target=${target#./}
echo $target
cd $target
- docker build --tag arvados/build:$target --build-arg HOSTTYPE=$HOSTTYPE .
+ docker build --tag arvados/build:$target --build-arg HOSTTYPE=$HOSTTYPE --build-arg BRANCH=$(git rev-parse --abbrev-ref HEAD) .
cd ..
done
# SPDX-License-Identifier: AGPL-3.0
ARG HOSTTYPE
+ARG BRANCH
FROM centos:7 as build_x86_64
# Install go
# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
cd /tmp/arvados/services/api && \
/usr/local/rvm/bin/rvm-exec default bundle install && \
cd /tmp/arvados/apps/workbench && \
# SPDX-License-Identifier: AGPL-3.0
ARG HOSTTYPE
+ARG BRANCH
## dont use debian:10 here since the word 'buster' is used for rvm precompiled binaries
FROM debian:buster as build_x86_64
# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
cd /tmp/arvados/services/api && \
/usr/local/rvm/bin/rvm-exec default bundle install && \
cd /tmp/arvados/apps/workbench && \
# SPDX-License-Identifier: AGPL-3.0
ARG HOSTTYPE
+ARG BRANCH
## dont use debian:11 here since the word 'bullseye' is used for rvm precompiled binaries
FROM debian:bullseye as build_x86_64
# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
cd /tmp/arvados/services/api && \
/usr/local/rvm/bin/rvm-exec default bundle install && \
cd /tmp/arvados/apps/workbench && \
# SPDX-License-Identifier: AGPL-3.0
ARG HOSTTYPE
+ARG BRANCH
FROM ubuntu:bionic as build_x86_64
# Install go
# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
cd /tmp/arvados/services/api && \
/usr/local/rvm/bin/rvm-exec default bundle install && \
cd /tmp/arvados/apps/workbench && \
# SPDX-License-Identifier: AGPL-3.0
ARG HOSTTYPE
+ARG BRANCH
FROM ubuntu:focal as build_x86_64
# Install go
# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
cd /tmp/arvados/services/api && \
/usr/local/rvm/bin/rvm-exec default bundle install && \
cd /tmp/arvados/apps/workbench && \
echo $TARGET
cd $TARGET
-time docker build --tag "$IMAGE" --build-arg HOSTTYPE=$HOSTTYPE .
+time docker build --tag "$IMAGE" --build-arg HOSTTYPE=$HOSTTYPE --build-arg BRANCH=$(git rev-parse --abbrev-ref HEAD) .
popd
if test -z "$packages" ; then
set +e
mv -f ${WORKSPACE}/packages/${TARGET}/* ${WORKSPACE}/packages/${TARGET}/processed/ 2>/dev/null
set -e
+ # give bundle (almost) all the cores. See also the MAKE env var that is passed into the
+ # docker run command below.
+ # Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
+ tmpfile=$(mktemp /tmp/run-build-packages-one-target.XXXXXX)
+ cores=$(let a=$(grep -c processor /proc/cpuinfo )-1; echo $a)
+ printf -- "---\nBUNDLE_JOBS: \"$cores\"" > $tmpfile
# Build packages.
if docker run \
--rm \
"${docker_volume_args[@]}" \
+ -v $tmpfile:/root/.bundle/config \
--env ARVADOS_BUILDING_VERSION="$ARVADOS_BUILDING_VERSION" \
--env ARVADOS_BUILDING_ITERATION="$ARVADOS_BUILDING_ITERATION" \
--env ARVADOS_DEBUG=$ARVADOS_DEBUG \
--env "ONLY_BUILD=$ONLY_BUILD" \
--env "FORCE_BUILD=$FORCE_BUILD" \
--env "ARCH=$ARCH" \
+ --env "MAKE=make --jobs $cores" \
"$IMAGE" $COMMAND
then
echo
FINAL_EXITCODE=$?
echo "ERROR: build packages on $IMAGE failed with exit status $FINAL_EXITCODE" >&2
fi
+ # Clean up the bundle config file
+ rm -f $tmpfile
fi
if test -n "$package_fails" ; then
cd "$srcdir"
mkdir -p tmp
git rev-parse HEAD >git-commit.version
- bundle package --all
+ bundle config set cache_all true
+ bundle package
)
if [[ 0 != "$?" ]] || ! cd "$WORKSPACE/packages/$TARGET"; then
echo "ERROR: $pkgname package prep failed" >&2
# We need to bundle to be ready even when we build a package without vendor directory
# because asset compilation requires it.
- bundle install --system >"$STDOUT_IF_DEBUG"
+ bundle config set --local system 'true' >"$STDOUT_IF_DEBUG"
+ bundle install >"$STDOUT_IF_DEBUG"
# clear the tmp directory; the asset generation step will recreate tmp/cache/assets,
# and we want that in the package, so it's easier to not exclude the tmp directory
- user/getting_started/community.html.textile.liquid
- Walkthough:
- user/tutorials/wgs-tutorial.html.textile.liquid
- - Run a workflow using Workbench:
+ - Using Workbench:
- user/getting_started/workbench.html.textile.liquid
- user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+ - user/topics/workbench-migration.html.textile.liquid
- Working at the Command Line:
- user/getting_started/setup-cli.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
h3. Conditions of creating a Collection
-The @portable_data_hash@ and @manifest_text@ attributes must be provided when creating a Collection. The cryptographic digest of the supplied @manifest_text@ must match the supplied @portable_data_hash@.
+If a new @portable_data_hash@ is specified when creating or updating a Collection, it must match the cryptographic digest of the supplied @manifest_text@.
h3. Side effects of creating a Collection
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
|collection|object||query||
+|replace_files|object|Initialize files and directories using content from other collections|query||
+
+The new collection's content can be initialized by providing a @manifest_text@ key in the provided @collection@ object, or by using the @replace_files@ option (see "replace_files":#replace_files below).
h3. delete
|_. Argument |_. Type |_. Description |_. Location |_. Example |
{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
|collection|object||query||
+|replace_files|object|Delete and replace files and directories using content from other collections|query||
+
+The collection's content can be updated by providing a @manifest_text@ key in the provided @collection@ object, or by using the @replace_files@ option (see "replace_files":#replace_files below).
h3. untrash
table(table table-bordered table-condensed).
|_. Argument |_. Type |_. Description |_. Location |_. Example |
{background:#ccffcc}.|uuid|string|The UUID of the Collection to get usage.|path||
+
+h2(#replace_files). Using "replace_files" to create/update collections
+
+The @replace_files@ option can be used with the @create@ and @update@ APIs to efficiently copy individual files and directory trees from other collections, and copy/rename/delete items within an existing collection, without transferring any file data.
+
+@replace_files@ keys indicate target paths in the new collection, and values specify sources that should be copied to the target paths.
+* Each target path must be an absolute canonical path beginning with @/@. It must not contain @.@ or @..@ components, consecutive @/@ characters, or a trailing @/@ after the final component.
+* Each source must be either an empty string (signifying that the target path is to be deleted), or @PDH/path@ where @PDH@ is the portable data hash of a collection on the cluster and @/path@ is a file or directory in that collection.
