Server-side components of Arvados contained in the apps/ and services/
-directories, including the API Server, Workbench, and Crunch, are licenced
+directories, including the API Server, Workbench, and Crunch, are licensed
under the GNU Affero General Public License version 3 (see agpl-3.0.txt)
The Arvados client Software Development Kits contained in the sdk/ directory,
sharing_popup
end
+ def update
+ @updates ||= params[@object.resource_param_name.to_sym]
+ if @updates && (@updates.keys - ["name", "description"]).empty?
+ # exclude manifest_text since only name or description is being updated
+ @object.manifest_text = nil
+ end
+ super
+ end
+
protected
def find_usable_token(token_list)
['tail_uuid', '=', current_user.uuid],
['link_class', '=', 'permission'],
])
- @my_repositories = Repository.where uuid: repo_links.collect(&:head_uuid)
+
+ owned_repositories = Repository.where(owner_uuid: current_user.uuid)
+
+ @my_repositories = (Repository.where(uuid: repo_links.collect(&:head_uuid)) |
+ owned_repositories).
+ uniq { |repo| repo.uuid }
+
+
@repo_writable = {}
repo_links.each do |link|
if link.name.in? ['can_write', 'can_manage']
end
end
+ owned_repositories.each do |repo|
+ @repo_writable[repo.uuid] = 'can_manage'
+ end
+
# virtual machines the current user can login into
@my_vm_logins = {}
Link.where(tail_uuid: current_user.uuid,
<div class="col-md-6">
<div class="panel panel-info">
<div class="panel-heading">
- <h3 class="panel-title">
+ <h3 class="panel-title">
<% if @name_link.nil? and @object.uuid.match /[0-9a-f]{32}/ %>
Content hash <%= @object.portable_data_hash %>
<% else %>
- <%= if @object.respond_to? :name
+ <%= if @object.respond_to? :name
render_editable_attribute @object, :name
else
@name_link.andand.name || @object.uuid
end %>
<% end %>
- </h3>
+ </h3>
</div>
<div class="panel-body">
<div class="arv-description-as-subtitle">
<%= render_editable_attribute @object, 'description', nil, { 'data-emptytext' => "(No description provided)", 'data-toggle' => 'manual' } %>
</div>
<img src="/favicon.ico" class="pull-right" alt="" style="opacity: 0.3"/>
- <p><i>Content hash:</i><br />
- <span class="arvados-uuid"><%= link_to @object.portable_data_hash, collection_path(@object.portable_data_hash) %></span>
+
<p><i>Content hash:</i><br />
+ <span class="arvados-uuid"><%= link_to @object.portable_data_hash, collection_path(@object.portable_data_hash) %></span>
</p>
<%= render partial: "show_source_summary" %>
</div>
<div class="col-md-3">
<div class="panel panel-default">
<div class="panel-heading">
- <h3 class="panel-title">
- Activity
- </h3>
+ <h3 class="panel-title">
+ Activity
+ </h3>
</div>
<div class="panel-body smaller-text">
<!--
- <input type="text" class="form-control" placeholder="Search"/>
+ <input type="text" class="form-control" placeholder="Search"/>
-->
- <div style="height:0.5em;"></div>
+
<div style="height:0.5em;"></div>
<% name_or_object = @name_link.andand.uuid ? @name_link : @object %>
<% if name_or_object.created_at and not @logs.andand.any? %>
<p>
</div>
</div>
</div>
+ <% if current_user %>
<div class="col-md-3">
<div class="panel panel-default">
<div class="panel-heading">
- <h3 class="panel-title">
- Sharing and permissions
- </h3>
+ <h3 class="panel-title">
+ Sharing and permissions
+ </h3>
</div>
<div class="panel-body">
<!--
- <input type="text" class="form-control" placeholder="Search"/>
+ <input type="text" class="form-control" placeholder="Search"/>
-->
<div id="sharing-button">
<%= render partial: 'sharing_button' %>
</div>
- <div style="height:0.5em;"></div>
+
<div style="height:0.5em;"></div>
<% if @projects.andand.any? %>
<p>Included in projects:<br />
<%= render_arvados_object_list_start(@projects, 'Show all projects',
</div>
</div>
</div>
+ <% else %>
+ <div class="col-md-3">
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h3 class="panel-title">
+ Welcome to Arvados
+ </h3>
+ </div>
+ <div class="panel-body">
+ You are accessing public data.
