PACKAGE_NAME=$1; shift
fi
-cd "/var/www/${PACKAGE_NAME%-server}/current"
+API_GEMS_LS="$(mktemp --tmpdir api-gems-XXXXXX.list)"
+trap 'rm -f "$API_GEMS_LS"' EXIT INT TERM QUIT
+
+cd "/var/www/${PACKAGE_NAME%-server}"
+
+check_gem_dirs() {
+ local when="$1"; shift
+ env -C shared/vendor_bundle/ruby ls -1 >"$API_GEMS_LS"
+ local ls_count="$(wc -l <"$API_GEMS_LS")"
+ if [ "$ls_count" = 1 ]; then
+ return 0
+ fi
+ echo "Package $PACKAGE_NAME FAILED: $ls_count gem directories created after $when:" >&2
+ case "${ARVADOS_DEBUG:-0}" in
+ 0) cat "$API_GEMS_LS" >&2 ;;
+ *) env -C shared/vendor_bundle/ruby find -maxdepth 3 -type d -ls >&2 ;;
+ esac
+ return 11
+}
+
+check_gem_dirs "initial install"
case "$TARGET" in
debian*|ubuntu*)
;;
esac
-bundle list >"$ARV_PACKAGES_DIR/$PACKAGE_NAME.gems"
+check_gem_dirs "package reinstall"
+env -C current bundle list >"$ARV_PACKAGES_DIR/$PACKAGE_NAME.gems"
set -e
-DATABASE_READY=1
-APPLICATION_READY=1
-
-report_not_ready() {
- local ready_flag="$1"; shift
- local config_file="$1"; shift
- if [ "1" != "$ready_flag" ]; then cat >&2 <<EOF
-
-PLEASE NOTE:
-
-The $PACKAGE_NAME package was not configured completely because
-$config_file needs some tweaking.
-Please refer to the documentation at
-<$DOC_URL> for more details.
-
-When $(basename "$config_file") has been modified,
-reconfigure or reinstall this package.
-
-EOF
- fi
-}
+for DISTRO_FAMILY in $(. /etc/os-release && echo "${ID:-} ${ID_LIKE:-}"); do
+ case "$DISTRO_FAMILY" in
+ debian)
+ RESETUP_CMD="dpkg-reconfigure $PACKAGE_NAME"
+ break ;;
+ rhel)
+ RESETUP_CMD="dnf reinstall $PACKAGE_NAME"
+ break ;;
+ esac
+done
+if [ -z "$RESETUP_CMD" ]; then
+ echo "$PACKAGE_NAME postinst skipped: don't recognize the distribution from /etc/os-release" >&2
+ exit 0
+fi
+# Default documentation URL. This can be set to a more specific URL.
+NOT_READY_DOC_URL="https://doc.arvados.org/install/install-api-server.html"
report_web_service_warning() {
local warning="$1"; shift
To override, set the WEB_SERVICE environment variable to the name of the service
hosting the Rails server.
-For Debian-based systems, then reconfigure this package with dpkg-reconfigure.
-
-For RPM-based systems, then reinstall this package.
-
+After you do that, resume $PACKAGE_NAME setup by running:
+ $RESETUP_CMD
EOF
}
run_and_report "Running db:migrate" \
bin/rake db:migrate
elif echo "$DB_MIGRATE_STATUS" | grep -q 'database .* does not exist'; then
- if ! run_and_report "Running db:setup" \
- bin/rake db:setup 2>/dev/null; then
- echo "Warning: unable to set up database." >&2
- DATABASE_READY=0
- fi
+ run_and_report "Running db:setup" bin/rake db:setup
else
- echo "Warning: Database is not ready to set up. Skipping database setup." >&2
- DATABASE_READY=0
+ # We don't have enough configuration to even check the database.
+ return 1
fi
}
"Multiple web services found. Choosing the first one ($WEB_SERVICE)"
fi
- if [ -e /etc/redhat-release ]; then
- # Recognize any service that starts with "nginx"; e.g., nginx16.
- if [ "$WEB_SERVICE" != "${WEB_SERVICE#nginx}" ]; then
- WWW_OWNER=nginx
- else
- WWW_OWNER=apache
- fi
- else
- # Assume we're on a Debian-based system for now.
- # Both Apache and Nginx run as www-data by default.
- WWW_OWNER=www-data
- fi
-
- echo
- echo "Assumption: $WEB_SERVICE is configured to serve Rails from"
- echo " $RELEASE_PATH"
- echo "Assumption: $WEB_SERVICE and passenger run as $WWW_OWNER"
- echo
-
- echo -n "Creating symlinks to configuration in $CONFIG_PATH ..."
- setup_confdirs /etc/arvados "$CONFIG_PATH"
- setup_conffile environments/production.rb environments/production.rb.example \
- || true
- setup_extra_conffiles
- echo "... done."
+ case "$DISTRO_FAMILY" in
+ debian) WWW_OWNER=www-data ;;
+ rhel) case "$WEB_SERVICE" in
+ httpd*) WWW_OWNER=apache ;;
+ nginx*) WWW_OWNER=nginx ;;
+ esac
+ ;;
+ esac
# Before we do anything else, make sure some directories and files are in place
if [ ! -e $SHARED_PATH/log ]; then mkdir -p $SHARED_PATH/log; fi
export RAILS_ENV=production
run_and_report "Installing bundler" gem install --conservative --version '~> 2.4.0' bundler
+ local ruby_minor_ver="$(ruby -e 'puts RUBY_VERSION.split(".")[..1].join(".")')"
local bundle="$(gem contents --version '~> 2.4.0' bundler | grep -E '/(bin|exe)/bundle$' | tail -n1)"
if ! [ -x "$bundle" ]; then
# Some distros (at least Ubuntu 24.04) append the Ruby version to the
# executable name, but that isn't reflected in the output of
# `gem contents`. Check for that version.
- bundle="$bundle$(ruby -e 'puts RUBY_VERSION.split(".")[..1].join(".")')"
+ bundle="$bundle$ruby_minor_ver"
if ! [ -x "$bundle" ]; then
echo "Error: failed to find \`bundle\` command after installing bundler gem" >&2
return 1
find vendor/cache -maxdepth 1 -name '*.gem' -print0 \
| run_and_report "Installing bundle gems" xargs -0r \
gem install --conservative --ignore-dependencies --local --quiet \
- --install-dir="$bundle_path/ruby/$(ruby -e 'puts RUBY_VERSION')"
+ --install-dir="$bundle_path/ruby/$ruby_minor_ver.0"
run_and_report "Running bundle install" "$bundle" install --prefer-local --quiet
run_and_report "Verifying bundle is complete" "$bundle" exec true
- echo -n "Ensuring directory and file permissions ..."
- # Ensure correct ownership of a few files
- chown "$WWW_OWNER:" $RELEASE_PATH/config/environment.rb
- chown "$WWW_OWNER:" $RELEASE_PATH/config.ru
- chown "$WWW_OWNER:" $RELEASE_PATH/Gemfile.lock
- chown -R "$WWW_OWNER:" $RELEASE_PATH/tmp || true
- chown -R "$WWW_OWNER:" $SHARED_PATH/log
- # Make sure postgres doesn't try to use a pager.
- export PAGER=
- case "$RAILSPKG_DATABASE_LOAD_TASK" in
- # db:structure:load was deprecated in Rails 6.1 and shouldn't be used.
- db:schema:load | db:structure:load)
- chown "$WWW_OWNER:" $RELEASE_PATH/db/schema.rb || true
- chown "$WWW_OWNER:" $RELEASE_PATH/db/structure.sql || true
- ;;
- esac
- chmod 644 $SHARED_PATH/log/*
- chmod -R 2775 $RELEASE_PATH/tmp || true
- echo "... done."
+ if [ -z "$WWW_OWNER" ]; then
+ NOT_READY_REASON="there is no web service account to own Arvados configuration"
+ NOT_READY_DOC_URL="https://doc.arvados.org/install/nginx.html"
+ else
+ cat <<EOF
+
+Assumption: $WEB_SERVICE is configured to serve Rails from
+ $RELEASE_PATH
+Assumption: $WEB_SERVICE and passenger run as $WWW_OWNER
+
+EOF
- if [ -n "$RAILSPKG_DATABASE_LOAD_TASK" ]; then
- prepare_database
+ echo -n "Creating symlinks to configuration in $CONFIG_PATH ..."
+ setup_confdirs /etc/arvados "$CONFIG_PATH"
+ setup_conffile environments/production.rb environments/production.rb.example \
+ || true
+ setup_extra_conffiles
+ echo "... done."
+
+ echo -n "Ensuring directory and file permissions ..."
+ # Ensure correct ownership of a few files
+ chown "$WWW_OWNER:" $RELEASE_PATH/config/environment.rb
+ chown "$WWW_OWNER:" $RELEASE_PATH/config.ru
+ chown "$WWW_OWNER:" $RELEASE_PATH/Gemfile.lock
+ chown -R "$WWW_OWNER:" $SHARED_PATH/log
+ # Make sure postgres doesn't try to use a pager.
+ export PAGER=
+ case "$RAILSPKG_DATABASE_LOAD_TASK" in
+ # db:structure:load was deprecated in Rails 6.1 and shouldn't be used.
+ db:schema:load | db:structure:load)
+ chown "$WWW_OWNER:" $RELEASE_PATH/db/schema.rb || true
+ chown "$WWW_OWNER:" $RELEASE_PATH/db/structure.sql || true
+ ;;
+ esac
+ chmod 644 $SHARED_PATH/log/*
+ echo "... done."
fi
- if [ -e /etc/arvados/config.yml ]; then
- # warn about config errors (deprecated/removed keys from
- # previous version, etc)
- run_and_report "Checking configuration for completeness" \
- bin/rake config:check || APPLICATION_READY=0
- else
- APPLICATION_READY=0
+ if [ -n "$NOT_READY_REASON" ]; then
+ :
+ # warn about config errors (deprecated/removed keys from
+ # previous version, etc)
+ elif ! run_and_report "Checking configuration for completeness" bin/rake config:check; then
+ NOT_READY_REASON="you must add required configuration settings to /etc/arvados/config.yml"
+ NOT_READY_DOC_URL="https://doc.arvados.org/install/install-api-server.html#update-config"
+ elif [ -z "$RAILSPKG_DATABASE_LOAD_TASK" ]; then
+ :
+ elif ! prepare_database; then
+ NOT_READY_REASON="database setup could not be completed"
fi
- chown -R "$WWW_OWNER:" $RELEASE_PATH/tmp
+ if [ -n "$WWW_OWNER" ]; then
+ chown -R "$WWW_OWNER:" $RELEASE_PATH/tmp
+ chmod -R 2775 $RELEASE_PATH/tmp
+ fi
- if [ -n "$SERVICE_MANAGER" ]; then
+ if [ -z "$NOT_READY_REASON" ] && [ -n "$SERVICE_MANAGER" ]; then
service_command "$SERVICE_MANAGER" restart "$WEB_SERVICE"
fi
}
-if [ "$1" = configure ]; then
- # This is a debian-based system
- configure_version
-elif [ "$1" = "0" ] || [ "$1" = "1" ] || [ "$1" = "2" ]; then
- # This is an rpm-based system
- configure_version
-fi
+configure_version
+if [ -n "$NOT_READY_REASON" ]; then
+ cat >&2 <<EOF
+NOTE: The $PACKAGE_NAME package was not configured completely because
+$NOT_READY_REASON.
+Please refer to the documentation for next steps:
+ <$NOT_READY_DOC_URL>
-report_not_ready "$APPLICATION_READY" "/etc/arvados/config.yml"
+After you do that, resume $PACKAGE_NAME setup by running:
+ $RESETUP_CMD
+EOF
+fi
else
local rpm_root
case "$TARGET" in
- rocky8) rpm_root="CentOS/8/dev" ;;
+ rocky8) rpm_root="RHEL/8/dev" ;;
*)
echo "FIXME: Don't know RPM URL path for $TARGET, building"
return 0
sdk/go/keepclient
sdk/go/health
sdk/go/httpserver
-sdk/go/manifest
sdk/go/blockdigest
sdk/go/asyncbuf
sdk/go/stats
<pre><code># <span class="userinput">tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
-baseurl=http://rpm.arvados.org/CentOS/$releasever/os/$basearch/
+baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
-gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF</span>
{%- if modules_to_enable != nil %}
# <span class="userinput">dnf module enable {{ modules_to_enable }}</span>
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
|name|string|||
-|description|text|||
+|description|text|Free text description of the group. May be HTML formatted, must be appropriately sanitized before display.||
|properties|hash|User-defined metadata, may be used in queries using "subproperty filters":{{site.baseurl}}/api/methods.html#subpropertyfilters ||
|portable_data_hash|string|The MD5 sum of the manifest text stripped of block hints other than the size hint.||
-|manifest_text|text|||
+|manifest_text|text|The manifest describing how to assemble blocks into files, in the "Arvados manifest format":{{site.baseurl}}/architecture/manifest-format.html||
|replication_desired|number|Minimum storage replication level desired for each data block referenced by this collection. A value of @null@ signifies that the site default replication level (typically 2) is desired.|@2@|
|replication_confirmed|number|Replication level most recently confirmed by the storage system. This field is null when a collection is first created, and is reset to null when the manifest_text changes in a way that introduces a new data block. An integer value indicates the replication level of the _least replicated_ data block in the collection.|@2@, null|
|replication_confirmed_at|datetime|When @replication_confirmed@ was confirmed. If @replication_confirmed@ is null, this field is also null.||
Data can be shared with other users via the Arvados permission model.
+h3(#trashing). Trashing collections
+
+Collections can be trashed by updating the record and setting the @trash_at@ field, or with the "delete":#delete method. The delete method sets @trash_at@ to "now".
+
+The value of @trash_at@ can be set to a time in the future as a feature to automatically expire collections.
+
+When @trash_at@ is set, @delete_at@ will also be set. Normally @delete_at = trash_at + Collections.DefaultTrashLifetime@. When the @trash_at@ time is past but @delete_at@ is in the future, the trashed collection is invisible to most API calls unless the @include_trash@ parameter is true. Collections in the trashed state can be "untrashed":#untrash so long as @delete_at@ has not past. Collections are also trashed if they are contained in a "trashed group":groups.html#trashing
+
+Once @delete_at@ is past, the collection and all of its previous versions will be deleted permanently and can no longer be untrashed.
+
+h3(#replace_files). Using "replace_files" to create/update collections
+
+The @replace_files@ option can be used with the "create":#create and "update":#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>
+
h2. Methods
See "Common resource methods":{{site.baseurl}}/api/methods.html for more information about @create@, @delete@, @get@, @list@, and @update@.
Supports federated @get@ only, which may be called with either a uuid or a portable data hash. When requesting a portable data hash which is not available on the home cluster, the query is forwarded to all the clusters listed in @RemoteClusters@ and returns the first successful result.
-h3. create
+h3(#create). create
Create a new Collection.
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
+h3(#delete). delete
Put a Collection in the trash. This sets the @trash_at@ field to @now@ and @delete_at@ field to @now@ + token TTL. A trashed collection is invisible to most API calls unless the @include_trash@ parameter is true.
filters: [["file_names", "ilike", "%dir1/dir2/dir3%"], ["file_names", "ilike", "%sample1234.fastq%"]]
</pre>
-h3. update
+h3(#update). update
Update attributes of an existing Collection.
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
+h3(#untrash). untrash
Remove a Collection from the trash. This sets the @trash_at@ and @delete_at@ fields to @null@.