+* In an @update@ request, sources may reference the current portable data hash of the collection being updated.
+
+Example: delete @foo.txt@ from a collection
+
+<notextile><pre>
+"replace_files": {
+ "/foo.txt": ""
+}
+</pre></notextile>
+
+Example: rename @foo.txt@ to @bar.txt@ in a collection with portable data hash @fa7aeb5140e2848d39b416daeef4ffc5+45@
+
+<notextile><pre>
+"replace_files": {
+ "/foo.txt": "",
+ "/bar.txt": "fa7aeb5140e2848d39b416daeef4ffc5+45/foo.txt"
+}
+</pre></notextile>
+
+Example: delete current contents, then add content from multiple collections
+
+<notextile><pre>
+"replace_files": {
+ "/": "",
+ "/copy of collection 1": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/",
+ "/copy of collection 2": "ea10d51bcf88862dbcc36eb292017dfd+45/"
+}
+</pre></notextile>
+
+Example: replace entire collection with a copy of a subdirectory from another collection
+
+<notextile><pre>
+"replace_files": {
+ "/": "1f4b0bc7583c2a7f9102c395f4ffc5e3+45/subdir"
+}
+</pre></notextile>
+
+A target path with a non-empty source cannot be the ancestor of another target path in the same request. For example, the following request is invalid:
+
+<notextile><pre>
+"replace_files": {
+ "/foo": "fa7aeb5140e2848d39b416daeef4ffc5+45/",
+ "/foo/this_will_return_an_error": ""
+}
+</pre></notextile>
{% endcomment %}
{% include 'notebox_begin' %}
-This guide covers the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". There is also a new Workbench web application under development called "Workbench 2". Sites which have both Workbench applications installed will have a dropdown menu option "Switch to Workbench 2" to switch between versions.
-
-This guide will be updated to cover "Workbench 2" in the future.
+This guide covers the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". There is also a new Workbench web application under development called "Workbench 2". This guide will be updated to cover "Workbench 2" in the future. See "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
{% include 'notebox_end' %}
You can access the Arvados Workbench used in this guide using this link:
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Workbench 2 migration"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Arvados is in the process of migrating from the classic web application, referred to as "Workbench 1", to a completely new web application, referred to as "Workbench 2".
+
+!{width: 90%}{{ site.baseurl }}/images/wb2-example.png!
+
+Workbench 2 is the new Workbench web application that will, over time, replace Workbench 1. Workbench 2 is being built based on user feedback, and it is approaching feature parity with Workbench 1. Workbench 2 has a modern look and feel and offers several advanced features and performance enhancements. Arvados clusters typically have both Workbench applications installed and have a dropdown menu option in the user menu to switch between versions.
+
+!{{ site.baseurl }}/images/switch-to-wb2.png!
+
+Workbench 2 is stable and recommended for general use, but still lacks some features available in the classic Workbench 1 application. When necessary, you can easily switch back:
+
+!{{ site.baseurl }}/images/switch-to-wb1.png!
+
+Some major improvements of Workbench 2 include:
+
+h2. General
+
+* More responsive, only loads data needed for display
+* More familiar user interface, modeled on the file explorer of MacOS and Windows.
+* Advanced search capabilities
+
+h2. Project browsing
+
+* Expanded informational columns
+* Expanded filtering options
+* Right side informational panel providing details about selected item without navigating away from the project
+* Support for adding and querying user-supplied metadata properties on Projects
+
+h2. Collection browsing
+
+* Able to browse collections with millions of files
+* Support for adding and querying user-supplied metadata properties on Collections
+* Support for viewing past versions of a collection
+
+h2. User and Group management
+
+* Able to create user groups through the GUI
+* Able to add/view/remove members of user groups, and what permissions are shared with the group
+* Able to add/view/remove permissions shared with individual users
import (
"context"
+ "fmt"
+ "net/http"
+ "os"
+ "sort"
+ "strings"
"time"
"git.arvados.org/arvados.git/sdk/go/arvados"
+ "git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/auth"
+ "git.arvados.org/arvados.git/sdk/go/httpserver"
)
// CollectionGet defers to railsProxy for everything except blob
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
+ if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, "", opts.Attrs, opts.ReplaceFiles); err != nil {
+ return arvados.Collection{}, err
+ }
resp, err := conn.railsProxy.CollectionCreate(ctx, opts)
if err != nil {
return resp, err
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
+ if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, opts.UUID, opts.Attrs, opts.ReplaceFiles); err != nil {
+ return arvados.Collection{}, err
+ }
resp, err := conn.railsProxy.CollectionUpdate(ctx, opts)
if err != nil {
return resp, err
}
coll.ManifestText = arvados.SignManifest(coll.ManifestText, token, exp, ttl, []byte(conn.cluster.Collections.BlobSigningKey))
}
+
+// If replaceFiles is non-empty, populate attrs["manifest_text"] by
+// starting with the content of fromUUID (or an empty collection if
+// fromUUID is empty) and applying the specified file/directory
+// replacements.
+//
+// Return value is the (possibly modified) attrs map.
+func (conn *Conn) applyReplaceFilesOption(ctx context.Context, fromUUID string, attrs map[string]interface{}, replaceFiles map[string]string) (map[string]interface{}, error) {
+ if len(replaceFiles) == 0 {
+ return attrs, nil
+ } else if mtxt, ok := attrs["manifest_text"].(string); ok && len(mtxt) > 0 {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "ambiguous request: both 'replace_files' and attrs['manifest_text'] values provided")
+ }
+
+ // Load the current collection (if any) and set up an
+ // in-memory filesystem.
+ var dst arvados.Collection
+ if _, replacingRoot := replaceFiles["/"]; !replacingRoot && fromUUID != "" {
+ src, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: fromUUID})
+ if err != nil {
+ return nil, err
+ }
+ dst = src
+ }
+ dstfs, err := dst.FileSystem(&arvados.StubClient{}, &arvados.StubClient{})
+ if err != nil {
+ return nil, err
+ }
+
+ // Sort replacements by source collection to avoid redundant
+ // reloads when a source collection is used more than
+ // once. Note empty sources (which mean "delete target path")
+ // sort first.
+ dstTodo := make([]string, 0, len(replaceFiles))
+ {
+ srcid := make(map[string]string, len(replaceFiles))
+ for dst, src := range replaceFiles {
+ dstTodo = append(dstTodo, dst)
+ if i := strings.IndexRune(src, '/'); i > 0 {
+ srcid[dst] = src[:i]
+ }
+ }
+ sort.Slice(dstTodo, func(i, j int) bool {
+ return srcid[dstTodo[i]] < srcid[dstTodo[j]]
+ })
+ }
+
+ // Reject attempt to replace a node as well as its descendant
+ // (e.g., a/ and a/b/), which is unsupported, except where the
+ // source for a/ is empty (i.e., delete).