+ </div>
+ </div>
+ </div>
+ <% end %>
</div>
<%= render file: 'application/show.html.erb', locals: local_assigns %>
assert /#{stage3_id}->#{stage3_out}/.match(used_by_svg)
end
+
+ test "view collection with empty properties" do
+ fixture_name = :collection_with_empty_properties
+ show_collection(fixture_name, :active)
+ assert_equal(api_fixture('collections')[fixture_name.to_s]['name'], assigns(:object).name)
+ assert_not_nil(assigns(:object).properties)
+ assert_empty(assigns(:object).properties)
+ end
+
+ test "view collection with one property" do
+ fixture_name = :collection_with_one_property
+ show_collection(fixture_name, :active)
+ fixture = api_fixture('collections')[fixture_name.to_s]
+ assert_equal(fixture['name'], assigns(:object).name)
+ assert_equal(fixture['properties'][0], assigns(:object).properties[0])
+ end
+
+ test "create collection with properties" do
+ post :create, {
+ collection: {
+ name: 'collection created with properties',
+ manifest_text: '',
+ properties: {
+ property_1: 'value_1'
+ },
+ },
+ format: :json
+ }, session_for(:active)
+ assert_response :success
+ assert_not_nil assigns(:object).uuid
+ assert_equal 'collection created with properties', assigns(:object).name
+ assert_equal 'value_1', assigns(:object).properties[:property_1]
+ end
+
+ test "update description and check manifest_text is not lost" do
+ collection = api_fixture("collections")["multilevel_collection_1"]
+ post :update, {
+ id: collection["uuid"],
+ collection: {
+ description: 'test description update'
+ },
+ format: :json
+ }, session_for(:active)
+ assert_response :success
+ assert_not_nil assigns(:object)
+ assert_equal 'test description update', assigns(:object).description
+ assert_equal collection['manifest_text'], assigns(:object).manifest_text
+ end
end
assert_includes editables, false, "should have a readonly repository"
end
+ test "show repositories lists linked as well as owned repositories" do
+ get :manage_account, {}, session_for(:active)
+ assert_response :success
+ repos = assigns(:my_repositories)
+ assert repos
+ repo_writables = assigns(:repo_writable)
+ assert_not_empty repo_writables, "repo_writables should not be empty"
+ assert_includes repo_writables, api_fixture('repositories')['repository4']['uuid'] # writable by active
+ assert_includes repo_writables, api_fixture('repositories')['repository2']['uuid'] # owned by active
+ end
+
test "request shell access" do
user = api_fixture('users')['spectator']
# in collection page
assert_no_selector 'input', text: 'Create sharing link'
+ assert_no_text 'Sharing and permissions'
assert_no_selector 'a', text: 'Upload'
assert_no_selector 'button', 'Selection'
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
-|locator|string|||
-|portable_data_hash|string|||
|name|string|||
-|redundancy|number|||
-|redundancy_confirmed_by_client_uuid|string|API client||
-|redundancy_confirmed_at|datetime|||
-|redundancy_confirmed_as|number|||
+|description|text|||
+|portable_data_hash|string|||
|manifest_text|text|||
+|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.||
print >>stderr, error
sys.exit(1)
- # Apply default replication, if none specified. TODO (#3410): Use
- # default replication given by discovery document.
- if args.replication <= 0:
- args.replication = 2
+ # write_copies diverges from args.replication here.
+ # args.replication is how many copies we will instruct Arvados to
+ # maintain (by passing it in collections().create()) after all
+ # data is written -- and if None was given, we'll use None there.
+ # Meanwhile, write_copies is how many copies of each data block we
+ # write to Keep, which has to be a number.
+ #
+ # If we simply changed args.replication from None to a default
+ # here, we'd end up erroneously passing the default replication
+ # level (instead of None) to collections().create().
