case "$TARGET" in
centos*)
- fpm_depends+=(git)
+ fpm_depends+=(git arvados-server)
;;
debian* | ubuntu*)
- fpm_depends+=(git g++)
+ fpm_depends+=(git g++ arvados-server)
;;
esac
test -d ubuntu1804/generated || mkdir ubuntu1804/generated
cp -rlt ubuntu1804/generated common-generated/*
-GOTARBALL=go1.10.1.linux-amd64.tar.gz
+GOTARBALL=go1.12.7.linux-amd64.tar.gz
NODETARBALL=node-v6.11.2-linux-x64.tar.xz
RVMKEY1=mpapis.asc
RVMKEY2=pkuczynski.asc
common-generated-all: common-generated/$(GOTARBALL) common-generated/$(NODETARBALL) common-generated/$(RVMKEY1) common-generated/$(RVMKEY2)
common-generated/$(GOTARBALL): common-generated
- wget -cqO common-generated/$(GOTARBALL) http://storage.googleapis.com/golang/$(GOTARBALL)
+ wget -cqO common-generated/$(GOTARBALL) https://dl.google.com/go/$(GOTARBALL)
common-generated/$(NODETARBALL): common-generated
wget -cqO common-generated/$(NODETARBALL) https://nodejs.org/dist/v6.11.2/$(NODETARBALL)
RUN wget http://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
RUN rpm -ivh epel-release-latest-7.noarch.rpm
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
# The version of setuptools that comes with CentOS is way too old
RUN pip install --upgrade setuptools
ADD generated/node-v6.11.2-linux-x64.tar.xz /usr/local/
RUN ln -s /usr/local/node-v6.11.2-linux-x64/bin/* /usr/local/bin/
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
ENV WORKSPACE /arvados
CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "debian8"]
ADD generated/node-v6.11.2-linux-x64.tar.xz /usr/local/
RUN ln -s /usr/local/node-v6.11.2-linux-x64/bin/* /usr/local/bin/
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
ENV WORKSPACE /arvados
CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "debian9"]
ADD generated/node-v6.11.2-linux-x64.tar.xz /usr/local/
RUN ln -s /usr/local/node-v6.11.2-linux-x64/bin/* /usr/local/bin/
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
ENV WORKSPACE /arvados
CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "ubuntu1404"]
ADD generated/node-v6.11.2-linux-x64.tar.xz /usr/local/
RUN ln -s /usr/local/node-v6.11.2-linux-x64/bin/* /usr/local/bin/
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
ENV WORKSPACE /arvados
CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "ubuntu1604"]
ADD generated/node-v6.11.2-linux-x64.tar.xz /usr/local/
RUN ln -s /usr/local/node-v6.11.2-linux-x64/bin/* /usr/local/bin/
-RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle && rm -rf /tmp/arvados
+RUN git clone --depth 1 git://git.curoverse.com/arvados.git /tmp/arvados && cd /tmp/arvados/services/api && /usr/local/rvm/bin/rvm-exec default bundle && cd /tmp/arvados/apps/workbench && /usr/local/rvm/bin/rvm-exec default bundle
+
+# Workbench depends on arvados-server for config manipulation
+ENV GOPATH /tmp
+RUN mkdir -p $GOPATH/src/git.curoverse.com && ln -sT /tmp/arvados $GOPATH/src/git.curoverse.com/arvados.git && cd $GOPATH/src/git.curoverse.com/arvados.git/cmd/arvados-server && go get -v github.com/kardianos/govendor && $GOPATH/bin/govendor sync && go get && go build && cp arvados-server /usr/local/bin/ && rm -rf /tmp/arvados
ENV WORKSPACE /arvados
CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "ubuntu1804"]
fi
report_not_ready "$DATABASE_READY" "$CONFIG_PATH/database.yml"
-report_not_ready "$APPLICATION_READY" "$CONFIG_PATH/application.yml"
+if printf '%s\n' "$CONFIG_PATH" | grep -Fqe "sso"; then
+ report_not_ready "$APPLICATION_READY" "$CONFIG_PATH/application.yml"
+else
+ report_not_ready "$APPLICATION_READY" "/etc/arvados/config.yml"
+fi
rm -rf tmp
mkdir tmp
- # Set up application.yml and production.rb so that asset precompilation works
- \cp config/application.yml.example config/application.yml -f
- \cp config/environments/production.rb.example config/environments/production.rb -f
- sed -i 's/secret_token: ~/secret_token: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx/' config/application.yml
- sed -i 's/keep_web_url: false/keep_web_url: exampledotcom/' config/application.yml
+ # Set up an appropriate config.yml
+ arvados-server config-dump -config <(cat /etc/arvados/config.yml 2>/dev/null || echo "Clusters: {zzzzz: {}}") > /tmp/x
+ mkdir -p /etc/arvados/
+ mv /tmp/x /etc/arvados/config.yml
+ perl -p -i -e 'BEGIN{undef $/;} s/WebDAV(.*?):\n( *)ExternalURL: ""/WebDAV$1:\n$2ExternalURL: "example.com"/g' /etc/arvados/config.yml
RAILS_ENV=production RAILS_GROUPS=assets bundle exec rake npm:install >/dev/null
RAILS_ENV=production RAILS_GROUPS=assets bundle exec rake assets:precompile >/dev/null