+ for _, dst := range dstTodo {
+ if dst != "/" && (strings.HasSuffix(dst, "/") ||
+ strings.HasSuffix(dst, "/.") ||
+ strings.HasSuffix(dst, "/..") ||
+ strings.Contains(dst, "//") ||
+ strings.Contains(dst, "/./") ||
+ strings.Contains(dst, "/../") ||
+ !strings.HasPrefix(dst, "/")) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "invalid replace_files target: %q", dst)
+ }
+ for i := 0; i < len(dst)-1; i++ {
+ if dst[i] != '/' {
+ continue
+ }
+ outerdst := dst[:i]
+ if outerdst == "" {
+ outerdst = "/"
+ }
+ if outersrc := replaceFiles[outerdst]; outersrc != "" {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "replace_files: cannot operate on target %q inside non-empty target %q", dst, outerdst)
+ }
+ }
+ }
+
+ var srcidloaded string
+ var srcfs arvados.FileSystem
+ // Apply the requested replacements.
+ for _, dst := range dstTodo {
+ src := replaceFiles[dst]
+ if src == "" {
+ if dst == "/" {
+ // In this case we started with a
+ // blank manifest, so there can't be
+ // anything to delete.
+ continue
+ }
+ err := dstfs.RemoveAll(dst)
+ if err != nil {
+ return nil, fmt.Errorf("RemoveAll(%s): %w", dst, err)
+ }
+ continue
+ }
+ srcspec := strings.SplitN(src, "/", 2)
+ srcid, srcpath := srcspec[0], "/"
+ if !arvadosclient.PDHMatch(srcid) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "invalid source %q for replace_files[%q]: must be \"\" or \"PDH\" or \"PDH/path\"", src, dst)
+ }
+ if len(srcspec) == 2 && srcspec[1] != "" {
+ srcpath = srcspec[1]
+ }
+ if srcidloaded != srcid {
+ srcfs = nil
+ srccoll, err := conn.CollectionGet(ctx, arvados.GetOptions{UUID: srcid})
+ if err != nil {
+ return nil, err
+ }
+ // We use StubClient here because we don't
+ // want srcfs to read/write any file data or
+ // sync collection state to/from the database.
+ srcfs, err = srccoll.FileSystem(&arvados.StubClient{}, &arvados.StubClient{})
+ if err != nil {
+ return nil, err
+ }
+ srcidloaded = srcid
+ }
+ snap, err := arvados.Snapshot(srcfs, srcpath)
+ if err != nil {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "error getting snapshot of %q from %q: %w", srcpath, srcid, err)
+ }
+ // Create intermediate dirs, in case dst is
+ // "newdir1/newdir2/dst".
+ for i := 1; i < len(dst)-1; i++ {
+ if dst[i] == '/' {
+ err = dstfs.Mkdir(dst[:i], 0777)
+ if err != nil && !os.IsExist(err) {
+ return nil, httpserver.Errorf(http.StatusBadRequest, "error creating parent dirs for %q: %w", dst, err)
+ }
+ }
+ }
+ err = arvados.Splice(dstfs, dst, snap)
+ if err != nil {
+ return nil, fmt.Errorf("error splicing snapshot onto path %q: %w", dst, err)
+ }
+ }
+ mtxt, err := dstfs.MarshalManifest(".")
+ if err != nil {
+ return nil, err
+ }
+ if attrs == nil {
+ attrs = make(map[string]interface{}, 1)
+ }
+ attrs["manifest_text"] = mtxt
+ return attrs, nil
+}
import (
"context"
+ "io/fs"
+ "path/filepath"
"regexp"
+ "sort"
"strconv"
+ "strings"
"time"
"git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/controller/rpc"
"git.arvados.org/arvados.git/sdk/go/arvados"
+ "git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/arvadostest"
"git.arvados.org/arvados.git/sdk/go/auth"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "git.arvados.org/arvados.git/sdk/go/keepclient"
check "gopkg.in/check.v1"
)
s.localdb.vocabularyCache = voc
}
-func (s *CollectionSuite) TestCollectionCreateWithProperties(c *check.C) {
+func (s *CollectionSuite) TestCollectionCreateAndUpdateWithProperties(c *check.C) {
s.setUpVocabulary(c, "")
ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
for _, tt := range tests {
c.Log(c.TestName()+" ", tt.name)
+ // Create with properties
coll, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
Select: []string{"uuid", "properties"},
Attrs: map[string]interface{}{
} else {
c.Assert(err, check.NotNil)
}
- }
-}
-
-func (s *CollectionSuite) TestCollectionUpdateWithProperties(c *check.C) {
- s.setUpVocabulary(c, "")
- ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
- tests := []struct {
- name string
- props map[string]interface{}
- success bool
- }{
- {"Invalid prop key", map[string]interface{}{"Priority": "IDVALIMPORTANCES1"}, false},
- {"Invalid prop value", map[string]interface{}{"IDTAGIMPORTANCES": "high"}, false},
- {"Valid prop key & value", map[string]interface{}{"IDTAGIMPORTANCES": "IDVALIMPORTANCES1"}, true},
- {"Empty properties", map[string]interface{}{}, true},
- }
- for _, tt := range tests {
- c.Log(c.TestName()+" ", tt.name)
- coll, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{})
+ // Create, then update with properties
+ coll, err = s.localdb.CollectionCreate(ctx, arvados.CreateOptions{})
c.Assert(err, check.IsNil)
coll, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
UUID: coll.UUID,
}
}
+func (s *CollectionSuite) TestCollectionReplaceFiles(c *check.C) {
+ ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.AdminToken}})
+ foo, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &foo)
+ foobarbaz, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": "./foo/bar 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &foobarbaz)
+ wazqux, err := s.localdb.railsProxy.CollectionCreate(ctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": "./waz d85b1213473c2fd7c2045020a6b9c62b+3 0:3:qux.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ s.localdb.signCollection(ctx, &wazqux)
+
+ ctx = auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
+
+ // Create using content from existing collections
+ dst, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
+ ReplaceFiles: map[string]string{
+ "/f": foo.PortableDataHash + "/foo.txt",
+ "/b": foobarbaz.PortableDataHash + "/foo/bar",
+ "/q": wazqux.PortableDataHash + "/",
+ "/w": wazqux.PortableDataHash + "/waz",
+ },
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "f", "b/baz.txt", "q/waz/qux.txt", "w/qux.txt")
+
+ // Delete a file and a directory
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ "/f": "",
+ "/q/waz": "",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/baz.txt", "q/", "w/qux.txt")
+
+ // Move and copy content within collection
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ // Note splicing content to /b/corge.txt but
+ // removing everything else from /b
+ "/b": "",
+ "/b/corge.txt": dst.PortableDataHash + "/b/baz.txt",
+ "/quux/corge.txt": dst.PortableDataHash + "/b/baz.txt",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/corge.txt", "q/", "w/qux.txt", "quux/corge.txt")
+
+ // Remove everything except one file
+ dst, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ "/": "",
+ "/b/corge.txt": dst.PortableDataHash + "/b/corge.txt",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "b/corge.txt")
+
+ // Copy entire collection to root
+ dstcopy, err := s.localdb.CollectionCreate(ctx, arvados.CreateOptions{
+ ReplaceFiles: map[string]string{
+ "/": dst.PortableDataHash,
+ }})
+ c.Check(err, check.IsNil)
+ c.Check(dstcopy.PortableDataHash, check.Equals, dst.PortableDataHash)
+ s.expectFiles(c, dstcopy, "b/corge.txt")
+
+ // Check invalid targets, sources, and combinations
+ for _, badrepl := range []map[string]string{
+ {
+ "/foo/nope": dst.PortableDataHash + "/b",
+ "/foo": dst.PortableDataHash + "/b",
+ },
+ {
+ "/foo": dst.PortableDataHash + "/b",
+ "/foo/nope": "",
+ },
+ {
+ "/": dst.PortableDataHash + "/",
+ "/nope": "",
+ },
+ {
+ "/": dst.PortableDataHash + "/",
+ "/nope": dst.PortableDataHash + "/b",
+ },
+ {"/bad/": ""},
+ {"/./bad": ""},
+ {"/b/./ad": ""},
+ {"/b/../ad": ""},
+ {"/b/.": ""},
+ {".": ""},
+ {"bad": ""},
+ {"": ""},
+ {"/bad": "/b"},
+ {"/bad": "bad/b"},
+ {"/bad": dst.UUID + "/b"},
+ } {
+ _, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: badrepl,
+ })
+ c.Logf("badrepl %#v\n... got err: %s", badrepl, err)
+ c.Check(err, check.NotNil)
+ }
+
+ // Check conflicting replace_files and manifest_text
+ _, err = s.localdb.CollectionUpdate(ctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{"/": ""},
+ Attrs: map[string]interface{}{
+ "manifest_text": ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:z\n",
+ }})
+ c.Logf("replace_files+manifest_text\n... got err: %s", err)
+ c.Check(err, check.ErrorMatches, "ambiguous request: both.*replace_files.*manifest_text.*")
+}
+
+// expectFiles checks coll's directory structure against the given
+// list of expected files and empty directories. An expected path with
+// a trailing slash indicates an empty directory.