+ write_copies = (args.replication or
+ api_client._rootDesc.get('defaultCollectionReplication', 2))
if args.progress:
reporter = progress_writer(human_progress)
writer = ArvPutCollectionWriter(
resume_cache, reporter, bytes_expected,
num_retries=args.retries,
- replication=args.replication)
+ replication=write_copies)
else:
writer = ArvPutCollectionWriter.from_cache(
resume_cache, reporter, bytes_expected,
num_retries=args.retries,
- replication=args.replication)
+ replication=write_copies)
# Install our signal handler for each code in CAUGHT_SIGNALS, and save
# the originals.
manifest_text = CollectionReader(manifest_text).manifest_text(normalize=True)
replication_attr = 'replication_desired'
if api_client._schema.schemas['Collection']['properties'].get(replication_attr, None) is None:
- # API calls it 'redundancy' until #3410.
+ # API called it 'redundancy' before #3410.
replication_attr = 'redundancy'
# Register the resulting collection in Arvados.
collection = api_client.collections().create(
def test_put_collection_with_default_redundancy(self):
collection = self.run_and_find_collection("")
- self.assertEqual(2, collection['replication_desired'])
+ self.assertEqual(None, collection['replication_desired'])
def test_put_collection_with_unnamed_project_link(self):
link = self.run_and_find_collection(
title: "Arvados API",
description: "The API to interact with Arvados.",
documentationLink: "http://doc.arvados.org/api/index.html",
+ defaultCollectionReplication: Rails.configuration.default_collection_replication,
protocol: "rest",
baseUrl: root_url + "arvados/v1/",
basePath: "/arvados/v1/",
include KindAndEtag
include CommonApiTemplate
+ serialize :properties, Hash
+
before_validation :check_encoding
before_validation :check_signatures
before_validation :strip_manifest_text
before_validation :set_portable_data_hash
+ before_validation :maybe_clear_replication_confirmed
validate :ensure_hash_matches_manifest_text
before_save :set_file_names
t.add :portable_data_hash
t.add :signed_manifest_text, as: :manifest_text
t.add :replication_desired
+ t.add :replication_confirmed
+ t.add :replication_confirmed_at
end
def self.attributes_required_columns
# API response, and never let clients select the
# manifest_text column.
'manifest_text' => ['manifest_text'],
-
- # This is a shim until the database column gets
- # renamed to replication_desired in #3410.
- 'replication_desired' => ['redundancy'],
)
end
end
end
- def replication_desired
- # Shim until database columns get fixed up in #3410.
- redundancy or 2
- end
-
- def redundancy_status
- if redundancy_confirmed_as.nil?
- 'unconfirmed'
- elsif redundancy_confirmed_as < redundancy
- 'degraded'
- else
- if redundancy_confirmed_at.nil?
- 'unconfirmed'
- elsif Time.now - redundancy_confirmed_at < 7.days
- 'OK'
- else
- 'stale'
- end
- end
- end
-
def signed_manifest_text
if has_attribute? :manifest_text
token = current_api_client_authorization.andand.api_token
def self.munge_manifest_locators! manifest
# Given a manifest text and a block, yield each locator,
# and replace it with whatever the block returns.
- manifest.andand.gsub!(/ [[:xdigit:]]{32}(\+[[:digit:]]+)?(\+\S+)/) do |word|
+ manifest.andand.gsub!(/ [[:xdigit:]]{32}(\+\S+)?/) do |word|
if loc = Keep::Locator.parse(word.strip)
" " + yield(loc)
else
end
end
+ def self.each_manifest_locator manifest
+ # Given a manifest text and a block, yield each locator.
+ manifest.andand.scan(/ ([[:xdigit:]]{32}(\+\S+)?)/) do |word, _|
+ if loc = Keep::Locator.parse(word)
+ yield loc
+ end
+ end
+ end
+
def self.normalize_uuid uuid
hash_part = nil
size_part = nil
def portable_manifest_text
portable_manifest = self[:manifest_text].dup
self.class.munge_manifest_locators!(portable_manifest) do |loc|
- loc.hash + '+' + loc.size.to_s
+ if loc.size
+ loc.hash + '+' + loc.size.to_s
+ else
+ loc.hash
+ end
end
portable_manifest
end
'+' +
portable_manifest.bytesize.to_s)
end
+
+ def maybe_clear_replication_confirmed
+ if manifest_text_changed?