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>
|group_class|string|Type of group. @project@ and @filter@ indicate that the group should be displayed by Workbench and arv-mount as a project for organizing and naming objects. @role@ is used as part of the "permission system":{{site.baseurl}}/api/permission-model.html. |@"filter"@
@"project"@
@"role"@|
-|description|text|||
+|description|text|Free text description of the group. May be HTML formatted, must be appropriately sanitized before display.||
|properties|hash|User-defined metadata, may be used in queries using "subproperty filters":{{site.baseurl}}/api/methods.html#subpropertyfilters ||
|writable_by|array|(Deprecated) List of UUID strings identifying Users and other Groups that have write permission for this Group. Users who are allowed to administer the Group will receive a list of user/group UUIDs that have permission via explicit permission links; permissions via parent/ancestor groups are not taken into account. Other users will receive a partial list including only the Group's owner_uuid and (if applicable) their own user UUID.||
|can_write|boolean|True if the current user has write permission on this group.||
|can_manage|boolean|True if the current user has manage permission on this group.||
-|trash_at|datetime|If @trash_at@ is non-null and in the past, this group and all objects directly or indirectly owned by the group will be hidden from API calls. May be untrashed.||
+|trash_at|datetime|If @trash_at@ is non-null and in the past, this group and all objects directly or indirectly owned by the group will be hidden from API calls. May be untrashed as long as @delete_at@ is in the future.||
|delete_at|datetime|If @delete_at@ is non-null and in the past, the group and all objects directly or indirectly owned by the group may be permanently deleted.||
|is_trashed|datetime|True if @trash_at@ is in the past, false if not.||
|frozen_by_uuid|string|For a frozen project, indicates the user who froze the project; null in all other cases. When a project is frozen, no further changes can be made to the project or its contents, even by admins. Attempting to add new items or modify, rename, move, trash, or delete the project or its contents, including any subprojects, will return an error.||
-h3(#frozen). Frozen projects
+h2. Group types and states
-A user with @manage@ permission can set the @frozen_by_uuid@ attribute of a @project@ group to their own user UUID. Once this is done, no further changes can be made to the project or its contents, including subprojects.
+h3(#project). Project groups
-The @frozen_by_uuid@ attribute can be cleared by an admin user. It can also be cleared by a user with @manage@ permission, unless the @API.UnfreezeProjectRequiresAdmin@ configuration setting is active.
+Groups with @group_class: project@ are used to organize objects and subprojects through ownership. When "trashed or deleted":#trashing, all items owned by the project (including subprojects, collections, or container requests) as well as permissions (permission links) granted to the project are also trashed or deleted.
-The optional @API.FreezeProjectRequiresDescription@ and @API.FreezeProjectRequiresProperties@ configuration settings can be used to prevent users from freezing projects that have empty @description@ and/or specified @properties@ entries.
+h3(#role). Role groups
+
+Groups with @group_class: role@ are used to grant permissions to users (or other groups) through permission links. Role groups can confer "can_manage" permission but cannot directly own objects. When "trashed and deleted":#trashing group membership and permission grants (expressed as permission links) are deleted as well.
h3(#filter). Filter groups
-@filter@ groups are virtual groups; they can not own other objects. Filter groups have a special @properties@ field named @filters@, which must be an array of filter conditions. See "list method filters":{{site.baseurl}}/api/methods.html#filters for details on the syntax of valid filters, but keep in mind that the attributes must include the object type (@collections@, @container_requests@, @groups@, @workflows@), separated with a dot from the field to be filtered on.
+Groups with @group_class: filter@ groups are virtual groups; they can not own other objects, but instead their contents (as returned by the "contents":#contents API method) are defined by a query. Filter groups have a special @properties@ field named @filters@, which must be an array of filter conditions. See "list method filters":{{site.baseurl}}/api/methods.html#filters for details on the syntax of valid filters, but keep in mind that the attributes must include the object type (@collections@, @container_requests@, @groups@, @workflows@), separated with a dot from the field to be filtered on.
Filters are applied with an implied *and* between them, but each filter only applies to the object type specified. The results are subject to the usual access controls - they are a subset of all objects the user can see. Here is an example:
},
</pre>
+"Trashed or deleting":#trashing a filter group causes the group itself to be hidden or deleted, but has no effect on the items returned in "contents", i.e. the database objects in "contents" are not hidden or deleted and may be accessed by other means.
+
+h3(#trashing). Trashing groups
+
+Groups can be trashed by updating the record and setting the @trash_at@ field, or with the "delete":#delete method. The delete method sets @trash_at@ to "now".
+
+The value of @trash_at@ can be set to a time in the future as a feature to automatically expire groups.
+
+When @trash_at@ is set, @delete_at@ will also be set. Normally @delete_at = trash_at + Collections.DefaultTrashLifetime@ for projects and filter groups, and @delete_at = trash_at@ for role groups. When the @trash_at@ time is past but @delete_at@ is in the future, the trashed group is invisible to most API calls unless the @include_trash@ parameter is true. All objects directly or indirectly owned by the group (including subprojects, collections, or container requests) are considered trashed as well. Groups in the trashed state can be "untrashed":#untrash so long as @delete_at@ has not past.
+
+Once @delete_at@ is past, the group will be deleted permanently and can no longer be untrashed. Different group types have different behavior when deleted, described above.
+
+Note: like other groups, "role" groups may have @trash_at@ set to date in the future, however roles groups are required to have @delete_at = trash_at@, so the trash time and delete time expire at the same time. This means once @trash_at@ expires the role group is deleted immediately. Role groups with @trash_at@ set can only be "untrashed":#untrash before they expire.
+
+h3(#frozen). Frozen projects
+
+A user with @manage@ permission can set the @frozen_by_uuid@ attribute of a @project@ group to their own user UUID. Once this is done, no further changes can be made to the project or its contents, including subprojects.
+
+The @frozen_by_uuid@ attribute can be cleared by an admin user. It can also be cleared by a user with @manage@ permission, unless the @API.UnfreezeProjectRequiresAdmin@ configuration setting is active.
+
+The optional @API.FreezeProjectRequiresDescription@ and @API.FreezeProjectRequiresProperties@ configuration settings can be used to prevent users from freezing projects that have empty @description@ and/or empty @properties@ entries.
+
h2. Methods
See "Common resource methods":{{site.baseurl}}/api/methods.html for more information about @create@, @delete@, @get@, @list@, and @update@.
|group|object||query||
|async|boolean (default false)|Defer the permissions graph update by a configured number of seconds. (By default, @async_permissions_update_interval@ is 20 seconds). On success, the response is 202 (Accepted).|query|@true@|
-h3. delete
+h3(#delete). delete
-Put a Group in the trash. This sets the @trash_at@ field to @now@ and @delete_at@ field to @now@ + token TTL. A trashed group is invisible to most API calls unless the @include_trash@ parameter is true. All objects directly or indirectly owned by the Group are considered trashed as well.
+Put a Group in the trash. See "Trashing groups":#trashing for details.
Arguments:
|group|object||query||
|async|boolean (default false)|Defer the permissions graph update by a configured number of seconds. (By default, @async_permissions_update_interval@ is 20 seconds). On success, the response is 202 (Accepted).|query|@true@|
-h3. untrash
+h3(#untrash). untrash
-Remove a Group from the trash. This sets the @trash_at@ and @delete_at@ fields to @null@.
+Remove a Group from the trash. Only valid when @delete_at@ is in the future. This sets the @trash_at@ and @delete_at@ fields to @null@.
Arguments:
github.com/gogo/protobuf v1.3.2
github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510
github.com/gorilla/mux v1.8.0
- github.com/hashicorp/go-retryablehttp v0.7.6
+ github.com/hashicorp/go-retryablehttp v0.7.7
github.com/hashicorp/golang-lru v1.0.2
github.com/hashicorp/yamux v0.1.1
github.com/jmcvetta/randutil v0.0.0-20150817122601-2bb1b664bcff
golang.org/x/sys v0.20.0
google.golang.org/api v0.181.0
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
- gopkg.in/square/go-jose.v2 v2.6.0
+ gopkg.in/go-jose/go-jose.v2 v2.6.3
rsc.io/getopt v0.0.0-20170811000552-20be20937449
)
github.com/hashicorp/go-cleanhttp v0.5.2/go.mod h1:kO/YDlP8L1346E6Sodw+PrpBSV4/SoxCXGY6BqNFT48=
github.com/hashicorp/go-hclog v1.6.3 h1:Qr2kF+eVWjTiYmU7Y31tYlP1h0q/X3Nl3tPGdaB11/k=
github.com/hashicorp/go-hclog v1.6.3/go.mod h1:W4Qnvbt70Wk/zYJryRzDRU/4r0kIg0PVHBcfoyhpF5M=
-github.com/hashicorp/go-retryablehttp v0.7.6 h1:TwRYfx2z2C4cLbXmT8I5PgP/xmuqASDyiVuGYfs9GZM=
-github.com/hashicorp/go-retryablehttp v0.7.6/go.mod h1:pkQpWZeYWskR+D1tR2O5OcBFOxfA7DoAO6xtkuQnHTk=
+github.com/hashicorp/go-retryablehttp v0.7.7 h1:C8hUCYzor8PIfXHa4UrZkU4VvK8o9ISHxT2Q8+VepXU=
+github.com/hashicorp/go-retryablehttp v0.7.7/go.mod h1:pkQpWZeYWskR+D1tR2O5OcBFOxfA7DoAO6xtkuQnHTk=
github.com/hashicorp/golang-lru v1.0.2 h1:dV3g9Z/unq5DpblPpw+Oqcv4dU/1omnb4Ok8iPY6p1c=
github.com/hashicorp/golang-lru v1.0.2/go.mod h1:iADmTwqILo4mZ8BN3D2Q6+9jd8WM5uGBxy+E8yxSoD4=
github.com/hashicorp/yamux v0.1.1 h1:yrQxtgseBDrq9Y652vSRDvsKCJKOUD+GzTS4Y0Y8pvE=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
+gopkg.in/go-jose/go-jose.v2 v2.6.3 h1:nt80fvSDlhKWQgSWyHyy5CfmlQr+asih51R8PTWNKKs=
+gopkg.in/go-jose/go-jose.v2 v2.6.3/go.mod h1:zzZDPkNNw/c9IE7Z9jr11mBZQhKQTMzoEEIoEdZlFBI=
gopkg.in/mgo.v2 v2.0.0-20180705113604-9856a29383ce/go.mod h1:yeKp02qBN3iKW1OzL3MGk2IdtZzaj7SFntXj72NppTA=
-gopkg.in/square/go-jose.v2 v2.6.0 h1:NGk74WTnPKBNUhNzQX7PYcTLUjoq7mzKk2OKbvwk2iI=
-gopkg.in/square/go-jose.v2 v2.6.0/go.mod h1:M9dMgbHiYLoDGQrXy7OpJDJWiKiU//h+vD76mk0e1AI=
gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
"strings"
"time"
+ "git.arvados.org/arvados.git/lib/ctrlctx"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/auth"
// them.
opts.Select = append([]string{"is_trashed", "trash_at"}, opts.Select...)
}
+ err = conn.lockUUID(ctx, opts.UUID)
+ if err != nil {
+ return arvados.Collection{}, err
+ }
if opts.Attrs, err = conn.applyReplaceFilesOption(ctx, opts.UUID, opts.Attrs, opts.ReplaceFiles); err != nil {
return arvados.Collection{}, err
}
coll.ManifestText = arvados.SignManifest(coll.ManifestText, token, exp, ttl, []byte(conn.cluster.Collections.BlobSigningKey))
}
+func (conn *Conn) lockUUID(ctx context.Context, uuid string) error {
+ tx, err := ctrlctx.CurrentTx(ctx)
+ if err != nil {
+ return err
+ }
+ _, err = tx.ExecContext(ctx, `insert into uuid_locks (uuid) values ($1) on conflict (uuid) do update set n=uuid_locks.n+1`, uuid)
+ if err != nil {
+ return err
+ }
+ return nil
+}
+
// 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
"sort"
"strconv"
"strings"
+ "sync"
"time"
"git.arvados.org/arvados.git/lib/ctrlctx"
c.Check(found, check.DeepEquals, expected)
}
+// Until #21701 it's hard to test from the outside whether the
+// uuid_lock mechanism is effectively serializing concurrent
+// replace_files updates to a single collection. For now, we're
+// really just checking that it doesn't cause updates to deadlock or
+// anything like that.
+func (s *CollectionSuite) TestCollectionUpdateLock(c *check.C) {
+ adminctx := ctrlctx.NewWithToken(s.ctx, s.cluster, arvadostest.AdminToken)
+ foo, err := s.localdb.railsProxy.CollectionCreate(adminctx, arvados.CreateOptions{
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ "manifest_text": ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo.txt\n",
+ }})
+ c.Assert(err, check.IsNil)
+ dst, err := s.localdb.CollectionCreate(s.userctx, arvados.CreateOptions{
+ ReplaceFiles: map[string]string{
+ "/foo.txt": foo.PortableDataHash + "/foo.txt",
+ },
+ Attrs: map[string]interface{}{
+ "owner_uuid": arvadostest.ActiveUserUUID,
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, dst, "foo.txt")
+
+ var wg sync.WaitGroup
+ for i := 0; i < 10; i++ {
+ name1, name2 := "a", "b"
+ if i&1 == 1 {
+ name1, name2 = "b", "a"
+ }
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ upd, err := s.localdb.CollectionUpdate(s.userctx, arvados.UpdateOptions{
+ UUID: dst.UUID,
+ ReplaceFiles: map[string]string{
+ "/" + name1: foo.PortableDataHash + "/foo.txt",
+ "/" + name2: "",
+ "/foo.txt": "",
+ }})
+ c.Assert(err, check.IsNil)
+ s.expectFiles(c, upd, name1)
+ }()
+ }
+ wg.Wait()
+}
+
func (s *CollectionSuite) TestSignatures(c *check.C) {
resp, err := s.localdb.CollectionGet(s.userctx, arvados.GetOptions{UUID: arvadostest.FooCollection})
c.Check(err, check.IsNil)
"golang.org/x/oauth2"
"google.golang.org/api/option"
"google.golang.org/api/people/v1"
- "gopkg.in/square/go-jose.v2/jwt"
+ "gopkg.in/go-jose/go-jose.v2/jwt"
)
var (
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/keepclient"
- "git.arvados.org/arvados.git/sdk/go/manifest"
"github.com/bmatcuk/doublestar/v4"
)
// copied from the local filesystem.
//
// Symlinks to mounted collections, and any collections mounted under
-// ctrOutputDir, are copied by transforming the relevant parts of the
-// existing manifests, without moving any data around.
+// ctrOutputDir, are copied by reference, without moving any data
+// around.
//
// Symlinks to other parts of the container's filesystem result in
// errors.
secretMounts map[string]arvados.Mount
logger printfer
- dirs []string
- files []filetodo
- manifest string
+ dirs []string
+ files []filetodo
+ staged arvados.CollectionFileSystem
- manifestCache map[string]*manifest.Manifest
+ manifestCache map[string]string
}
// Copy copies data as needed, and returns a new manifest.
+//
+// Copy should not be called more than once.
func (cp *copier) Copy() (string, error) {
- err := cp.walkMount("", cp.ctrOutputDir, limitFollowSymlinks, true)
+ var err error
+ cp.staged, err = (&arvados.Collection{}).FileSystem(cp.client, cp.keepClient)
if err != nil {
- return "", fmt.Errorf("error scanning files to copy to output: %v", err)
+ return "", fmt.Errorf("error creating Collection.FileSystem: %v", err)
}
- collfs, err := (&arvados.Collection{ManifestText: cp.manifest}).FileSystem(cp.client, cp.keepClient)
+ err = cp.walkMount("", cp.ctrOutputDir, limitFollowSymlinks, true)
if err != nil {
- return "", fmt.Errorf("error creating Collection.FileSystem: %v", err)
+ return "", fmt.Errorf("error scanning files to copy to output: %v", err)
}
- // Remove files/dirs that don't match globs (the ones that
- // were added during cp.walkMount() by copying subtree
- // manifests into cp.manifest).
- err = cp.applyGlobsToCollectionFS(collfs)
+ // Remove files/dirs that don't match globs (the files/dirs
+ // that were added during cp.walkMount() by copying subtree
+ // manifests into cp.staged).
+ err = cp.applyGlobsToStaged()
if err != nil {
return "", fmt.Errorf("error while removing non-matching files from output collection: %w", err)
}
- // Remove files/dirs that don't match globs (the ones that are
- // stored on the local filesystem and would need to be copied
- // in copyFile() below).
+ // Remove files/dirs that don't match globs (the files/dirs
+ // that are stored on the local filesystem and would need to
+ // be copied in copyFile() below).
cp.applyGlobsToFilesAndDirs()
for _, d := range cp.dirs {
- err = collfs.Mkdir(d, 0777)
+ err = cp.staged.Mkdir(d, 0777)
if err != nil && err != os.ErrExist {
return "", fmt.Errorf("error making directory %q in output collection: %v", d, err)
}
// open so f's data can be packed with it).
dir, _ := filepath.Split(f.dst)
if dir != lastparentdir || unflushed > keepclient.BLOCKSIZE {
- if err := collfs.Flush("/"+lastparentdir, dir != lastparentdir); err != nil {
+ if err := cp.staged.Flush("/"+lastparentdir, dir != lastparentdir); err != nil {
return "", fmt.Errorf("error flushing output collection file data: %v", err)
}
unflushed = 0
}
lastparentdir = dir
- n, err := cp.copyFile(collfs, f)
+ n, err := cp.copyFile(cp.staged, f)
if err != nil {
return "", fmt.Errorf("error copying file %q into output collection: %v", f, err)
}
unflushed += n
}
- return collfs.MarshalManifest(".")