+func (s *CollectionSuite) expectFiles(c *check.C, coll arvados.Collection, expected ...string) {
+ client := arvados.NewClientFromEnv()
+ ac, err := arvadosclient.New(client)
+ c.Assert(err, check.IsNil)
+ kc, err := keepclient.MakeKeepClient(ac)
+ c.Assert(err, check.IsNil)
+ cfs, err := coll.FileSystem(arvados.NewClientFromEnv(), kc)
+ c.Assert(err, check.IsNil)
+ var found []string
+ nonemptydirs := map[string]bool{}
+ fs.WalkDir(arvados.FS(cfs), "/", func(path string, d fs.DirEntry, err error) error {
+ dir, _ := filepath.Split(path)
+ nonemptydirs[dir] = true
+ if d.IsDir() {
+ if path != "/" {
+ path += "/"
+ }
+ if !nonemptydirs[path] {
+ nonemptydirs[path] = false
+ }
+ } else {
+ found = append(found, path)
+ }
+ return nil
+ })
+ for d, nonempty := range nonemptydirs {
+ if !nonempty {
+ found = append(found, d)
+ }
+ }
+ for i, path := range found {
+ if path != "/" {
+ found[i] = strings.TrimPrefix(path, "/")
+ }
+ }
+ sort.Strings(found)
+ sort.Strings(expected)
+ c.Check(found, check.DeepEquals, expected)
+}
+
func (s *CollectionSuite) TestSignatures(c *check.C) {
ctx := auth.NewContext(context.Background(), &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
def test_small_collection
uuid = Digest::MD5.hexdigest(foo_manifest) + '+' + foo_manifest.size.to_s
+ ok = nil
out, err = capture_subprocess_io do
- assert_arv('--format', 'uuid', 'collection', 'create', '--collection', {
- uuid: uuid,
- manifest_text: foo_manifest
- }.to_json)
+ ok = arv('--format', 'uuid', 'collection', 'create', '--collection', {
+ uuid: uuid,
+ manifest_text: foo_manifest
+ }.to_json)
end
- assert(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(out))
- assert_equal '', err
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, out)
+ end
+
+ def test_collection_replace_files
+ ok = nil
+ uuid, err = capture_subprocess_io do
+ ok = arv('--format', 'uuid', 'collection', 'create', '--collection', '{}')
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, uuid)
+ uuid = uuid.strip
+
+ out, err = capture_subprocess_io do
+ ok = arv('--format', 'uuid',
+ 'collection', 'update',
+ '--uuid', uuid,
+ '--collection', '{}',
+ '--replace-files', {
+ "/gpl.pdf": "b519d9cb706a29fc7ea24dbea2f05851+93/GNU_General_Public_License,_version_3.pdf",
+ }.to_json)
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_equal(uuid, out.strip)
+
+ ok = nil
+ out, err = capture_subprocess_io do
+ ok = arv('--format', 'json', 'collection', 'get', '--uuid', uuid)
+ end
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/\. 6a4ff0499484c6c79c95cd8c566bd25f\+249025.* 0:249025:gpl.pdf\\n/, out)
end
def test_read_resource_object_from_file
begin
tempfile.write({manifest_text: foo_manifest}.to_json)
tempfile.close
+ ok = nil
out, err = capture_subprocess_io do
- assert_arv('--format', 'uuid',
- 'collection', 'create', '--collection', tempfile.path)
+ ok = arv('--format', 'uuid',
+ 'collection', 'create', '--collection', tempfile.path)
end
- assert(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(out))
- assert_equal '', err
+ assert_equal('', err)
+ assert_equal(true, ok)
+ assert_match(/^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/, out)
ensure
tempfile.unlink
end
end
protected
- def assert_arv(*args)
- expect = case args.first
- when true, false
- args.shift
- else
- true
- end
- assert_equal(expect,
- system(['./bin/arv', 'arv'], *args),
- "`arv #{args.join ' '}` " +
- "should exit #{if expect then 0 else 'non-zero' end}")
+ def arv(*args)
+ system(['./bin/arv', 'arv'], *args)
end
def foo_manifest
EnsureUniqueName bool `json:"ensure_unique_name"`
Select []string `json:"select"`
Attrs map[string]interface{} `json:"attrs"`
+ // ReplaceFiles only applies when creating a collection.
+ ReplaceFiles map[string]string `json:"replace_files"`
}
type UpdateOptions struct {
Attrs map[string]interface{} `json:"attrs"`
Select []string `json:"select"`
BypassFederation bool `json:"bypass_federation"`
+ // ReplaceFiles only applies when updating a collection.