+ # If the new manifest_text contains locators whose hashes
+ # weren't in the old manifest_text, storage replication is no
+ # longer confirmed.
+ in_old_manifest = {}
+ self.class.each_manifest_locator(manifest_text_was) do |loc|
+ in_old_manifest[loc.hash] = true
+ end
+ self.class.each_manifest_locator(manifest_text) do |loc|
+ if not in_old_manifest[loc.hash]
+ self.replication_confirmed_at = nil
+ self.replication_confirmed = nil
+ break
+ end
+ end
+ end
+ end
+
+ def ensure_permission_to_save
+ if (not current_user.andand.is_admin and
+ (replication_confirmed_at_changed? or replication_confirmed_changed?) and
+ not (replication_confirmed_at.nil? and replication_confirmed.nil?))
+ raise ArvadosModel::PermissionDeniedError.new("replication_confirmed and replication_confirmed_at attributes cannot be changed, except by setting both to nil")
+ end
+ super
+ end
end
# Permit insecure (OpenSSL::SSL::VERIFY_NONE) connections to the Single Sign
# On (sso) server. Should only be enabled during development when the SSO
# server is using a self-signed cert.
- sso_insecure: false
\ No newline at end of file
+ sso_insecure: false
+
+ # Default replication level for collections. This is used when a
+ # collection's replication_desired attribute is nil.
+ default_collection_replication: 2
--- /dev/null
+class RenameReplicationAttributes < ActiveRecord::Migration
+ RENAME = [[:redundancy, :replication_desired],
+ [:redundancy_confirmed_as, :replication_confirmed],
+ [:redundancy_confirmed_at, :replication_confirmed_at]]
+
+ def up
+ RENAME.each do |oldname, newname|
+ rename_column :collections, oldname, newname
+ end
+ remove_column :collections, :redundancy_confirmed_by_client_uuid
+ Collection.reset_column_information
+
+ # Removing that column dropped some search indexes. Let's put them back.
+ add_index :collections, ["owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "portable_data_hash", "uuid", "name", "file_names"], name: 'collections_search_index'
+ execute "CREATE INDEX collections_full_text_search_idx ON collections USING gin(#{Collection.full_text_tsvector});"
+ end
+
+ def down
+ remove_index :collections, name: 'collections_search_index'
+ add_column :collections, :redundancy_confirmed_by_client_uuid, :string
+ RENAME.reverse.each do |oldname, newname|
+ rename_column :collections, newname, oldname
+ end
+ remove_index :collections, :name => 'collections_full_text_search_idx'
+ Collection.reset_column_information
+
+ execute "CREATE INDEX collections_full_text_search_idx ON collections USING gin(#{Collection.full_text_tsvector});"
+ add_index :collections, ["owner_uuid", "modified_by_client_uuid", "modified_by_user_uuid", "portable_data_hash", "uuid", "name", "file_names", "redundancy_confirmed_by_client_uuid"], name: 'collections_search_index'
+ end
+end
modified_by_user_uuid character varying(255),
modified_at timestamp without time zone,
portable_data_hash character varying(255),
- redundancy integer,
- redundancy_confirmed_by_client_uuid character varying(255),
- redundancy_confirmed_at timestamp without time zone,
- redundancy_confirmed_as integer,
+ replication_desired integer,
+ replication_confirmed_at timestamp without time zone,
+ replication_confirmed integer,
updated_at timestamp without time zone NOT NULL,
uuid character varying(255),
manifest_text text,
-- Name: collections_full_text_search_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
--
-CREATE INDEX collections_full_text_search_idx ON collections USING gin (to_tsvector('english'::regconfig, (((((((((((((((((((COALESCE(owner_uuid, ''::character varying))::text || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(portable_data_hash, ''::character varying))::text) || ' '::text) || (COALESCE(redundancy_confirmed_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || COALESCE(properties, ''::text)) || ' '::text) || (COALESCE(file_names, ''::character varying))::text)));