+ return cp.staged.MarshalManifest(".")
}
func (cp *copier) matchGlobs(path string, isDir bool) bool {
cp.files = keepfiles
}
-// Delete files in collfs that do not match cp.globs. Also delete
+// Delete files in cp.staged that do not match cp.globs. Also delete
// directories that are empty (after deleting non-matching files) and
// do not match cp.globs themselves.
-func (cp *copier) applyGlobsToCollectionFS(collfs arvados.CollectionFileSystem) error {
+func (cp *copier) applyGlobsToStaged() error {
if len(cp.globs) == 0 {
return nil
}
include := make(map[string]bool)
- err := fs.WalkDir(arvados.FS(collfs), "", func(path string, ent fs.DirEntry, err error) error {
+ err := fs.WalkDir(arvados.FS(cp.staged), "", func(path string, ent fs.DirEntry, err error) error {
if cp.matchGlobs(path, ent.IsDir()) {
for i, c := range path {
if i > 0 && c == '/' {
if err != nil {
return err
}
- err = fs.WalkDir(arvados.FS(collfs), "", func(path string, ent fs.DirEntry, err error) error {
+ err = fs.WalkDir(arvados.FS(cp.staged), "", func(path string, ent fs.DirEntry, err error) error {
if err != nil || path == "" {
return err
}
if !include[path] {
- err := collfs.RemoveAll(path)
+ err := cp.staged.RemoveAll(path)
if err != nil {
return err
}
return n, dst.Close()
}
-// Append to cp.manifest, cp.files, and cp.dirs so as to copy src (an
+// Add to cp.staged, cp.files, and cp.dirs so as to copy src (an
// absolute path in the container's filesystem) to dest (an absolute
// path in the output collection, or "" for output root).
//
if err != nil {
return err
}
- cp.manifest += mft.Extract(srcRelPath, dest).Text
+ err = cp.copyFromCollection(dest, &arvados.Collection{ManifestText: mft}, srcRelPath)
+ if err != nil {
+ return err
+ }
default:
cp.logger.Printf("copying %q", outputRelPath)
hostRoot, err := cp.hostRoot(srcRoot)
if err != nil {
return err
}
- mft := manifest.Manifest{Text: coll.ManifestText}
- cp.manifest += mft.Extract(srcRelPath, dest).Text
+ err = cp.copyFromCollection(dest, &coll, srcRelPath)
+ if err != nil {
+ return err
+ }
}
if walkMountsBelow {
return cp.walkMountsBelow(dest, src)
return nil
}
+func (cp *copier) copyFromCollection(dest string, coll *arvados.Collection, srcRelPath string) error {
+ tmpfs, err := coll.FileSystem(cp.client, cp.keepClient)
+ if err != nil {
+ return err
+ }
+ snap, err := arvados.Snapshot(tmpfs, srcRelPath)
+ if err != nil {
+ return err
+ }
+ // Create ancestors of dest, if necessary.
+ for i, c := range dest {
+ if i > 0 && c == '/' {
+ err = cp.staged.Mkdir(dest[:i], 0777)
+ if err != nil && !os.IsExist(err) {
+ return err
+ }
+ }
+ }
+ return arvados.Splice(cp.staged, dest, snap)
+}
+
func (cp *copier) walkMountsBelow(dest, src string) error {
for mnt, mntinfo := range cp.mounts {
if !strings.HasPrefix(mnt, src+"/") {
return m.Kind == "text" || m.Kind == "json" || (m.Kind == "collection" && m.Writable)
}
-func (cp *copier) getManifest(pdh string) (*manifest.Manifest, error) {
+func (cp *copier) getManifest(pdh string) (string, error) {
if mft, ok := cp.manifestCache[pdh]; ok {
return mft, nil
}
var coll arvados.Collection
err := cp.client.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+pdh, nil, nil)
if err != nil {
- return nil, fmt.Errorf("error retrieving collection record for %q: %s", pdh, err)
+ return "", fmt.Errorf("error retrieving collection record for %q: %s", pdh, err)
}
- mft := &manifest.Manifest{Text: coll.ManifestText}
if cp.manifestCache == nil {
- cp.manifestCache = map[string]*manifest.Manifest{pdh: mft}
- } else {
- cp.manifestCache[pdh] = mft
+ cp.manifestCache = make(map[string]string)
}
- return mft, nil
+ cp.manifestCache[pdh] = coll.ManifestText
+ return coll.ManifestText, nil
}
import (
"bytes"
+ "encoding/json"
+ "fmt"
"io"
"io/fs"
"os"
"syscall"
"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/keepclient"
"github.com/sirupsen/logrus"
check "gopkg.in/check.v1"
)
func (s *copierSuite) SetUpTest(c *check.C) {
tmpdir := c.MkDir()
s.log = bytes.Buffer{}
+
+ cl, err := arvadosclient.MakeArvadosClient()
+ c.Assert(err, check.IsNil)
+ kc, err := keepclient.MakeKeepClient(cl)
+ c.Assert(err, check.IsNil)
+ collfs, err := (&arvados.Collection{}).FileSystem(arvados.NewClientFromEnv(), kc)
+ c.Assert(err, check.IsNil)
+
s.cp = copier{
client: arvados.NewClientFromEnv(),
+ keepClient: kc,
hostOutputDir: tmpdir,
ctrOutputDir: "/ctr/outdir",
mounts: map[string]arvados.Mount{
"/secret_text": {Kind: "text", Content: "xyzzy"},
},
logger: &logrus.Logger{Out: &s.log, Formatter: &logrus.TextFormatter{}, Level: logrus.InfoLevel},
+ staged: collfs,
}
}
err = s.cp.walkMount("", s.cp.ctrOutputDir, 10, true)
c.Check(err, check.IsNil)
- c.Check(s.cp.manifest, check.Matches, `(?ms)\./l_dir acbd\S+ 0:3:foo\n\. acbd\S+ 0:3:l_file\n\. 37b5\S+ 0:3:l_file_w\n`)
+ s.checkStagedFile(c, "l_dir/foo", 3)
+ s.checkStagedFile(c, "l_file", 3)
+ s.checkStagedFile(c, "l_file_w", 3)
+}
+
+func (s *copierSuite) checkStagedFile(c *check.C, path string, size int64) {
+ fi, err := s.cp.staged.Stat(path)
+ if c.Check(err, check.IsNil) {
+ c.Check(fi.Size(), check.Equals, size)
+ }
}
func (s *copierSuite) TestSymlink(c *check.C) {
}
}
+func (s *copierSuite) TestCopyFromLargeCollection_Readonly(c *check.C) {
+ s.testCopyFromLargeCollection(c, false)
+}
+
+func (s *copierSuite) TestCopyFromLargeCollection_Writable(c *check.C) {
+ s.testCopyFromLargeCollection(c, true)
+}
+
+func (s *copierSuite) testCopyFromLargeCollection(c *check.C, writable bool) {
+ bindtmp := c.MkDir()
+ mtxt := arvadostest.FakeManifest(100, 100, 2, 4<<20)
+ pdh := arvados.PortableDataHash(mtxt)
+ json, err := json.Marshal(arvados.Collection{ManifestText: mtxt, PortableDataHash: pdh})
+ c.Assert(err, check.IsNil)
+ err = os.WriteFile(bindtmp+"/.arvados#collection", json, 0644)
+ // This symlink tricks walkHostFS into calling walkMount on
+ // the fakecollection dir. If we did the obvious thing instead
+ // (i.e., mount a collection under the output dir) walkMount
+ // would see that our fakecollection dir is actually a regular
+ // directory, conclude that the mount has been deleted and
+ // replaced by a regular directory tree, and process the tree
+ // as regular files, bypassing the manifest-copying code path
+ // we're trying to test.
+ err = os.Symlink("/fakecollection", s.cp.hostOutputDir+"/fakecollection")
+ c.Assert(err, check.IsNil)
+ s.cp.mounts["/fakecollection"] = arvados.Mount{
+ Kind: "collection",
+ PortableDataHash: pdh,
+ Writable: writable,
+ }
+ s.cp.bindmounts = map[string]bindmount{
+ "/fakecollection": bindmount{HostPath: bindtmp, ReadOnly: !writable},
+ }
+ s.cp.manifestCache = map[string]string{pdh: mtxt}
+ err = s.cp.walkMount("", s.cp.ctrOutputDir, 10, true)
+ c.Check(err, check.IsNil)
+ c.Log(s.log.String())
+
+ // Check some files to ensure they were copied properly.
+ // Specifically, arbitrarily check every 17th file in every
+ // 13th dir. (This is better than checking all of the files
+ // only in that it's less likely to show up as a distracting
+ // signal in CPU profiling.)
+ for i := 0; i < 100; i += 13 {
+ for j := 0; j < 100; j += 17 {
+ fnm := fmt.Sprintf("/fakecollection/dir%d/dir%d/file%d", i, j, j)
+ _, err := s.cp.staged.Stat(fnm)
+ c.Assert(err, check.IsNil, check.Commentf("%s", fnm))
+ }
+ }
+}
+
func (s *copierSuite) TestMountBelowExcludedByGlob(c *check.C) {
bindtmp := c.MkDir()
s.cp.mounts["/ctr/outdir/include/includer"] = arvados.Mount{
c.Check(s.cp.files, check.DeepEquals, []filetodo{
{src: s.cp.hostOutputDir + "/include/includew/foo", dst: "/include/includew/foo", size: 3},
})
- c.Check(s.cp.manifest, check.Matches, `(?ms).*\./include/includer .*`)
- c.Check(s.cp.manifest, check.Not(check.Matches), `(?ms).*exclude.*`)
+ manifest, err := s.cp.staged.MarshalManifest(".")
+ c.Assert(err, check.IsNil)
+ c.Check(manifest, check.Matches, `(?ms).*\./include/includer .*`)
+ c.Check(manifest, check.Not(check.Matches), `(?ms).*exclude.*`)
c.Check(s.log.String(), check.Matches, `(?ms).*not copying \\"exclude/excluder\\".*`)
c.Check(s.log.String(), check.Matches, `(?ms).*not copying \\"nonexistent/collection\\".*`)
}
}
// applyGlobsToFilesAndDirs uses the same glob-matching code as
-// applyGlobsToCollectionFS, so we don't need to test all of the same
+// applyGlobsToStaged, so we don't need to test all of the same
// glob-matching behavior covered in TestApplyGlobsToCollectionFS. We
// do need to check that (a) the glob is actually being used to filter
// out files, and (b) non-matching dirs still included if and only if
c.Logf("=== globs: %q", trial.globs)
collfs, err := (&arvados.Collection{ManifestText: ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo 0:0:bar 0:0:baz/quux 0:0:baz/parent1/item1\n"}).FileSystem(nil, nil)
c.Assert(err, check.IsNil)
- cp := copier{globs: trial.globs}
- err = cp.applyGlobsToCollectionFS(collfs)
+ cp := copier{globs: trial.globs, staged: collfs}
+ err = cp.applyGlobsToStaged()
if !c.Check(err, check.IsNil) {
continue
}
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/keepclient"
- "git.arvados.org/arvados.git/sdk/go/manifest"
"golang.org/x/sys/unix"
)
type IKeepClient interface {
BlockWrite(context.Context, arvados.BlockWriteOptions) (arvados.BlockWriteResponse, error)
ReadAt(locator string, p []byte, off int) (int, error)
- ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
LocalLocator(locator string) (string, error)
SetStorageClasses(sc []string)
}
"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/manifest"
. "gopkg.in/check.v1"
)
return errors.New("not implemented")
}
-func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
- if filename == hwImageID+".tar" {
- rdr := ioutil.NopCloser(&bytes.Buffer{})
- client.Called = true
- return FileWrapper{rdr, 1321984}, nil
- } else if filename == "/file1_in_main.txt" {
- rdr := ioutil.NopCloser(strings.NewReader("foo"))
- client.Called = true
- return FileWrapper{rdr, 3}, nil
- }
- return nil, nil
-}
-
type apiStubServer struct {
server *httptest.Server
proxy *httputil.ReverseProxy
KeepTestClient
}
-func (*KeepErrorTestClient) ManifestFileReader(manifest.Manifest, string) (arvados.File, error) {
- return nil, errors.New("KeepError")
-}
-
func (*KeepErrorTestClient) BlockWrite(context.Context, arvados.BlockWriteOptions) (arvados.BlockWriteResponse, error) {
return arvados.BlockWriteResponse{}, errors.New("KeepError")
}
return 0, errors.New("KeepError")
}
-type ErrorReader struct {
- FileWrapper
-}
-
-func (ErrorReader) Read(p []byte) (n int, err error) {
- return 0, errors.New("ErrorReader")
-}
-
-func (ErrorReader) Seek(int64, int) (int64, error) {
- return 0, errors.New("ErrorReader")
-}
-
-func (*KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
- return ErrorReader{}, nil
-}
-
func dockerLog(fd byte, msg string) []byte {
by := []byte(msg)
header := make([]byte, 8+len(by))
func (s *integrationSuite) TestRunTrivialContainerWithSingularity(c *C) {
s.engine = "singularity"
s.testRunTrivialContainer(c)
- c.Check(s.logFiles["crunch-run.txt"], Matches, `(?ms).*Using container runtime: singularity.* version 3\.\d+.*`)
+ c.Check(s.logFiles["crunch-run.txt"], Matches, `(?ms).*Using container runtime: singularity.* version [34]\.\d+.*`)
}
func (s *integrationSuite) TestRunTrivialContainerWithLocalKeepstore(c *C) {
package deduplicationreport
import (
+ "bytes"
"flag"
"fmt"
"io"
"git.arvados.org/arvados.git/lib/cmd"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
- "git.arvados.org/arvados.git/sdk/go/manifest"
+ "git.arvados.org/arvados.git/sdk/go/blockdigest"
"github.com/dustin/go-humanize"
"github.com/sirupsen/logrus"
func blockList(collection arvados.Collection) (blocks map[string]int) {
blocks = make(map[string]int)
- m := manifest.Manifest{Text: collection.ManifestText}
- blockChannel := m.BlockIterWithDuplicates()
- for b := range blockChannel {
- blocks[b.Digest.String()] = b.Size
+ for _, token := range bytes.Split([]byte(collection.ManifestText), []byte{' '}) {
+ if blockdigest.IsBlockLocator(string(token)) {
+ loc, _ := blockdigest.ParseBlockLocator(string(token))
+ blocks[loc.Digest.String()] = loc.Size
+ }
}
return
}
"libxslt1-dev",
"libyaml-dev",
"linkchecker",
+ "locales",
"lsof",
"make",
"net-tools",
"r-cran-xml",
"rsync",
"sudo",
+ "unzip",
"uuid-dev",
"wget",
"xvfb",
Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands::
- sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<EOF
+ sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
- baseurl=http://rpm.arvados.org/CentOS/\$releasever/os/\$basearch/
+ baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
- gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+ gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-arvados-cwl-runner
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package arvadostest
+
+import (
+ "bytes"
+ "fmt"
+ "math/rand"
+)
+
+func FakeManifest(dirCount, filesPerDir, blocksPerFile, interleaveChunk int) string {
+ const blksize = 1 << 26
+ mb := bytes.NewBuffer(make([]byte, 0, 40000000))
+ blkid := 0
+ for i := 0; i < dirCount; i++ {
+ fmt.Fprintf(mb, "./dir%d", i)
+ for j := 0; j < filesPerDir; j++ {
+ for k := 0; k < blocksPerFile; k++ {
+ blkid++
+ fmt.Fprintf(mb, " %032x+%d+A%040x@%08x", blkid, blksize, blkid, blkid)
+ }
+ }
+ for j := 0; j < filesPerDir; j++ {
+ if interleaveChunk == 0 {
+ fmt.Fprintf(mb, " %d:%d:dir%d/file%d", (filesPerDir-j-1)*blocksPerFile*blksize, blocksPerFile*blksize, j, j)
+ continue
+ }
+ for todo := int64(blocksPerFile) * int64(blksize); todo > 0; todo -= int64(interleaveChunk) {
+ size := int64(interleaveChunk)
+ if size > todo {
+ size = todo
+ }
+ offset := rand.Int63n(int64(blocksPerFile)*int64(blksize)*int64(filesPerDir) - size)
+ fmt.Fprintf(mb, " %d:%d:dir%d/file%d", offset, size, j, j)
+ }
+ }
+ mb.Write([]byte{'\n'})
+ }
+ return mb.String()
+}
"time"
"gopkg.in/check.v1"
- "gopkg.in/square/go-jose.v2"
- "gopkg.in/square/go-jose.v2/jwt"
+ "gopkg.in/go-jose/go-jose.v2"
+ "gopkg.in/go-jose/go-jose.v2/jwt"
)
type OIDCProvider struct {
return LocatorPattern.MatchString(s)
}
-func ParseBlockLocator(s string) (b BlockLocator, err error) {
+func ParseBlockLocator(s string) (BlockLocator, error) {
if !LocatorPattern.MatchString(s) {
- err = fmt.Errorf("String \"%s\" does not match BlockLocator pattern "+
- "\"%s\".",
- s,
- LocatorPattern.String())
- } else {
- tokens := strings.Split(s, "+")
- var blockSize int64
- var blockDigest BlockDigest
- // We expect both of the following to succeed since LocatorPattern
- // restricts the strings appropriately.