+ ReplaceFiles map[string]string `json:"replace_files"`
}
type GroupContentsOptions struct {
import (
"context"
+ "errors"
"io"
)
type apiClient interface {
RequestAndDecode(dst interface{}, method, path string, body io.Reader, params interface{}) error
}
+
+var errStubClient = errors.New("stub client")
+
+type StubClient struct{}
+
+func (*StubClient) ReadAt(string, []byte, int) (int, error) { return 0, errStubClient }
+func (*StubClient) LocalLocator(loc string) (string, error) { return loc, nil }
+func (*StubClient) BlockWrite(context.Context, BlockWriteOptions) (BlockWriteResponse, error) {
+ return BlockWriteResponse{}, errStubClient
+}
+func (*StubClient) RequestAndDecode(_ interface{}, _, _ string, _ io.Reader, _ interface{}) error {
+ return errStubClient
+}
"errors"
"fmt"
"io"
+ "io/fs"
"log"
"net/http"
"os"
MemorySize() int64
}
+type fsFS struct {
+ FileSystem
+}
+
+// FS returns an fs.FS interface to the given FileSystem, to enable
+// the use of fs.WalkDir, etc.
+func FS(fs FileSystem) fs.FS { return fsFS{fs} }
+func (fs fsFS) Open(path string) (fs.File, error) {
+ f, err := fs.FileSystem.Open(path)
+ return f, err
+}
+
type inode interface {
SetParent(parent inode, name string)
Parent() inode
default:
return nil, fmt.Errorf("invalid flags 0x%x", flag)
}
- if !writable && parent.IsDir() {
+ if parent.IsDir() {
// A directory can be opened via "foo/", "foo/.", or
// "foo/..".
switch name {
case ".", "":
- return &filehandle{inode: parent}, nil
+ return &filehandle{inode: parent, readable: readable, writable: writable}, nil
case "..":
- return &filehandle{inode: parent.Parent()}, nil
+ return &filehandle{inode: parent.Parent(), readable: readable, writable: writable}, nil
}
}
createMode := flag&os.O_CREATE != 0
f, err = fs.OpenFile(target, os.O_CREATE|os.O_WRONLY, 0700)
}
if err != nil {
- return err
+ return fmt.Errorf("open %s: %w", target, err)
}
defer f.Close()
return f.Splice(newsubtree)
func (dn *dirnode) Splice(repl inode) error {
repl, err := repl.Snapshot()
if err != nil {
- return err
+ return fmt.Errorf("cannot copy snapshot: %w", err)
}
switch repl := repl.(type) {
default:
defer dn.Unlock()
_, err = dn.parent.Child(dn.fileinfo.name, func(inode) (inode, error) { return repl, nil })
if err != nil {
- return err
+ return fmt.Errorf("error replacing filenode: dn.parent.Child(): %w", err)
}
repl.fs = dn.fs
}
}
}
+func (s *CollectionFSSuite) TestSnapshotSplice(c *check.C) {
+ filedata1 := "hello snapshot+splice world\n"
+ fs, err := (&Collection{}).FileSystem(s.client, s.kc)
+ c.Assert(err, check.IsNil)
+ {
+ f, err := fs.OpenFile("file1", os.O_CREATE|os.O_RDWR, 0700)
+ c.Assert(err, check.IsNil)
+ _, err = f.Write([]byte(filedata1))
+ c.Assert(err, check.IsNil)
+ err = f.Close()
+ c.Assert(err, check.IsNil)
+ }
+
+ snap, err := Snapshot(fs, "/")
+ c.Assert(err, check.IsNil)
+ err = Splice(fs, "dir1", snap)
+ c.Assert(err, check.IsNil)
+ f, err := fs.Open("dir1/file1")
+ c.Assert(err, check.IsNil)
+ buf, err := io.ReadAll(f)
+ c.Assert(err, check.IsNil)
+ c.Check(string(buf), check.Equals, filedata1)
+}
+
func (s *CollectionFSSuite) TestRefreshSignatures(c *check.C) {
filedata1 := "hello refresh signatures world\n"
fs, err := (&Collection{}).FileSystem(s.client, s.kc)
import (
"io"
+ "io/fs"
"os"
)
return
}
+// dirEntry implements fs.DirEntry, see (*filehandle)ReadDir().
+type dirEntry struct {
+ os.FileInfo
+}
+
+func (ent dirEntry) Type() fs.FileMode {
+ return ent.Mode().Type()
+}
+func (ent dirEntry) Info() (fs.FileInfo, error) {
+ return ent, nil
+}
+
+// ReadDir implements fs.ReadDirFile.
+func (f *filehandle) ReadDir(count int) ([]fs.DirEntry, error) {
+ fis, err := f.Readdir(count)
+ if len(fis) == 0 {
+ return nil, err
+ }
+ ents := make([]fs.DirEntry, len(fis))
+ for i, fi := range fis {
+ ents[i] = dirEntry{fi}
+ }
+ return ents, err
+}
+
func (f *filehandle) Readdir(count int) ([]os.FileInfo, error) {
if !f.inode.IsDir() {
return nil, ErrInvalidOperation
"io/ioutil"
"net/http"
"os"
+ "strings"
"syscall"
"time"
c.Check(string(buf), check.Equals, string(thisfile))
}
- // Cannot splice a file onto a collection root, or anywhere
- // outside a collection
+ // Cannot splice a file onto a collection root; cannot splice
+ // anything to a target outside a collection.
for _, badpath := range []string{
+ dstPath + "/",
dstPath,
+ "/home/A Project/newnodename/",
"/home/A Project/newnodename",
+ "/home/A Project/",
"/home/A Project",
+ "/home/newnodename/",
"/home/newnodename",
+ "/home/",
"/home",
+ "/newnodename/",
"/newnodename",
+ "/",
} {
err = Splice(s.fs, badpath, snapFile)
c.Check(err, check.NotNil)
- c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %s"))
- if badpath == dstPath {
- c.Check(err, check.ErrorMatches, `cannot use Splice to attach a file at top level of \*arvados.collectionFileSystem: invalid operation`, check.Commentf("badpath: %s", badpath))
+ if strings.Contains(badpath, "newnodename") && strings.HasSuffix(badpath, "/") {
+ c.Check(err, ErrorIs, os.ErrNotExist, check.Commentf("badpath %q", badpath))
+ } else {
+ c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %q", badpath))
+ }
+ if strings.TrimSuffix(badpath, "/") == dstPath {
+ c.Check(err, check.ErrorMatches, `cannot use Splice to attach a file at top level of \*arvados.collectionFileSystem: invalid operation`, check.Commentf("badpath: %q", badpath))
continue
}
- err = Splice(s.fs, badpath, snap1)
- c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %s"))
- }
- // Destination cannot have trailing slash
- for _, badpath := range []string{
- dstPath + "/ctxlog/",
- dstPath + "/",
- "/home/A Project/",
- "/home/",
- "/",
- "",
- } {
err = Splice(s.fs, badpath, snap1)
- c.Check(err, ErrorIs, ErrInvalidArgument, check.Commentf("badpath %s", badpath))
- err = Splice(s.fs, badpath, snapFile)
- c.Check(err, ErrorIs, ErrInvalidArgument, check.Commentf("badpath %s", badpath))
+ if strings.Contains(badpath, "newnodename") && strings.HasSuffix(badpath, "/") {