+CREATE INDEX collections_full_text_search_idx ON collections USING gin (to_tsvector('english'::regconfig, (((((((((((((((((COALESCE(owner_uuid, ''::character varying))::text || ' '::text) || (COALESCE(modified_by_client_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(modified_by_user_uuid, ''::character varying))::text) || ' '::text) || (COALESCE(portable_data_hash, ''::character varying))::text) || ' '::text) || (COALESCE(uuid, ''::character varying))::text) || ' '::text) || (COALESCE(name, ''::character varying))::text) || ' '::text) || (COALESCE(description, ''::character varying))::text) || ' '::text) || COALESCE(properties, ''::text)) || ' '::text) || (COALESCE(file_names, ''::character varying))::text)));
--
-- Name: collections_search_index; Type: INDEX; Schema: public; Owner: -; Tablespace:
--
-CREATE INDEX collections_search_index ON collections USING btree (owner_uuid, modified_by_client_uuid, modified_by_user_uuid, portable_data_hash, redundancy_confirmed_by_client_uuid, uuid, name, file_names);
+CREATE INDEX collections_search_index ON collections USING btree (owner_uuid, modified_by_client_uuid, modified_by_user_uuid, portable_data_hash, uuid, name, file_names);
--
INSERT INTO schema_migrations (version) VALUES ('20150203180223');
-INSERT INTO schema_migrations (version) VALUES ('20150206210804');
\ No newline at end of file
+INSERT INTO schema_migrations (version) VALUES ('20150206210804');
+
+INSERT INTO schema_migrations (version) VALUES ('20150206230342');
\ No newline at end of file
name: collection_with_some_unique_words
description: The quick_brown_fox jumps over the lazy_dog
+replication_undesired_unconfirmed:
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2015-02-07 00:19:28.596506247 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2015-02-07 00:19:28.596338465 Z
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ replication_desired: ~
+ replication_confirmed_at: ~
+ replication_confirmed: ~
+ updated_at: 2015-02-07 00:19:28.596236608 Z
+ uuid: zzzzz-4zz18-wjxq7uzx2m9jj4a
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: replication want=null have=null
+
+replication_desired_2_unconfirmed:
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2015-02-07 00:21:35.050333515 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2015-02-07 00:21:35.050189104 Z
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ replication_desired: 2
+ replication_confirmed_at: ~
+ replication_confirmed: ~
+ updated_at: 2015-02-07 00:21:35.050126576 Z
+ uuid: zzzzz-4zz18-3t236wrz4769h7x
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: replication want=2 have=null
+
+replication_desired_2_confirmed_2:
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2015-02-07 00:19:28.596506247 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2015-02-07 00:19:28.596338465 Z
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ replication_desired: 2
+ replication_confirmed_at: 2015-02-07 00:24:52.983381227 Z
+ replication_confirmed: 2
+ updated_at: 2015-02-07 00:24:52.983381227 Z
+ uuid: zzzzz-4zz18-434zv1tnnf2rygp
+ manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 37b51d194a7513e45b56f6524f2d51f2+3 0:3:foo 3:6:bar\n"
+ name: replication want=2 have=2
+
+collection_with_empty_properties:
+ uuid: zzzzz-4zz18-emptyproperties
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2015-02-13T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2015-02-13T17:22:54Z
+ updated_at: 2015-02-13T17:22:54Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: collection with empty properties
+ properties: {}
+
+collection_with_one_property:
+ uuid: zzzzz-4zz18-withoneproperty
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2015-02-13T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2015-02-13T17:22:54Z
+ updated_at: 2015-02-13T17:22:54Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: collection with one property
+ properties:
+ property1: value1
+
# Test Helper trims the rest of the file
# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
end
[1, 5, nil].each do |ask|
- test "Set replication_desired=#{ask} using redundancy attr" do
- # The Python SDK checks the Collection schema in the discovery
- # doc, then asks for 'redundancy' or 'replication_desired'
- # accordingly, so it isn't necessary to maintain backward
- # compatibility here when the attribute changes to
- # replication_desired.
