Keep as a filesystem":{{site.baseurl}}/user/tutorials/tutorial-keep-mount.html tutorial for more information.
\ No newline at end of file
+Please refer to the "Accessing Keep from GNU/Linux":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html tutorial for more information.
---
layout: default
navsection: userguide
-title: "Mounting Keep as a filesystem"
+title: "Accessing Keep from GNU/Linux"
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-This tutoral describes how to access Arvados collections using traditional filesystem tools by mounting Keep as a file system using @arv-mount@.
+This tutoral describes how to access Arvados collections on GNU/Linux using traditional filesystem tools by mounting Keep as a file system using @arv-mount@.
{% include 'tutorial_expectations' %}
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Accessing Keep from OS X"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+OS X users can browse Keep read-only via WebDAV. Specific collections can also be accessed read-write via WebDAV.
+
+h3. Browsing Keep (read-only)
+
+In Finder, use "Connect to Server..." under the "Go" menu and enter @https://collections.uuid_prefix.your.domain/@ in popup dialog. When prompted for credentials, put a valid Arvados token in the @Password@ field and anything in the Name field (it will be ignored by Arvados).
+
+This mount is read-only. Write support for the @/users/@ directory is planned for a future release.
+
+h3. Accessing a specific collection in Keep (read-write)
+
+In Finder, use "Connect to Server..." under the "Go" menu and enter @https://collections.uuid_prefix.your.domain/@ in popup dialog. When prompted for credentials, put a valid Arvados token in the @Password@ field and anything in the Name field (it will be ignored by Arvados).
+
+This collection is now accessible read/write.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Accessing Keep from Windows"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Windows users can browse Keep read-only via WebDAV. Specific collections can also be accessed read-write via WebDAV.
+
+h3. Browsing Keep (read-only)
+
+Use the 'Map network drive' functionality, and enter @https://collections.uuid_prefix.your.domain/@ in the Folder field. When prompted for credentials, you can fill in an arbitrary string for @Username@, it is ignored by Arvados. Windows will not accept an empty @Username@. Put a valid Arvados token in the @Password@ field.
+
+This mount is read-only. Write support for the @/users/@ directory is planned for a future release.
+
+h3. Accessing a specific collection in Keep (read-write)
+
+Use the 'Map network drive' functionality, and enter @https://collections.uuid_prefix.your.domain/c=your-collection-uuid@ in the Folder field. When prompted for credentials, you can fill in an arbitrary string for @Username@, it is ignored by Arvados. Windows will not accept an empty @Username@. Put a valid token in the @Password@ field.
+
+This collection is now accessible read/write.
exit
end
-git_latest_tag = `git describe --abbrev=0`
+git_latest_tag = `git tag -l |sort -V -r |head -n1`
git_latest_tag = git_latest_tag.encode('utf-8').strip
git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
git_timestamp = Time.at(git_timestamp.to_i).utc
SETUP_DIR = os.path.dirname(__file__) or '.'
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def choose_version_from():
sdk_ts = subprocess.check_output(
from source package), leave it alone.
"""
def git_latest_tag(self):
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag(self):
gitinfo = subprocess.check_output(
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
from source package), leave it alone.
"""
def git_latest_tag(self):
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag(self):
gitinfo = subprocess.check_output(
exit
end
-git_latest_tag = `git describe --abbrev=0`
+git_latest_tag = `git tag -l |sort -V -r |head -n1`
git_latest_tag = git_latest_tag.encode('utf-8').strip
git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
git_timestamp = Time.at(git_timestamp.to_i).utc
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
exit
end
-git_latest_tag = `git describe --abbrev=0`
+git_latest_tag = `git tag -l |sort -V -r |head -n1`
git_latest_tag = git_latest_tag.encode('utf-8').strip
git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
git_timestamp = Time.at(git_timestamp.to_i).utc
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
--- /dev/null
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+=lwu7
+-----END PGP PUBLIC KEY BLOCK-----
VOLUME /var/log/nginx
VOLUME /etc/ssl/private
-RUN apt-key adv --no-tty --keyserver hkp://pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D || \
- apt-key adv --no-tty --keyserver hkp://pgp.mit.edu:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
+ADD 58118E89F3A912897C070ADBF76221572C52609D.asc /tmp/
+RUN apt-key add --no-tty /tmp/58118E89F3A912897C070ADBF76221572C52609D.asc && \
+ rm -f /tmp/58118E89F3A912897C070ADBF76221572C52609D.asc
RUN mkdir -p /etc/apt/sources.list.d && \
echo deb https://apt.dockerproject.org/repo debian-stretch main > /etc/apt/sources.list.d/docker.list && \
import re
def git_latest_tag():
- gitinfo = subprocess.check_output(
- ['git', 'describe', '--abbrev=0']).strip()
- return str(gitinfo.decode('utf-8'))
+ gittags = subprocess.check_output(['git', 'tag', '-l']).split()
+ gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
+ return str(next(iter(gittags)).decode('utf-8'))
def git_timestamp_tag():
gitinfo = subprocess.check_output(
projects / arvados.git / commitdiff