+ c.Check(err, ErrorIs, os.ErrNotExist, check.Commentf("badpath %q", badpath))
+ } else {
+ c.Check(err, ErrorIs, ErrInvalidOperation, check.Commentf("badpath %q", badpath))
+ }
}
// Destination's parent must already exist
}
snap2, err := Snapshot(s.fs, dstPath+"/ctxlog-copy")
- c.Check(err, check.IsNil)
- err = Splice(s.fs, dstPath+"/ctxlog-copy-copy", snap2)
- c.Check(err, check.IsNil)
+ if c.Check(err, check.IsNil) {
+ err = Splice(s.fs, dstPath+"/ctxlog-copy-copy", snap2)
+ c.Check(err, check.IsNil)
+ }
// Snapshot entire collection, splice into same collection at
// a new path, remove file from original location, verify
_, err = s.fs.Open(dstPath + "/arvados/fs_site_test.go")
c.Check(err, check.Equals, os.ErrNotExist)
f, err = s.fs.Open(dstPath + "/copy2/arvados/fs_site_test.go")
- c.Check(err, check.IsNil)
- defer f.Close()
- buf, err := ioutil.ReadAll(f)
- c.Check(err, check.IsNil)
- c.Check(string(buf), check.Equals, string(thisfile))
+ if c.Check(err, check.IsNil) {
+ defer f.Close()
+ buf, err := ioutil.ReadAll(f)
+ c.Check(err, check.IsNil)
+ c.Check(string(buf), check.Equals, string(thisfile))
+ }
}
import (
"encoding/json"
+ "fmt"
"net/http"
)
+func Errorf(status int, tmpl string, args ...interface{}) error {
+ return errorWithStatus{fmt.Errorf(tmpl, args...), status}
+}
+
func ErrorWithStatus(err error, status int) error {
return errorWithStatus{err, status}
}
curl.setopt(pycurl.HEADERFUNCTION, self._headerfunction)
if self.insecure:
curl.setopt(pycurl.SSL_VERIFYPEER, 0)
+ curl.setopt(pycurl.SSL_VERIFYHOST, 0)
else:
curl.setopt(pycurl.CAINFO, arvados.util.ca_certs_path())
if method == "HEAD":
curl.setopt(pycurl.HEADERFUNCTION, self._headerfunction)
if self.insecure:
curl.setopt(pycurl.SSL_VERIFYPEER, 0)
+ curl.setopt(pycurl.SSL_VERIFYHOST, 0)
else:
curl.setopt(pycurl.CAINFO, arvados.util.ca_certs_path())
self._setcurltimeouts(curl, timeout)
self.assertEqual(
mock.responses[0].getopt(pycurl.SSL_VERIFYPEER),
0)
+ self.assertEqual(
+ mock.responses[0].getopt(pycurl.SSL_VERIFYHOST),
+ 0)
api_client.insecure = False
with tutil.mock_keep_responses(b'foo', 200) as mock:
self.assertEqual(
mock.responses[0].getopt(pycurl.SSL_VERIFYPEER),
None)
+ self.assertEqual(
+ mock.responses[0].getopt(pycurl.SSL_VERIFYHOST),
+ None)
def test_refresh_signature(self):
blk_digest = '6f5902ac237024bdd0c176cb93063dc4+11'
gem 'jquery-rails'
-gem 'rvm-capistrano', :group => :test
-
gem 'acts_as_api'
gem 'passenger'
multi_json (>= 1.0.0)
builder (3.2.4)
byebug (11.0.1)
- capistrano (2.15.9)
- highline
- net-scp (>= 1.0.0)
- net-sftp (>= 2.0.0)
- net-ssh (>= 2.0.14)
- net-ssh-gateway (>= 1.1.0)
concurrent-ruby (1.1.9)
crass (1.0.6)
erubi (1.10.0)
multi_json (~> 1.11)
os (>= 0.9, < 2.0)
signet (~> 0.7)
- highline (2.0.1)
httpclient (2.8.3)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
metaclass (~> 0.0.1)
multi_json (1.15.0)
multipart-post (2.1.1)
- net-scp (2.0.0)
- net-ssh (>= 2.6.5, < 6.0.0)
- net-sftp (2.1.2)
- net-ssh (>= 2.6.5)
- net-ssh (5.2.0)
- net-ssh-gateway (2.0.0)
- net-ssh (>= 4.0.0)
nio4r (2.5.8)
nokogiri (1.13.3)
mini_portile2 (~> 2.8.0)
railties (>= 4.2.0, < 6.0)
retriable (1.4.1)
ruby-prof (0.15.9)
- rvm-capistrano (1.5.6)
- capistrano (~> 2.15.4)
safe_yaml (1.0.5)
signet (0.11.0)
addressable (~> 2.3)
rails-perftest
responders (~> 2.0)
ruby-prof (~> 0.15.0)
- rvm-capistrano
safe_yaml
signet (< 0.12)
simplecov (~> 0.7.1)
end
end
+ # The 'replace_files' option is implemented in lib/controller,
+ # not Rails -- we just need to add it here so discovery-aware
+ # clients know how to validate it.
+ [:create, :update].each do |action|
+ discovery[:resources]['collections'][:methods][action][:parameters]['replace_files'] = {
+ type: 'object',
+ description: 'Files and directories to initialize/replace with content from other collections.',
+ required: false,
+ location: 'query',
+ properties: {},
+ additionalProperties: {type: 'string'},
+ }
+ end
+
discovery[:resources]['configs'] = {
methods: {
get: {
desc "Remove old container log entries from the logs table"
task delete_old_container_logs: :environment do
- delete_sql = "DELETE FROM logs WHERE id in (SELECT logs.id FROM logs JOIN containers ON logs.object_uuid = containers.uuid WHERE event_type IN ('stdout', 'stderr', 'arv-mount', 'crunch-run', 'crunchstat') AND containers.log IS NOT NULL AND clock_timestamp() - containers.finished_at > interval '#{Rails.configuration.Containers.Logging.MaxAge.to_i} seconds')"
+ delete_sql = "DELETE FROM logs WHERE id in (SELECT logs.id FROM logs JOIN containers ON logs.object_uuid = containers.uuid WHERE event_type IN ('stdout', 'stderr', 'arv-mount', 'crunch-run', 'crunchstat') AND containers.log IS NOT NULL AND now() - containers.finished_at > interval '#{Rails.configuration.Containers.Logging.MaxAge.to_i} seconds')"
ActiveRecord::Base.connection.execute(delete_sql)
end
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-# This task finds jobs that have been finished for at least as long as
-# the duration specified in the `clean_job_log_rows_after`
-# configuration setting, and deletes their stderr logs from the logs table.
-
-namespace :db do
- desc "Remove old job stderr entries from the logs table"
- task delete_old_job_logs: :environment do
- delete_sql = "DELETE FROM logs WHERE id in (SELECT logs.id FROM logs JOIN jobs ON logs.object_uuid = jobs.uuid WHERE event_type = 'stderr' AND jobs.log IS NOT NULL AND clock_timestamp() - jobs.finished_at > interval '#{Rails.configuration.Containers.Logging.MaxAge.to_i} seconds')"
-
- ActiveRecord::Base.connection.execute(delete_sql)
- end
-end
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-require 'current_api_client'
-
-# This is needed instead of just including CurrentApiClient so that its
-# methods don't get imported as Object's class methods; this is a problem because
-# the methods would be imported only on test environment. See #15716 for more info.