+ test "Set replication_desired=#{ask.inspect}" do
+ Rails.configuration.default_collection_replication = 2
authorize_with :active
put :update, {
- id: collections(:collection_owned_by_active).uuid,
+ id: collections(:replication_undesired_unconfirmed).uuid,
collection: {
- redundancy: ask,
+ replication_desired: ask,
},
}
assert_response :success
- assert_equal (ask or 2), json_response['replication_desired']
+ assert_equal ask, json_response['replication_desired']
end
end
+
+ test "get collection with properties" do
+ authorize_with :active
+ get :show, {id: collections(:collection_with_one_property).uuid}
+ assert_response :success
+ assert_not_nil json_response['uuid']
+ assert_equal 'value1', json_response['properties']['property1']
+ end
+
+ test "create collection with properties" do
+ authorize_with :active
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47",
+ properties: {'property_1' => 'value_1'}
+ }
+ }
+ assert_response :success
+ assert_not_nil json_response['uuid']
+ assert_equal 'value_1', json_response['properties']['property_1']
+ end
end
assert_equal first_item['description'], 'The quick_brown_fox jumps over the lazy_dog'
end
end
+
+ test "create and get collection with properties" do
+ # create collection to be searched for
+ signed_manifest = Collection.sign_manifest(". bad42fa702ae3ea7d888fef11b46f450+44 0:44:my_test_file.txt\n", api_token(:active))
+ post "/arvados/v1/collections", {
+ format: :json,
+ collection: {manifest_text: signed_manifest}.to_json,
+ }, auth(:active)
+ assert_response 200
+ assert_not_nil json_response['uuid']
+ assert_not_nil json_response['properties']
+ assert_empty json_response['properties']
+
+ # update collection's description
+ put "/arvados/v1/collections/#{json_response['uuid']}", {
+ format: :json,
+ collection: { properties: {'property_1' => 'value_1'} }
+ }, auth(:active)
+ assert_response :success
+ assert_equal 'value_1', json_response['properties']['property_1']
+ end
end
indexes = ActiveRecord::Base.connection.indexes(table)
search_index_by_columns = indexes.select do |index|
- index.columns == search_index_columns
+ index.columns.sort == search_index_columns.sort
end
search_index_by_name = indexes.select do |index|
index.name == "#{table}_search_index"
end
end
+ test 'portable data hash with missing size hints' do
+ [[". d41d8cd98f00b204e9800998ecf8427e+0+Bar 0:0:x",
+ ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:x"],
+ [". d41d8cd98f00b204e9800998ecf8427e+Foo 0:0:x",
+ ". d41d8cd98f00b204e9800998ecf8427e 0:0:x"],
+ [". d41d8cd98f00b204e9800998ecf8427e 0:0:x",
+ ". d41d8cd98f00b204e9800998ecf8427e 0:0:x"],
+ ].each do |unportable, portable|
+ c = Collection.new(manifest_text: unportable)
+ assert c.valid?
+ assert_equal(Digest::MD5.hexdigest(portable)+"+#{portable.length}",
+ c.portable_data_hash)
+ end
+ end
+
[0, 2, 4, nil].each do |ask|
- test "replication_desired reports #{ask or 2} if redundancy is #{ask}" do
+ test "set replication_desired to #{ask.inspect}" do
+ Rails.configuration.default_collection_replication = 2
act_as_user users(:active) do
- c = collections(:collection_owned_by_active)
- c.update_attributes redundancy: ask
- assert_equal (ask or 2), c.replication_desired
+ c = collections(:replication_undesired_unconfirmed)
+ c.update_attributes replication_desired: ask
+ assert_equal ask, c.replication_desired
+ end
+ end
+ end
+
+ test "replication_confirmed* can be set by admin user" do
+ c = collections(:replication_desired_2_unconfirmed)
+ act_as_user users(:admin) do
+ assert c.update_attributes(replication_confirmed: 2,
+ replication_confirmed_at: Time.now)
+ end
+ end
+
+ test "replication_confirmed* cannot be set by non-admin user" do
+ act_as_user users(:active) do
+ c = collections(:replication_desired_2_unconfirmed)
+ # Cannot set just one at a time.