# Remove generated configuration files so they don't go in the package.
- rm config/application.yml config/environments/production.rb
+ rm -rf /etc/arvados/
)
if [[ "$?" != "0" ]]; then
echo -n 'go: '
go version \
|| fatal "No go binary. See http://golang.org/doc/install"
- [[ $(go version) =~ go1.([0-9]+) ]] && [[ ${BASH_REMATCH[1]} -ge 10 ]] \
- || fatal "Go >= 1.10 required. See http://golang.org/doc/install"
+ [[ $(go version) =~ go1.([0-9]+) ]] && [[ ${BASH_REMATCH[1]} -ge 12 ]] \
+ || fatal "Go >= 1.12 required. See http://golang.org/doc/install"
echo -n 'gcc: '
gcc --version | egrep ^gcc \
|| fatal "No gcc. Try: apt-get install build-essential"
|@is_a@|string|Arvados object type|@["head_uuid","is_a","arvados#collection"]@|
|@exists@|string|Test if a subproperty is present.|@["properties","exists","my_subproperty"]@|
+
+h4(#substringsearchfilter). Filtering using substring search
+
+Resources can also be filtered by searching for a substring in attributes of type @string@, @array of strings@, @text@, and @hash@, which are indexed in the database specifically for search. To use substring search, the filter must:
+
+* Specify @any@ as the attribute
+* Use either the @like@ or @ilike@ operator
+* Have an operand of type @string@ that is wrapped in the SQL pattern match wildcard character @%@
+
+For example, the @["any", "like", "%foo%"]@ filter will return all resources that contain @foo@ in the content of at least one attribute of the previously defined types. This is the recommended way to do keyword and file name search across the entire database. Note that only exact substring matches are returned and results are unranked and returned in the order specified by the @list@ @order@ argument.
+
h4(#subpropertyfilters). Filtering on subproperties
-Some record type have an additional @properties@ attribute that allows recording and filtering on additional key-value pairs. To filter on a subproperty, the value in the @attribute@ position has the form @properties.user_property@. You may also use JSON-LD / RDF style URIs for property keys by enclosing them in @<...>@ for example @properties.<http://example.com/user_property>@. Alternately you may also provide a JSON-LD "@context" field, however at this time JSON-LD contexts are not interpreted by Arvados.
+Some record types have an additional @properties@ attribute that allows recording and filtering on additional key-value pairs. To filter on a subproperty, the value in the @attribute@ position has the form @properties.user_property@. You may also use JSON-LD / RDF style URIs for property keys by enclosing them in @<...>@ for example @properties.<http://example.com/user_property>@. Alternately you may also provide a JSON-LD "@context" field, however at this time JSON-LD contexts are not interpreted by Arvados.
table(table table-bordered table-condensed).
|_. Operator|_. Operand type|_. Description|_. Example|
@arv collection list --filters '[["name", "=", "PGP VAR inputs"], ["created_at", ">=", "2014-10-01"]]'@
-will return a list of all collections visible to the current user which are named "PGP VAR inputs" and were created on or after October 1, 2014.
+will return a list of all collections visible to the current user which are named "PGP VAR inputs" and were created on or after October 1, 2014. See the "Common resource methods":{{site.baseurl}}/api/methods.html#index page for more details on using @list@ and @--filters@.
case "$TARGET" in
centos*)
- fpm_depends+=(libcurl-devel postgresql-devel)
+ fpm_depends+=(libcurl-devel postgresql-devel arvados-server)
;;
debian* | ubuntu*)
- fpm_depends+=(libcurl-ssl-dev libpq-dev g++)
+ fpm_depends+=(libcurl-ssl-dev libpq-dev g++ arvados-server)
;;
esac
ExternalURL: "https://$localip:${services[keep-web-ssl]}/"
Composer:
ExternalURL: "http://$localip:${services[composer]}"
-
+ Controller:
+ ExternalURL: "https://$localip:${services[controller-ssl]}"
NodeProfiles: # to be deprecated in favor of "Services" section
"*":
arvados-controller:
bundle exec passenger-config build-native-support
bundle exec passenger-config install-standalone-runtime
mkdir -p /usr/src/arvados/apps/workbench/tmp
-RAILS_GROUPS=assets bundle exec rake npm:install
if test "$1" = "--only-deps" ; then
- exit
+ # Workaround for validation that asserts there's a download URL
+ # configured, which breaks rake if it is missing.
+cat >config/application.yml <<EOF
+$RAILS_ENV:
+ keep_web_url: https://example.com/c=%{uuid_or_pdh}
+EOF
+ RAILS_GROUPS=assets bundle exec rake npm:install
+ rm config/application.yml
+ exit
fi
set -u
(cd config && /usr/local/lib/arvbox/yml_override.py application.yml)
fi
+RAILS_GROUPS=assets bundle exec rake npm:install
bundle exec rake assets:precompile