- blockDigest, err = FromString(tokens[0])
- if err != nil {
- return
- }
- blockSize, err = strconv.ParseInt(tokens[1], 10, 0)
- if err != nil {
- return
- }
- b.Digest = blockDigest
- b.Size = int(blockSize)
- b.Hints = tokens[2:]
+ return BlockLocator{}, fmt.Errorf("String %q does not match block locator pattern %q.", s, LocatorPattern.String())
}
- return
+ tokens := strings.Split(s, "+")
+ // We expect both of the following to succeed since
+ // LocatorPattern restricts the strings appropriately.
+ blockDigest, err := FromString(tokens[0])
+ if err != nil {
+ return BlockLocator{}, err
+ }
+ blockSize, err := strconv.ParseInt(tokens[1], 10, 0)
+ if err != nil {
+ return BlockLocator{}, err
+ }
+ return BlockLocator{
+ Digest: blockDigest,
+ Size: int(blockSize),
+ Hints: tokens[2:],
+ }, nil
}
"os"
"git.arvados.org/arvados.git/sdk/go/arvados"
- "git.arvados.org/arvados.git/sdk/go/manifest"
)
// ErrNoManifest indicates the given collection has no manifest
}
return fs.OpenFile(filename, os.O_RDONLY, 0)
}
-
-func (kc *KeepClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
- fs, err := (&arvados.Collection{ManifestText: m.Text}).FileSystem(nil, kc)
- if err != nil {
- return nil, err
- }
- return fs.OpenFile(filename, os.O_RDONLY, 0)
-}
+++ /dev/null
-// Copyright (C) The Arvados Authors. All rights reserved.
-//
-// SPDX-License-Identifier: Apache-2.0
-
-/* Deals with parsing Manifest Text. */
-
-// Inspired by the Manifest class in arvados/sdk/ruby/lib/arvados/keep.rb
-
-package manifest
-
-import (
- "errors"
- "fmt"
- "path"
- "regexp"
- "sort"
- "strconv"
- "strings"
-
- "git.arvados.org/arvados.git/sdk/go/blockdigest"
-)
-
-var ErrInvalidToken = errors.New("Invalid token")
-
-type Manifest struct {
- Text string
- Err error
-}
-
-type BlockLocator struct {
- Digest blockdigest.BlockDigest
- Size int
- Hints []string
-}
-
-// FileSegment is a portion of a file that is contained within a
-// single block.
-type FileSegment struct {
- Locator string
- // Offset (within this block) of this data segment
- Offset int
- Len int
-}
-
-// FileStreamSegment is a portion of a file described as a segment of a stream.
-type FileStreamSegment struct {
- SegPos uint64
- SegLen uint64
- Name string
-}
-
-// ManifestStream represents a single line from a manifest.
-type ManifestStream struct {
- StreamName string
- Blocks []string
- blockOffsets []uint64
- FileStreamSegments []FileStreamSegment
- Err error
-}
-
-// Array of segments referencing file content
-type segmentedFile []FileSegment
-
-// Map of files to list of file segments referencing file content
-type segmentedStream map[string]segmentedFile
-
-// Map of streams
-type segmentedManifest map[string]segmentedStream
-
-var escapeSeq = regexp.MustCompile(`\\([0-9]{3}|\\)`)
-
-func unescapeSeq(seq string) string {
- if seq == `\\` {
- return `\`
- }
- i, err := strconv.ParseUint(seq[1:], 8, 8)
- if err != nil {
- // Invalid escape sequence: can't unescape.
- return seq
- }
- return string([]byte{byte(i)})
-}
-
-func EscapeName(s string) string {
- raw := []byte(s)
- escaped := make([]byte, 0, len(s))
- for _, c := range raw {
- if c <= 32 {
- oct := fmt.Sprintf("\\%03o", c)
- escaped = append(escaped, []byte(oct)...)
- } else {
- escaped = append(escaped, c)
- }
- }
- return string(escaped)
-}
-
-func UnescapeName(s string) string {
- return escapeSeq.ReplaceAllStringFunc(s, unescapeSeq)
-}
-
-func ParseBlockLocator(s string) (b BlockLocator, err error) {
- if !blockdigest.LocatorPattern.MatchString(s) {
- err = fmt.Errorf("String \"%s\" does not match BlockLocator pattern "+
- "\"%s\".",
- s,
- blockdigest.LocatorPattern.String())
- } else {
- tokens := strings.Split(s, "+")
- var blockSize int64
- var blockDigest blockdigest.BlockDigest
- // We expect both of the following to succeed since LocatorPattern
- // restricts the strings appropriately.
- blockDigest, err = blockdigest.FromString(tokens[0])
- if err != nil {
- return
- }
- blockSize, err = strconv.ParseInt(tokens[1], 10, 0)
- if err != nil {
- return
- }
- b.Digest = blockDigest
- b.Size = int(blockSize)
- b.Hints = tokens[2:]
- }
- return
-}
-
-func parseFileStreamSegment(tok string) (ft FileStreamSegment, err error) {
- parts := strings.SplitN(tok, ":", 3)
- if len(parts) != 3 {
- err = ErrInvalidToken
- return
- }
- ft.SegPos, err = strconv.ParseUint(parts[0], 10, 64)
- if err != nil {
- return
- }
- ft.SegLen, err = strconv.ParseUint(parts[1], 10, 64)
- if err != nil {
- return
- }
- ft.Name = UnescapeName(parts[2])
- return
-}
-
-func (s *ManifestStream) FileSegmentIterByName(filepath string) <-chan *FileSegment {
- ch := make(chan *FileSegment, 64)
- go func() {
- s.sendFileSegmentIterByName(filepath, ch)
- close(ch)
- }()
- return ch
-}
-
-func firstBlock(offsets []uint64, rangeStart uint64) int {
- // rangeStart/blockStart is the inclusive lower bound
- // rangeEnd/blockEnd is the exclusive upper bound
-
- hi := len(offsets) - 1
- var lo int
- i := ((hi + lo) / 2)
- blockStart := offsets[i]
- blockEnd := offsets[i+1]
-
- // perform a binary search for the first block
- // assumes that all of the blocks are contiguous, so rangeStart is guaranteed
- // to either fall into the range of a block or be outside the block range entirely
- for !(rangeStart >= blockStart && rangeStart < blockEnd) {
- if lo == i {
- // must be out of range, fail
- return -1
- }
- if rangeStart > blockStart {
- lo = i
- } else {
- hi = i
- }
- i = ((hi + lo) / 2)
- blockStart = offsets[i]
- blockEnd = offsets[i+1]
- }
- return i
-}
-
-func (s *ManifestStream) sendFileSegmentIterByName(filepath string, ch chan<- *FileSegment) {
- // This is what streamName+"/"+fileName will look like:
- target := fixStreamName(filepath)
- for _, fTok := range s.FileStreamSegments {
- wantPos := fTok.SegPos
- wantLen := fTok.SegLen
- name := fTok.Name
-
- if s.StreamName+"/"+name != target {
- continue
- }
- if wantLen == 0 {
- ch <- &FileSegment{Locator: "d41d8cd98f00b204e9800998ecf8427e+0", Offset: 0, Len: 0}
- continue
- }
-
- // Binary search to determine first block in the stream
- i := firstBlock(s.blockOffsets, wantPos)
- if i == -1 {
- // Shouldn't happen, file segments are checked in parseManifestStream
- panic(fmt.Sprintf("File segment %v extends past end of stream", fTok))
- }
- for ; i < len(s.Blocks); i++ {
- blockPos := s.blockOffsets[i]
- blockEnd := s.blockOffsets[i+1]
- if blockEnd <= wantPos {
- // Shouldn't happen, FirstBlock() should start
- // us on the right block, so if this triggers
- // that means there is a bug.
- panic(fmt.Sprintf("Block end %v comes before start of file segment %v", blockEnd, wantPos))
- }
- if blockPos >= wantPos+wantLen {
- // current block comes after current file span
- break
- }
-
- fseg := FileSegment{
- Locator: s.Blocks[i],
- Offset: 0,
- Len: int(blockEnd - blockPos),
- }
- if blockPos < wantPos {
- fseg.Offset = int(wantPos - blockPos)
- fseg.Len -= fseg.Offset
- }
- if blockEnd > wantPos+wantLen {
- fseg.Len = int(wantPos+wantLen-blockPos) - fseg.Offset
- }
- ch <- &fseg
- }
- }
-}
-
-func parseManifestStream(s string) (m ManifestStream) {
- tokens := strings.Split(s, " ")
-
- m.StreamName = UnescapeName(tokens[0])
- if m.StreamName != "." && !strings.HasPrefix(m.StreamName, "./") {
- m.Err = fmt.Errorf("Invalid stream name: %s", m.StreamName)
- return
- }
-
- tokens = tokens[1:]
- var i int
- for i = 0; i < len(tokens); i++ {
- if !blockdigest.IsBlockLocator(tokens[i]) {
- break
- }
- }
- m.Blocks = tokens[:i]
- fileTokens := tokens[i:]
-
- if len(m.Blocks) == 0 {
- m.Err = fmt.Errorf("No block locators found")
- return
- }
-
- m.blockOffsets = make([]uint64, len(m.Blocks)+1)
- var streamoffset uint64
- for i, b := range m.Blocks {
- bl, err := ParseBlockLocator(b)
- if err != nil {
- m.Err = err
- return
- }
- m.blockOffsets[i] = streamoffset
- streamoffset += uint64(bl.Size)
- }
- m.blockOffsets[len(m.Blocks)] = streamoffset
-
- if len(fileTokens) == 0 {
- m.Err = fmt.Errorf("No file tokens found")
- return
- }
-
- for _, ft := range fileTokens {
- pft, err := parseFileStreamSegment(ft)
- if err != nil {
- m.Err = fmt.Errorf("Invalid file token: %s", ft)
- break
- }
- if pft.SegPos+pft.SegLen > streamoffset {
- m.Err = fmt.Errorf("File segment %s extends past end of stream %d", ft, streamoffset)
- break
- }
- m.FileStreamSegments = append(m.FileStreamSegments, pft)
- }
-
- return
-}
-
-func fixStreamName(sn string) string {
- sn = path.Clean(sn)
- if strings.HasPrefix(sn, "/") {
- sn = "." + sn
- } else if sn != "." {
- sn = "./" + sn
- }
- return sn
-}
-
-func splitPath(srcpath string) (streamname, filename string) {
- pathIdx := strings.LastIndex(srcpath, "/")
- if pathIdx >= 0 {
- streamname = srcpath[0:pathIdx]
- filename = srcpath[pathIdx+1:]
- } else {
- streamname = srcpath
- filename = ""
- }
- return
-}
-
-func (m *Manifest) segment() (*segmentedManifest, error) {
- files := make(segmentedManifest)
-
- for stream := range m.StreamIter() {
- if stream.Err != nil {
- // Stream has an error
- return nil, stream.Err
- }
- currentStreamfiles := make(map[string]bool)
- for _, f := range stream.FileStreamSegments {
- sn := stream.StreamName
- if strings.HasSuffix(sn, "/") {
- sn = sn[0 : len(sn)-1]
- }
- path := sn + "/" + f.Name
- streamname, filename := splitPath(path)
- if files[streamname] == nil {
- files[streamname] = make(segmentedStream)
- }
- if !currentStreamfiles[path] {
- segs := files[streamname][filename]
- for seg := range stream.FileSegmentIterByName(path) {
- if seg.Len > 0 {
- segs = append(segs, *seg)
- }
- }
- files[streamname][filename] = segs
- currentStreamfiles[path] = true
- }
- }
- }
-
- return &files, nil
-}
-
-func (stream segmentedStream) normalizedText(name string) string {
- var sortedfiles []string
- for k := range stream {
- sortedfiles = append(sortedfiles, k)
- }
- sort.Strings(sortedfiles)
-
- streamTokens := []string{EscapeName(name)}
-
- blocks := make(map[blockdigest.BlockDigest]int64)
- var streamoffset int64
-
- // Go through each file and add each referenced block exactly once.
- for _, streamfile := range sortedfiles {
- for _, segment := range stream[streamfile] {
- b, _ := ParseBlockLocator(segment.Locator)
- if _, ok := blocks[b.Digest]; !ok {
- streamTokens = append(streamTokens, segment.Locator)
- blocks[b.Digest] = streamoffset
- streamoffset += int64(b.Size)
- }
- }
- }
-
- if len(streamTokens) == 1 {
- streamTokens = append(streamTokens, "d41d8cd98f00b204e9800998ecf8427e+0")
- }
-
- for _, streamfile := range sortedfiles {
- // Add in file segments
- spanStart := int64(-1)
- spanEnd := int64(0)
- fout := EscapeName(streamfile)
- for _, segment := range stream[streamfile] {
- // Collapse adjacent segments
- b, _ := ParseBlockLocator(segment.Locator)
- streamoffset = blocks[b.Digest] + int64(segment.Offset)
- if spanStart == -1 {
- spanStart = streamoffset
- spanEnd = streamoffset + int64(segment.Len)
- } else {
- if streamoffset == spanEnd {
- spanEnd += int64(segment.Len)
- } else {
- streamTokens = append(streamTokens, fmt.Sprintf("%d:%d:%s", spanStart, spanEnd-spanStart, fout))
- spanStart = streamoffset
- spanEnd = streamoffset + int64(segment.Len)
- }
- }
- }
-
- if spanStart != -1 {
- streamTokens = append(streamTokens, fmt.Sprintf("%d:%d:%s", spanStart, spanEnd-spanStart, fout))
- }
-
- if len(stream[streamfile]) == 0 {
- streamTokens = append(streamTokens, fmt.Sprintf("0:0:%s", fout))
- }
- }
-
- return strings.Join(streamTokens, " ") + "\n"
-}
-
-func (m segmentedManifest) manifestTextForPath(srcpath, relocate string) string {
- srcpath = fixStreamName(srcpath)
-
- var suffix string
- if strings.HasSuffix(relocate, "/") {
- suffix = "/"
- }
- relocate = fixStreamName(relocate) + suffix
-
- streamname, filename := splitPath(srcpath)
-
- if stream, ok := m[streamname]; ok {
- // check if it refers to a single file in a stream
- filesegs, okfile := stream[filename]
- if okfile {
- newstream := make(segmentedStream)
- relocateStream, relocateFilename := splitPath(relocate)
- if relocateFilename == "" {
- relocateFilename = filename
- }
- newstream[relocateFilename] = filesegs
- return newstream.normalizedText(relocateStream)
- }
- }
-
- // Going to extract multiple streams
- prefix := srcpath + "/"
-
- if strings.HasSuffix(relocate, "/") {
- relocate = relocate[0 : len(relocate)-1]
- }
-
- var sortedstreams []string
- for k := range m {
- sortedstreams = append(sortedstreams, k)
- }
- sort.Strings(sortedstreams)
-
- manifest := ""
- for _, k := range sortedstreams {
- if strings.HasPrefix(k, prefix) || k == srcpath {
- manifest += m[k].normalizedText(relocate + k[len(srcpath):])
- }
- }
- return manifest
-}
-
-// Extract extracts some or all of the manifest and returns the extracted
-// portion as a normalized manifest. This is a swiss army knife function that
-// can be several ways:
-//
-// If 'srcpath' and 'relocate' are '.' it simply returns an equivalent manifest
-// in normalized form.