+ assert_raise ArvadosModel::PermissionDeniedError do
+ c.update_attributes replication_confirmed: 1
+ end
+ assert_raise ArvadosModel::PermissionDeniedError do
+ c.update_attributes replication_confirmed_at: Time.now
+ end
+ # Cannot set both at once, either.
+ assert_raise ArvadosModel::PermissionDeniedError do
+ c.update_attributes(replication_confirmed: 1,
+ replication_confirmed_at: Time.now)
+ end
+ end
+ end
+
+ test "replication_confirmed* can be cleared (but only together) by non-admin user" do
+ act_as_user users(:active) do
+ c = collections(:replication_desired_2_confirmed_2)
+ # Cannot clear just one at a time.
+ assert_raise ArvadosModel::PermissionDeniedError do
+ c.update_attributes replication_confirmed: nil
end
+ c.reload
+ assert_raise ArvadosModel::PermissionDeniedError do
+ c.update_attributes replication_confirmed_at: nil
+ end
+ # Can clear both at once.
+ c.reload
+ assert c.update_attributes(replication_confirmed: nil,
+ replication_confirmed_at: nil)
+ end
+ end
+
+ test "clear replication_confirmed* when introducing a new block in manifest" do
+ c = collections(:replication_desired_2_confirmed_2)
+ act_as_user users(:active) do
+ assert c.update_attributes(manifest_text: collections(:user_agreement).signed_manifest_text)
+ assert_nil c.replication_confirmed
+ assert_nil c.replication_confirmed_at
+ end
+ end
+
+ test "don't clear replication_confirmed* when just renaming a file" do
+ c = collections(:replication_desired_2_confirmed_2)
+ act_as_user users(:active) do
+ new_manifest = c.signed_manifest_text.sub(':bar', ':foo')
+ assert c.update_attributes(manifest_text: new_manifest)
+ assert_equal 2, c.replication_confirmed
+ assert_not_nil c.replication_confirmed_at
+ end
+ end
+
+ test "don't clear replication_confirmed* when just deleting a data block" do
+ c = collections(:replication_desired_2_confirmed_2)
+ act_as_user users(:active) do
+ new_manifest = c.signed_manifest_text
+ new_manifest.sub!(/ \S+:bar/, '')
+ new_manifest.sub!(/ acbd\S+/, '')
+
+ # Confirm that we did just remove a block from the manifest (if
+ # not, this test would pass without testing the relevant case):
+ assert_operator new_manifest.length+40, :<, c.signed_manifest_text.length
+
+ assert c.update_attributes(manifest_text: new_manifest)
+ assert_equal 2, c.replication_confirmed
+ assert_not_nil c.replication_confirmed_at
+ end
+ end
+
+ test "create collection with properties" do
+ act_as_system_user do
+ c = Collection.create(manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo\n",
+ properties: {'property_1' => 'value_1'})
+ assert c.valid?
+ assert_equal 'value_1', c.properties['property_1']
end
end
end
def convertTime(t):
- '''Parse Arvados timestamp to unix time.'''
+ """Parse Arvados timestamp to unix time."""
+ if not t:
+ return 0
try:
return calendar.timegm(time.strptime(t, "%Y-%m-%dT%H:%M:%SZ"))
except (TypeError, ValueError):
self.collection_object = None
if isinstance(collection, dict):
self.collection_locator = collection['uuid']
+ self._mtime = convertTime(collection.get('modified_at'))
else:
self.collection_locator = collection
+ self._mtime = 0
def same(self, i):
return i['uuid'] == self.collection_locator or i['portable_data_hash'] == self.collection_locator
def new_collection(self, new_collection_object, coll_reader):
self.collection_object = new_collection_object
+ self._mtime = convertTime(self.collection_object.get('modified_at'))
+
if self.collection_object_file is not None:
self.collection_object_file.update(self.collection_object)
else:
return super(CollectionDirectory, self).__contains__(k)
- def mtime(self):
- self.checkupdate()
- return convertTime(self.collection_object["modified_at"]) if self.collection_object is not None and 'modified_at' in self.collection_object else 0
-
class MagicDirectory(Directory):
'''A special directory that logically contains the set of all extant keep
projects / arvados.git / commitdiff