-class CurrentApiClientHelper
- extend CurrentApiClient
-end
-
-def has_symbols? x
- if x.is_a? Hash
- x.each do |k,v|
- return true if has_symbols?(k) or has_symbols?(v)
- end
- elsif x.is_a? Array
- x.each do |k|
- return true if has_symbols?(k)
- end
- elsif x.is_a? Symbol
- return true
- elsif x.is_a? String
- return true if x.start_with?(':') && !x.start_with?('::')
- end
- false
-end
-
-def check_for_serialized_symbols rec
- jsonb_cols = rec.class.columns.select{|c| c.type == :jsonb}.collect{|j| j.name}
- (jsonb_cols + rec.class.serialized_attributes.keys).uniq.each do |colname|
- if has_symbols? rec.attributes[colname]
- st = recursive_stringify rec.attributes[colname]
- puts "Found value potentially containing Ruby symbols in #{colname} attribute of #{rec.uuid}, current value is\n#{rec.attributes[colname].to_s[0..1024]}\nrake symbols:stringify will update it to:\n#{st.to_s[0..1024]}\n\n"
- end
- end
-end
-
-def recursive_stringify x
- if x.is_a? Hash
- Hash[x.collect do |k,v|
- [recursive_stringify(k), recursive_stringify(v)]
- end]
- elsif x.is_a? Array
- x.collect do |k|
- recursive_stringify k
- end
- elsif x.is_a? Symbol
- x.to_s
- elsif x.is_a? String and x.start_with?(':') and !x.start_with?('::')
- x[1..-1]
- else
- x
- end
-end
-
-def stringify_serialized_symbols rec
- # ensure_serialized_attribute_type should prevent symbols from
- # getting into the database in the first place. If someone managed
- # to get them into the database (perhaps using an older version)
- # we'll convert symbols to strings when loading from the
- # database. (Otherwise, loading and saving an object with existing
- # symbols in a serialized field will crash.)
- jsonb_cols = rec.class.columns.select{|c| c.type == :jsonb}.collect{|j| j.name}
- (jsonb_cols + rec.class.serialized_attributes.keys).uniq.each do |colname|
- if has_symbols? rec.attributes[colname]
- begin
- st = recursive_stringify rec.attributes[colname]
- puts "Updating #{colname} attribute of #{rec.uuid} from\n#{rec.attributes[colname].to_s[0..1024]}\nto\n#{st.to_s[0..1024]}\n\n"
- rec.write_attribute(colname, st)
- rec.save!
- rescue => e
- puts "Failed to update #{rec.uuid}: #{e}"
- end
- end
- end
-end
-
-namespace :symbols do
- desc 'Warn about serialized values starting with ":" that may be symbols'
- task check: :environment do
- [ApiClientAuthorization, ApiClient,
- AuthorizedKey, Collection,
- Container, ContainerRequest, Group,
- Human, Job, JobTask, KeepDisk, KeepService, Link,
- Node, PipelineInstance, PipelineTemplate,
- Repository, Specimen, Trait, User, VirtualMachine,
- Workflow].each do |klass|
- CurrentApiClientHelper.act_as_system_user do
- klass.all.each do |c|
- check_for_serialized_symbols c
- end
- end
- end
- end
-
- task stringify: :environment do
- [ApiClientAuthorization, ApiClient,
- AuthorizedKey, Collection,
- Container, ContainerRequest, Group,
- Human, Job, JobTask, KeepDisk, KeepService, Link,
- Node, PipelineInstance, PipelineTemplate,
- Repository, Specimen, Trait, User, VirtualMachine,
- Workflow].each do |klass|
- CurrentApiClientHelper.act_as_system_user do
- klass.all.each do |c|
- stringify_serialized_symbols c
- end
- end
- end
- end
-end
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-require 'test_helper'
-require 'rake'
-
-Rake.application.rake_require "tasks/delete_old_job_logs"
-Rake::Task.define_task(:environment)
-
-class DeleteOldJobLogsTaskTest < ActiveSupport::TestCase
- TASK_NAME = "db:delete_old_job_logs"
-
- def log_uuids(*fixture_names)
- fixture_names.map { |name| logs(name).uuid }
- end
-
- def run_with_expiry(clean_after)
- Rails.configuration.Containers.Logging.MaxAge = clean_after
- Rake::Task[TASK_NAME].reenable
- Rake.application.invoke_task TASK_NAME
- end
-
- def job_stderr_logs
- Log.where("object_uuid LIKE :pattern AND event_type = :etype",
- pattern: "_____-8i9sb-_______________",
- etype: "stderr")
- end
-
- def check_existence(test_method, fixture_uuids)
- uuids_now = job_stderr_logs.map(&:uuid)
- fixture_uuids.each do |expect_uuid|
- send(test_method, uuids_now, expect_uuid)
- end
- end
-
- test "delete all logs" do
- uuids_to_keep = log_uuids(:crunchstat_for_running_job)
- uuids_to_clean = log_uuids(:crunchstat_for_previous_job,
- :crunchstat_for_ancient_job)
- run_with_expiry(1)
- check_existence(:assert_includes, uuids_to_keep)
- check_existence(:refute_includes, uuids_to_clean)
- end
-
- test "delete only old logs" do
- uuids_to_keep = log_uuids(:crunchstat_for_running_job,
- :crunchstat_for_previous_job)
- uuids_to_clean = log_uuids(:crunchstat_for_ancient_job)
- run_with_expiry(360.days)
- check_existence(:assert_includes, uuids_to_keep)
- check_existence(:refute_includes, uuids_to_clean)
- end
-end
"region": "{{user `aws_default_region`}}",
"ena_support": "true",
"source_ami": "{{user `aws_source_ami`}}",
- "instance_type": "m4.large",
+ "instance_type": "m5.large",
"vpc_id": "{{user `vpc_id`}}",
"subnet_id": "{{user `subnet_id`}}",
"associate_public_ip_address": "{{user `associate_public_ip_address`}}",
"launch_block_device_mappings": [{
"device_name": "/dev/xvda",
"volume_size": 20,
- "volume_type": "gp2",
+ "volume_type": "gp3",
"delete_on_termination": true
}],
"ami_block_device_mappings": [
done
}
+# $DIST should not have a dot if there is one in /etc/os-release (e.g. 18.04)
+DIST=$(. /etc/os-release; echo $ID$VERSION_ID | tr -d '.')
+
# Run apt-get update
$SUDO DEBIAN_FRONTEND=noninteractive apt-get --yes update
TMP_LSB=`/usr/bin/lsb_release -c -s`
LSB_RELEASE_CODENAME=${TMP_LSB//[$'\t\r\n ']}
+SET_RESOLVER=
+if [ -n "$RESOLVER" ]; then
+ SET_RESOLVER="--dns ${RESOLVER}"
+fi
+
# Add the arvados apt repository
echo "# apt.arvados.org" |$SUDO tee --append /etc/apt/sources.list.d/apt.arvados.org.list
echo "deb http://apt.arvados.org/$LSB_RELEASE_CODENAME $LSB_RELEASE_CODENAME${REPOSUFFIX} main" |$SUDO tee --append /etc/apt/sources.list.d/apt.arvados.org.list
# Install the Arvados packages we need
wait_for_apt_locks && $SUDO DEBIAN_FRONTEND=noninteractive apt-get -qq --yes install \
python3-arvados-fuse \
- arvados-docker-cleaner \
- docker.io
+ arvados-docker-cleaner
+
+# We want Docker 20.10 or later so that we support glibc 2.33 and up in the container, cf.
+# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005906
+dockerversion=5:20.10.13~3-0
+if [[ "$DIST" =~ ^debian ]]; then
+ family="debian"
+ if [ "$DIST" == "debian10" ]; then
+ distro="buster"
+ elif [ "$DIST" == "debian11" ]; then
+ distro="bullseye"
+ fi
+elif [[ "$DIST" =~ ^ubuntu ]]; then
+ family="ubuntu"
+ if [ "$DIST" == "ubuntu1804" ]; then
+ distro="bionic"
+ elif [ "$DIST" == "ubuntu2004" ]; then
+ distro="focal"
+ fi
+else
+ echo "Unsupported distribution $DIST"
+ exit 1
+fi
+curl -fsSL https://download.docker.com/linux/$family/gpg | $SUDO gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+echo deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/$family/ $distro stable | \
+ $SUDO tee /etc/apt/sources.list.d/docker.list
+$SUDO apt-get update
+$SUDO apt-get -yq --no-install-recommends install docker-ce=${dockerversion}~${family}-${distro}
+
+# Set a higher ulimit and the resolver (if set) for docker
+$SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
+ /lib/systemd/system/docker.service \
+ > /etc/systemd/system/docker.service
+
+$SUDO systemctl daemon-reload
+
+# docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
+# and the BootProbeCommand might be "docker ps -q"
+$SUDO systemctl disable docker
# Get Go and build singularity
goversion=1.17.1
$SUDO sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
$SUDO update-grub
-# Set a higher ulimit and the resolver (if set) for docker
-if [ "x$RESOLVER" != "x" ]; then
- SET_RESOLVER="--dns ${RESOLVER}"
-fi
-
-$SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
- /lib/systemd/system/docker.service \
- > /etc/systemd/system/docker.service
-
-$SUDO systemctl daemon-reload
-
-# docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
-# and the BootProbeCommand might be "docker ps -q"
-$SUDO systemctl disable docker
-
# Make sure user_allow_other is set in fuse.conf
$SUDO sed -i 's/#user_allow_other/user_allow_other/g' /etc/fuse.conf
$SUDO sed -i "s/#prepend domain-name-servers 127.0.0.1;/prepend domain-name-servers ${RESOLVER};/" /etc/dhcp/dhclient.conf
fi
-if [ "$AWS_EBS_AUTOSCALE" != "1" ]; then
+# AWS_EBS_AUTOSCALE is not always set, work around unset variable check
+EBS_AUTOSCALE=${AWS_EBS_AUTOSCALE:-}
+
+if [ "$EBS_AUTOSCALE" != "1" ]; then
# Set up the cloud-init script that will ensure encrypted disks
$SUDO mv /tmp/usr-local-bin-ensure-encrypted-partitions.sh /usr/local/bin/ensure-encrypted-partitions.sh
else
$SUDO chown root:root /etc/cloud/cloud.cfg.d/07_compute_arvados_dispatch_cloud.cfg
if [ "$NVIDIA_GPU_SUPPORT" == "1" ]; then
- # $DIST should not have a dot if there is one in /etc/os-release (e.g. 18.04)
- DIST=$(. /etc/os-release; echo $ID$VERSION_ID | tr -d '.')
# We need a kernel and matching headers
if [[ "$DIST" =~ ^debian ]]; then
$SUDO apt-get -y install linux-image-cloud-amd64 linux-headers-cloud-amd64
$SUDO apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/7fa2af80.pub
$SUDO apt-get -y install software-properties-common
$SUDO add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$DIST/x86_64/ /"
- $SUDO add-apt-repository contrib
+ # Ubuntu 18.04's add-apt-repository does not understand 'contrib'
+ $SUDO add-apt-repository contrib || true
$SUDO apt-get update
$SUDO apt-get -y install cuda
$SUDO tee /etc/apt/sources.list.d/libnvidia-container.list
fi
- if [ "$DIST" == "debian10" ]; then
- # Debian 10 comes with Docker 18.xx, we need 19.03 or later
- curl -fsSL https://download.docker.com/linux/debian/gpg | $SUDO gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
- echo deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian/ buster stable | \
- $SUDO tee /etc/apt/sources.list.d/docker.list
- $SUDO apt-get update
- $SUDO apt-get -yq --no-install-recommends install docker-ce=5:19.03.15~3-0~debian-buster
-
- $SUDO sed "s/ExecStart=\(.*\)/ExecStart=\1 --default-ulimit nofile=10000:10000 ${SET_RESOLVER}/g" \
- /lib/systemd/system/docker.service \
- > /etc/systemd/system/docker.service
-
- $SUDO systemctl daemon-reload
-
- # docker should not start on boot: we restart it inside /usr/local/bin/ensure-encrypted-partitions.sh,
- # and the BootProbeCommand might be "docker ps -q"
- $SUDO systemctl disable docker
- fi
$SUDO apt-get update
$SUDO apt-get -y install libnvidia-container1 libnvidia-container-tools nvidia-container-toolkit
# This service fails to start when the image is booted without Nvidia GPUs present, which makes
exit 0
fi
-# FIXME! #16992 Temporary fix for psql call in arvados-api-server
-if [ -e /root/.psqlrc ]; then
- if ! ( grep 'pset pager off' /root/.psqlrc ); then
- RESTORE_PSQL="yes"
- cp /root/.psqlrc /root/.psqlrc.provision.backup
- fi
-else
- DELETE_PSQL="yes"
-fi
-
-echo '\pset pager off' >> /root/.psqlrc
-# END FIXME! #16992 Temporary fix for psql call in arvados-api-server
-
# Now run the install
salt-call --local state.apply -l ${LOG_LEVEL}
sed -i 's/^manage_etc_hosts: true/#manage_etc_hosts: true/g' /etc/cloud/cloud.cfg.d/*
fi
-# FIXME! #16992 Temporary fix for psql call in arvados-api-server
-if [ "x${DELETE_PSQL}" = "xyes" ]; then
- echo "Removing .psql file"
- rm /root/.psqlrc
-fi
-
-if [ "x${RESTORE_PSQL}" = "xyes" ]; then
- echo "Restoring .psql file"
- mv -v /root/.psqlrc.provision.backup /root/.psqlrc
-fi
-# END FIXME! #16992 Temporary fix for psql call in arvados-api-server
-
# Leave a copy of the Arvados CA so the user can copy it where it's required
if [ "$DEV_MODE" = "yes" ]; then
echo "Copying the Arvados CA certificate to the installer dir, so you can import it"
projects / arvados.git / commitdiff