-//
-// Extract(".", ".") // return entire normalized manfest text
-//
-// If 'srcpath' points to a single file, it will return manifest text for just that file.
-// The value of "relocate" is can be used to rename the file or set the file stream.
-//
-// Extract("./foo", ".") // extract file "foo" and put it in stream "."
-// Extract("./foo", "./bar") // extract file "foo", rename it to "bar" in stream "."
-// Extract("./foo", "./bar/") // extract file "foo", rename it to "./bar/foo"
-// Extract("./foo", "./bar/baz") // extract file "foo", rename it to "./bar/baz")
-//
-// Otherwise it will return the manifest text for all streams with the prefix in "srcpath" and place
-// them under the path in "relocate".
-//
-// Extract("./stream", ".") // extract "./stream" to "." and "./stream/subdir" to "./subdir")
-// Extract("./stream", "./bar") // extract "./stream" to "./bar" and "./stream/subdir" to "./bar/subdir")
-func (m Manifest) Extract(srcpath, relocate string) (ret Manifest) {
- segmented, err := m.segment()
- if err != nil {
- ret.Err = err
- return
- }
- ret.Text = segmented.manifestTextForPath(srcpath, relocate)
- return
-}
-
-func (m *Manifest) StreamIter() <-chan ManifestStream {
- ch := make(chan ManifestStream)
- go func(input string) {
- // This slice holds the current line and the remainder of the
- // manifest. We parse one line at a time, to save effort if we
- // only need the first few lines.
- lines := []string{"", input}
- for {
- lines = strings.SplitN(lines[1], "\n", 2)
- if len(lines[0]) > 0 {
- // Only parse non-blank lines
- ch <- parseManifestStream(lines[0])
- }
- if len(lines) == 1 {
- break
- }
- }
- close(ch)
- }(m.Text)
- return ch
-}
-
-func (m *Manifest) FileSegmentIterByName(filepath string) <-chan *FileSegment {
- ch := make(chan *FileSegment, 64)
- filepath = fixStreamName(filepath)
- go func() {
- for stream := range m.StreamIter() {
- if !strings.HasPrefix(filepath, stream.StreamName+"/") {
- continue
- }
- stream.sendFileSegmentIterByName(filepath, ch)
- }
- close(ch)
- }()
- return ch
-}
-
-// BlockIterWithDuplicates iterates over the block locators of a manifest.
-//
-// Blocks may appear multiple times within the same manifest if they
-// are used by multiple files. In that case this Iterator will output
-// the same block multiple times.
-//
-// In order to detect parse errors, caller must check m.Err after the returned channel closes.
-func (m *Manifest) BlockIterWithDuplicates() <-chan blockdigest.BlockLocator {
- blockChannel := make(chan blockdigest.BlockLocator)
- go func(streamChannel <-chan ManifestStream) {
- for ms := range streamChannel {
- if ms.Err != nil {
- m.Err = ms.Err
- continue
- }
- for _, block := range ms.Blocks {
- if b, err := blockdigest.ParseBlockLocator(block); err == nil {
- blockChannel <- b
- } else {
- m.Err = err
- }
- }
- }
- close(blockChannel)
- }(m.StreamIter())
- return blockChannel
-}
+++ /dev/null
-// Copyright (C) The Arvados Authors. All rights reserved.
-//
-// SPDX-License-Identifier: Apache-2.0
-
-package manifest
-
-import (
- "fmt"
- "git.arvados.org/arvados.git/sdk/go/arvadostest"
- "git.arvados.org/arvados.git/sdk/go/blockdigest"
- "io/ioutil"
- "reflect"
- "regexp"
- "runtime"
- "testing"
-)
-
-func getStackTrace() string {
- buf := make([]byte, 1000)
- bytesWritten := runtime.Stack(buf, false)
- return "Stack Trace:\n" + string(buf[:bytesWritten])
-}
-
-func expectFromChannel(t *testing.T, c <-chan string, expected string) {
- actual, ok := <-c
- if !ok {
- t.Fatalf("Expected to receive %s but channel was closed. %s",
- expected,
- getStackTrace())
- }
- if actual != expected {
- t.Fatalf("Expected %s but got %s instead. %s",
- expected,
- actual,
- getStackTrace())
- }
-}
-
-func expectChannelClosed(t *testing.T, c <-chan interface{}) {
- received, ok := <-c
- if ok {
- t.Fatalf("Expected channel to be closed, but received %v instead. %s",
- received,
- getStackTrace())
- }
-}
-
-func expectEqual(t *testing.T, actual interface{}, expected interface{}) {
- if actual != expected {
- t.Fatalf("Expected %v but received %v instead. %s",
- expected,
- actual,
- getStackTrace())
- }
-}
-
-func expectStringSlicesEqual(t *testing.T, actual []string, expected []string) {
- if len(actual) != len(expected) {
- t.Fatalf("Expected %v (length %d), but received %v (length %d) instead. %s", expected, len(expected), actual, len(actual), getStackTrace())
- }
- for i := range actual {
- if actual[i] != expected[i] {
- t.Fatalf("Expected %v but received %v instead (first disagreement at position %d). %s", expected, actual, i, getStackTrace())
- }
- }
-}
-
-func expectFileStreamSegmentsEqual(t *testing.T, actual []FileStreamSegment, expected []FileStreamSegment) {
- if !reflect.DeepEqual(actual, expected) {
- t.Fatalf("Expected %v but received %v instead. %s", expected, actual, getStackTrace())
- }
-}
-
-func expectManifestStream(t *testing.T, actual ManifestStream, expected ManifestStream) {
- expectEqual(t, actual.StreamName, expected.StreamName)
- expectStringSlicesEqual(t, actual.Blocks, expected.Blocks)
- expectFileStreamSegmentsEqual(t, actual.FileStreamSegments, expected.FileStreamSegments)
-}
-
-func expectBlockLocator(t *testing.T, actual blockdigest.BlockLocator, expected blockdigest.BlockLocator) {
- expectEqual(t, actual.Digest, expected.Digest)
- expectEqual(t, actual.Size, expected.Size)
- expectStringSlicesEqual(t, actual.Hints, expected.Hints)
-}
-
-func TestParseManifestStreamSimple(t *testing.T) {
- m := parseManifestStream(". 365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf 0:2310:qr1hi-8i9sb-ienvmpve1a0vpoi.log.txt")
- expectManifestStream(t, m, ManifestStream{StreamName: ".",
- Blocks: []string{"365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf"},
- FileStreamSegments: []FileStreamSegment{{0, 2310, "qr1hi-8i9sb-ienvmpve1a0vpoi.log.txt"}}})
-}
-
-func TestParseBlockLocatorSimple(t *testing.T) {
- b, err := ParseBlockLocator("365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf")
- if err != nil {
- t.Fatalf("Unexpected error parsing block locator: %v", err)
- }
- d, err := blockdigest.FromString("365f83f5f808896ec834c8b595288735")
- if err != nil {
- t.Fatalf("Unexpected error during FromString for block locator: %v", err)
- }
- expectBlockLocator(t, blockdigest.BlockLocator{b.Digest, b.Size, b.Hints},
- blockdigest.BlockLocator{Digest: d,
- Size: 2310,
- Hints: []string{"K@qr1hi",
- "Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf"}})
-}
-
-func TestStreamIterShortManifestWithBlankStreams(t *testing.T) {
- content, err := ioutil.ReadFile("testdata/short_manifest")
- if err != nil {
- t.Fatalf("Unexpected error reading manifest from file: %v", err)
- }
- manifest := Manifest{Text: string(content)}
- streamIter := manifest.StreamIter()
-
- firstStream := <-streamIter
- expectManifestStream(t,
- firstStream,
- ManifestStream{StreamName: ".",
- Blocks: []string{"b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c"},
- FileStreamSegments: []FileStreamSegment{{0, 15693477, "chr10_band0_s0_e3000000.fj"}}})
-
- received, ok := <-streamIter
- if ok {
- t.Fatalf("Expected streamIter to be closed, but received %v instead.",
- received)
- }
-}
-
-func TestBlockIterLongManifest(t *testing.T) {
- content, err := ioutil.ReadFile("testdata/long_manifest")
- if err != nil {
- t.Fatalf("Unexpected error reading manifest from file: %v", err)
- }
- manifest := Manifest{Text: string(content)}
- blockChannel := manifest.BlockIterWithDuplicates()
-
- firstBlock := <-blockChannel
- d, err := blockdigest.FromString("b746e3d2104645f2f64cd3cc69dd895d")
- if err != nil {
- t.Fatalf("Unexpected error during FromString for block: %v", err)
- }
- expectBlockLocator(t,
- firstBlock,
- blockdigest.BlockLocator{Digest: d,
- Size: 15693477,
- Hints: []string{"E2866e643690156651c03d876e638e674dcd79475@5441920c"}})
- blocksRead := 1
- var lastBlock blockdigest.BlockLocator
- for lastBlock = range blockChannel {
- blocksRead++
- }
- expectEqual(t, blocksRead, 853)
-
- d, err = blockdigest.FromString("f9ce82f59e5908d2d70e18df9679b469")
- if err != nil {
- t.Fatalf("Unexpected error during FromString for block: %v", err)
- }
- expectBlockLocator(t,
- lastBlock,
- blockdigest.BlockLocator{Digest: d,
- Size: 31367794,
- Hints: []string{"E53f903684239bcc114f7bf8ff9bd6089f33058db@5441920c"}})
-}
-
-func TestUnescape(t *testing.T) {
- for _, testCase := range [][]string{
- {`\040`, ` `},
- {`\009`, `\009`},
- {`\\\040\\`, `\ \`},
- {`\\040\`, `\040\`},
- } {
- in := testCase[0]
- expect := testCase[1]
- got := UnescapeName(in)
- if expect != got {
- t.Errorf("For '%s' got '%s' instead of '%s'", in, got, expect)
- }
- }
-}
-
-type fsegtest struct {
- mt string // manifest text
- f string // filename
- want []FileSegment // segments should be received on channel
-}
-
-func TestFileSegmentIterByName(t *testing.T) {
- mt := arvadostest.PathologicalManifest
- for _, testCase := range []fsegtest{
- {mt: mt, f: "zzzz", want: nil},
- // This case is too sensitive: it would be acceptable
- // (even preferable) to return only one empty segment.
- {mt: mt, f: "foo/zero", want: []FileSegment{{"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}, {"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}}},
- {mt: mt, f: "zero@0", want: []FileSegment{{"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}}},
- {mt: mt, f: "zero@1", want: []FileSegment{{"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}}},
- {mt: mt, f: "zero@4", want: []FileSegment{{"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}}},
- {mt: mt, f: "zero@9", want: []FileSegment{{"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}}},
- {mt: mt, f: "f", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 0, 1}}},
- {mt: mt, f: "ooba", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 1, 2}, {"37b51d194a7513e45b56f6524f2d51f2+3", 0, 2}}},
- {mt: mt, f: "overlapReverse/o", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 2, 1}}},
- {mt: mt, f: "overlapReverse/oo", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 1, 2}}},
- {mt: mt, f: "overlapReverse/ofoo", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 2, 1}, {"acbd18db4cc2f85cedef654fccc4a4d8+3", 0, 3}}},
- {mt: mt, f: "foo bar/baz", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 0, 3}}},
- // This case is too sensitive: it would be better to
- // omit the empty segment.
- {mt: mt, f: "segmented/frob", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 0, 1}, {"37b51d194a7513e45b56f6524f2d51f2+3", 2, 1}, {"acbd18db4cc2f85cedef654fccc4a4d8+3", 1, 1}, {"d41d8cd98f00b204e9800998ecf8427e+0", 0, 0}, {"37b51d194a7513e45b56f6524f2d51f2+3", 0, 1}}},
- {mt: mt, f: "segmented/oof", want: []FileSegment{{"acbd18db4cc2f85cedef654fccc4a4d8+3", 1, 2}, {"acbd18db4cc2f85cedef654fccc4a4d8+3", 0, 1}}},
- } {
- m := Manifest{Text: testCase.mt}
- var got []FileSegment
- for fs := range m.FileSegmentIterByName(testCase.f) {
- got = append(got, *fs)
- }
- if !reflect.DeepEqual(got, testCase.want) {
- t.Errorf("For %#v:\n got %#v\n want %#v", testCase.f, got, testCase.want)
- }
- }
-}
-
-func TestBlockIterWithBadManifest(t *testing.T) {
- testCases := [][]string{
- {"badstream acbd18db4cc2f85cedef654fccc4a4d8+3 0:1:file1.txt", "Invalid stream name: badstream"},
- {"/badstream acbd18db4cc2f85cedef654fccc4a4d8+3 0:1:file1.txt", "Invalid stream name: /badstream"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 file1.txt", "Invalid file token: file1.txt"},
- {". acbd18db4cc2f85cedef654fccc4a4+3 0:1:file1.txt", "No block locators found"},
- {". acbd18db4cc2f85cedef654fccc4a4d8 0:1:file1.txt", "No block locators found"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 0:1:file1.txt file2.txt 1:2:file3.txt", "Invalid file token: file2.txt"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 0:1:file1.txt. bcde18db4cc2f85cedef654fccc4a4d8+3 1:2:file3.txt", "Invalid file token: bcde18db4cc2f85cedef654fccc4a4d8.*"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 0:1:file1.txt\n. acbd18db4cc2f85cedef654fccc4a4d8+3 ::file2.txt\n", "Invalid file token: ::file2.txt"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 bcde18db4cc2f85cedef654fccc4a4d8+3\n", "No file tokens found"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3 ", "Invalid file token"},
- {". acbd18db4cc2f85cedef654fccc4a4d8+3", "No file tokens found"},
- {". 0:1:file1.txt\n", "No block locators found"},
- {".\n", "No block locators found"},
- }
-
- for _, testCase := range testCases {
- manifest := Manifest{Text: string(testCase[0])}
- blockChannel := manifest.BlockIterWithDuplicates()
-
- for block := range blockChannel {
- _ = block
- }
-
- // completed reading from blockChannel; now check for errors
- if manifest.Err == nil {
- t.Fatalf("Expected error")
- }
-
- matched, _ := regexp.MatchString(testCase[1], manifest.Err.Error())
- if !matched {
- t.Fatalf("Expected error not found. Expected: %v; Found: %v", testCase[1], manifest.Err.Error())
- }
- }
-}
-
-func TestNormalizeManifest(t *testing.T) {
- m1 := Manifest{Text: `. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
-. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
-. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
-`}
- expectEqual(t, m1.Extract(".", ".").Text,
- `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
-`)
-
- m2 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
-`}
- expectEqual(t, m2.Extract(".", ".").Text, m2.Text)
-
- m3 := Manifest{Text: `. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
-. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
-. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
-`}
- expectEqual(t, m3.Extract(".", ".").Text, `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
-`)
- expectEqual(t, m3.Extract("/md5sum.txt", "/wiggle.txt").Text, `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:wiggle.txt
-`)
-
- m4 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`}
-
- expectEqual(t, m4.Extract(".", ".").Text,
- `./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-`)
-
- expectEqual(t, m4.Extract("./foo", ".").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
- expectEqual(t, m4.Extract("./foo", "./baz").Text, "./baz 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
- expectEqual(t, m4.Extract("./foo/bar", ".").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
- expectEqual(t, m4.Extract("./foo/bar", "./baz").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:baz 67108864:3:baz\n")
- expectEqual(t, m4.Extract("./foo/bar", "./quux/").Text, "./quux 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
- expectEqual(t, m4.Extract("./foo/bar", "./quux/baz").Text, "./quux 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:baz 67108864:3:baz\n")
- expectEqual(t, m4.Extract(".", ".").Text, `./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-`)
- expectEqual(t, m4.Extract(".", "./zip").Text, `./zip/foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
-./zip/zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-`)
-
- expectEqual(t, m4.Extract("foo/.//bar/../../zzz/", "/waz/").Text, `./waz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-`)
-
