[ARVADOS] updated: 1.2.0-457-gf9038f303
Git user
git at public.curoverse.com
Wed Nov 28 22:57:30 EST 2018
Summary of changes:
.licenseignore | 1 +
build/run-build-packages.sh | 31 +++++-
.../58118E89F3A912897C070ADBF76221572C52609D.asc | 106 +++++++++++++++++++++
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 5 +-
4 files changed, 137 insertions(+), 6 deletions(-)
create mode 100644 tools/arvbox/lib/arvbox/docker/58118E89F3A912897C070ADBF76221572C52609D.asc
via f9038f303e54dd99e87e99f9631a9097cc93e591 (commit)
via afaca89ea95ab66f770ea5e878875eca11dc1c9b (commit)
from 1b183250a9d496cebe189360f7e0c867be0ca62d (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit f9038f303e54dd99e87e99f9631a9097cc93e591
Author: Ward Vandewege <wvandewege at veritasgenetics.com>
Date: Wed Nov 28 22:23:34 2018 -0500
Work around ruamel.yaml packaging issue.
closes #14552
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege at veritasgenetics.com>
diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index fe01e4b2e..73e2e6286 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -327,6 +327,28 @@ package_go_binary tools/keep-rsync keep-rsync \
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 $i-9")
+ else
+ echo "Encountered ruamel dependency that I can't parse. Aborting..."
+ exit 1
+ fi
+done
+
+
# The Python SDK
# Please resist the temptation to add --no-python-fix-name to the fpm call here
# (which would remove the python- prefix from the package name), because this
@@ -339,7 +361,8 @@ rm -rf "$WORKSPACE/sdk/python/build"
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
@@ -355,7 +378,7 @@ else
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[@]}" "${iterargs[@]}"
fi
# schema_salad. This is a python dependency of arvados-cwl-runner,
@@ -381,9 +404,9 @@ fi
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
cwltoolversion=$(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
commit afaca89ea95ab66f770ea5e878875eca11dc1c9b
Author: Ward Vandewege <wvandewege at veritasgenetics.com>
Date: Wed Nov 28 15:12:19 2018 -0500
Stop relying on the keyservers during arvbox docker image build, they are too
unreliable.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege at veritasgenetics.com>
diff --git a/.licenseignore b/.licenseignore
index ba4c2dc38..83c81b2fc 100644
--- a/.licenseignore
+++ b/.licenseignore
@@ -71,3 +71,4 @@ sdk/R/NAMESPACE
sdk/R/.Rbuildignore
sdk/R/ArvadosR.Rproj
*.Rd
+*.asc
diff --git a/tools/arvbox/lib/arvbox/docker/58118E89F3A912897C070ADBF76221572C52609D.asc b/tools/arvbox/lib/arvbox/docker/58118E89F3A912897C070ADBF76221572C52609D.asc
new file mode 100644
index 000000000..086bab3e0
--- /dev/null
+++ b/tools/arvbox/lib/arvbox/docker/58118E89F3A912897C070ADBF76221572C52609D.asc
@@ -0,0 +1,106 @@
+-----BEGIN PGP PUBLIC KEY BLOCK-----
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+-----END PGP PUBLIC KEY BLOCK-----
diff --git a/tools/arvbox/lib/arvbox/docker/Dockerfile.base b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
index f54bf832a..4f915946f 100644
--- a/tools/arvbox/lib/arvbox/docker/Dockerfile.base
+++ b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
@@ -51,8 +51,9 @@ VOLUME /var/lib/docker
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 && \
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