- m5 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
-`}
- expectEqual(t, m5.Extract(".", ".").Text,
- `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-`)
-
- m8 := Manifest{Text: `./a\040b\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\040world.txt
-`}
- expectEqual(t, m8.Extract(".", ".").Text, m8.Text)
-
- m9 := Manifest{Text: ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:10:one 20:10:two 10:10:one 30:10:two\n"}
- expectEqual(t, m9.Extract("", "").Text, ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:20:one 20:20:two\n")
-
- m10 := Manifest{Text: ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:10:one 20:10:two 10:10:one 30:10:two\n"}
- expectEqual(t, m10.Extract("./two", "./three").Text, ". acbd18db4cc2f85cedef654fccc4a4d8+40 20:20:three\n")
-
- m11 := Manifest{Text: arvadostest.PathologicalManifest}
- expectEqual(t, m11.Extract(".", ".").Text, `. acbd18db4cc2f85cedef654fccc4a4d8+3 37b51d194a7513e45b56f6524f2d51f2+3 73feffa4b7f6bb68e44cf984c85f6e88+3+Z+K@xyzzy 0:1:f 1:4:ooba 5:1:r 5:4:rbaz 0:0:zero@0 0:0:zero@1 0:0:zero@4 0:0:zero@9
-./foo acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo 0:3:foo 0:0:zero
-./foo\040bar acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:baz 0:3:baz\040waz
-./overlapReverse acbd18db4cc2f85cedef654fccc4a4d8+3 2:1:o 2:1:ofoo 0:3:ofoo 1:2:oo
-./segmented acbd18db4cc2f85cedef654fccc4a4d8+3 37b51d194a7513e45b56f6524f2d51f2+3 0:1:frob 5:1:frob 1:1:frob 3:1:frob 1:2:oof 0:1:oof
-`)
-
- m12 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
-./foo/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`}
-
- expectEqual(t, m12.Extract("./foo", ".").Text, `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-./baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`)
- expectEqual(t, m12.Extract("./foo", "./blub").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`)
- expectEqual(t, m12.Extract("./foo", "./blub/").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`)
- expectEqual(t, m12.Extract("./foo/", "./blub/").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
-`)
-
- m13 := Manifest{Text: `foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
-`}
-
- expectEqual(t, m13.Extract(".", ".").Text, ``)
- expectEqual(t, m13.Extract(".", ".").Err.Error(), "Invalid stream name: foo")
-
- m14 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 67108863:3:bar
-`}
-
- expectEqual(t, m14.Extract(".", ".").Text, ``)
- expectEqual(t, m14.Extract(".", ".").Err.Error(), "File segment 67108863:3:bar extends past end of stream 67108864")
-
- m15 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3bar
-`}
-
- expectEqual(t, m15.Extract(".", ".").Text, ``)
- expectEqual(t, m15.Extract(".", ".").Err.Error(), "Invalid file token: 0:3bar")
-}
-
-func TestFirstBlock(t *testing.T) {
- fmt.Println("ZZZ")
- expectEqual(t, firstBlock([]uint64{1, 2, 3, 4}, 3), 2)
- expectEqual(t, firstBlock([]uint64{1, 2, 3, 4, 5, 6}, 4), 3)
-}
+++ /dev/null
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+++ /dev/null
-. b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c 0:15693477:chr10_band0_s0_e3000000.fj
Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands::
- sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<EOF
+ sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
- baseurl=http://rpm.arvados.org/CentOS/\$releasever/os/\$basearch/
+ baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
- gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+ gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-arvados-python-client
logger.debug("Getting block %s", word)
data = src_keep.get(word)
put_queue.put((word, data))
- except e:
+ except Exception as e:
logger.error("Error getting block %s: %s", word, e)
transfer_error.append(e)
try:
bytes_written += loc.size
if progress_writer:
progress_writer.report(obj_uuid, bytes_written, bytes_expected)
- except e:
+ except Exception as e:
logger.error("Error putting block %s (%s bytes): %s", blockhash, loc.size, e)
try:
# Drain the 'get' queue so we end early
GEM
remote: https://rubygems.org/
specs:
- actioncable (7.0.8.1)
- actionpack (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ actioncable (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
nio4r (~> 2.0)
websocket-driver (>= 0.6.1)
- actionmailbox (7.0.8.1)
- actionpack (= 7.0.8.1)
- activejob (= 7.0.8.1)
- activerecord (= 7.0.8.1)
- activestorage (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ actionmailbox (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ activejob (= 7.0.8.4)
+ activerecord (= 7.0.8.4)
+ activestorage (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
mail (>= 2.7.1)
net-imap
net-pop
net-smtp
- actionmailer (7.0.8.1)
- actionpack (= 7.0.8.1)
- actionview (= 7.0.8.1)
- activejob (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ actionmailer (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ actionview (= 7.0.8.4)
+ activejob (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
mail (~> 2.5, >= 2.5.4)
net-imap
net-pop
net-smtp
rails-dom-testing (~> 2.0)
- actionpack (7.0.8.1)
- actionview (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ actionpack (7.0.8.4)
+ actionview (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
rack (~> 2.0, >= 2.2.4)
rack-test (>= 0.6.3)
rails-dom-testing (~> 2.0)
rails-html-sanitizer (~> 1.0, >= 1.2.0)
- actiontext (7.0.8.1)
- actionpack (= 7.0.8.1)
- activerecord (= 7.0.8.1)
- activestorage (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ actiontext (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ activerecord (= 7.0.8.4)
+ activestorage (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
globalid (>= 0.6.0)
nokogiri (>= 1.8.5)
- actionview (7.0.8.1)
- activesupport (= 7.0.8.1)
+ actionview (7.0.8.4)
+ activesupport (= 7.0.8.4)
builder (~> 3.1)
erubi (~> 1.4)
rails-dom-testing (~> 2.0)
rails-html-sanitizer (~> 1.1, >= 1.2.0)
- activejob (7.0.8.1)
- activesupport (= 7.0.8.1)
+ activejob (7.0.8.4)
+ activesupport (= 7.0.8.4)
globalid (>= 0.3.6)
- activemodel (7.0.8.1)
- activesupport (= 7.0.8.1)
- activerecord (7.0.8.1)
- activemodel (= 7.0.8.1)
- activesupport (= 7.0.8.1)
- activestorage (7.0.8.1)
- actionpack (= 7.0.8.1)
- activejob (= 7.0.8.1)
- activerecord (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ activemodel (7.0.8.4)
+ activesupport (= 7.0.8.4)
+ activerecord (7.0.8.4)
+ activemodel (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
+ activestorage (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ activejob (= 7.0.8.4)
+ activerecord (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
marcel (~> 1.0)
mini_mime (>= 1.1.0)
- activesupport (7.0.8.1)
+ activesupport (7.0.8.4)
concurrent-ruby (~> 1.0, >= 1.0.2)
i18n (>= 1.6, < 2)
minitest (>= 5.1)
extlib (>= 0.9.15)
multi_json (>= 1.0.0)
base64 (0.2.0)
- builder (3.2.4)
+ builder (3.3.0)
byebug (11.1.3)
- concurrent-ruby (1.2.3)
+ concurrent-ruby (1.3.3)
crass (1.0.6)
date (3.3.4)
docile (1.4.0)
- erubi (1.12.0)
+ erubi (1.13.0)
extlib (0.9.16)
factory_bot (6.2.1)
activesupport (>= 5.0.0)
os (>= 0.9, < 2.0)
signet (>= 0.16, < 2.a)
httpclient (2.8.3)
- i18n (1.14.4)
+ i18n (1.14.5)
concurrent-ruby (~> 1.0)
jquery-rails (4.6.0)
rails-dom-testing (>= 1, < 3)
net-pop
net-smtp
marcel (1.0.4)
- method_source (1.0.0)
+ method_source (1.1.0)
mini_mime (1.1.5)
- mini_portile2 (2.8.5)
+ mini_portile2 (2.8.7)
minitest (5.10.3)
mocha (2.1.0)
ruby2_keywords (>= 0.0.5)
multi_json (1.15.0)
multipart-post (2.4.0)
- net-imap (0.3.7)
+ net-imap (0.4.14)
date
net-protocol
net-pop (0.1.2)
timeout
net-smtp (0.5.0)
net-protocol
- nio4r (2.7.1)
+ nio4r (2.7.3)
nokogiri (1.15.6)
mini_portile2 (~> 2.8.2)
racc (~> 1.4)
pg (1.5.4)
power_assert (2.0.3)
public_suffix (5.0.4)
- racc (1.7.3)
+ racc (1.8.0)
rack (2.2.9)
rack-test (2.1.0)
rack (>= 1.3)
- rails (7.0.8.1)
- actioncable (= 7.0.8.1)
- actionmailbox (= 7.0.8.1)
- actionmailer (= 7.0.8.1)
- actionpack (= 7.0.8.1)
- actiontext (= 7.0.8.1)
- actionview (= 7.0.8.1)
- activejob (= 7.0.8.1)
- activemodel (= 7.0.8.1)
- activerecord (= 7.0.8.1)
- activestorage (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ rails (7.0.8.4)
+ actioncable (= 7.0.8.4)
+ actionmailbox (= 7.0.8.4)
+ actionmailer (= 7.0.8.4)
+ actionpack (= 7.0.8.4)
+ actiontext (= 7.0.8.4)
+ actionview (= 7.0.8.4)
+ activejob (= 7.0.8.4)
+ activemodel (= 7.0.8.4)
+ activerecord (= 7.0.8.4)
+ activestorage (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
bundler (>= 1.15.0)
- railties (= 7.0.8.1)
+ railties (= 7.0.8.4)
rails-controller-testing (1.0.5)
actionpack (>= 5.0.1.rc1)
actionview (>= 5.0.1.rc1)
rails-observers (0.1.5)
activemodel (>= 4.0)
rails-perftest (0.0.7)
- railties (7.0.8.1)
- actionpack (= 7.0.8.1)
- activesupport (= 7.0.8.1)
+ railties (7.0.8.4)
+ actionpack (= 7.0.8.4)
+ activesupport (= 7.0.8.4)
method_source
rake (>= 12.2)
thor (~> 1.0)
websocket-driver (0.7.6)
websocket-extensions (>= 0.1.0)
websocket-extensions (0.1.5)
- zeitwerk (2.6.13)
+ zeitwerk (2.6.16)
zlib (3.1.0)
PLATFORMS
skip_before_action :find_object_by_uuid, only: :shared
skip_before_action :render_404_if_no_object, only: :shared
- TRASHABLE_CLASSES = ['project']
-
def self._index_requires_parameters
(super rescue {}).
merge({
end
end
- def destroy
- if !TRASHABLE_CLASSES.include?(@object.group_class)
- @object.destroy
- show
- else
- super # Calls destroy from TrashableController module
- end
- end
-
def render_404_if_no_object
if params[:action] == 'contents'
if !params[:uuid]
in_batches(of: 15).
update_all('is_trashed = true')
- # Sweep trashed projects and their contents (as well as role
- # groups that were trashed before #18340 when that was
- # disallowed)
+ # Want to make sure the #update_trash hook on the Group class
+ # runs. It does a couple of important things:
+ #
+ # - For projects, puts all the subprojects in the trashed_groups table.
+ #
+ # - For role groups, outbound permissions are deleted.
Group.
- where('delete_at is not null and delete_at < statement_timestamp()').each do |project|
- delete_project_and_contents(project.uuid)
+ where("is_trashed = false and trash_at < statement_timestamp()").each do |grp|
+ grp.is_trashed = true
+ grp.save
end
+
+ # Sweep groups and their contents that are ready to be deleted
Group.
- where('is_trashed = false and trash_at < statement_timestamp()').
- update_all('is_trashed = true')
+ where('delete_at is not null and delete_at < statement_timestamp()').each do |group|
+ delete_project_and_contents(group.uuid)
+ end
# Sweep expired tokens
ActiveRecord::Base.connection.execute("DELETE from api_client_authorizations where expires_at <= statement_timestamp()")
+
+ # Sweep unused uuid_locks entries
+ ActiveRecord::Base.connection.execute("DELETE FROM uuid_locks WHERE uuid IN (SELECT uuid FROM uuid_locks FOR UPDATE SKIP LOCKED)")
end
head :no_content
end
if !p
raise "can't sweep group '#{p_uuid}', it may not exist"
end
- # First delete sub projects
- Group.where({group_class: 'project', owner_uuid: p_uuid}).each do |sub_project|
- delete_project_and_contents(sub_project.uuid)
- end
- # Next, iterate over all tables which have owner_uuid fields, with some
- # exceptions, and delete records owned by this project
- skipped_classes = ['Group', 'User']
- ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |klass|
- if !skipped_classes.include?(klass.name) && klass.columns.collect(&:name).include?('owner_uuid')
- klass.where({owner_uuid: p_uuid}).in_batches(of: 15).destroy_all
+ if p.group_class == 'project'
+ # First delete sub projects and owned filter groups
+ Group.where({owner_uuid: p_uuid}).each do |sub_project|
+ delete_project_and_contents(sub_project.uuid)
+ end
+ # Next, iterate over all tables which have owner_uuid fields, with some
+ # exceptions, and delete records owned by this project
+ skipped_classes = ['Group', 'User']
+ ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |klass|
+ if !skipped_classes.include?(klass.name) && klass.columns.collect(&:name).include?('owner_uuid')
+ klass.where({owner_uuid: p_uuid}).in_batches(of: 15).destroy_all
+ end
end
end
- # Finally delete the project itself
+ # Finally delete the group itself
p.destroy
end
end
t.add :can_manage
end
+ def default_delete_after_trash_interval
+ if self.group_class == 'role'
+ ActiveSupport::Duration.build(0)
+ else
+ super
+ end
+ end
+
+ def minimum_delete_after_trash_interval
+ if self.group_class == 'role'
+ ActiveSupport::Duration.build(0)
+ else
+ super
+ end
+ end
+
+ def validate_trash_and_delete_timing
+ if self.group_class == 'role' && delete_at && delete_at != trash_at
+ errors.add :delete_at, "must be == trash_at for role groups"
+ else
+ super
+ end
+ end
+
# check if admins are allowed to make changes to the project, e.g. it
# isn't trashed or frozen.
def admin_change_permitted
[self.uuid,
TrashedGroup.find_by_group_uuid(self.owner_uuid).andand.trash_at,
self.trash_at])
+
if frozen_descendants.any?
raise ArgumentError.new("cannot trash project containing frozen project #{frozen_descendants[0]["uuid"]}")
end
+ if self.trash_at and self.group_class == 'role'
+ # if this is a role group that is now in the trash, it loses all
+ # of its outgoing permissions.
+ Link.where(link_class: 'permission', tail_uuid: self.uuid).destroy_all
+ end
+
ActiveRecord::Base.connection.exec_query(%{
with temptable as (select * from project_subtree_with_trash_at($1, LEAST($2, $3)::timestamp)),
end
def clear_permissions_trash_frozen
+ Link.where(link_class: 'permission', tail_uuid: self.uuid).destroy_all
ComputedPermission.where(target_uuid: uuid).delete_all
ActiveRecord::Base.connection.exec_delete(
"delete from trashed_groups where group_uuid=$1",
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+class CreateUuidLocks < ActiveRecord::Migration[7.0]
+ def change
+ create_table :uuid_locks, id: false do |t|
+ t.string :uuid, null: false, index: {unique: true}
+ t.integer :n, null: false, default: 0
+ end
+ end
+end
ALTER SEQUENCE public.users_id_seq OWNED BY public.users.id;
+--
+-- Name: uuid_locks; Type: TABLE; Schema: public; Owner: -
+--
+
+CREATE TABLE public.uuid_locks (
+ uuid character varying NOT NULL,
+ n integer DEFAULT 0 NOT NULL
+);
+
+
--
-- Name: virtual_machines; Type: TABLE; Schema: public; Owner: -
--
CREATE UNIQUE INDEX index_users_on_uuid ON public.users USING btree (uuid);
+--
+-- Name: index_uuid_locks_on_uuid; Type: INDEX; Schema: public; Owner: -
+--
+
+CREATE UNIQUE INDEX index_uuid_locks_on_uuid ON public.uuid_locks USING btree (uuid);
+
+
--
-- Name: index_virtual_machines_on_created_at_and_uuid; Type: INDEX; Schema: public; Owner: -
--
('20231013000000'),
('20240329173437'),
('20240402162733'),
-('20240604183200');
+('20240604183200'),
+('20240618121312');
'repositories',
'specimens',
'traits',
+ 'uuid_locks',
])
klass = t.classify.constantize
next unless klass and 'owner_uuid'.in?(klass.columns.collect(&:name))
true
end
+ def default_delete_after_trash_interval
+ Rails.configuration.Collections.DefaultTrashLifetime
+ end
+
+ def minimum_delete_after_trash_interval
+ Rails.configuration.Collections.BlobSigningTTL
+ end
+
def default_trash_interval
if trash_at_changed? && !delete_at_changed?
# If trash_at is updated without touching delete_at,
if trash_at.nil?
self.delete_at = nil
else
- self.delete_at = trash_at + Rails.configuration.Collections.DefaultTrashLifetime.seconds
+ self.delete_at = trash_at + self.default_delete_after_trash_interval
end
elsif !trash_at || !delete_at || trash_at > delete_at
# Not trash, or bogus arguments? Just validate in
earliest_delete = [
@validation_timestamp,
trash_at_was,
- ].compact.min + Rails.configuration.Collections.BlobSigningTTL
+ ].compact.min + minimum_delete_after_trash_interval
# The previous value of delete_at is also an upper bound on the
# longest-lived permission token. For example, if TTL=14,
if !@object.is_trashed
@object.update!(trash_at: db_current_time)
end
- earliest_delete = (@object.trash_at +
- Rails.configuration.Collections.BlobSigningTTL)
+ earliest_delete = (@object.trash_at + @object.minimum_delete_after_trash_interval)
if @object.delete_at > earliest_delete
@object.update!(delete_at: earliest_delete)
end
end
def untrash
- if @object.is_trashed
- @object.trash_at = nil
+ if !@object.is_trashed
+ raise ArvadosModel::InvalidStateTransitionError.new("Item is not trashed, cannot untrash")
+ end
- if params[:ensure_unique_name]
- @object.save_with_unique_name!
- else
- @object.save!
- end
+ if db_current_time >= @object.delete_at
+ raise ArvadosModel::InvalidStateTransitionError.new("delete_at time has already passed, cannot untrash")
+ end
+
+ @object.trash_at = nil
+
+ if params[:ensure_unique_name]
+ @object.save_with_unique_name!
else
- raise ArvadosModel::InvalidStateTransitionError.new("Item is not trashed, cannot untrash")
+ @object.save!
end
+
show
end
name: trashed project
group_class: project
trash_at: 2001-01-01T00:00:00Z
- delete_at: 2008-03-01T00:00:00Z
+ delete_at: 2038-03-01T00:00:00Z
is_trashed: true
modified_at: 2001-01-01T00:00:00Z
delete_at: 2038-03-01T00:00:00Z
is_trashed: false
modified_at: 2001-01-01T00:00:00Z
+
+trashed_role_on_next_sweep:
+ uuid: zzzzz-j7d0g-soontobetrashd2
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: soon to be trashed role group
+ group_class: role
+ trash_at: 2001-01-01T00:00:00Z
+ delete_at: 2001-01-01T00:00:00Z
+ is_trashed: false
+ modified_at: 2001-01-01T00:00:00Z
name: can_write
head_uuid: zzzzz-j7d0g-fffffffffffffff
properties: {}
+
+foo_file_readable_by_soon_to_be_trashed_role:
+ uuid: zzzzz-o0j2j-5s8ry7sn7bwxb7w
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-000000000000000
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-soontobetrashd2
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ properties: {}
format: :json,
}
assert_response :success
- # Should not be trashed
- assert_nil Group.find_by_uuid(groups(grp).uuid)
+ # Should be trashed
+ assert Group.find_by_uuid(groups(grp).uuid).is_trashed
end
end
assert_not_empty Group.where('uuid=? and is_trashed=true', p.uuid)
end
+ test "trash_sweep - role groups are deleted" do
+ p = groups(:trashed_role_on_next_sweep)
+ assert_empty Group.where('uuid=? and is_trashed=true', p.uuid)
+ assert_not_empty Link.where(uuid: links(:foo_file_readable_by_soon_to_be_trashed_role).uuid)
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ assert_empty Group.where(uuid: p.uuid)
+ assert_empty Link.where(uuid: links(:foo_file_readable_by_soon_to_be_trashed_role).uuid)
+ end
+
test "trash_sweep - delete projects and their contents" do
g_foo = groups(:trashed_project)
g_bar = groups(:trashed_subproject)
assert_not_empty ContainerRequest.where(uuid: cr.uuid)
authorize_with :admin
+ Group.find_by_uuid(g_foo.uuid).update!(delete_at: Time.now - 1.second)
+
post :trash_sweep
assert_response :success
assert_equal user_nr_was, User.all.length
assert_equal coll_nr_was-2, # collection_in_trashed_subproject
Collection.all.length # & deleted_on_next_sweep collections
- assert_equal group_nr_was, Group.where('group_class<>?', 'project').length
+ assert_equal group_nr_was-1, # trashed_role_on_next_sweep
+ Group.where('group_class<>?', 'project').length
assert_equal project_nr_was-3, Group.where(group_class: 'project').length
assert_equal cr_nr_was-1, ContainerRequest.all.length
end
+ test "trash_sweep - delete unused uuid_locks" do
+ uuid_active = "zzzzz-zzzzz-uuidlockstest11"
+ uuid_inactive = "zzzzz-zzzzz-uuidlockstest00"
+
+ ready = Queue.new
+ insertsql = "INSERT INTO uuid_locks (uuid) VALUES ($1) ON CONFLICT (uuid) do UPDATE SET n = uuid_locks.n+1"
+ url = ENV["DATABASE_URL"].sub(/\?.*/, '')
+ Thread.new do
+ conn = PG::Connection.new(url)
+ conn.exec_params(insertsql, [uuid_active])
+ conn.exec_params(insertsql, [uuid_inactive])
+ conn.transaction do |conn|
+ conn.exec_params(insertsql, [uuid_active])
+ ready << true
+ # If we keep this transaction open while trash_sweep runs, the
+ # uuid_active row shouldn't get deleted.
+ sleep 10
+ rescue
+ # Unblock main thread
+ ready << false
+ raise
+ end
+ end
+ assert_equal true, ready.pop
+ authorize_with :admin
+ post :trash_sweep
+ rows = ActiveRecord::Base.connection.exec_query("SELECT uuid FROM uuid_locks ORDER BY uuid", "", []).rows
+ assert_includes(rows, [uuid_active], "row with active lock (still held by thread) should not have been deleted")
+ refute_includes(rows, [uuid_inactive], "row with inactive lock should have been deleted")
+ end
end
assert_response 404
end
+ test "adding can_read links from group to collection, user to group, then trash group" do
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response 404
+
+ # add permission for group to read collection
+ post "/arvados/v1/links",
+ params: {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private_role).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response 404
+
+ # add permission for spectator to read group
+ post "/arvados/v1/links",
+ params: {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:private_role).uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
+ u = json_response['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response :success
+
+ # put the group in the trash, this should keep the group members
+ # but delete the permissions.
+ post "/arvados/v1/groups/#{groups(:private_role).uuid}/trash",
+ params: {:format => :json},
+ headers: auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator, should fail now
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response 404
+
+ # should not be able to grant permission to a trashed group
+ post "/arvados/v1/links",
+ params: {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private_role).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
+ assert_response 422
+
+ # can't take group out of the trash
+ post "/arvados/v1/groups/#{groups(:private_role).uuid}/untrash",
+ params: {:format => :json},
+ headers: auth(:admin)
+ assert_response 422
+
+ # when a role group is untrashed the permissions don't
+ # automatically come back
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response 404
+
+ # can't add permission for group to read collection either
+ post "/arvados/v1/links",
+ params: {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private_role).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ },
+ headers: auth(:admin)
+ assert_response 422
+
+ # still can't read foo file
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}",
+ params: {:format => :json},
+ headers: auth(:spectator)
+ assert_response 404
+ end
+
test "read-only group-admin cannot modify administered user" do
put "/arvados/v1/users/#{users(:active).uuid}",
params: {
Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands::
- sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<EOF
+ sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
- baseurl=http://rpm.arvados.org/CentOS/\$releasever/os/\$basearch/
+ baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
- gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+ gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-arvados-fuse
import { FilterBuilder } from 'services/api/filter-builder';
import { ProcessStatusFilter, buildProcessStatusFilters } from 'store/resource-type-filters/resource-type-filters';
import {act} from "react-dom/test-utils";
+import { updateResources } from 'store/resources/resources-actions';
configure({ adapter: new Adapter() });
it("requests subprocess progress stats for stopped processes and displays progress", async () => {
// when
+ const containerRequest = {
+ uuid: 'zzzzz-xvhdp-000000000000000',
+ containerUuid: 'zzzzz-dz642-000000000000000',
+ };
const process = {
container: {
state: ContainerState.COMPLETE,
},
- containerRequest: {
- containerUuid: 'zzzzz-dz642-000000000000000',
- },
+ containerRequest: containerRequest,
} as Process;
+ await store.dispatch(updateResources([containerRequest, process]));
statusResponse = {
[ProcessStatusFilter.COMPLETED]: 100,
});
it("dislays correct progress bar widths with different values", async () => {
+ const containerRequest = {
+ uuid: 'zzzzz-xvhdp-000000000000001',
+ containerUuid: 'zzzzz-dz642-000000000000001',
+ };
const process = {
container: {
state: ContainerState.COMPLETE,
},
- containerRequest: {
- containerUuid: 'zzzzz-dz642-000000000000001',
- },
+ containerRequest: containerRequest,
} as Process;
+ await store.dispatch(updateResources([containerRequest, process]));
statusResponse = {
[ProcessStatusFilter.COMPLETED]: 50,
import { StyleRulesCallback, Tooltip, WithStyles, withStyles } from "@material-ui/core";
import { CProgressStacked, CProgress } from '@coreui/react';
import { useAsyncInterval } from "common/use-async-interval";
-import { Process } from "store/processes/process";
+import { Process, isProcessRunning } from "store/processes/process";
import { connect } from "react-redux";
import { Dispatch } from "redux";
-import { fetchProcessProgressBarStatus } from "store/subprocess-panel/subprocess-panel-actions";
+import { fetchProcessProgressBarStatus, isProcess } from "store/subprocess-panel/subprocess-panel-actions";
import { ProcessStatusFilter, serializeOnlyProcessTypeFilters } from "store/resource-type-filters/resource-type-filters";
import { ProjectResource } from "models/project";
import { getDataExplorer } from "store/data-explorer/data-explorer-reducer";
}
export interface ProgressBarActionProps {
- fetchProcessProgressBarStatus: (parentResource
: Process | ProjectResource, typeFilter?: string) => Promise<ProgressBarStatus | undefined>;
+ fetchProcessProgressBarStatus: (parentResource
Uuid: string, typeFilter?: string) => Promise<ProgressBarStatus | undefined>;
}
type ProgressBarProps = ProgressBarDataProps & ProgressBarActionProps & WithStyles<CssRules>;
export type ProgressBarStatus = {
counts: ProgressBarCounts;
- isRunning: boolean;
+ shouldPollProject: boolean;
};
const mapStateToProps = (state: RootState, props: ProgressBarDataProps) => {
};
const mapDispatchToProps = (dispatch: Dispatch): ProgressBarActionProps => ({
- fetchProcessProgressBarStatus: (parentResource: Process | ProjectResource, typeFilter?: string) => {
- return dispatch<any>(fetchProcessProgressBarStatus(parentResource, typeFilter));
+ fetchProcessProgressBarStatus: (parentResourceUuid: string, typeFilter?: string) => {
+ return dispatch<any>(fetchProcessProgressBarStatus(parentResourceUuid, typeFilter));
},
});
({ parentResource, typeFilter, classes, fetchProcessProgressBarStatus }: ProgressBarProps) => {
const [progressCounts, setProgressData] = useState<ProgressBarCounts | undefined>(undefined);
- const [isRunning, setIsRunning] = useState<boolean>(false);
-
+ const [shouldPollProject, setShouldPollProject] = useState<boolean>(false);
+ const shouldPollProcess = isProcess(parentResource) ? isProcessRunning(parentResource) : false;
+
+ // Should polling be active based on container status
+ // or result of aggregated project process contents
+ const shouldPoll = shouldPollProject || shouldPollProcess;
+
+ const parentUuid = parentResource
+ ? isProcess(parentResource)
+ ? parentResource.containerRequest.uuid
+ : parentResource.uuid
+ : "";
+
+ // Runs periodically whenever polling should be happeing
+ // Either when the workflow is running (shouldPollProcess) or when the
+ // project contains steps in an active state (shouldPollProject)
useAsyncInterval(async () => {
- if (parentResource) {
- fetchProcessProgressBarStatus(parentResource, typeFilter)
+ if (parentUuid) {
+ fetchProcessProgressBarStatus(parentUuid, typeFilter)
.then(result => {
if (result) {
setProgressData(result.counts);
- setIsRunning(result.isRunning);
+ setShouldPollProject(result.shouldPollProject);
}
});
}
- }, isRunning ? 5000 : null);
-
+ }, shouldPoll ? 5000 : null);
+
+ // Runs fetch on first load for processes and projects, except when
+ // process is running since polling will be enabled by shouldPoll.
+ // Project polling starts false so this is still needed for project
+ // initial load to set shouldPollProject and kick off shouldPoll
+ // Watches shouldPollProcess but not shouldPollProject
+ // * This runs a final fetch when process ends & is updated through
+ // websocket / store
+ // * We ignore shouldPollProject entirely since it changes to false
+ // as a result of a fetch so the data is already up to date
useEffect(() => {
- if (!isRunning && parentResource) {
- fetchProcessProgressBarStatus(parentResource, typeFilter)
+ if (!shouldPollProcess && parentUuid) {
+ fetchProcessProgressBarStatus(parentUuid, typeFilter)
.then(result => {
if (result) {
setProgressData(result.counts);
- setIsRunning(result.isRunning);
+ setShouldPollProject(result.shouldPollProject);
}
});
}
- }, [fetchProcessProgressBarStatus, isRunning, parentResource, typeFilter]);
+ }, [fetchProcessProgressBarStatus, shouldPollProcess, parentUuid, typeFilter]);
let tooltip = "";
if (progressCounts) {
import { ProjectResource } from "models/project";
import { getProcess } from "store/processes/process";
import { filterCollectionFilesBySelection } from "store/collection-panel/collection-panel-files/collection-panel-files-state";
+import { selectOne, deselectAllOthers } from "store/multiselect/multiselect-actions";
export const contextMenuActions = unionize({
OPEN_CONTEXT_MENU: ofType<{ position: ContextMenuPosition; resource: ContextMenuResource }>(),
export const openContextMenu = (event: React.MouseEvent<HTMLElement>, resource: ContextMenuResource) => (dispatch: Dispatch) => {
event.preventDefault();
+ dispatch<any>(selectOne(resource.uuid));
+ dispatch<any>(deselectAllOthers(resource.uuid));
const { left, top } = event.currentTarget.getBoundingClientRect();
dispatch(
contextMenuActions.OPEN_CONTEXT_MENU({
import { FilterBuilder, joinFilters } from 'services/api/filter-builder';
import { ProgressBarStatus, ProgressBarCounts } from 'components/subprocess-progress-bar/subprocess-progress-bar';
import { ProcessStatusFilter, buildProcessStatusFilters } from 'store/resource-type-filters/resource-type-filters';
-import { Process, isProcessRunning } from 'store/processes/process';
+import { Process } from 'store/processes/process';
import { ProjectResource } from 'models/project';
+import { getResource } from 'store/resources/resources';
+import { ContainerRequestResource } from 'models/container-request';
+import { Resource } from 'models/resource';
export const SUBPROCESS_PANEL_ID = "subprocessPanel";
export const SUBPROCESS_ATTRIBUTES_DIALOG = 'subprocessAttributesDialog';
processStatus: ProcessStatusFilter;
};
-const isProcess = (resource: Process | ProjectResource | undefined): resource is Process => {
+/**
+ * Type guard to distinguish Processes from other Resources
+ * @param resource The item to check
+ * @returns if the resource is a Process
+ */
+export const isProcess = <T extends Resource>(resource: T | Process | undefined): resource is Process => {
return !!resource && 'containerRequest' in resource;
};
-export const fetchProcessProgressBarStatus = (parentResource: Process | ProjectResource, typeFilter?: string) =>
+/**
+ * Type guard to distinguish ContainerRequestResources from Resources
+ * @param resource The item to check
+ * @returns if the resource is a ContainerRequestResource
+ */
+const isContainerRequest = <T extends Resource>(resource: T | ContainerRequestResource | undefined): resource is ContainerRequestResource => {
+ return !!resource && 'containerUuid' in resource;
+};
+
+export const fetchProcessProgressBarStatus = (parentResourceUuid: string, typeFilter?: string) =>
async (dispatch: Dispatch, getState: () => RootState, services: ServiceRepository): Promise<ProgressBarStatus | undefined> => {
+ const resources = getState().resources;
+ const parentResource = getResource<ProjectResource | ContainerRequestResource>(parentResourceUuid)(resources);
+
const requestContainerStatusCount = async (fb: FilterBuilder) => {
return await services.containerRequestService.list({
limit: 0,
});
}
- let baseFilter = "";
- if (isProcess(parentResource)) {
- baseFilter = new FilterBuilder().addEqual('requesting_container_uuid', parentResource.containerRequest.containerUuid).getFilters();
- } else {
+ let baseFilter: string = "";
+ if (isContainerRequest(parentResource) && parentResource.containerUuid) {
+ // Prevent CR without containerUuid from generating baseFilter
+ baseFilter = new FilterBuilder().addEqual('requesting_container_uuid', parentResource.containerUuid).getFilters();
+ } else if (parentResource && !isContainerRequest(parentResource)) {
+ // isCR type narrowing needed since CR without container may fall through
baseFilter = new FilterBuilder().addEqual('owner_uuid', parentResource.uuid).getFilters();
}
- if (typeFilter) {
- baseFilter = joinFilters(baseFilter, typeFilter);
- }
+ if (parentResource && baseFilter) {
+ // Add type filters from consumers that want to sync progress stats with filters
+ if (typeFilter) {
+ baseFilter = joinFilters(baseFilter, typeFilter);
+ }
- if (baseFilter) {
try {
// Create return object
let result: ProgressBarCounts = {
result[singleResult.status] += singleResult.count;
});
- let isRunning = result[ProcessStatusFilter.RUNNING] + result[ProcessStatusFilter.QUEUED] > 0;
-
- if (isProcess(parentResource)) {
- isRunning = isProcessRunning(parentResource);
- }
-
- return {counts: result, isRunning};
+ // CR polling is handled in progress bar based on store updates
+ // This bool triggers polling without causing a final fetch when disabled
+ // The shouldPoll logic here differs slightly from shouldPollProcess:
+ // * Process gets websocket updates through the store so using isProcessRunning
+ // ignores Queued
+ // * In projects, we get no websocket updates on CR state changes so we treat
+ // Queued processes as running in order to let polling keep us up to date
+ // when anything transitions to Running. This also means that a project with
+ // CRs in a stopped state won't start polling if CRs are started elsewhere
+ const shouldPollProject = isContainerRequest(parentResource)
+ ? false
+ : (result[ProcessStatusFilter.RUNNING] + result[ProcessStatusFilter.QUEUED]) > 0;
+
+ return {counts: result, shouldPollProject};
} catch (e) {
return undefined;
}
- } else {
- return undefined;
}
+ return undefined;
};
export const viewDetailsAction = {
icon: DetailsIcon,
name: ContextMenuActionNames.VIEW_DETAILS,
- execute: dispatch => {
- dispatch(toggleDetailsPanel());
+ execute: (dispatch, resources) => {
+ dispatch(toggleDetailsPanel(resources[0].uuid));
},
};
Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands::
- sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<EOF
+ sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
- baseurl=http://rpm.arvados.org/CentOS/\$releasever/os/\$basearch/
+ baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
- gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+ gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-crunchstat-summary
--- /dev/null
+---
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+postgresql_external_service:
+ db_host: "__DATABASE_EXTERNAL_SERVICE_HOST_OR_IP__"
+ db_port: 5432
+ db_name: "__DATABASE_NAME__"
+ db_user: "__DATABASE_USER__"
+ db_password: "__DATABASE_PASSWORD__"
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+{%- set pg_svc = pillar.get('postgresql_external_service', {}) %}
+
+{%- if pg_svc %}
+__CLUSTER___external_trgm_extension:
+ postgres_extension.present:
+ - name: pg_trgm
+ - if_not_exists: true
+ - schema: public
+ - db_host: {{ pg_svc.db_host }}
+ - db_port: 5432
+ - db_user: {{ pg_svc.db_user }}
+ - db_password: {{ pg_svc.db_password }}
+ - require:
+ - pkg: postgresql-client-libs
+{%- endif %}
\ No newline at end of file
logfile=terraform-$(date -Iseconds).log
(cd terraform/vpc && terraform apply -auto-approve) 2>&1 | tee -a $logfile
(cd terraform/data-storage && terraform apply -auto-approve) 2>&1 | tee -a $logfile
- (cd terraform/services && terraform apply -auto-approve) 2>&1 | grep -v letsencrypt_iam_secret_access_key | tee -a $logfile
- (cd terraform/services && echo -n 'letsencrypt_iam_secret_access_key = ' && terraform output letsencrypt_iam_secret_access_key) 2>&1 | tee -a $logfile
+ (cd terraform/services && \
+ terraform apply -auto-approve) 2>&1 | \
+ grep -v letsencrypt_iam_secret_access_key | \
+ grep -v database_password | \
+ tee -a $logfile
+ (cd terraform/services && \
+ echo -n 'letsencrypt_iam_secret_access_key = ' && \
+ terraform output letsencrypt_iam_secret_access_key && \
+ echo -n 'database_password = ' && \
+ terraform output database_password) 2>&1 | tee -a $logfile
;;
terraform-destroy)
for R in ${ROLES:-}; do
case "${R}" in
"database")
+ # Skip if using an external service
+ if [[ "${DATABASE_EXTERNAL_SERVICE_HOST_OR_IP:-}" != "" ]]; then
+ continue
+ fi
# States
grep -q "\- postgres$" ${STATES_TOP} || echo " - postgres" >> ${STATES_TOP}
grep -q "extra.prometheus_pg_exporter" ${STATES_TOP} || echo " - extra.prometheus_pg_exporter" >> ${STATES_TOP}
fi
echo " - extra.passenger_rvm" >> ${STATES_TOP}
grep -q "^ - postgres\\.client$" ${STATES_TOP} || echo " - postgres.client" >> ${STATES_TOP}
+ if [[ "${DATABASE_EXTERNAL_SERVICE_HOST_OR_IP:-}" != "" ]]; then
+ grep -q " - extra.postgresql_external" ${STATES_TOP} || echo " - extra.postgresql_external" >> ${STATES_TOP}
+ fi
### If we don't install and run LE before arvados-api-server, it fails and breaks everything
### after it. So we add this here as we are, after all, sharing the host for api and controller
grep -q "nginx_api_configuration" ${PILLARS_TOP} || echo " - nginx_api_configuration" >> ${PILLARS_TOP}
grep -q "nginx_controller_configuration" ${PILLARS_TOP} || echo " - nginx_controller_configuration" >> ${PILLARS_TOP}
+ if [[ "${DATABASE_EXTERNAL_SERVICE_HOST_OR_IP:-}" != "" ]]; then
+ grep -q " - postgresql_external" ${PILLARS_TOP} || echo " - postgresql_external" >> ${PILLARS_TOP}
+ fi
+
if [ "${ENABLE_BALANCER}" == "no" ]; then
if [ "${SSL_MODE}" = "lets-encrypt" ]; then
if [ "${USE_LETSENCRYPT_ROUTE53}" = "yes" ]; then
}
private_subnet_id = data.terraform_remote_state.vpc.outputs.private_subnet_id
public_subnet_id = data.terraform_remote_state.vpc.outputs.public_subnet_id
+ additional_rds_subnet_id = data.terraform_remote_state.vpc.outputs.additional_rds_subnet_id
arvados_sg_id = data.terraform_remote_state.vpc.outputs.arvados_sg_id
eip_id = data.terraform_remote_state.vpc.outputs.eip_id
keepstore_iam_role_name = data.terraform_remote_state.data-storage.outputs.keepstore_iam_role_name
+ use_rds = (var.use_rds && data.terraform_remote_state.vpc.outputs.use_rds)
+ rds_username = var.rds_username != "" ? var.rds_username : "${local.cluster_name}_arvados"
+ rds_password = var.rds_password != "" ? var.rds_password : one(random_string.default_rds_password[*].result)
+ rds_allocated_storage = var.rds_allocated_storage
+ rds_max_allocated_storage = max(var.rds_max_allocated_storage, var.rds_allocated_storage)
+ rds_instance_type = var.rds_instance_type
+ rds_backup_retention_period = var.rds_backup_retention_period
+ rds_backup_before_deletion = var.rds_backup_before_deletion
+ rds_final_backup_name = var.rds_final_backup_name != "" ? var.rds_final_backup_name : "arvados-${local.cluster_name}-db-final-snapshot"
+ rds_postgresql_version = var.rds_postgresql_version
}
}
}
+provider "random" {}
+
+resource "random_string" "default_rds_password" {
+ count = (local.use_rds && var.rds_password == "") ? 1 : 0
+ length = 32
+ special = false
+}
+
resource "aws_iam_instance_profile" "keepstore_instance_profile" {
name = "${local.cluster_name}-keepstore-00-iam-role"
role = data.terraform_remote_state.data-storage.outputs.keepstore_iam_role_name
}
}
+resource "aws_db_subnet_group" "arvados_db_subnet_group" {
+ count = local.use_rds ? 1 : 0
+ name = "${local.cluster_name}_db_subnet_group"
+ subnet_ids = [local.private_subnet_id, local.additional_rds_subnet_id]
+}
+
+resource "aws_db_instance" "postgresql_service" {
+ count = local.use_rds ? 1 : 0
+ allocated_storage = local.rds_allocated_storage
+ max_allocated_storage = local.rds_max_allocated_storage
+ engine = "postgres"
+ engine_version = local.rds_postgresql_version
+ instance_class = local.rds_instance_type
+ db_name = "${local.cluster_name}_arvados"
+ username = local.rds_username
+ password = local.rds_password
+ skip_final_snapshot = !local.rds_backup_before_deletion
+ final_snapshot_identifier = local.rds_final_backup_name
+
+ vpc_security_group_ids = [local.arvados_sg_id]
+ db_subnet_group_name = aws_db_subnet_group.arvados_db_subnet_group[0].name
+
+ backup_retention_period = local.rds_backup_retention_period
+ publicly_accessible = false
+ storage_encrypted = true
+ multi_az = false
+
+ lifecycle {
+ ignore_changes = [
+ username,
+ ]
+ }
+
+ tags = {
+ Name = "${local.cluster_name}_postgresql_service"
+ }
+}
+
resource "aws_iam_policy" "compute_node_ebs_autoscaler" {
name = "${local.cluster_name}_compute_node_ebs_autoscaler"
policy = jsonencode({
output "ssl_password_secret_name" {
value = aws_secretsmanager_secret.ssl_password_secret.name
-}
\ No newline at end of file
+}
+
+output "database_address" {
+ value = one(aws_db_instance.postgresql_service[*].address)
+}
+
+output "database_name" {
+ value = one(aws_db_instance.postgresql_service[*].db_name)
+}
+
+output "database_username" {
+ value = one(aws_db_instance.postgresql_service[*].username)
+}
+
+output "database_password" {
+ value = one(aws_db_instance.postgresql_service[*].password)
+ sensitive = true
+}
+
+output "database_version" {
+ value = one(aws_db_instance.postgresql_service[*].engine_version_actual)
+}
# controller = 300
# }
+# Use an RDS instance for database. For this to work, make sure to also set
+# 'use_rds' to true in '../vpc/terraform.tfvars'.
+# use_rds = true
+#
+# Provide custom values if needed.
+# rds_username = ""
+# rds_password = ""
+# rds_instance_type = "db.m5.xlarge"
+# rds_postgresql_version = "16.3"
+# rds_allocated_storage = 200
+# rds_max_allocated_storage = 1000
+# rds_backup_retention_period = 30
+# rds_backup_before_deletion = false
+# rds_final_backup_name = ""
+
# AWS secret's name which holds the SSL certificate private key's password.
# Default: "arvados-ssl-privkey-password"
# ssl_password_secret_name_suffix = "some-name-suffix"
description = "The EC2 instance AMI to use on the nodes"
type = string
default = ""
-}
\ No newline at end of file
+}
+
+variable "use_rds" {
+ description = "Enable to create an RDS instance as the cluster's database service"
+ type = bool
+ default = false
+}
+
+variable "rds_username" {
+ description = "RDS instance's username. Default: <cluster_name>_arvados"
+ type = string
+ default = ""
+}
+
+variable "rds_password" {
+ description = "RDS instance's password. Default: randomly-generated 32 chars"
+ type = string
+ default = ""
+}
+
+variable "rds_instance_type" {
+ description = "RDS instance type"
+ type = string
+ default = "db.m5.large"
+}
+
+variable "rds_allocated_storage" {
+ description = "RDS initial storage size (GiB)"
+ type = number
+ default = 60
+}
+
+variable "rds_max_allocated_storage" {
+ description = "RDS maximum storage size that will autoscale to (GiB)"
+ type = number
+ default = 300
+}
+
+variable "rds_backup_retention_period" {
+ description = "RDS Backup retention (days). Set to 0 to disable"
+ type = number
+ default = 7
+ validation {
+ condition = (var.rds_backup_retention_period <= 35)
+ error_message = "rds_backup_retention_period should be less than 36 days"
+ }
+}
+
+variable "rds_backup_before_deletion" {
+ description = "Create a snapshot before deleting the RDS instance"
+ type = bool
+ default = true
+}
+
+variable "rds_final_backup_name" {
+ description = "Snapshot name to use for the RDS final snapshot"
+ type = string
+ default = ""
+}
+
+variable "rds_postgresql_version" {
+ description = "RDS PostgreSQL version"
+ type = string
+ default = "15"
+}
private_subnet_id = one(aws_subnet.private_subnet[*]) != null ? one(aws_subnet.private_subnet[*]).id : var.private_subnet_id
public_subnet_id = one(aws_subnet.public_subnet[*]) != null ? one(aws_subnet.public_subnet[*]).id : var.public_subnet_id
+ additional_rds_subnet_id = one(aws_subnet.additional_rds_subnet[*]) != null ? one(aws_subnet.additional_rds_subnet[*]).id : var.additional_rds_subnet_id
public_hosts = var.private_only ? [] : var.user_facing_hosts
private_hosts = concat(
}
]
])
+ use_rds = var.use_rds
}
}
}
+#
+# Additional subnet on a different AZ is required if RDS is enabled
+#
+resource "aws_subnet" "additional_rds_subnet" {
+ count = (var.additional_rds_subnet_id == "" && local.use_rds) ? 1 : 0
+ vpc_id = local.arvados_vpc_id
+ availability_zone = data.aws_availability_zones.available.names[1]
+ cidr_block = "10.1.3.0/24"
+
+ lifecycle {
+ precondition {
+ condition = (var.vpc_id == "")
+ error_message = "additional_rds_subnet_id should be set if vpc_id is also set"
+ }
+ }
+}
+
#
# VPC S3 access
#
value = local.arvados_sg_id
}
+output "additional_rds_subnet_id" {
+ value = local.use_rds ? local.additional_rds_subnet_id : ""
+}
+
output "eip_id" {
value = { for k, v in aws_eip.arvados_eip: k => v.id }
}
output "custom_tags" {
value = var.custom_tags
}
+
+output "use_rds" {
+ value = var.use_rds
+}
# Optional networking options. Set existing resources to be used instead of
# creating new ones.
# NOTE: We only support fully managed or fully custom networking, not a mix of both.
+#
# vpc_id = "vpc-aaaa"
# sg_id = "sg-bbbb"
# public_subnet_id = "subnet-cccc"
# private_subnet_id = "subnet-dddd"
+#
+# RDS related parameters:
+# use_rds = true
+# additional_rds_subnet_id = "subnet-eeee"
# Optional custom tags to add to every resource. Default: {}
# custom_tags = {
default = ""
}
+variable "additional_rds_subnet_id" {
+ description = "Use existing subnet for RDS instead of creating one for the cluster"
+ type = string
+ default = ""
+}
+
variable "private_subnet_id" {
description = "Use existing private subnet instead of creating one for the cluster"
type = string
description = "Apply customized tags to every resource on the cluster"
type = map(string)
default = {}
+}
+
+variable "use_rds" {
+ description = "Enable this to create an RDS instance as the cluster's database service"
+ type = bool
+ default = false
}
\ No newline at end of file
Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands::
- sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<EOF
+ sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
- baseurl=http://rpm.arvados.org/CentOS/\$releasever/os/\$basearch/
+ baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
- gpgkey=http://rpm.arvados.org/CentOS/RPM-GPG-KEY-arvados
+ gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-arvados-user-activity
projects / arvados.git / commitdiff